[protege-discussion] Exception in inference api

[Soha Said]

Why using inferrence api from java shows me TopObjectProperty and 
TopDataProperty to each individual?
and
This is another the trace from protege when I use classify from reasoner menu


Error 2 Logged at Thu Oct 14 00:29:36 EET 2010
NullPointerException: null
    org.semanticweb.HermiT.hierarchy.InstanceManager.getTypes(Unknown Source)
    org.semanticweb.HermiT.Reasoner.getTypes(Unknown Source)
   
 org.protege.editor.owl.ui.frame.individual.OWLClassAssertionAxiomTypeFrameSection$1.run(OWLClassAssertionAxiomTypeFrameSection.java:73)

   
 org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:181)

   
 org.protege.editor.owl.ui.frame.individual.OWLClassAssertionAxiomTypeFrameSection.refillInferred(OWLClassAssertionAxiomTypeFrameSection.java:70)

   
 org.protege.editor.owl.ui.frame.AbstractOWLFrameSection.setRootObject(AbstractOWLFrameSection.java:232)

   
 org.protege.editor.owl.ui.frame.AbstractOWLFrame.refill(AbstractOWLFrame.java:94)

   
 org.protege.editor.owl.ui.frame.AbstractOWLFrame.setRootObject(AbstractOWLFrame.java:86)

   
 org.protege.editor.owl.ui.framelist.OWLFrameList.setRootObject(OWLFrameList.java:349)

   
 org.protege.editor.owl.ui.view.individual.OWLIndividualDescriptionViewComponent.updateView(OWLIndividualDescriptionViewComponent.java:41)

   
 org.protege.editor.owl.ui.view.individual.AbstractOWLIndividualViewComponent.updateView(AbstractOWLIndividualViewComponent.java:41)

   
 org.protege.editor.owl.ui.view.individual.AbstractOWLIndividualViewComponent.updateView(AbstractOWLIndividualViewComponent.java:17)

   
 org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.updateViewContentAndHeader(AbstractOWLSelectionViewComponent.java:194)

   
 org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.selectionChanged(AbstractOWLSelectionViewComponent.java:72)

   
 org.protege.editor.owl.model.selection.OWLSelectionModelImpl.fireSelectionChanged(OWLSelectionModelImpl.java:192)

   
 org.protege.editor.owl.model.selection.OWLSelectionModelImpl.updateSelectedObject(OWLSelectionModelImpl.java:180)

   
 org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelectedObject(OWLSelectionModelImpl.java:168)

   
 org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelectedEntity(OWLSelectionModelImpl.java:203)

   
 org.protege.editor.owl.model.OWLWorkspace.verifySelection(OWLWorkspace.java:378)

   
 org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:298)

    org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:132)
   
 org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:221)
   
 org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:763)

   
 org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$2.run(OWLReasonerManagerImpl.java:244)

    java.awt.event.InvocationEvent.dispatch(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.Dialog$1.run(Unknown Source)
    java.awt.Dialog$2.run(Unknown Source)
    java.security.AccessController.doPrivileged(Native Method)
    java.awt.Dialog.show(Unknown Source)
    java.awt.Component.show(Unknown Source)
    java.awt.Component.setVisible(Unknown Source)
   
 org.protege.editor.owl.ui.inference.ReasonerProgressUI$3.run(ReasonerProgressUI.java:156)

    java.awt.event.InvocationEvent.dispatch(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.run(Unknown Source)
-----------------------------------------------------------------------------------------------------------------------------


You still did not send the stack trace for your exception.  An example 
of a stack trace for an exception would be something like this:

    java.lang.ClassCastException:
    uk.ac.manchester.cs.owl.owlapi.OWLObjectAllValuesFromImpl cannot be cast
      to org.semanticweb.owlapi.model.OWLClass
      
atuk.ac.manchester.cs.owl.owlapi.OWLClassImpl.compareObjectOfSameType(OWLClassImpl.java:434)

      
at uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:167)

      at 
uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:41)
      at java.util.TreeMap.put(TreeMap.java:562)
      at java.util.TreeSet.add(TreeSet.java:255)
      
at uk.ac.manchester.cs.owl.owlapi.OWLClassImpl.getSuperClasses(OWLClassImpl.java:206)

      


Each line in such a trace provides some additional information for a 
developer to analyze.

I would say that the API is working because I have modified some code in 
Protege 4 recently that looks very much like what you are writing.  The 
code invoked by Protege 4.1 by File->Export Inferred Hierarchy is very 
similar to yours.

-Timothy


On 10/12/2010 09:28 AM, Soha Said wrote:
> Hello,
> I trace the error and I find the error in this line:
> InferredGenerator.add(new InferredClassAssertionAxiomGenerator());
> when I replced with this line:
> InferredGenerator.add(new InferredPropertyAssertionGenerator());
> it worked without error, but when I open the protege, the object 
> properties are not saved correctly.
> for example, each individual will have its object properties and 
> linked to the other individuals by TopObjectProperty like individual x 
> and y, and x has TopObjectProperty is y and vise versa.
> when i classify from the protege interface, it inferred the properties 
> correctly, but using api i think there is some problem.
>
> On 10/10/2010 07:06 AM, Soha Said wrote:
> > I used protege 4.1 beta build 209 api, and I have a problem in
> > inference api.
> > This is the snapshot of code that I used to get inferencing:
> > OWLOntologyManager 
> ontologymanager=OWLManager.createOWLOntologyManager();
> >            OWLOntology
> > ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
> >            OWLDataFactory factory=ontologymanager.getOWLDataFactory();
> >            OWLReasonerFactory reasonerfactory= new
> > Reasoner.ReasonerFactory();
> >            OWLReasoner
> > owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
> >
> > owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
> >
> > List<InferredAxiomGenerator<? extends OWLAxiom>> InferredGenerator =
> > new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
> >            InferredGenerator.add(new
> > InferredClassAssertionAxiomGenerator());
> >            InferredOntologyGenerator ontologygenerator=new
> > InferredOntologyGenerator(owlreasoner,InferredGenerator);
> >            ontologygenerator.fillOntology(ontologymanager,ontology);
> >            ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
> > but I have an exception in this line:
> > ontologygenerator.fillOntology(ontologymanager,ontology);
> > this exception says: java.lang.NullPointerException
> >  I don't know what i should do and what is wrong.
> > Thanks in advance
> > Soha Said
> >


      
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