Re: [OWLAPI-developer] 3.4.1: OWLOntologyManager.getOntology() & OWLOntology.getDirectImportDocumen

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On 27 October 2012 01:52, Rouquette, Nicolas F (313K)
<nic...@jp...> wrote:
> Ignazio,
>
> In our infrastructure, we need an explicit ontology of OWL2 including
> datatype maps.
> We started from this: http://www.w3.org/2007/OWL/wiki/Owl2.owl6
> And we added the imported ontologies (or approximations of them based on
> what we could find).
>
> We settled on the following kernel of 6 ontologies whose import relations
> induces a strongly connected directed graph:
>
> http://purl.org/dc/elements/1.1
> http://www.w3.org/2000/01/rdf-schema
> http://www.w3.org/2002/07/owl
> http://www.w3.org/1999/02/22-rdf-syntax-ns
> http://www.w3.org/2003/g/data-view
> http://www.w3.org/2001/XMLSchema
>
> (if there are official / bug-free versions of these, we'd love to use
> them!)
>
> To avoid confusion with whatever is available (or not), we use an OASIS
> XML Catalog technique like Protégé to remap the above IRIs to local files
> (attached).
>
>

Thank you, I'll look at what went wrong.

>
> According to the comments on OWLOntology.getDirectImports(), there can be
> fewer ontologies in the result than imported documents if some ontologies
> aren't loaded for some reason.
> We consider this possibility a silent failure so we use
> ont.getDirectImportDocuments() instead and verify that each imported
> document IRI resolves to an ontology whose version IRI (if any) or
> ontology IRI matches that document IRI.

Another reason might be that two different imports resolve to the same
ontology - in that case, the results are equivalent.

However there are three variables at play here: ontology IRI, document
IRI and version IRI (when there is one) need not be the same. I
suspect what's missing is a check through the loaded documents.
I.

>
> - Nicolas.
>
> On 10/26/12 2:51 PM, "Ignazio Palmisano" <ipa...@gm...>
> wrote:
>
>>On 26 October 2012 22:05, Rouquette, Nicolas F (313K)
>><nic...@jp...> wrote:
>>> With 3.4.1 (revision 2092), our code fails when we try to get an
>>>imported
>>> ontology like this:
>>>
>>> OWLOntologyManager ontManager = Š;
>>>
>>> OWLOntology ont = Š;
>>>
>>> for (IRI directImportDocumentIRI : ont.getDirectImportsDocuments()) {
>>>         OWLOntology directImportOntology =
>>> ontManager.getOntology(directImportDocumentIRI); // << throws
>>> OWLOntologyDocumentAlreadyExistsException
>>>         Š
>>>
>>> The exception comes from OWLOntologyManagerImpl, line 295 below:
>>>
>>>
>>
>>Thanks for reporting this, it looks to me like a problem with the
>>relations between document names and ontology iris.
>>Can you print out the directImportDocumentIRIs and the ontology ids
>>for the ontologies in the import closure - or share the ontology on
>>which this happens?
>>I'm trying to figure out if there is a mismatch between document iris
>>and ontology iris, and how to work it out.
>>In the meantime, ontology.getDirectImports() should return the set of
>>imported ontologies without the need for you to manually retrieve
>>them.
>>HTH,
>>I.
>>
>>>     public OWLOntology getOntology(IRI ontologyIRI) {
>>>         OWLOntologyID ontologyID = new OWLOntologyID(ontologyIRI);
>>>         // return getOntology(ontologyID);
>>>         OWLOntology result = ontologiesByID.get(ontologyID);
>>>         if (result == null) {
>>>             for (OWLOntologyID nextOntologyID :
>>>ontologiesByID.keySet()) {
>>>                 if (ontologyIRI.equals(nextOntologyID.getVersionIRI()))
>>>{
>>>                     result = ontologiesByID.get(nextOntologyID);
>>>                 }
>>>             }
>>>         }
>>>         // HACK: This extra clause is necessary to make getOntology
>>>match
>>> the
>>>         // behaviour of createOntology
>>>         // in cases where a documentIRI has been recorded, based on the
>>> mappers,
>>>         // but an ontology has not
>>>         // been stored in ontologiesByID
>>>         if (result == null) {
>>>             IRI documentIRI = getDocumentIRIFromMappers(ontologyID,
>>>true);
>>>             if (documentIRI == null) {
>>>                 if (!ontologyID.isAnonymous()) {
>>>                     documentIRI = ontologyID.getDefaultDocumentIRI();
>>>                 } else {
>>>                     documentIRI = IRI.generateDocumentIRI();
>>>                 }
>>>                 Collection<IRI> existingDocumentIRIs =
>>> documentIRIsByID.values();
>>>                 while (existingDocumentIRIs.contains(documentIRI)) {
>>>                     documentIRI = IRI.generateDocumentIRI();
>>>                 }
>>>             }
>>>             if (documentIRIsByID.values().contains(documentIRI)) {
>>>                 throw new RuntimeException(new
>>> OWLOntologyDocumentAlreadyExistsException(  // line 295
>>>                         documentIRI));
>>>             }
>>>         }
>>>         return result;
>>>     }
>>>
>>>
>>>
>>> What is the rationale for getOntology(IRI) to throw
>>> OWLOntologyDocumentAlreadyExistsException when we precisely want to
>>> retrieve the ontology document?
>>>
>>> - Nicolas.
>>>
>>>
>>>
>>>-------------------------------------------------------------------------
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>>
>>--------------------------------------------------------------------------
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>
>
> ------------------------------------------------------------------------------
> WINDOWS 8 is here.
> Millions of people.  Your app in 30 days.
> Visit The Windows 8 Center at Sourceforge for all your go to resources.
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> _______________________________________________
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>

Re: [OWLAPI-developer] 3.4.1: OWLOntologyManager.getOntology() & OWLOntology.getDirectImportDocumen

Re: [OWLAPI-developer] 3.4.1: OWLOntologyManager.getOntology() & OWLOntology.getDirectImportDocuments()