Unable to open SPARQL query view

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Unable to open SPARQL query view

Hjuls
Hi,
I can't open SPARQL query view in my ontology with 1.500.000 axioms.
The issue seems related with the weight of the ontology, because it shows up only if the ontology is already loaded. Instead, without opening  any ontology, the SPARQL successfully.
I've already see a previous conversation on a similar topic https://github.com/protegeproject/protege/issues/625#issuecomment-293424694 and I followed the istructions, but that solution didn't worked.
I tried to reinstall Protege from the beginning with the previous solution suggested plugins also, but it didn't worked too. Any suggestion?
Thanks,
Julio
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Re: Unable to open SPARQL query view

Rafael Gonçalves
Hi Julio,

This is due to a known issue in the SPARQL Query plugin: https://github.com/protegeproject/rdf-library/issues/3, which we haven’t gotten around to fixing yet. The conversion of OWL axioms to RDF triples (that’s done when the SPARQL tab is activated) is sub-optimal, and so there is a delay. Because of the size of the ontology, lack of space may be contributing to the delay or the halting—How much memory do you allocate to Protege?

Cheers,
Rafael

On May 17, 2017, at 07:40, Hjuls <[hidden email]> wrote:

Hi,
I can't open SPARQL query view in my ontology with 1.500.000 axioms.
The issue seems related with the weight of the ontology, because it shows up
only if the ontology is already loaded. Instead, without opening  any
ontology, the SPARQL successfully.
I've already see a previous conversation on a similar topic
https://github.com/protegeproject/protege/issues/625#issuecomment-293424694
<https://github.com/protegeproject/protege/issues/625#issuecomment-293424694>  
and I followed the istructions, but that solution didn't worked.
I tried to reinstall Protege from the beginning with the previous solution
suggested plugins also, but it didn't worked too. Any suggestion?
Thanks,
Julio



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Re: Unable to open SPARQL query view

Rafael Gonçalves
Alternatively, you can use the Snap SPARQL plugin that works with the OWL entailment regime (and because of that, Snap requires that you reason over the ontology first).

Cheers,
Rafael

On May 17, 2017, at 10:58, Rafael Gonçalves <[hidden email]> wrote:

Hi Julio,

This is due to a known issue in the SPARQL Query plugin: https://github.com/protegeproject/rdf-library/issues/3, which we haven’t gotten around to fixing yet. The conversion of OWL axioms to RDF triples (that’s done when the SPARQL tab is activated) is sub-optimal, and so there is a delay. Because of the size of the ontology, lack of space may be contributing to the delay or the halting—How much memory do you allocate to Protege?

Cheers,
Rafael

On May 17, 2017, at 07:40, Hjuls <[hidden email]> wrote:

Hi,
I can't open SPARQL query view in my ontology with 1.500.000 axioms.
The issue seems related with the weight of the ontology, because it shows up
only if the ontology is already loaded. Instead, without opening  any
ontology, the SPARQL successfully.
I've already see a previous conversation on a similar topic
https://github.com/protegeproject/protege/issues/625#issuecomment-293424694
<https://github.com/protegeproject/protege/issues/625#issuecomment-293424694>  
and I followed the istructions, but that solution didn't worked.
I tried to reinstall Protege from the beginning with the previous solution
suggested plugins also, but it didn't worked too. Any suggestion?
Thanks,
Julio



--
View this message in context: http://protege-project.136.n4.nabble.com/Unable-to-open-SPARQL-query-view-tp4668535.html
Sent from the Protege User mailing list archive at Nabble.com.
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Re: Unable to open SPARQL query view

Hjuls
Thanks for the suggestion regarding Snap plugin.
However I allocated a minimum memory value equal to 466M to a maximun equal to 4048M (editing the run.bat file).
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Re: Unable to open SPARQL query view

Matthew Horridge-2
Administrator
Is the problem with reasoning or executing the query after reasoning has been performed?

Could you upload (zipped) your ontology somewhere so that we can take a look at it?

