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[protege-owl] Null Pointer Exception on Property URI rename/delete

Timothy Redmond tredmond at stanford.edu
Thu Apr 15 08:47:56 PDT 2010


Thank you for a very nice error report.  Everything that I could ask for 
is there.  So I can tell you one thing right off.  This error is an 
exception that is getting generated filling the client cache.  The name 
change has gone to the server and has presumably succeeded.  If you 
start another client after this happens you will see the refactor.

Unfortunately there are no line numbers (this is our issue and is out of 
your control) and I didn't manage to replicate the issue.  So I don't 
know exactly what caused the exception yet.

There is a bug fix in svn involving refactors of URI's and based purely 
on the behavior of Protege it doesn't look like that fix got into build 
572.  Also I saw that there are many refresh problems in the user 
interface when I change the name of a property.  It looks like the 
change went through but apparently Protege has trouble noticing that the 
name changed.

-Timothy



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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