Protege 4.3 Pellet reasoner show NullPointerException: null

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Protege 4.3 Pellet reasoner show NullPointerException: null

Hamizah Hamka
Greetings team of expert.

I have questions to ask.
I am currently running Pellet reasoner in Protege 4.3,
, at first it popup with list of red highlighted
property that inconsistent in my ontology.
And while the Pellet running, i delete the inconsistent 
property and try to synchronize back the reasoner.
But it point out with the red triangle warning symbol 
and i caught up with the NullPointerException: null.
How can i resolve this issues?
Thank you in advance for any suggestions.

--
“Time is like a sword: if you don’t cut it, it will cut you. Second is yourself: if you don’t busy it with right, it will busy you with wrong.” --Imam Shafi'i


Best Regards,

Nurhamizah Binti Mohd Hamka
MC113037
Master in Science (Software Engineering)
Faculty of Computing
Universiti Teknologi Malaysia
Skudai, Johor

_______________________________________________
p4-feedback mailing list
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Re: Protege 4.3 Pellet reasoner show NullPointerException: null

Timothy Redmond
On 01/08/2014 12:33 AM, mieza hamka wrote:
Greetings team of expert.

I have questions to ask.
I am currently running Pellet reasoner in Protege 4.3,
, at first it popup with list of red highlighted
property that inconsistent in my ontology.
And while the Pellet running, i delete the inconsistent 
property and try to synchronize back the reasoner.
But it point out with the red triangle warning symbol 
and i caught up with the NullPointerException: null.
How can i resolve this issues?
Thank you in advance for any suggestions.

To figure this out we will probably need a bit more information.  Without more information we can't tell if this is a pellet issue or a protege bug.  The minimal information that would get us started would be to see the full listing of the exception information that you see when you click on the red triangle.  Better would be to get a look at the logs with the exception (they are a bit awkward to get but they are in ".Protege/logs" under the home directory).

The other question would be if you see the null pointer exception if you restart Protege and then pellet. This would give a hint as to whether the exception comes from some issue with the synchronization logic.

Finally - if it is possible - best is to send a copy of the ontology with the steps to repeat the issue.

-Timothy




--
“Time is like a sword: if you don’t cut it, it will cut you. Second is yourself: if you don’t busy it with right, it will busy you with wrong.” --Imam Shafi'i


Best Regards,

Nurhamizah Binti Mohd Hamka
MC113037
Master in Science (Software Engineering)
Faculty of Computing
Universiti Teknologi Malaysia
Skudai, Johor


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


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Re: Protege 4.3 Pellet reasoner show NullPointerException: null

Hamizah Hamka
Thank you Sir.

Well.
This is the copy of the error from the Protege.

