Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Stephen Larson slarson at ucsd.edu
Mon Aug 13 18:48:26 PDT 2007


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>
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>

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

mitTransaction(Unknown Source)
        at
edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore .
commitTransaction(Unknown Source)
        at 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()
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/protege-owl/attachments/20070813/f8837f1c/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: nullpointer.png
Type: image/png
Size: 6133 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/protege-owl/attachments/20070813/f8837f1c/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: search.png
Type: image/png
Size: 5011 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/protege-owl/attachments/20070813/f8837f1c/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: sao(3).owl
Type: application/octet-stream
Size: 896827 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/protege-owl/attachments/20070813/f8837f1c/attachment.owl>


More information about the protege-owl mailing list