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

Timothy Redmond tredmond at stanford.edu
Thu Apr 15 13:24:29 PDT 2010


> 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)?
Actually - better than that - this feature should be in the core 
protege.  But if you write such a plugin and we like it then we will 
include it in the default Protege distribution.

-Timothy



On 04/15/2010 01:01 PM, Gray, Trevor wrote:
>
> "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> 
> [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 
> <mailto: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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