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[protege-discussion] Export ontology from Protege server

Jie Zheng jiezheng at pcbi.upenn.edu
Mon Jun 27 07:43:31 PDT 2011


Hi Tania,

Thanks a lot for fixing the problem with detailed explanation.

Jie

On 6/24/2011 7:16 PM, Tania Tudorache wrote:
> Hi Jie,
>
> We analyzed what happened. The export of this particular ontology was 
> corrupted because of an invalid statement in the ontology. If you look 
> at the attached screenshot, you will see that the class "matrix" has 
> one statement: rdfs:subClassOf Cls(@A25...) that has type string. This 
> is an invalid statement, and I am not sure how it got in there. In any 
> case, I removed this statement from the WebProtege server (the 
> enhanced OBI project), and the export works now fine.
>
> We were able to reproduce the corrupted exported file. What happened 
> is that the export process would throw an exception about the invalid 
> statement in the Protege client console, but then it would continue 
> the export in a bad state. So, it corrupted the output file. The 
> export process should have stopped with an error message. We'll try to 
> fix this for the next Protege release.
>
> In any case, I am glad that we identified the exact cause of this 
> problem, and we were able to fix the ontology.
>
> Tania
>
>
>
>
> On 06/22/2011 01:22 PM, Jie Zheng wrote:
>> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> protege-discussion mailing list
>>>> protege-discussion at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>>>
>>>> Instructions for unsubscribing:http://protege.stanford.edu/doc/faq.html#01a.03
>>>
>>>
>>> _______________________________________________
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>>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>>
>>> Instructions for unsubscribing:http://protege.stanford.edu/doc/faq.html#01a.03
>>
>
>
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