____________
Error 1 Logged at Fri Jan 10 13:54:53 SGT 2014
NullPointerException: null
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection$1.run(OWLClassAssertionAxiomMembersSection.java:89)
    org.protege.editor.owl.model.inference.DisplayedInferencePreferences.executeTask(DisplayedInferencePreferences.java:119)
    org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:183)
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection.refillInferred(OWLClassAssertionAxiomMembersSection.java:80)
    org.protege.editor.owl.ui.frame.AbstractOWLFrameSection.setRootObject(AbstractOWLFrameSection.java:306)
    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:343)
    org.protege.editor.owl.ui.view.cls.OWLClassDescriptionViewComponent.updateView(OWLClassDescriptionViewComponent.java:57)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:36)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:19)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.updateViewContentAndHeader(AbstractOWLSelectionViewComponent.java:202)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.selectionChanged(AbstractOWLSelectionViewComponent.java:80)
    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:435)
    org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:334)
    org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:140)
    org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:253)
    org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:818)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner$1.run(OWLReasonerManagerImpl.java:430)
    java.awt.event.InvocationEvent.dispatch(Unknown Source)
    java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    java.awt.EventQueue.access$000(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.security.AccessController.doPrivileged(Native Method)
    java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(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)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Fri Jan 10 13:54:53 SGT 2014
NullPointerException: null
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection$1.run(OWLClassAssertionAxiomMembersSection.java:89)
    org.protege.editor.owl.model.inference.DisplayedInferencePreferences.executeTask(DisplayedInferencePreferences.java:119)
    org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:183)
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection.refillInferred(OWLClassAssertionAxiomMembersSection.java:80)
    org.protege.editor.owl.ui.frame.AbstractOWLFrameSection.setRootObject(AbstractOWLFrameSection.java:306)
    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:343)
    org.protege.editor.owl.ui.view.cls.OWLClassDescriptionViewComponent.updateView(OWLClassDescriptionViewComponent.java:57)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:36)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:19)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.updateViewContentAndHeader(AbstractOWLSelectionViewComponent.java:202)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.selectionChanged(AbstractOWLSelectionViewComponent.java:80)
    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:435)
    org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:346)
    org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:140)
    org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:253)
    org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:818)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$2.run(OWLReasonerManagerImpl.java:311)
    java.awt.event.InvocationEvent.dispatch(Unknown Source)
    java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    java.awt.EventQueue.access$000(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.security.AccessController.doPrivileged(Native Method)
    java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(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)
---------------------------------------------------------------------------------------------------

and I attached my ontology (still need more validation).
Whenever i open and start running the Pellet,
it popup with the red triangle warning message as above.
Thank you for any advises regarding this matters.
Hope to get some knowledge whether my structural ontology have problem
or any additional problem.



On Thu, Jan 9, 2014 at 9:52 PM, Timothy Redmond <[hidden email]> wrote:
On 01/08/2014 12:33 AM, mieza hamka wrote:
Greetings team of expert.

I have questions to ask.
I am currently running Pellet reasoner in Protege 4.3,
, at first it popup with list of red highlighted
property that inconsistent in my ontology.
And while the Pellet running, i delete the inconsistent 
property and try to synchronize back the reasoner.
But it point out with the red triangle warning symbol 
and i caught up with the NullPointerException: null.
How can i resolve this issues?
Thank you in advance for any suggestions.

To figure this out we will probably need a bit more information.  Without more information we can't tell if this is a pellet issue or a protege bug.  The minimal information that would get us started would be to see the full listing of the exception information that you see when you click on the red triangle.  Better would be to get a look at the logs with the exception (they are a bit awkward to get but they are in ".Protege/logs" under the home directory).

The other question would be if you see the null pointer exception if you restart Protege and then pellet. This would give a hint as to whether the exception comes from some issue with the synchronization logic.

Finally - if it is possible - best is to send a copy of the ontology with the steps to repeat the issue.

-Timothy




--
“Time is like a sword: if you don’t cut it, it will cut you. Second is yourself: if you don’t busy it with right, it will busy you with wrong.” --Imam Shafi'i


Best Regards,

Nurhamizah Binti Mohd Hamka
MC113037
Master in Science (Software Engineering)
Faculty of Computing
Universiti Teknologi Malaysia
Skudai, Johor


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback




--
“Time is like a sword: if you don’t cut it, it will cut you. Second is yourself: if you don’t busy it with right, it will busy you with wrong.” --Imam Shafi'i


Best Regards,

Nurhamizah Binti Mohd Hamka
MC113037
Master in Science (Software Engineering)
Faculty of Computing
Universiti Teknologi Malaysia
Skudai, Johor

_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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Re: Protege 4.3 Pellet reasoner show NullPointerException: null

Timothy Redmond

Thanks - this looks like it is a reasoner bug.  I will investigate it and see if it needs to be reported to the pellet group or if something else needs to happen.

Meanwhile, this bug does not appear to be fatal.  It prevents Protege from showing the full list of inferred members of the Thing class but otherwise the reasoner still seems to work.  In addition, the HermiT reasoner does not seem to have this problem.

