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[protege-discussion] Export ontology from Protege server

Jie Zheng jiezheng at pcbi.upenn.edu
Wed Jun 22 08:34:47 PDT 2011


Hi,

I am working with WebProtege which both Protege server and Protege rich 
client is Protege 3.4.6. I used Desktop protege to export the ontology 
from the server using "Export to Format' XML. I got error message when I 
open the exported ontology using both Protege 3.4.6 and Protege 4.1.

The error message got using Protege 3.4.6:
"Errors found performing operation.

1. An error occurred at parsing the OWL ontology

     http://purl.obolibrary.org/obo/opl.owl

     at line 2045 and column 737.
     Jena parse error message: XML document structures must start and 
end within the same entity.
     Exception class org.xml.sax.SAXParseException.  Message: XML 
document structures must start and end within the same entity.

See console and log for more details."

The error message got using Protege 4.1:
"Export ontology using Protege, export format as XML, when open using 
Protege 4.1 got following error

org.xml.sax.SAXParseException: XML document structures must start and 
end within the same entity.


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

org.coode.owlapi.rdfxml.parser.OWLRDFXMLParserSAXException: 
org.xml.sax.SAXParseException: XML document structures must start and 
end within the same entity.
     at 
org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:129)
     at 
uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:204)
     at 
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:725)
     at 
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:682)
     at 
org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:317)
     at 
org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:180)
     at 
org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:174)
     at 
org.protege.editor.core.ProtegeManager.openAndSetupEditorKit(ProtegeManager.java:157)
     at 
org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$2.actionPerformed(ProtegeWelcomeFrame.java:139)
     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.pumpOneEventForFilters(Unknown Source)
     at java.awt.EventDispatchThread.pumpEventsForFilter(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: XML document structures must 
start and end within the same entity.
     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.XMLScanner.reportFatalError(Unknown 
Source)
     at 
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.endEntity(Unknown 
Source)
     at 
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.endEntity(Unknown 
Source)
     at 
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.endEntity(Unknown 
Source)
     at 
com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(Unknown 
Source)
     at 
com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.peekChar(Unknown Source)
     at 
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(Unknown 
Source)
     at 
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown 
Source)
     at 
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(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 
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown 
Source)
     at javax.xml.parsers.SAXParser.parse(Unknown Source)
     at 
org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:173)
     at 
org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:119)
     ... 31 more"

I attached the exported owl file (opl_inferred_export.owl) and the 
original file stored in the Protege server (opl_inferred_server.owl).

Any idea of why it happen? Is it a bug of protege or did I do something 
wrong?

Thanks,

Jie
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