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[protege-owl] Null Pointer Exception onProperty URIrename/delete

Gray, Trevor tgray at globalspec.com
Thu Apr 15 13:01:15 PDT 2010


"Is there any reason you can't update the client to 3.4.4?"

 

Other than I hadn't gotten around to it yet, nope.  I had no idea that it would make such a big difference.  

 

Using version 3.4.4 for the client seems to have fixed the issue.  This will be the first thing I check the next time someone has a problem.

 

Should I consider writing a plug-in so users who are connecting with a different version of Protégé will be notified (and prompted to install/use the correct one)?

 

Thanks!

-Trevor

 

________________________________

From: protege-owl-bounces at lists.stanford.edu [mailto:protege-owl-bounces at lists.stanford.edu] On Behalf Of Timothy Redmond
Sent: Thursday, April 15, 2010 3:40 PM
To: protege-owl at lists.stanford.edu
Subject: Re: [protege-owl] Null Pointer Exception onProperty URIrename/delete

 





"Is there anything else that might be a factor?"

The only one I can think of is that the server is running version 3.4.4 while the client is using 3.4.3.  You mentioned that "the server and the client would (probably) need to have the same version", is there a specific reason for this? 


This is very probably the problem.  The interfaces on the server and the client need to correspond.   The default behavior of java is to be very conservative about this.  So it is possible that what you are seeing is that we have not over-ridden this conservative behavior somewhere.  However if that were the case you would probably be seeing some other errors regarding bad serialization.  So I suspect that the difference is some real (probably small) difference in the behavior of the server and the client.

Is there any reason you can't update the client to 3.4.4?

-Timothy



On 04/15/2010 12:19 PM, Gray, Trevor wrote: 

"Does this exception occur consistently or is it rare?"

It happens every time.  Restarting the server and/or clients doesn't affect when the error fires.

 

 

"Is there anything else that might be a factor?"

The only one I can think of is that the server is running version 3.4.4 while the client is using 3.4.3.  You mentioned that "the server and the client would (probably) need to have the same version", is there a specific reason for this? 

 

I'm still in the evaluation/planning phase of integrating Protégé into our production processes.  I'll look into using the nightly build with the client first, then the server and test what happens in between.

 

-Trevor

 

________________________________

From: protege-owl-bounces at lists.stanford.edu [mailto:protege-owl-bounces at lists.stanford.edu] On Behalf Of Timothy Redmond
Sent: Thursday, April 15, 2010 1:27 PM
To: protege-owl at lists.stanford.edu
Subject: Re: [protege-owl] Null Pointer Exception on Property URIrename/delete

 


So I didn't talk about how to move forward on this issue.   We will continue to try to replicate it here.  (It is still the start of the day and I just did a quick test.)  One question about this - does this exception occur consistently or is it rare?  Is there anything else that might be a factor?

One approach - depending on your needs - is that you pull a nightly Protege build and run that.  This may not make sense for you and it includes a different set of plugins than the distribution.  Also the server and the client would (probably) need to have the same version of Protege.  But we would get line numbers and the line number would probably tell us what happened.

-Timothy

[1] http://smi-protege.stanford.edu/protege3/Protege-3-nightly.zip


On 04/14/2010 08:11 AM, Gray, Trevor wrote: 

Problem/Error

-------------

 

When I change the URI of an Object/Data Property I get a NullPointerException (see below for the trace). Also, I can't set the property back to its original URI (the URI string turns red in the UI and won't let me submit the change).  I get a similar error when I delete a Property.

 

Things to Note

--------------

 

- The client is connected over the LAN to a protégé server.  

- This first happened while working with a collaborative project that is stored in an OWL/RDF database.

- This also happens with the collaborative pizza project, which isn't stored in a database.

- This also happens with a non-collaborative pizza project on the server.

- This does not happen with a local (non-server), non-collaborative project.

- I get the same error for both Object and Data Properties.

- I do not get an error when renaming or deleting Classes.

- Once I reload the project I can change back to the original URI, but get the same error message and issues.

 

>From these bullets I guess that the issue is with the protégé server having trouble committing changes to Properties submitted by the clients.

 

Any ideas on what the issue is, or how I can go about fixing it will be greatly appreciated!

 

Sincerely,

Trevor Gray

 

 

Protégé/Project Info

--------------------

 

Protege 3.4.3 Build 572, JVM 1.5.0_11-b03, memory=520M, Windows XP, encoding=UTF-8, language=en, country=US

Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin

Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya

Loaded plugin dfki.protege.ontoviz

Loaded plugin edu.stanford.smi.protegex.standard_extensions - Graph Widget, Table Widget

Loaded plugin edu.stanford.bmir.protegex.bp.ref - BioPortal Reference Plugin

Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF Backend

Loaded plugin edu.stanford.smi.protegex.changes - Changes tab

Loaded plugin edu.stanford.smi.protegex.chatPlugin - Chat

Loaded plugin edu.stanford.smi.protege.collab - Collaborative Protege

Loaded plugin edu.stanford.smi.protege.script - Script Plugin

Loaded plugin edu.stanford.smi.protege.stringsearch - String Search Tab

Loaded plugin edu.stanford.smi.protegex.datamaster - DataMaster Tab

Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs

Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab

Loaded plugin edu.stanford.smi.protegex.facets_tab

Loaded plugin edu.stanford.smi.protegex.instance_tree

Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab

Loaded plugin edu.stanford.smi.protegex.metaanalysis - MetaAnalysis Tab

Loaded plugin edu.stanford.smi.protegex.owl.inference.pellet - Protege Pellet Reasoner