I am assuming that since you sent us the ontology, I can forward this ontology to the pellet group for study?

-Timothy


On 01/09/2014 09:58 PM, mieza hamka wrote:
Thank you Sir.

Well.
This is the copy of the error from the Protege.

____________
Error 1 Logged at Fri Jan 10 13:54:53 SGT 2014
NullPointerException: null
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection$1.run(OWLClassAssertionAxiomMembersSection.java:89)
    org.protege.editor.owl.model.inference.DisplayedInferencePreferences.executeTask(DisplayedInferencePreferences.java:119)
    org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:183)
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection.refillInferred(OWLClassAssertionAxiomMembersSection.java:80)
    org.protege.editor.owl.ui.frame.AbstractOWLFrameSection.setRootObject(AbstractOWLFrameSection.java:306)
    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:343)
    org.protege.editor.owl.ui.view.cls.OWLClassDescriptionViewComponent.updateView(OWLClassDescriptionViewComponent.java:57)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:36)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:19)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.updateViewContentAndHeader(AbstractOWLSelectionViewComponent.java:202)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.selectionChanged(AbstractOWLSelectionViewComponent.java:80)
    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:435)
    org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:334)
    org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:140)
    org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:253)
    org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:818)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner$1.run(OWLReasonerManagerImpl.java:430)
    java.awt.event.InvocationEvent.dispatch(Unknown Source)
    java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    java.awt.EventQueue.access$000(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.security.AccessController.doPrivileged(Native Method)
    java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(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)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Fri Jan 10 13:54:53 SGT 2014
NullPointerException: null
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection$1.run(OWLClassAssertionAxiomMembersSection.java:89)
    org.protege.editor.owl.model.inference.DisplayedInferencePreferences.executeTask(DisplayedInferencePreferences.java:119)
    org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:183)
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection.refillInferred(OWLClassAssertionAxiomMembersSection.java:80)
    org.protege.editor.owl.ui.frame.AbstractOWLFrameSection.setRootObject(AbstractOWLFrameSection.java:306)
    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:343)
    org.protege.editor.owl.ui.view.cls.OWLClassDescriptionViewComponent.updateView(OWLClassDescriptionViewComponent.java:57)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:36)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:19)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.updateViewContentAndHeader(AbstractOWLSelectionViewComponent.java:202)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.selectionChanged(AbstractOWLSelectionViewComponent.java:80)
    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:435)
    org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:346)
    org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:140)
    org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:253)
    org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:818)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$2.run(OWLReasonerManagerImpl.java:311)
    java.awt.event.InvocationEvent.dispatch(Unknown Source)
    java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    java.awt.EventQueue.access$000(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.security.AccessController.doPrivileged(Native Method)
    java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(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)
---------------------------------------------------------------------------------------------------

and I attached my ontology (still need more validation).
Whenever i open and start running the Pellet,
it popup with the red triangle warning message as above.
Thank you for any advises regarding this matters.
Hope to get some knowledge whether my structural ontology have problem
or any additional problem.



On Thu, Jan 9, 2014 at 9:52 PM, Timothy Redmond <[hidden email]> wrote:
On 01/08/2014 12:33 AM, mieza hamka wrote:
Greetings team of expert.

I have questions to ask.
I am currently running Pellet reasoner in Protege 4.3,
, at first it popup with list of red highlighted
property that inconsistent in my ontology.
And while the Pellet running, i delete the inconsistent 
property and try to synchronize back the reasoner.
But it point out with the red triangle warning symbol 
and i caught up with the NullPointerException: null.
How can i resolve this issues?
Thank you in advance for any suggestions.

To figure this out we will probably need a bit more information.  Without more information we can't tell if this is a pellet issue or a protege bug.  The minimal information that would get us started would be to see the full listing of the exception information that you see when you click on the red triangle.  Better would be to get a look at the logs with the exception (they are a bit awkward to get but they are in ".Protege/logs" under the home directory).

