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[protege-owl] import problem in b504

Tania Tudorache tudorache at stanford.edu
Tue Feb 3 12:09:50 PST 2009


Hi Ralf,

I know it's been a long time, but this problem should be fixed in the 
next beta release. You should be able to upgrade to 5.4 beta > 520. At 
least the imports work fine.

Tania


Ralf Weinand wrote:
> Hi Tania,
>
> thanks a lot.
>
> Yes, the two xxxInput.owl files themselves (without the context of the 
> other files),
> contain a lot of "undefined" entities. But they refer to concepts 
> defined in the other
> files. So if everything gets imported into one big model, Protege 
> should not need
> to guess anymore, but should know what is meant.
> Isn´t that right?
>
> At the moment I´m still working with b130, since b504 is to unstable 
> for my use cases.
> When do you expect the next release of Protege?
>
> Cheers,
> Ralf
>
>
>
> On Fri, Jul 11, 2008 at 3:16 AM, Tania Tudorache 
> <tudorache at stanford.edu <mailto:tudorache at stanford.edu>> wrote:
>
>     Hi Ralf,
>
>     Thanks a lot for the bug report. We'll fix the problem and get
>     back to you.
>
>     It might be that SWRL did not convert all individuals, because of the
>     loading problems.
>
>     The file that you sent me is somewhere at the limit of the parser,
>     because all entities in it are undefined. So the parser has to make a
>     lot of guess of the type of entities. The parser does handle untyped
>     entities, but in your ontology, everything is untyped, and some
>     heuristics used by the parser to guess the type were not handling this
>     case well.
>
>     Tania
>
>
>     Ralf Weinand wrote:
>     > Hi,
>     >
>     > I had a problem in protege 3.4 b130 with transfering knowledge from
>     > OWL to Jess
>     > (the problem was that not all individuals got transfered) so I tried
>     > the latest build 504,
>     > but there even the steps before failed.
>     >
>     > I did want to perform the following steps:
>     > 1. Open file Composition1Input.owl
>     > 2. Import from file: GetResidentInfoInput.owl  [THIS FAILED IN
>     PROTEGE
>     > b504]
>     > 3. Import from file: dataflow4GetResidentInfoInput.owl
>     > 4. OWL --> Jess [NOT ALL INDIVIDUALS COPIED IN b130]
>     > 5. RUN Jess
>     > 6. Jess --> OWL
>     > (You need the ServiceAnchor.owl in a lokal Web Server.)
>     >
>     > The interesting thing is that, when I do this in b130 and save
>     the project
>     > and load the project in b504, then the import works, but SWRL
>     TAB throws
>     > the following exception at step 4:
>     >
>     > Exception importing SWRL rules and OWL knowledge:
>     >
>     edu.stanford.smi.protegex.owl.swrl.bridge.exceptions.OWLFactoryException:
>     > empty property name in SWRLDatavaluedPropertyAtom
>     > 'rdfs:label(?p2:Composition1, "Composition1Process")'
>     >
>     > Cheers,
>     > Ralf
>     >
>     > PS: I know that the XXXInput.owl files to not conform to the
>     OWL-files
>     > generated by Protege.
>     > I get these ontologies from another system, so I (respectively
>     > protege) have to cope with it...
>     >
>     >
>     > The following exception was thrown in b504 at the second step:
>     >
>     > Postprocess: Possibly typed entities (19 resources) ... WARNING:
>     Wrong
>     > type: Def
>     > aultRDFIndividual(@PARSE_A0 of
>     > [DefaultRDFSNamedClass(http://localhost:8080/onto
>     > logies/ServiceAnchor.owl#Process)]) --
>     > DefaultKnowledgeBase.getFrameOfType()
>     > WARNING: Exception caught java.lang.NullPointerException --
>     > EventDispatchFrameSt
>     > ore.dispatchEvents()
>     > WARNING: use fine logging for more details --
>     > EventDispatchFrameStore.dispatchEv
>     > ents()
>     > WARNING: Wrong type: DefaultRDFIndividual(@PARSE_A3 of
>     > [DefaultRDFSNamedClass(ht
>     >
>     tp://localhost:8080/PublicServices/ResidentRegistry/ResidentRegistryOntology.owl
>     > #Birth)]) -- DefaultKnowledgeBase.getFrameOfType()
>     > WARNING: Exception caught java.lang.NullPointerException --
>     > EventDispatchFrameSt
>     > ore.dispatchEvents()
>     > WARNING: use fine logging for more details --
