Examples of OntModel

com.hp.hpl.jena.ontology.OntModel
An enhanced view of a Jena model that is known to contain ontology data, under a given ontology {@link Profile vocabulary} (such as OWL).This class does not by itself compute the deductive extension of the graph under the semantic rules of the language. Instead, we wrap an underlying model with this ontology interface, that presents a convenience syntax for accessing the language elements. Depending on the inference capability of the underlying model, the OntModel will appear to contain more or less triples. For example, if this class is used to wrap a plain memory or database model, only the relationships asserted by the document will be reported through this convenience API. Alternatively, if the OntModel wraps an OWL inferencing model, the inferred triples from the extension will be reported as well. For example, assume the following ontology fragment:
```
 :A rdf:type owl:Class . :B rdf:type owl:Class ; rdfs:subClassOf :A . :widget rdf:type :B . 
```
In a non-inferencing model, the rdf:type of the widget will be reported as class :B only. In a model that can process the OWL semantics, the widget's types will include :B, :A, and owl:Thing.

Note: that OntModel is an extension to the {@link InfModel} interface. This is to support the case where an ontology modelwraps an inference graph, and we want to make the special capabilities of the InfModel, for example global consistency checking, accessible to client programs. Since not all ont models use a reasoner, using these methods may result in a runtime exception, though the typical behaviour is that such calls will be silently ignored.

Examples of com.hp.hpl.jena.ontology.OntModel

  
  private static OntModel createDefaultOntModel() {
    OntModelSpec spec = new OntModelSpec(OntModelSpec.OWL_MEM);
    OntDocumentManager docMang = new OntDocumentManager();
    spec.setDocumentManager(docMang);
    OntModel model = ModelFactory.createOntologyModel(spec, null);
    // removeNotNeccesaryNamespaces(model);


    return model;
  }

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Examples of com.hp.hpl.jena.ontology.OntModel

      }
    }
    


    if ( model instanceof OntModel ) {
      OntModel ontModel = (OntModel) model;
      ExtendedIterator<Individual> iter = ontModel.listIndividuals(termRes);
      if ( iter.hasNext() ) {
        while ( iter.hasNext() ) {
          Resource idv = (Resource) iter.next();


          termModel.add(idv, RDF.type, termRes);

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Examples of com.hp.hpl.jena.ontology.OntModel

  }


  private void _loadOntology(OntologyInfo ontology, String full_path) {
    final Model model2update = _getEffectiveModel(_getInfModel() != null);
    if ( USE_UNVERSIONED ) {
      OntModel model = JenaUtil2.loadModel("file:" +full_path, false);


      if ( OntUtil.isOntResolvableUri(ontology.getUri()) ) {
        MmiUri mmiUri;
        try {
          mmiUri = new MmiUri(ontology.getUri());
          OntModel unversionedModel = UnversionedConverter.getUnversionedModel(model, mmiUri);
          model2update.add(unversionedModel);
        }
        catch (URISyntaxException e) {
          log.error("shouldn't happen", e);
          return;

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Examples of com.hp.hpl.jena.ontology.OntModel

  private void _loadOntology(_Conn _conn, OntologyInfo ontology, String graphId, String full_path, boolean clearGraphFirst) {
    
    String graphUri;
    
    String ontologyUri = ontology.getUri();
    OntModel model;
    
    if ( USE_UNVERSIONED ) {
      model = JenaUtil2.loadModel("file:" +full_path, false);


      if ( OntUtil.isOntResolvableUri(ontologyUri) ) {

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Examples of com.hp.hpl.jena.ontology.OntModel

    }
    
    
    String uriFile = file.toURI().toString();
    try {
      OntModel model = _loadModel(uriFile, lang, false);
      return model;
    }
    catch ( Throwable jenaExc ) {
      // XML parse exception?
      String errorMessage = getXmlParseExceptionErrorMessage(jenaExc);

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Examples of com.hp.hpl.jena.ontology.OntModel

    }  
  }
  
  private static OntModel _loadModel(String uriModel, String lang, boolean processImports) {


    OntModel model = null;
    uriModel = JenaUtil2.removeTrailingFragment(uriModel);
    model = _createDefaultOntModel();
    model.setDynamicImports(false);
    model.getDocumentManager().setProcessImports(processImports);
    if ( log.isDebugEnabled() ) {
      log.debug("loading model " + uriModel + "  LANG=" +lang);
    }
    model.read(uriModel, lang);
    return model;
  }

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Examples of com.hp.hpl.jena.ontology.OntModel

  }
  private static OntModel _createDefaultOntModel() {
    OntModelSpec spec = new OntModelSpec(OntModelSpec.OWL_MEM);
    OntDocumentManager docMang = new OntDocumentManager();
    spec.setDocumentManager(docMang);
    OntModel model = ModelFactory.createOntologyModel(spec, null);
    // removeNotNeccesaryNamespaces(model);


    return model;
  }

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Examples of com.hp.hpl.jena.ontology.OntModel

      );
    }


    // original model:
    final String uriFile = file.toURI().toString();
    final OntModel originalModel = JenaUtil2.loadModel(uriFile, false);


    if ( originalModel == null ) {
      // This should not happen.
      return new InternalErrorResponse(
          file.getAbsolutePath()+ ": internal error: uploaded file "
          + "cannot be read as an ontology model. "
          + "Please, report this bug."
      );
    }


    // corresponding unversioned model in case is requested: 
    OntModel unversionedModel = null;
    
    if ( unversionedRequest ) {


      unversionedModel = UnversionedConverter.getUnversionedModel(originalModel, ontReq.mmiUri);
      
      if ( unversionedModel != null ) {
        if ( log.isDebugEnabled() ) {
          log.debug("_getResponseForMmiUri: obtained unversioned model");
        }
      }
      else {
        // error in conversion to unversioned version.
        // this is unexpected. 
        // Continue with original model, if necessary; see below.
        log.error("_getResponseForMmiUri: unexpected: error in conversion to unversioned version.  But continuing with original model");
      }
    }


    String term = ontReq.mmiUri.getTerm();
    
    OntModel model = unversionedModel != null ? unversionedModel : originalModel;


    if ( term.length() == 0 ) {
      return new OntologyResponse(model);
    }
    else {

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Examples of com.hp.hpl.jena.ontology.OntModel

      resp = new InternalErrorResponse(error);
    }
    else {
      // original model:
      final String uriFile = file.toURI().toString();
      final OntModel originalModel = JenaUtil2.loadModel(uriFile, false);


      if ( originalModel == null ) {
        // This should not happen.
        String error = file.getAbsolutePath()+ ": internal error: uploaded file "
          + "cannot be read as an ontology model. "
          + "Please, report this bug."
        ;
        log.warn(error);
        resp = new InternalErrorResponse(error);
      }
      else {
        OntModel model = originalModel;


        // no explicit version requested and it's an unversioned MmiUri?
        if ( ontReq.version == null && ontReq.mmiUri != null && ontReq.mmiUri.getVersion() == null ) {
          model = UnversionedConverter.getUnversionedModel(originalModel, ontReq.mmiUri);
        }

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Examples of com.hp.hpl.jena.ontology.OntModel

      }
    }
    


    if ( model instanceof OntModel ) {
      OntModel ontModel = (OntModel) model;
      ExtendedIterator<Individual> iter = ontModel.listIndividuals(termRes);
      if ( iter.hasNext() ) {
        out.println("<br/>");
        out.println("<table class=\"inline\" width=\"100%\">");
        out.printf("<tr>%n");
        out.printf("<th>Individuals</th>");

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