Protege won't read the owl from Template Specifications List
Posted: Tue Jul 30, 2013 2:31 pm
Hello
I was looking at the Template Specifications List (http://15926.org/15926_template_specs.php) with Lillian and it was fairly heavy reading. So I thought I would look at the OWL file instead with Protege since that often makes the data a bit easier to read.
Protege 4.3 gives a string out of range exception at a chartAt method. It is below the SAX parser, so I think the XML is valid. The first method above the actualy exception is a getOWLLiteral method, so there must be something wonky with a literal definition.
It opens in Protege 3.5, but on closer inspection there doesn't really seem to be anything there and after a bit of browsing it just crashes.
Anyone managed to open the owl file in protege?
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Error 1 Logged at Tue Jul 30 16:29:49 CEST 2013
StringIndexOutOfBoundsException: String index out of range: 0
java.lang.String.charAt(String.java:686)
uk.ac.manchester.cs.owl.owlapi.InternalsNoCache.getOWLLiteral(InternalsNoCache.java:211)
uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryInternalsImpl.getOWLLiteral(OWLDataFactoryInternalsImpl.java:149)
uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl.getOWLLiteral(OWLDataFactoryImpl.java:1635)
org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.getOWLLiteral(OWLRDFConsumer.java:1805)
org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.handleStreaming(OWLRDFConsumer.java:1781)
org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.statementWithLiteralValue(OWLRDFConsumer.java:1702)
org.semanticweb.owlapi.rdf.syntax.RDFParser.statementWithLiteralValue(RDFParser.java:597)
org.semanticweb.owlapi.rdf.syntax.RDFParser$ResourceOrLiteralPropertyElement.endElement(RDFParser.java:998)
org.semanticweb.owlapi.rdf.syntax.RDFParser.endElement(RDFParser.java:293)
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:601)
com.sun.org.apache.xerces.internal.impl.dtd.XMLNSDTDValidator.endNamespaceScope(XMLNSDTDValidator.java:263)
com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.handleEndElement(XMLDTDValidator.java:2028)
com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endElement(XMLDTDValidator.java:901)
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1782)
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2939)
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:647)
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:140)
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:170)
org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:119)
uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:206)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:906)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:843)
org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:313)
org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:190)
org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:184)
org.protege.editor.core.ProtegeManager.openAndSetupEditorKit(ProtegeManager.java:173)
org.protege.editor.core.ui.action.OpenAction.openInNewWorkspace(OpenAction.java:57)
org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:216)
org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
javax.swing.AbstractButton.doClick(AbstractButton.java:389)
com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95)
java.awt.MenuItem.processActionEvent(MenuItem.java:650)
java.awt.MenuItem.processEvent(MenuItem.java:609)
java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:343)
java.awt.MenuComponent.dispatchEvent(MenuComponent.java:331)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:720)
java.awt.EventQueue.access$400(EventQueue.java:82)
java.awt.EventQueue$2.run(EventQueue.java:676)
java.awt.EventQueue$2.run(EventQueue.java:674)
java.security.AccessController.doPrivileged(Native Method)
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
java.awt.EventQueue$3.run(EventQueue.java:690)
java.awt.EventQueue$3.run(EventQueue.java:688)
java.security.AccessController.doPrivileged(Native Method)
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
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I was looking at the Template Specifications List (http://15926.org/15926_template_specs.php) with Lillian and it was fairly heavy reading. So I thought I would look at the OWL file instead with Protege since that often makes the data a bit easier to read.
Protege 4.3 gives a string out of range exception at a chartAt method. It is below the SAX parser, so I think the XML is valid. The first method above the actualy exception is a getOWLLiteral method, so there must be something wonky with a literal definition.
It opens in Protege 3.5, but on closer inspection there doesn't really seem to be anything there and after a bit of browsing it just crashes.
Anyone managed to open the owl file in protege?
-----------------------------------------------------------------------------------------------------------------------------------------------------------------
Error 1 Logged at Tue Jul 30 16:29:49 CEST 2013
StringIndexOutOfBoundsException: String index out of range: 0
java.lang.String.charAt(String.java:686)
uk.ac.manchester.cs.owl.owlapi.InternalsNoCache.getOWLLiteral(InternalsNoCache.java:211)
uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryInternalsImpl.getOWLLiteral(OWLDataFactoryInternalsImpl.java:149)
uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl.getOWLLiteral(OWLDataFactoryImpl.java:1635)
org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.getOWLLiteral(OWLRDFConsumer.java:1805)
org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.handleStreaming(OWLRDFConsumer.java:1781)
org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.statementWithLiteralValue(OWLRDFConsumer.java:1702)
org.semanticweb.owlapi.rdf.syntax.RDFParser.statementWithLiteralValue(RDFParser.java:597)
org.semanticweb.owlapi.rdf.syntax.RDFParser$ResourceOrLiteralPropertyElement.endElement(RDFParser.java:998)
org.semanticweb.owlapi.rdf.syntax.RDFParser.endElement(RDFParser.java:293)
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:601)
com.sun.org.apache.xerces.internal.impl.dtd.XMLNSDTDValidator.endNamespaceScope(XMLNSDTDValidator.java:263)
com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.handleEndElement(XMLDTDValidator.java:2028)
com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endElement(XMLDTDValidator.java:901)
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1782)
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2939)
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:647)
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:140)
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:170)
org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:119)
uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:206)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:906)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:843)
org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:313)
org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:190)
org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:184)
org.protege.editor.core.ProtegeManager.openAndSetupEditorKit(ProtegeManager.java:173)
org.protege.editor.core.ui.action.OpenAction.openInNewWorkspace(OpenAction.java:57)
org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:216)
org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
javax.swing.AbstractButton.doClick(AbstractButton.java:389)
com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95)
java.awt.MenuItem.processActionEvent(MenuItem.java:650)
java.awt.MenuItem.processEvent(MenuItem.java:609)
java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:343)
java.awt.MenuComponent.dispatchEvent(MenuComponent.java:331)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:720)
java.awt.EventQueue.access$400(EventQueue.java:82)
java.awt.EventQueue$2.run(EventQueue.java:676)
java.awt.EventQueue$2.run(EventQueue.java:674)
java.security.AccessController.doPrivileged(Native Method)
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
java.awt.EventQueue$3.run(EventQueue.java:690)
java.awt.EventQueue$3.run(EventQueue.java:688)
java.security.AccessController.doPrivileged(Native Method)
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
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