>     > EventDispatchFrameStore.dispatchEv
>     > ents()
>     > WARNING: Wrong type: DefaultOWLIndividual(@PARSE_A1 of
>     > [DefaultOWLNamedClass(htt
>     > p://localhost:8080/ontologies/ServiceAnchor.owl#Input)]) --
>     > DefaultKnowledgeBase
>     > .getFrameOfType()
>     > WARNING: Exception caught java.lang.NullPointerException --
>     > EventDispatchFrameSt
>     > ore.dispatchEvents()
>     > WARNING: use fine logging for more details --
>     > EventDispatchFrameStore.dispatchEv
>     > ents()
>     > 60 ms
>     > Updating underlying frames model in 0 ms
>     > java.lang.NullPointerException
>     >         at
>     >
>     edu.stanford.smi.protegex.owl.ui.cls.ClassTreeNode.dispose(Unknown So
>     > urce)
>     >         at
>     edu.stanford.smi.protege.util.LazyTreeNode.dispose(Unknown
>     > Source)
>     >         at
>     >
>     edu.stanford.smi.protegex.owl.ui.cls.ClassTreeNode.dispose(Unknown So
>     > urce)
>     >         at
>     edu.stanford.smi.protege.util.LazyTreeNode.dispose(Unknown
>     > Source)
>     >         at
>     > edu.stanford.smi.protege.util.LazyTreeModel.removeRoot(Unknown
>     Source
>     > )
>     >         at
>     edu.stanford.smi.protege.util.LazyTreeModel.dispose(Unknown
>     > Source)
>     >         at
>     > edu.stanford.smi.protege.util.SelectableTree.dispose(Unknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities$1.apply(Unknown
>     Sour
>     > ce)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     >
>     edu.stanford.smi.protege.util.ComponentUtilities.applyToDescendents(U
>     > nknown Source)
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.apply(Unknown
>     Source
>     > )
>     >         at
>     > edu.stanford.smi.protege.util.ComponentUtilities.dispose(Unknown
>     Sour
>     > ce)
>     >         at edu.stanford.smi.protege.ui.ProjectView.reloadAll(Unknown
>     > Source)
>     >         at
>     edu.stanford.smi.protege.ui.ProjectView.reload(Unknown Source)
>     >         at
>     edu.stanford.smi.protegex.owl.ui.ProtegeUI.reloadUI(Unknown
>     > Source)
>     >         at
>     edu.stanford.smi.protegex.owl.ui.ProtegeUI.reloadUI(Unknown
>     > Source)
>     >         at
>     edu.stanford.smi.protegex.owl.ui.ProtegeUI.reloadUI(Unknown
>     > Source)
>     >         at
>     >
>     edu.stanford.smi.protegex.owl.model.util.ImportHelper.importOntologie
>     > s(Unknown Source)
>     >         at
>     >
>     edu.stanford.smi.protegex.owl.model.util.ImportHelper.importOntologie
>     > s(Unknown Source)
>     >         at
>     >
>     edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.addImpo
>     > rt(Unknown Source)
>     >         at
>     >
>     edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.access$
>     > 100(Unknown Source)
>     >         at
>     >
>     edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel$2.actio
>     > nPerformed(Unknown Source)
>     >         at
>     >
>     javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:18
>     > 49)
>     >         at
>     >
>     javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.jav
>     > a:2169)
>     >         at
>     >
>     javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel
>     > .java:420)
>     >         at
>     >
>     javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258
>     > )
>     >         at
>     >
>     javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonL
>     > istener.java:236)
>     >         at
>     >
>     java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:2
>     > 31)
>     >         at java.awt.Component.processMouseEvent(Component.java:5517)
>     >         at
>     javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
>     >         at java.awt.Component.processEvent(Component.java:5282)
>     >         at java.awt.Container.processEvent(Container.java:1966)
>     >         at java.awt.Component.dispatchEventImpl(Component.java:3984)
>     >         at java.awt.Container.dispatchEventImpl(Container.java:2024)
>     >         at java.awt.Component.dispatchEvent(Component.java:3819)
>     >         at
>     >
>     java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212
