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[protege-discussion] [SPAM:##] Re: Exception in inference api

Timothy Redmond tredmond at stanford.edu
Sun Oct 17 10:31:53 PDT 2010



On 10/13/2010 04:03 PM, Soha Said wrote:
> Yes, Done with no error
> Thanks very much
> But about topobjectproperty and topDataproperty
> how can I avoid it.

Here I don't know what you mean.  If you are talking about an issue in 
Protege then this is my problem.  Check that it happens with the latest 
release and the latest updates (File->Check for Plugins), report it so 
that I can repeat the problem here and I will remove the inference.

If you are talking about a problem in your code then you simply need to 
adjust.  If some of the inferences being generated by the reasoner are 
too trivial and you don't want to see them, then you can programatically 
remove the information that you don't want to see.

> Also, object properties inferred correctly from protege interface
> but not inferred using api

All of the details are missing here so it is hard to know what you 
mean.  It is clear that some code is not behaving as you expect.  The 
best way to report such an issue is to send a small example which does 
not have the desired behavior and explain what you think it is doing 
wrong.  Preferably you will be working with the latest version of the 
software because it is not clear what to do with a bug report about 
something that has already been fixed.  The very best bug reports 
include enough information that the issue can be easily replicated here.

-Timothy



> It was working correct in previous version and data properties not and 
> now vise versa.
> ------------------------------------------------
> Yes this is much more informative.  I was beginning to suspect what was
> wrong in your last message.  You are using an old version of HermiT.  I
> remember this exception.  I know that this was present in Hermit 1.2.5
> but HermiT is now on version 1.3.1.
>
> If you need HermiT outside of Protege, you can obtain it from [1].  If
> you are using Protege Build 209, you can update to HermiT by clicking
> File->Check For Plugins and then install the HermiT plugin.  In the
> latter case, I would recommend also updating the OWL editor plugin.  I
> have recently fixed and improved the export inferred ontology method
> which you seem to be using.
>
> I was able to replicate your exception with older versions of HermiT
> using the attached ontology.
>
> -Timothy
>
> [1] http://hermit-reasoner.com/
>
>
> On 10/13/2010 03:09 PM, Soha Said wrote:
> > the trace is
> > java.lang.NullPointerException
> >        at
> > org.semanticweb.HermiT.hierarchy.InstanceManager.getTypes(Unknown 
> Source)
> >        at org.semanticweb.HermiT.Reasoner.getTypes(Unknown Source)
> >        at
> > 
> org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator.addAxioms(InferredClassAssertionAxiomGenerator.java:46)
> >        at
> > 
> org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator.addAxioms(InferredClassAssertionAxiomGenerator.java:42)
> >        at
> > 
> org.semanticweb.owlapi.util.InferredEntityAxiomGenerator.createAxioms(InferredEntityAxiomGenerator.java:49)
> >        at
> > 
> org.semanticweb.owlapi.util.InferredOntologyGenerator.fillOntology(InferredOntologyGenerator.java:111)
> >        at
> > prototype.PrototypeFrame.InferredInstances(PrototypeFrame.java:898)
> >        at
> > 
> prototype.PrototypeFrame.BtnInferenceActionPerformed(PrototypeFrame.java:203)
> >        at prototype.PrototypeFrame.access$200(PrototypeFrame.java:36)
> >        at
> > prototype.PrototypeFrame$4.actionPerformed(PrototypeFrame.java:98)
> >        at
> > javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
> >        at
> > 
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
> >        at
> > 
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
> >        at
> > javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
> >        at
> > 
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
> >        at java.awt.Component.processMouseEvent(Component.java:6263)
> >        at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
> >        at java.awt.Component.processEvent(Component.java:6028)
> >        at java.awt.Container.processEvent(Container.java:2041)
> >        at java.awt.Component.dispatchEventImpl(Component.java:4630)
> >        at java.awt.Container.dispatchEventImpl(Container.java:2099)
> >        at java.awt.Component.dispatchEvent(Component.java:4460)
> >        at
> > java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
> >        at
> > java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
> >        at
> > java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
> >        at java.awt.Container.dispatchEventImpl(Container.java:2085)
> >        at java.awt.Window.dispatchEventImpl(Window.java:2478)
> >        at java.awt.Component.dispatchEvent(Component.java:4460)
> >        at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
> >        at
> > 
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
> >        at
> > 
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
> >        at
> > 
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
> >        at
> > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
> >        at
> > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
> >        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> >
> > 
> -------------------------------------------------------------------------
> > 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 <http://uk.ac.manchester.cs/>
> > <http://uk.ac.manchester.cs/>.owl.owlapi.OWLObjectAllValuesFromImpl
> > cannot be cast
> >      to org.semanticweb.owlapi.model.OWLClass
> > atuk.ac.manchester.cs <http://atuk.ac.manchester.cs/>
> > 
> <http://uk.ac.manchester.cs.owl.owlapi.owlclassimpl.com/>.owl.owlapi.OWLClassImpl.compareObjectOfSameType(OWLClassImpl.java:434)
> >      at uk.ac.manchester.cs
> > 
> <http://uk.ac.manchester.cs.owl.owlapi.owlobjectimpl.com/>.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:167)
> >      at
> > uk.ac.manchester.cs 
> <http://uk.ac.manchester.cs.owl.owlapi.owlobjectimpl.com/>.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
> > 
> <http://uk.ac.manchester.cs.owl.owlapi.owlclassimpl.ge/>.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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