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[protege-discussion] Export ontology from Protege server

Jie Zheng jiezheng at pcbi.upenn.edu
Wed Jun 22 13:22:55 PDT 2011 

Hi Tania,

I saw the pop-up window you mentioned and the exported ontology is 
worked this time. However, the export process is incredible slow. I 
waited for about 7 minutes until the pop-up window showed up.

However, I got error again when exporting another ontology from same 
Protege server. *The error message when open the exported ontology using 
Protege 4.1 is:*
" org.semanticweb.owlapi.rdf.syntax.RDFParserException: 
[line=553:column=56] Cannot answer characters when object properties are 
excepted.
org.semanticweb.owlapi.rdf.syntax.RDFParserException: 
[line=553:column=56] Cannot answer characters when object properties are 
excepted.


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

org.coode.owlapi.rdfxml.parser.OWLRDFXMLParserSAXException: 
org.semanticweb.owlapi.rdf.syntax.RDFParserException: 
[line=553:column=56] Cannot answer characters when object properties are 
excepted.
     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$1.mouseReleased(LinkLabel.java:68)
     at java.awt.Component.processMouseEvent(Unknown Source)
     at javax.swing.JComponent.processMouseEvent(Unknown Source)
     at java.awt.Component.processEvent(Unknown Source)
     at java.awt.Container.processEvent(Unknown Source)
     at java.awt.Component.dispatchEventImpl(Unknown Source)
     at java.awt.Container.dispatchEventImpl(Unknown Source)
     at java.awt.Component.dispatchEvent(Unknown Source)
     at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
     at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
     at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
     at java.awt.Container.dispatchEventImpl(Unknown Source)
     at java.awt.Window.dispatchEventImpl(Unknown Source)
     at java.awt.Component.dispatchEvent(Unknown Source)
     at java.awt.EventQueue.dispatchEvent(Unknown Source)
     at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
     at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
     at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
     at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
     at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
     at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: org.semanticweb.owlapi.rdf.syntax.RDFParserException: 
[line=553:column=56] Cannot answer characters when object properties are 
excepted.
     at 
org.semanticweb.owlapi.rdf.syntax.RDFParser$PropertyElementList.characters(RDFParser.java:938)
     at 
org.semanticweb.owlapi.rdf.syntax.RDFParser.characters(RDFParser.java:307)
     at 
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.characters(Unknown 
Source)
     at 
com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.characters(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"
---------------------------------

*There are up to 1549 errors when opened using Protege 3.4.6. Part of 
the error message is:*
"Errors found performing operation.

1. An error occurred at parsing the OWL ontology

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

     at line 550 and column 54.
     Jena parse error message: {E201} rdf:about not allowed as attribute 
here.
     Exception class com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1.  
Message: {E201} rdf:about not allowed as attribute here.

2. An error occurred at parsing the OWL ontology

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

     at line 551 and column 63.
     Jena parse error message: {E201} rdf:resource not allowed as 
attribute here.
     Exception class com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1.  
Message: {E201} rdf:resource not allowed as attribute here.
....."
-----------------------------------

Although the export ontology is succeeded, I saw *the error message 
during the export:*
"SEVERE: Exception caught -- java.lang.ClassCastException: 
java.lang.String cannot be cast to 
edu.stanford.smi.protegex.owl.model.RDFSClass
         at 
edu.stanford.smi.protegex.owl.writer.rdfxml.renderer.RDFAxiomRenderer.renderClassAxioms(Unknown 
Source)
         at 
edu.stanford.smi.protegex.owl.writer.rdfxml.renderer.RDFAxiomRenderer.visitOWLNamedClass(Unknown 
Source)
         at 
edu.stanford.smi.protegex.owl.model.impl.DefaultOWLNamedClass.accept(Unknown 
Source)
         at 
edu.stanford.smi.protegex.owl.writer.rdfxml.renderer.RDFAxiomRenderer.write(Unknown 
Source)
         at 
edu.stanford.smi.protegex.owl.writer.rdfxml.rdfwriter.OWLModelContentWriter.writeContent(Unknown 
Source)
         at 
edu.stanford.smi.protegex.owl.writer.rdfxml.rdfwriter.RDFXMLDocumentWriter.writeDocument(Unknown 
Source)
         at 
edu.stanford.smi.protegex.owl.writer.rdfxml.rdfwriter.OWLModelWriter.write(Unknown 
Source)
         at 
edu.stanford.smi.protegex.owl.writer.rdfxml.rdfwriter.OWLModelAllTripleStoresWriter.write(Unknown 
Source)
         at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.save(Unknown 
Source)
         at 
edu.stanford.smi.protegex.owl.jena.export.JenaExportPlugin.exportProject(Unknown 
Source)
         at 
edu.stanford.smi.protegex.owl.jena.export.JenaExportPlugin.handleExportRequest(Unknown 
Source)
         at 
edu.stanford.smi.protege.ui.ProjectManager.exportProjectRequest(Unknown 
Source)
         at 
edu.stanford.smi.protege.action.ExportPluginAction.actionPerformed(Unknown 
Source)
         at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
         at javax.swing.AbstractButton$Handler.actionPerformed(Unknown 
Source)
         at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown 
Source)
         at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
         at javax.swing.AbstractButton.doClick(Unknown Source)
         at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
         at 
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
         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)

... saving successful.
WARNING: No ProjectView registered for project obi-webservices-export -- 
Protege UI.getProjectView()"
---------------------------

I attached the exported owl file (webServiceWithNewChanges-export.owl) 
and the original file stored in the Protege server 
(webServiceWithNewChanges.owl).

Thanks for your help.

Jie


On 6/22/2011 3:26 PM, Tania Tudorache wrote:
> Hi Jie,
>
> I suppose you exported by going to the File menu -> Export and the 
> selected OWL as a format.
>
> I checked the files that you sent, and the exported one is incomplete. 
> If you open it in a text editor, and scroll at the end of the file, 
> you will see that the OWL file is cut at some point. This probably 
> happened if the export process was terminated before the export 
> actually finished. That is why you get errors when trying to load it 
> into any of the Proteges.
>
> If the export finished successfully, you will get pop-up window saying 
> that export successful, and the path where it was created.
>
> I just made a test with exporting the OPL copy we have on the the 
> WebProtege server using the same method that you used, and it worked 
> with no problem.
>
> Tania
>
>
> On 06/22/2011 08:34 AM, Jie Zheng wrote:
>> 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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>> protege-discussion at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
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>
>
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