Loaded plugin edu.stanford.smi.protegex.query.lucene - LuceneQueryTab

Loaded plugin edu.stanford.smi.protegex.umls_tab - UMLS Tab

Loaded plugin edu.stanford.smi.protegex.wordnet - WordNet Tab

Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab

Loaded plugin org.algernon - Algernon

Loaded plugin org.protege.owl.axiome - Axiome Plugin

Loaded plugin org.protege.owl.mappingmaster - MappingMaster Plugin

Loaded plugin se.liu.ida.JessTab - JessTab Plugin

Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab

Loaded plugin uk.ac.man.cs.mig.coode.debugger

Loaded plugin uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor

Loaded plugin uk.ac.man.cs.mig.coode.owldoc

Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab

Loaded plugin uk.ac.man.cs.mig.coode.owlviz

Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic Wizards

Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl - OWL Wizards

Preloading frame values: OWLDatabaseModel(KB_080337)

Preloading frame values: DefaultKnowledgeBase(KB_589606)

Started Collaborative Protege on Wed Apr 14 09:43:53 EDT 2010

Preloading frame values: DefaultKnowledgeBase(KB_286730)

Preloading frame values: DefaultKnowledgeBase(KB_456634)

UI display time = 9 sec

 

 

Rename Error

------------

 

SEVERE: Exception caught -- java.lang.NullPointerException

        at edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.processValueUpdate(Unknown Source)

        at edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.replaceFrame(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.replaceFrame(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.replaceFrame(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.replaceFrame(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.replaceFrame(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.replaceFrame(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.replaceFrame(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.DefaultFrameFactory.rename(Unknown Source)

        at edu.stanford.smi.protege.model.DefaultKnowledgeBase.rename(Unknown Source)

        at edu.stanford.smi.protege.model.DefaultFrame.rename(Unknown Source)

        at edu.stanford.smi.protege.model.DefaultSlot.rename(Unknown Source)

        at edu.stanford.smi.protege.model.DefaultSlot.rename(Unknown Source)

        at edu.stanford.smi.protegex.owl.ui.resourcedisplay.InstanceNameEditor.attemptCommit(Unknown Source)

        at edu.stanford.smi.protegex.owl.ui.resourcedisplay.InstanceNameEditor$4.keyPressed(Unknown Source)

        at java.awt.Component.processKeyEvent(Unknown Source)

        at javax.swing.JComponent.processKeyEvent(Unknown Source)

        at java.awt.Component.processEvent(Unknown Source)

        at java.awt.Container.processEvent(Unknown Source)

        at java.awt.Component.dispatchEventImpl(Unknown Source)

        at java.awt.Container.dispatchEventImpl(Unknown Source)

        at java.awt.Component.dispatchEvent(Unknown Source)

        at java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)

        at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(Unknown Source)

 

        at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(Unknown Source)

        at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Source)

        at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)

        at java.awt.Component.dispatchEventImpl(Unknown Source)

        at java.awt.Container.dispatchEventImpl(Unknown Source)

        at java.awt.Window.dispatchEventImpl(Unknown Source)

        at java.awt.Component.dispatchEvent(Unknown Source)

        at java.awt.EventQueue.dispatchEvent(Unknown Source)

        at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)

 

        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)

        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

        at java.awt.EventDispatchThread.run(Unknown Source)

 

 

Delete Error

------------

 

SEVERE: Exception caught -- java.lang.NullPointerException

        at edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.processValueUpdate(Unknown Source)

        at edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.deleteSlot(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.deleteSlot(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.deleteSlot(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.deleteSlot(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.deleteSlot(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.deleteSlot(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.deleteSlot(Unknown Source)

        at edu.stanford.smi.protege.model.DefaultKnowledgeBase.deleteSlot(Unknown Source)

        at edu.stanford.smi.protege.model.DefaultKnowledgeBase.deleteFrame(Unknown Source)

        at edu.stanford.smi.protege.model.DefaultFrame.delete(Unknown Source)

        at edu.stanford.smi.protegex.owl.ui.properties.OWLSubpropertyPane.handleDelete(Unknown Source)

        at edu.stanford.smi.protegex.owl.ui.properties.OWLSubpropertyPane$8.onDelete(Unknown Source)

        at edu.stanford.smi.protege.util.DeleteAction.onDelete(Unknown Source)

        at edu.stanford.smi.protege.util.DeleteAction.actionPerformed(Unknown Source)

        at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)

        at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)

        at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)

        at javax.swing.DefaultButtonModel.setPressed(Unknown Source)

        at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)

        at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)

        at java.awt.Component.processMouseEvent(Unknown Source)

        at javax.swing.JComponent.processMouseEvent(Unknown Source)

        at java.awt.Component.processEvent(Unknown Source)

        at java.awt.Container.processEvent(Unknown Source)

        at java.awt.Component.dispatchEventImpl(Unknown Source)

        at java.awt.Container.dispatchEventImpl(Unknown Source)

        at java.awt.Component.dispatchEvent(Unknown Source)

        at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)

        at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)

        at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)

        at java.awt.Container.dispatchEventImpl(Unknown Source)

        at java.awt.Window.dispatchEventImpl(Unknown Source)

        at java.awt.Component.dispatchEvent(Unknown Source)

        at java.awt.EventQueue.dispatchEvent(Unknown Source)

        at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)

 

        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)

        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

        at java.awt.EventDispatchThread.run(Unknown Source)

 
 
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