Error when trying to load a different version of an ontology in the same window

[csnyulas]

To reproduce:

1. Open an ontology in Protege
2. Try to open either the same ontology file again or another version of that ontology (having the same ontology IRI), and asked whether you want to open the new ontology in the current window, choose "Yes"
   
3. The following error message is shown (see the details below):
   

Note: This is a long standing issue, inherited from Protege 4, which can be very annoying, especially if people don't know why they are getting this error.

Desired behaviour: In case someone is trying to open an ontology that is already opened in the current workspace (or different version of the same ontology), the common sense behaviour would be to replace the content in the workspace with the newly opened ontology content, or if there are unsaved changes, at least ask the user to decide what should Protege do with the currently loaded ontology.

Details:
This is the error message we get

Ontology already exists. OntologyID(OntologyIRI(<http://protege.stanford.edu/ontologies/groceries>) VersionIRI(<null>))

And here is the stack trace:

Ontology already exists. OntologyID(OntologyIRI(<http://protege.stanford.edu/ontologies/groceries>) VersionIRI(<null>))


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

org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI(<http://protege.stanford.edu/ontologies/groceries>) VersionIRI(<null>))
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1048)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:972)
    at org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:278)
    at org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:201)
    at org.protege.editor.owl.OWLEditorKit.handleLoadRecentRequest(OWLEditorKit.java:189)
    at org.protege.editor.core.ui.action.OpenRecentAction$RecentEditorKitAction.openInCurrentWorkspace(OpenRecentAction.java:95)
    at org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:221)
    at org.protege.editor.core.ui.action.OpenRecentAction$RecentEditorKitAction.actionPerformed(OpenRecentAction.java:76)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
    at java.awt.Component.processMouseEvent(Component.java:6525)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
    at java.awt.Component.processEvent(Component.java:6290)
    at java.awt.Container.processEvent(Container.java:2234)
    at java.awt.Component.dispatchEventImpl(Component.java:4881)
    at java.awt.Container.dispatchEventImpl(Container.java:2292)
    at java.awt.Component.dispatchEvent(Component.java:4703)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
    at java.awt.Container.dispatchEventImpl(Container.java:2278)
    at java.awt.Window.dispatchEventImpl(Window.java:2750)
    at java.awt.Component.dispatchEvent(Component.java:4703)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:702)
    at java.awt.EventQueue$3.run(EventQueue.java:696)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
    at java.awt.EventQueue$4.run(EventQueue.java:724)
    at java.awt.EventQueue$4.run(EventQueue.java:722)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:721)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI(<http://protege.stanford.edu/ontologies/groceries>) VersionIRI(<null>))
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:721)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:555)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:583)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:671)
    at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:652)
    at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2864)
    at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:183)
    at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1507)
    at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:365)
    at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:331)
    at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:399)
    at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:196)
    at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509)
    at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:182)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:356)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2786)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:117)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777)
    at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
    at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
    at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:649)
    at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:333)
    at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:140)
    at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:212)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1035)
    ... 45 more

[MengtianYin]

Hi, I face the same issue. Have u solved it?

[pafournier]

I finaly guess I face this problem everytime I forget to launch the reasoner before closing Protégé 5. 5.0, although it seems to me it was not the case previously (meanwhile I loaded and installed proposed add on recently).
As I am facing another time this situation my latest rdf ontology version is empty : any idea to reactivate the file opening capacity. ? Thank you.

[danielbakas]

I'm having the same issue when trying to import RDFS 😢

[marimeireles]

Hi, having the same issue why is this closed? Is there some solution marked somewhere else?

I'm getting the same error.

Here is some more information: I've stashed all my changes, so the file that used to be able to be opened by Protege is not being opened anymore and still throwing the same error.
It seems to me like it's some sort of full cache problem with protege?

Another problem is that my error log is truncated so I can't properly follow all that's happening.

[marimeireles]

I've read the rest of "similar" issues on GH and none of them attend to my specific problem.
I see there's a commit related to this issue. Maybe I should open a new one?
Though it is the same error message...

[marimeireles]

Okay, so the problem in my case was that because I got an error in the previous time I was importing my TTL my XML got misformatted and that messed everything up.
The good news is, just erasing that and running Protege again will generate a new one for you that works.