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[protege-owl] Fwd: Exception thrown in Multi-user Protege

Timothy Redmond tredmond at stanford.edu
Tue Aug 21 11:32:52 PDT 2007


I apologize for not getting back to you (twice).  Your message was an 
excellent bug report with all the information we needed to analyze the 
problem.

Tania helped me debug this.  You are experiencing a bug that Tania has 
recently fixed.  If you go to the latest svn (get protege core and 
protege owl) or you wait for a release coming very soon this will be fixed.

In 414, if you have a file based project and turn on change tracking 
then all commits and rollbacks end up throwing a null pointer 
exception.  It turns out that (having analyzed what happened) the 
operations you were doing succeeded but you will get an exception every 
time.  (Also - of course - you don't have any way of knowing that these 
exceptions are harmless...)

-Timothy




Stephen Larson wrote:
> Hi Protege Team,
>
>    Did you ever get a chance to look at this?  Is there some better 
> place for me to file this bug report?
>
> Thanks,
>   Stephen
>
> ---------- Forwarded message ----------
> From: *Stephen Larson* <slarson at ucsd.edu <mailto:slarson at ucsd.edu>>
> Date: Jul 27, 2007 1:17 PM
> Subject: Exception thrown in Multi-user Protege
> To: User support for the Protege-OWL editor < 
> protege-owl at mailman.stanford.edu 
> <mailto:protege-owl at mailman.stanford.edu>>
>
> Hi,
>
>    I'm getting a scary exception thrown when using the client-server 
> mode of Protege, and I think it has been responsible for corrupting 
> our ontology file.  The error is pictured in nullpointer.png , 
> attached.  The ontology we are using is available at 
> http://ccdb.ucsd.edu/SAO/1.2/SAO.owl.  We have created an annotation 
> ontology for it using the steps described on the collaborative Protege 
> page.  We have also changed the label to the rdfs:label on the server 
> side.  Before the error popped up, I created a new class under "Cell" 
> using the button to create a child subclass.  Then I removed the 
> class.  This is when the error popped up.  These were the only things 
> that we had done in a client-server session.. so it should be 
> reproducible.
>
>    I'm including the result of using the annotation tab to "search" 
> without any arguments, to show what changes the ontology has 
> experienced.  Note that there are "missing frame name" warnings in there.
>
>    The exception shown in the java console (on the client side) is 
> pasted below.
>
>    I'm also attaching a corrupted version of the same ontology we are 
> using.  This corruption did not result from this error this time.  But 
> some other series of events led to it being corrupted before.  We are 
> only using a file-based project on the server end, and we have set it 
> to save at regular intervals.  We are using build 414.
>
> Thanks,
>    Stephen
>
>
> ********************EXCEPTION FOLLOWS:**********************
>
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>         at 
> edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.rol
> lbackTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.
> rollbackTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.rol
> lbackTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.rollbackT
> ransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.rollbackT
> ransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.rollbackT
> ransaction(Unknown Source)
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
>         at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown 
> Source)
>         at java.lang.reflect.Method.invoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocatio
> nHandler.invoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocatio
> nHandler.invoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.framestore.LocalizeFrameStoreHandler.
> handleInvoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocatio
> nHandler.invoke(Unknown Source)
>         at $Proxy0.rollbackTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.framestore.ServerFrameStore.rollbackT
> ransaction(Unknown Source)
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
>         at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
>         at java.lang.reflect.Method.invoke(Unknown Source)
>         at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source)
>         at sun.rmi.transport.Transport$1.run(Unknown Source)
>         at java.security.AccessController.doPrivileged (Native Method)
>         at sun.rmi.transport.Transport.serviceCall(Unknown Source)
>         at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown 
> Source)
>         at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0 
> (Unknown Sou
> rce)
>         at 
> sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Sour
> ce)
>         at 
> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source
> )
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run (Unknown 
> Source)
>         at java.lang.Thread.run(Unknown Source)
>         at 
> sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(Unknow
> n Source)
>         at sun.rmi.transport.StreamRemoteCall.executeCall (Unknown Source)
>         at sun.rmi.server.UnicastRef.invoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.framestore.ServerFrameStore_Stub.roll
> backTransaction(Unknown Source)
>         at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
>         at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
>         at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
>         at java.lang.reflect.Method.invoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore$2.i
> nvoke(Unknown Source)
>         at $Proxy1.rollbackTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.rol
> lbackTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.rol
> lbackTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore .
> rollbackTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.rol
> lbackTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.rollbackT
> ransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.rollbackT
> ransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.DefaultKnowledgeBase.rollbackTransacti
> on(Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.ui.cls.CreateSubclassAction.performActi
> on(Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.ui.cls.AssertedClassesPanel.createSubcl
> ass(Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.ui.cls.AssertedClassesPanel.access$100(
> Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.ui.cls.AssertedClassesPanel$2.actionPer
> formed(Unknown Source)
>         at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>         at javax.swing.AbstractButton$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 Sour
> ce)
>         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)
> SEVERE: Exception caught -- java.lang.NullPointerException
>         at 
> edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.com 
> <http://edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.com>
> mitTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore .
> commitTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.com 
> <http://edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.com>
> mitTransaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.commitTra
> nsaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.commitTra
> nsaction(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameSt
> ore.deleteCls(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.deleteCls
> (Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.model.framestore.OWLFrameStore.deleteNa
> medClass(Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.model.framestore.OWLFrameStore.deleteCl
> s(Unknown Source)
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
>         at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown 
> Source)
>         at java.lang.reflect.Method.invoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocatio
> nHandler.invoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocatio
> nHandler.invoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.framestore.LocalizeFrameStoreHandler.
> handleInvoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocatio
> nHandler.invoke(Unknown Source)
>         at $Proxy0.deleteCls(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.framestore.ServerFrameStore.deleteCls
> (Unknown Source)
>         at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
>         at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
>         at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
>         at java.lang.reflect.Method.invoke(Unknown Source)
>         at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source)
>         at sun.rmi.transport.Transport$1.run(Unknown Source)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at sun.rmi.transport.Transport.serviceCall(Unknown Source)
>         at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown 
> Source)
>         at 
> sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(Unknown Sou
> rce)
>         at 
> sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Sour
> ce)
>         at 
> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source
> )
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run (Unknown 
> Source)
>         at java.lang.Thread.run(Unknown Source)
>         at 
> sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(Unknow
> n Source)
>         at sun.rmi.transport.StreamRemoteCall.executeCall (Unknown Source)
>         at sun.rmi.server.UnicastRef.invoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.framestore.ServerFrameStore_Stub.dele
> teCls(Unknown Source)
>         at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
>         at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
>         at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
>         at java.lang.reflect.Method.invoke(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore$2.i
> nvoke(Unknown Source)
>         at $Proxy1.deleteCls(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.del
> eteCls(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.del
> eteCls(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.
> deleteCls(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.del
> eteCls(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.deleteCls
> (Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameSt
> ore.deleteFrame(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameSt
> ore.internalDeleteFrame(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameSt
> ore.internalDeleteInstance(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameSt
> ore.internalDeleteCls(Unknown Source)
>         at 
> edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameSt
> ore.deleteCls(Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.model.impl.AbstractOWLModel.deleteCls (U
> nknown Source)
>         at 
> edu.stanford.smi.protege.model.DefaultKnowledgeBase.deleteFrame(Unkno
> wn Source)
>         at edu.stanford.smi.protege.model.DefaultFrame.delete(Unknown 
> Source)
>         at 
> edu.stanford.smi.protegex.owl.ui.cls.DeleteClassAction.performAction (
> Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.ui.cls.AssertedClassesPanel$AllowableDe
> leteAction.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 Sour
> ce)
>         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)
>
> WARNING: Cannot find current name for Created and Deleted Object -- 
> ChangesKbFra
> meListener.updateCaches()
>
> ------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------
>
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