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[p4-feedback] Protege 4.1 seems to be hanging when I load ontology

McGibbney, Lewis John Lewis.McGibbney at gcu.ac.uk
Thu Apr 28 04:39:28 PDT 2011


Hi Timothy,

>I wasn't able to replicate your exact situation.   Does it happen with
any ontology (e.g. pizza? [1])?

Yes it does, I get the following if I try to open the ontology in [1]

org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.


Full Stack Trace
-----------------------------------------------------------------------------------------

org.coode.owlapi.rdfxml.parser.OWLRDFXMLParserSAXException: org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.
        at org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:90)
        at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:687)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:644)
        at org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:317)
        at org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:179)
        at org.protege.editor.core.ProtegeManager.loadAndSetupEditorKitFromURI(ProtegeManager.java:179)
        at org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel.handleOpenFromURI(ProtegeWelcomeFrame.java:188)
        at org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel.access$000(ProtegeWelcomeFrame.java:71)
        at org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$3.actionPerformed(ProtegeWelcomeFrame.java:146)
        at org.protege.editor.core.ui.util.LinkLabel.activateLink(LinkLabel.java:102)
        at org.protege.editor.core.ui.util.LinkLabel.access$100(LinkLabel.java:30)
        at org.protege.editor.core.ui.util.LinkLabel$1.mouseReleased(LinkLabel.java:68)
        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)
Caused by: org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.
        at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
        at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLScanner.scanExternalID(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(Unknown Source)
        at org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:153)
        at org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:80)
        ... 31 more


>Does this problem happen consistently
or is it intermittent?

It appears to be consitent now...

>Could a firewall issue be involved?
  No

>Do you have something similar that gives you a
hint?

Nothing apart from the stack traces and error messages I have alrerady posted!

>One thing that makes this explanation more
possible is that you said it also happens for downloaded ontologies.  If
they had an import it would also go to the network which could imply
delays even for local copies of your ontology.

The strange thing is that when I load the ontology locally, it seems to load but the UI simply displays a blank java canvas.

>If there is an import, what happens when you try to pull it up in a
browser?
The ontology loads fine, here it is here
http://content.screencast.com/users/WOMBRA/folders/Default/media/cd58d70f-c01c-4d6d-8261-937fd9be5ad4/section6energydomestic2010rdf.owl

>Do you see owl content or something else?
RDF/XML content

>The other thing that occurred to me was that this could somehow involve
dtd.  OWL files don't usually have (as far as I know) a system id or a
public id.   I was wondering if dtd files might.  OWL ontologies also
don't usually include a dtd but maybe yours does?

This cannot be the case, I have nothing like this within the ontology file.

Thank you for all of your suggestions, I will try a clean install for my platform and post if there are any changes in circumstance.

Lewis

Glasgow Caledonian University is a registered Scottish charity, number SC021474

Winner: Times Higher Education’s Widening Participation Initiative of the Year 2009 and Herald Society’s Education Initiative of the Year 2009.
http://www.gcu.ac.uk/newsevents/news/bycategory/theuniversity/1/name,6219,en.html

Winner: Times Higher Education’s Outstanding Support for Early Career Researchers of the Year 2010, GCU as a lead with Universities Scotland partners.
http://www.gcu.ac.uk/newsevents/news/bycategory/theuniversity/1/name,15691,en.html


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