Cheers,

Matthew


> On 17 May 2017, at 11:34, Hjuls <[hidden email]> wrote:
>
> Thanks for the suggestion regarding Snap plugin.
> However I allocated a minimum memory value equal to 466M to a maximun equal
> to 4048M (editing the run.bat file).
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Unable-to-open-SPARQL-query-view-tp4668535p4668540.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Unable to open SPARQL query view

刘栋在线
In reply to this post by Hjuls
I encountered the same problem recently. Actually I think it is related with the recent updates. I can open SPARQL view in Protégé 5.0 but not in Protégé 5.2. The same phenomenon happened on my friend's computer. In the logfile of protégé, it says:
2017-05-19 10:35:04.044 [AWT-EventQueue-0] ERROR ProtegeApplication    Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V
 at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]
 at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]
 at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
 at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
 at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
 at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
 at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:44) ~[na:na]
 at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:34) ~[na:na]
 at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
 at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
 at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
 at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
 at java.awt.Component.processHierarchyEvent(Component.java:6692) ~[na:1.8.0_40]
 at java.awt.Component.processEvent(Component.java:6311) ~[na:1.8.0_40]
 at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]
 at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]
 at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]
 at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]
 at java.awt.Component.createHierarchyEvents(Component.java:5541) ~[na:1.8.0_40]
 at java.awt.Container.createHierarchyEvents(Container.java:1443) ~[na:1.8.0_40]
 at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
 at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
 at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
 at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
 at java.awt.Component.show(Component.java:1622) ~[na:1.8.0_40]
 at java.awt.Component.show(Component.java:1654) ~[na:1.8.0_40]
 at java.awt.Component.setVisible(Component.java:1606) ~[na:1.8.0_40]
 at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_40]
 at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_40]
 at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_40]
 at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_40]
 at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_40]
 at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_40]
 at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_40]
 at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_40]
 at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_40]
 at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_40]
 at java.awt.Component.processMouseEvent(Component.java:6522) ~[na:1.8.0_40]
 at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_40]
 at java.awt.Component.processEvent(Component.java:6290) ~[na:1.8.0_40]
 at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]
 at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]
 at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]
 at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]
 at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) ~[na:1.8.0_40]
 at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4530) ~[na:1.8.0_40]
 at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) ~[na:1.8.0_40]
 at java.awt.Container.dispatchEventImpl(Container.java:2278) ~[na:1.8.0_40]
 at java.awt.Window.dispatchEventImpl(Window.java:2750) ~[na:1.8.0_40]
 at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751) ~[na:1.8.0_40]
 at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_40]
 at java.awt.EventQueue$3.run(EventQueue.java:702) ~[na:1.8.0_40]
 at java.awt.EventQueue$3.run(EventQueue.java:696) ~[na:1.8.0_40]
 at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]
 at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]
 at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) ~[na:1.8.0_40]
 at java.awt.EventQueue$4.run(EventQueue.java:724) ~[na:1.8.0_40]
 at java.awt.EventQueue$4.run(EventQueue.java:722) ~[na:1.8.0_40]
 at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]
 at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:721) ~[na:1.8.0_40]
 at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_40]
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_40]
 at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_40]
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_40]
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_40]
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_40]
Dong Liu
Wuhan University

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Re: Unable to open SPARQL query view

Rafael Gonçalves
This is a separate issue—it is related to plugin versions.

Could you clarify what versions of the ‘OWLAPI RDF Library' and 'SPARQL Query Plugin’ bundles you have installed? This can be checked from the ‘About Protege’ menu item.

Make sure that the latest versions of both of these plugins are installed in Protege 5.2. There were OWL API version updates in between, which may be why the error is occurring.

