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[p4-feedback] OWL file transformation

Timothy Redmond tredmond at stanford.edu
Thu Dec 16 08:55:25 PST 2010


> I have tried to do a bit of reading regarding bundles, although I have 
> learnt a bit this option has proved less than fruitful. Can anyone 
> please explain
>

Use a more recent version of Protege - this bug is nasty and has since 
been fixed.

I remembered it right away but it took longer for me to remember the 
cause of the bug.  It occurs when you double click an OWL file.  The 
problem is that Protege is layered on the Felix OSGi implementation.  
The bundles that you see generated have nothing to do with the OWL 
file.  They are Felix's response to the double click operation.

-Timothy


On 12/15/2010 09:46 AM, McGibbney, Lewis John wrote:
>
> Hi List,
>
> I have recently been constructing an ontology using 4.1 alpha using 
> Windows XP. I downloaded the OWLviz plug-in along with Graphviz 2.26.3 
> and configured the DOT application path to the 
> ProgramFiles\Graphviz\bin\dot application, however upon restarting 
> Protégé, my saved ontology has transformed from an OWL file to a 
> folder named after my ontology ending in .owl! The folder contains 16 
> bundles which all have the following contents
>
> Folder: version0.0
>
> File: bundle.id
>
> File:bundle.lastmodified
>
> File: bundle.location
>
> File: bundle.startlevel
>
> File: bundle.state
>
> When I try to open my ontology at the Protégé start-up screen I see 
> the following output
>
> Error 1 Logged at Wed Dec 15 17:41:16 GMT 2010
>
> NullPointerException: null
>
>     java.util.Hashtable.put(Unknown Source)
>
>     javax.swing.text.SimpleAttributeSet.addAttribute(Unknown Source)
>
>     javax.swing.text.StyleContext.addAttribute(Unknown Source)
>
>     javax.swing.text.StyleContext$NamedStyle.addAttribute(Unknown Source)
>
>     javax.swing.text.StyleConstants.setForeground(Unknown Source)
>
>     
> org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareStyles(OWLCellRenderer.java:597) 
>
>
>     
> org.protege.editor.owl.ui.renderer.OWLCellRenderer.<init>(OWLCellRenderer.java:144) 
>
>
>     
> org.protege.editor.owl.model.OWLWorkspace.createOWLCellRenderer(OWLWorkspace.java:826) 
>
>
>     
> org.protege.editor.owl.model.OWLWorkspace.createOWLCellRenderer(OWLWorkspace.java:821) 
>
>
>     
> org.protege.editor.owl.ui.find.EntityFinderField.<init>(EntityFinderField.java:77) 
>
>
>     
> org.protege.editor.owl.model.OWLWorkspace.createActiveOntologyPanel(OWLWorkspace.java:629) 
>
>
>     
> org.protege.editor.owl.model.OWLWorkspace.initialise(OWLWorkspace.java:201) 
>
>
>     
> org.protege.editor.owl.OWLEditorKit.getWorkspace(OWLEditorKit.java:113)
>
>     
> org.protege.editor.owl.ui.error.OntologyLoadErrorHandlerUI.handleErrorLoadingOntology(OntologyLoadErrorHandlerUI.java:99) 
>
>
>     
> org.protege.editor.owl.model.OWLModelManagerImpl.finishedLoadingOntology(OWLModelManagerImpl.java:336) 
>
>
>     
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.fireFinishedLoadingEvent(OWLOntologyManagerImpl.java:1049) 
>
>
>     
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:656) 
>
>
>     
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:590) 
>
>
>     
> org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:313) 
>
>
>     
> org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:152)
>
>     
> org.protege.editor.owl.OWLEditorKit.handleLoadRecentRequest(OWLEditorKit.java:140) 
>
>
>     
> org.protege.editor.core.ProtegeManager.openAndSetupRecentEditorKit(ProtegeManager.java:173) 
>
>
>     
> org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$6.actionPerformed(ProtegeWelcomeFrame.java:264) 
>
>
>     
> org.protege.editor.core.ui.util.LinkLabel.activateLink(LinkLabel.java:102) 
>
>
>     
> org.protege.editor.core.ui.util.LinkLabel.access$100(LinkLabel.java:30)
>
>     
> org.protege.editor.core.ui.util.LinkLabel$1.mouseReleased(LinkLabel.java:68) 
>
>
>     java.awt.Component.processMouseEvent(Unknown Source)
>
>     javax.swing.JComponent.processMouseEvent(Unknown Source)
>
>     java.awt.Component.processEvent(Unknown Source)
>
>     java.awt.Container.processEvent(Unknown Source)
>
>     java.awt.Component.dispatchEventImpl(Unknown Source)
>
>     java.awt.Container.dispatchEventImpl(Unknown Source)
>
>     java.awt.Component.dispatchEvent(Unknown Source)
>
>     java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
>
>     java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
>
>     java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
>
>     java.awt.Container.dispatchEventImpl(Unknown Source)
>
>     java.awt.Window.dispatchEventImpl(Unknown Source)
>
>     java.awt.Component.dispatchEvent(Unknown Source)
>
>     java.awt.EventQueue.dispatchEvent(Unknown Source)
>
>     java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
>
>     java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>
>     java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
>
>     java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>
>     java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>
>     java.awt.EventDispatchThread.run(Unknown Source)
>
> I have tried to do a bit of reading regarding bundles, although I have 
> learnt a bit this option has proved less than fruitful. Can anyone 
> please explain
>
> Thank you
>
> Lewis
>
>
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>
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