Protege Plugin not works with import section for Ontology

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1.) Load Ontology with imports declaration.
2.) After restart protege imports list is empty...

Original issue reported on code.google.com by v.gordievskiy@gmail.com on 5 Dec 2014 at 6:28

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I tried save the ontology (with import declaration) by programmatically way.
And have this exception: 

java.lang.NullPointerException
        at org.hypergraphdb.app.owl.HGDBOntologyInternalsImpl.findEqualImportsDeclaration(HGDBOntologyInternalsImpl.java:526)
        at org.hypergraphdb.app.owl.HGDBOntologyInternalsImpl.containsImportDeclaration(HGDBOntologyInternalsImpl.java:535)
        at org.hypergraphdb.app.owl.HGDBOntologyInternalsImpl$11.call(HGDBOntologyInternalsImpl.java:543)
        at org.hypergraphdb.app.owl.HGDBOntologyInternalsImpl$11.call(HGDBOntologyInternalsImpl.java:1)
        at org.hypergraphdb.transaction.HGTransactionManager.transact(HGTransactionManager.java:396)
        at org.hypergraphdb.transaction.HGTransactionManager.ensureTransaction(HGTransactionManager.java:323)
        at org.hypergraphdb.transaction.HGTransactionManager.ensureTransaction(HGTransactionManager.java:294)
        at org.hypergraphdb.app.owl.HGDBOntologyInternalsImpl.addImportsDeclaration(HGDBOntologyInternalsImpl.java:541)
        at org.hypergraphdb.app.owl.HGDBOntologyImpl$OWLOntologyChangeFilter.visit(HGDBOntologyImpl.java:1742)
        at org.semanticweb.owlapi.model.AddImport.accept(AddImport.java:100)
        at org.hypergraphdb.app.owl.HGDBOntologyImpl.applyChange(HGDBOntologyImpl.java:1645)
        at org.hypergraphdb.app.owl.HGDBStorer.storeOntology(HGDBStorer.java:112)
        at org.hypergraphdb.app.owl.HGDBStorer.storeOntology(HGDBStorer.java:156)
        at org.hypergraphdb.app.owl.HGDBStorer.storeOntology(HGDBStorer.java:54)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:991)
        at Implementation.OntoManager.HGDBOntoManager.NewOntology(HGDBOntoManager.java:199)

Original comment by v.gordievskiy@gmail.com on 5 Dec 2014 at 7:05

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Note: 
Implementation.OntoManager.HGDBOntoManager.NewOntology(HGDBOntoManager.java:199)
 - is part of code from my test.

Original comment by v.gordievskiy@gmail.com on 5 Dec 2014 at 7:06

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[deleted comment]

[GoogleCodeExporter]

Seems a reason in:

apps/owl/src/java/org/hypergraphdb/app/owl/HGDBOntologyImpl.java 

@SuppressWarnings("unchecked")
    @Override
    public List<HGHandle> findAll(HGQueryCondition condition)
    {
        // TODO Auto-generated method stub
        return null;
    }

Original comment by v.gordievskiy@gmail.com on 6 Dec 2014 at 1:32

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Hi, I'm traveling at the moment. Will look at those at the beginning of next 
week. Thanks much for the detailed reports! You are using the latest SVN 
codebase I assume?

Original comment by borislav...@gmail.com on 6 Dec 2014 at 10:26

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Hi! Yes, I checkout Revision: 2964.

I made a workaround for this in my working copy. Just return the empty 
ArrayList in the method presented above and all fine works with import 
declaration.

Original comment by v.gordievskiy@gmail.com on 6 Dec 2014 at 10:40

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Ok, I committed an implementation for that method. If you have a test case that 
I could add to unit testing, please pass it on, it would be useful!!

If you update from svn, please get the core module also, I made a small change 
there to avoid duplication of some fields in HGOntologyImpl.

Original comment by borislav...@gmail.com on 9 Dec 2014 at 5:01

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Thanks!

I shall do manual testing for this and preparing a code for test case.

Original comment by v.gordievskiy@gmail.com on 9 Dec 2014 at 9:04