>     > )
>     >         at
>     >
>     java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
>     >
>     >         at
>     > java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
>     >         at java.awt.Container.dispatchEventImpl(Container.java:2010)
>     >         at java.awt.Window.dispatchEventImpl(Window.java:1791)
>     >         at java.awt.Component.dispatchEvent(Component.java:3819)
>     >         at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>     >         at
>     >
>     java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchTh
>     > read.java:242)
>     >         at
>     >
>     java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
>     > ad.java:163)
>     >         at
>     >
>     java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
>     >
>     >         at
>     >
>     java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
>     >
>     >         at
>     java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>     > WARNING: Exception caught by default exception handler --
>     > java.lang.NullPointerE
>     > xception
>     >         at
>     edu.stanford.smi.protege.ui.FrameRenderer.load(Unknown Source)
>     >         at
>     > edu.stanford.smi.protegex.owl.ui.ResourceRenderer.load(Unknown
>     Source
>     > )
>     >         at
>     edu.stanford.smi.protege.util.DefaultRenderer.setup(Unknown
>     > Source)
>     >         at
>     >
>     edu.stanford.smi.protege.util.DefaultRenderer.getTreeCellRendererComp
>     > onent(Unknown Source)
>     >         at
>     >
>     javax.swing.plaf.basic.BasicTreeUI$NodeDimensionsHandler.getNodeDimen
>     > sions(BasicTreeUI.java:2693)
>     >         at
>     >
>     javax.swing.tree.AbstractLayoutCache.getNodeDimensions(AbstractLayout
>     > Cache.java:475)
>     >         at
>     >
>     javax.swing.tree.FixedHeightLayoutCache.getBounds(FixedHeightLayoutCa
>     > che.java:535)
>     >         at
>     >
>     javax.swing.tree.FixedHeightLayoutCache.getBounds(FixedHeightLayoutCa
>     > che.java:181)
>     >         at
>     >
>     javax.swing.tree.AbstractLayoutCache.getPreferredWidth(AbstractLayout
>     > Cache.java:228)
>     >         at
>     >
>     javax.swing.plaf.basic.BasicTreeUI.updateCachedPreferredSize(BasicTre
>     > eUI.java:1731)
>     >         at
>     >
>     javax.swing.plaf.basic.BasicTreeUI.getPreferredSize(BasicTreeUI.java:
>     > 1901)
>     >         at
>     >
>     javax.swing.plaf.basic.BasicTreeUI.getPreferredSize(BasicTreeUI.java:
>     > 1889)
>     >         at
>     javax.swing.JComponent.getPreferredSize(JComponent.java:1624)
>     >         at
>     >
>     javax.swing.ScrollPaneLayout.layoutContainer(ScrollPaneLayout.java:76
>     > 9)
>     >         at java.awt.Container.layout(Container.java:1401)
>     >         at java.awt.Container.doLayout(Container.java:1390)
>     >         at java.awt.Container.validateTree(Container.java:1473)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validateTree(Container.java:1480)
>     >         at java.awt.Container.validate(Container.java:1448)
>     >         at
>     >
>     javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.j
>     > ava:379)
>     >         at
>     >
>     javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(System
>     > EventQueueUtilities.java:113)
>     >         at
>     > java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>     >         at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
>     >         at
>     >
>     java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchTh
>     > read.java:242)
>     >         at
>     >
>     java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
>     > ad.java:163)
>     >         at
>     >
>     java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
>     >
>     >         at
>     >
>     java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
>     >
>     >         at
>     java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>     >
>     >
>     >
>     ------------------------------------------------------------------------
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