The other question would be if you see the null pointer exception if you restart Protege and then pellet. This would give a hint as to whether the exception comes from some issue with the synchronization logic.

Finally - if it is possible - best is to send a copy of the ontology with the steps to repeat the issue.

-Timothy




--
“Time is like a sword: if you don’t cut it, it will cut you. Second is yourself: if you don’t busy it with right, it will busy you with wrong.” --Imam Shafi'i


Best Regards,

Nurhamizah Binti Mohd Hamka
MC113037
Master in Science (Software Engineering)
Faculty of Computing
Universiti Teknologi Malaysia
Skudai, Johor


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback




--
“Time is like a sword: if you don’t cut it, it will cut you. Second is yourself: if you don’t busy it with right, it will busy you with wrong.” --Imam Shafi'i


Best Regards,

Nurhamizah Binti Mohd Hamka
MC113037
Master in Science (Software Engineering)
Faculty of Computing
Universiti Teknologi Malaysia
Skudai, Johor


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback
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Re: Protege 4.3 Pellet reasoner show NullPointerException: null

Hamizah Hamka
Sir,
Thank you for your concern.
Before you forward the ontology, it is such an appreciation if you can validate my ontology.
The scope of my ontology is to come out with concept of
element that needs to be taken care of during evaluation of domain type of ontology.
I list out thing to consider during evaluating domain ontology for web service description 
and construct it in the form of ontology.
Any comments or idea regarding the structure or the elements within my ontology
are much appreciated.
And yeah, you can forward my ontology for the pellet group study.
Hope groups of experts successfully resolve the issue.
Thank you again Sir.
Wishing you a beautiful day ahead.



On Fri, Jan 10, 2014 at 8:09 PM, Timothy Redmond <[hidden email]> wrote:

Thanks - this looks like it is a reasoner bug.  I will investigate it and see if it needs to be reported to the pellet group or if something else needs to happen.

Meanwhile, this bug does not appear to be fatal.  It prevents Protege from showing the full list of inferred members of the Thing class but otherwise the reasoner still seems to work.  In addition, the HermiT reasoner does not seem to have this problem.

I am assuming that since you sent us the ontology, I can forward this ontology to the pellet group for study?

-Timothy



On 01/09/2014 09:58 PM, mieza hamka wrote:
Thank you Sir.

Well.
This is the copy of the error from the Protege.

____________
Error 1 Logged at Fri Jan 10 13:54:53 SGT 2014
NullPointerException: null
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection$1.run(OWLClassAssertionAxiomMembersSection.java:89)
    org.protege.editor.owl.model.inference.DisplayedInferencePreferences.executeTask(DisplayedInferencePreferences.java:119)
    org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:183)
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection.refillInferred(OWLClassAssertionAxiomMembersSection.java:80)
    org.protege.editor.owl.ui.frame.AbstractOWLFrameSection.setRootObject(AbstractOWLFrameSection.java:306)
    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:343)
    org.protege.editor.owl.ui.view.cls.OWLClassDescriptionViewComponent.updateView(OWLClassDescriptionViewComponent.java:57)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:36)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:19)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.updateViewContentAndHeader(AbstractOWLSelectionViewComponent.java:202)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.selectionChanged(AbstractOWLSelectionViewComponent.java:80)
    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:435)
    org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:334)
    org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:140)
    org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:253)
    org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:818)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner$1.run(OWLReasonerManagerImpl.java:430)
    java.awt.event.InvocationEvent.dispatch(Unknown Source)
    java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    java.awt.EventQueue.access$000(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.security.AccessController.doPrivileged(Native Method)
    java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(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)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Fri Jan 10 13:54:53 SGT 2014
NullPointerException: null
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection$1.run(OWLClassAssertionAxiomMembersSection.java:89)
    org.protege.editor.owl.model.inference.DisplayedInferencePreferences.executeTask(DisplayedInferencePreferences.java:119)
    org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:183)
    org.protege.editor.owl.ui.frame.cls.OWLClassAssertionAxiomMembersSection.refillInferred(OWLClassAssertionAxiomMembersSection.java:80)
    org.protege.editor.owl.ui.frame.AbstractOWLFrameSection.setRootObject(AbstractOWLFrameSection.java:306)
    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:343)
    org.protege.editor.owl.ui.view.cls.OWLClassDescriptionViewComponent.updateView(OWLClassDescriptionViewComponent.java:57)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:36)
    org.protege.editor.owl.ui.view.cls.AbstractOWLClassViewComponent.updateView(AbstractOWLClassViewComponent.java:19)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.updateViewContentAndHeader(AbstractOWLSelectionViewComponent.java:202)
    org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.selectionChanged(AbstractOWLSelectionViewComponent.java:80)
    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:435)
    org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:346)
    org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:140)
    org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:253)
    org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:818)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$2.run(OWLReasonerManagerImpl.java:311)
    java.awt.event.InvocationEvent.dispatch(Unknown Source)
    java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    java.awt.EventQueue.access$000(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.awt.EventQueue$1.run(Unknown Source)
    java.security.AccessController.doPrivileged(Native Method)
    java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(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)
---------------------------------------------------------------------------------------------------