Cheers,
Rafael

> On May 18, 2017, at 19:38, 刘栋在线 <[hidden email]> wrote:
>
> I encountered the same problem recently. Actually I think it is related with the recent updates. I can open SPARQL view in Protégé 5.0 but not in Protégé 5.2. The same phenomenon happened on my friend's computer. In the logfile of protégé, it says:
> 2017-05-19 10:35:04.044 [AWT-EventQueue-0] ERROR ProtegeApplication    Uncaught Exception in thread 'AWT-EventQueue-0'
> java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V
>  at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]
>  at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]
>  at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
>  at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
>  at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
>  at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
>  at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:44) ~[na:na]
>  at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:34) ~[na:na]
>  at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
>  at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
>  at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
>  at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
>  at java.awt.Component.processHierarchyEvent(Component.java:6692) ~[na:1.8.0_40]
>  at java.awt.Component.processEvent(Component.java:6311) ~[na:1.8.0_40]
>  at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]
>  at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]
>  at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]
>  at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]
>  at java.awt.Component.createHierarchyEvents(Component.java:5541) ~[na:1.8.0_40]
>  at java.awt.Container.createHierarchyEvents(Container.java:1443) ~[na:1.8.0_40]
>  at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
>  at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
>  at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
>  at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
>  at java.awt.Component.show(Component.java:1622) ~[na:1.8.0_40]
>  at java.awt.Component.show(Component.java:1654) ~[na:1.8.0_40]
>  at java.awt.Component.setVisible(Component.java:1606) ~[na:1.8.0_40]
>  at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_40]
>  at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_40]
>  at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_40]
>  at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_40]
>  at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_40]
>  at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_40]
>  at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_40]
>  at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_40]
>  at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_40]
>  at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_40]
>  at java.awt.Component.processMouseEvent(Component.java:6522) ~[na:1.8.0_40]
>  at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_40]
>  at java.awt.Component.processEvent(Component.java:6290) ~[na:1.8.0_40]
>  at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]
>  at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]
>  at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]
>  at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]
>  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) ~[na:1.8.0_40]
>  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4530) ~[na:1.8.0_40]
>  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) ~[na:1.8.0_40]
>  at java.awt.Container.dispatchEventImpl(Container.java:2278) ~[na:1.8.0_40]
>  at java.awt.Window.dispatchEventImpl(Window.java:2750) ~[na:1.8.0_40]
>  at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]
>  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751) ~[na:1.8.0_40]
>  at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_40]
>  at java.awt.EventQueue$3.run(EventQueue.java:702) ~[na:1.8.0_40]
>  at java.awt.EventQueue$3.run(EventQueue.java:696) ~[na:1.8.0_40]
>  at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]
>  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]
>  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) ~[na:1.8.0_40]
>  at java.awt.EventQueue$4.run(EventQueue.java:724) ~[na:1.8.0_40]
>  at java.awt.EventQueue$4.run(EventQueue.java:722) ~[na:1.8.0_40]
>  at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]
>  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]
>  at java.awt.EventQueue.dispatchEvent(EventQueue.java:721) ~[na:1.8.0_40]
>  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_40]
>  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_40]
>  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_40]
>  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_40]
>  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_40]
>  at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_40]
> Dong Liu
> Wuhan University
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Unable to open SPARQL query view

Rafael Gonçalves
In reply to this post by Hjuls
That doesn’t look like enough memory for the ontology, but we’d have to have a look to confirm. Can you increase the maximum memory allocated?

Cheers,
Rafael

> On May 17, 2017, at 11:34, Hjuls <[hidden email]> wrote:
>
> Thanks for the suggestion regarding Snap plugin.
> However I allocated a minimum memory value equal to 466M to a maximun equal
> to 4048M (editing the run.bat file).
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Unable-to-open-SPARQL-query-view-tp4668535p4668540.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Unable to open SPARQL query view

Hjuls
In reply to this post by Matthew Horridge-2
None of these,it seems. In fact I can't even open the SPARQL tab, and it doesn't matter if the reasoner has been performed or not.
I confirm the opinion related to the cause is merely a memory problem.
On my machine the installed RAM is 8GB, so I raised memory up to 7168M but, taking a look to task manager and resource management, I saw that the java process make commit for up to 4GB of memory but, even after I've raised the memory, the max allocated is 3.5GB because of the limited  actual avalaible memory (I'm limited by the cached memory).
Cheers,
Julio


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Re: Unable to open SPARQL query view

Hjuls
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Re: Unable to open SPARQL query view

Lorenz Buehmann
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To be honest, I cannot follow this thread. For me the SPARQL query tab works with Protege 5.2.0 and latest update of the OWL RDF API 2.0.3.

None of these,it seems. In fact I can't even open the SPARQL tab, and it
doesn't matter if the reasoner has been performed or not.
I confirm the opinion related to the cause is merely a memory problem.
On my machine the installed RAM is 8GB, so I raised memory up to 7168M but,
taking a look to task manager and resource management, I saw that the java
process make commit for up to 4GB of memory but, even after I've raised the
memory, the max allocated is 3.5GB because of the limited  actual avalaible
memory (I'm limited by the cached memory).
Cheers,
Julio






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Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

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