and I attached my ontology (still need more validation).
Whenever i open and start running the Pellet,
it popup with the red triangle warning message as above.
Thank you for any advises regarding this matters.
Hope to get some knowledge whether my structural ontology have problem
or any additional problem.



On Thu, Jan 9, 2014 at 9:52 PM, Timothy Redmond <[hidden email]> wrote:
On 01/08/2014 12:33 AM, mieza hamka wrote:
Greetings team of expert.

I have questions to ask.
I am currently running Pellet reasoner in Protege 4.3,
, at first it popup with list of red highlighted
property that inconsistent in my ontology.
And while the Pellet running, i delete the inconsistent 
property and try to synchronize back the reasoner.
But it point out with the red triangle warning symbol 
and i caught up with the NullPointerException: null.
How can i resolve this issues?
Thank you in advance for any suggestions.

To figure this out we will probably need a bit more information.  Without more information we can't tell if this is a pellet issue or a protege bug.  The minimal information that would get us started would be to see the full listing of the exception information that you see when you click on the red triangle.  Better would be to get a look at the logs with the exception (they are a bit awkward to get but they are in ".Protege/logs" under the home directory).

The other question would be if you see the null pointer exception if you restart Protege and then pellet. This would give a hint as to whether the exception comes from some issue with the synchronization logic.

Finally - if it is possible - best is to send a copy of the ontology with the steps to repeat the issue.

-Timothy




--
“Time is like a sword: if you don’t cut it, it will cut you. Second is yourself: if you don’t busy it with right, it will busy you with wrong.” --Imam Shafi'i


Best Regards,

Nurhamizah Binti Mohd Hamka
MC113037
Master in Science (Software Engineering)
Faculty of Computing
Universiti Teknologi Malaysia
Skudai, Johor


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback




--
“Time is like a sword: if you don’t cut it, it will cut you. Second is yourself: if you don’t busy it with right, it will busy you with wrong.” --Imam Shafi'i


Best Regards,

Nurhamizah Binti Mohd Hamka
MC113037
Master in Science (Software Engineering)
Faculty of Computing
Universiti Teknologi Malaysia
Skudai, Johor


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback




--
“Time is like a sword: if you don’t cut it, it will cut you. Second is yourself: if you don’t busy it with right, it will busy you with wrong.” --Imam Shafi'i


Best Regards,

Nurhamizah Binti Mohd Hamka
MC113037
Master in Science (Software Engineering)
Faculty of Computing
Universiti Teknologi Malaysia
Skudai, Johor

_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback