Пример #1
0
  @Override
  public KuabaRepository load(String url) throws RepositoryLoadException {

    IRI iri;
    File f = new File(url);
    if (!url.contains(":/")) {
      iri = IRI.create(f);
    } else iri = IRI.create(url);

    try {
      OWLOntology inst = manager.loadOntologyFromOntologyDocument(iri);

      if (inst == null) throw new RepositoryLoadException(url, "Invalid Location.");
      if (inst.getOntologyID().getOntologyIRI() == null) {
        // An anonymous Ontology was loaded, and they are not supported by the Kuaba Subsystem
        manager.removeOntology(inst);
        throw new RepositoryLoadException(url, "It is probably an incompatible or malformed file.");
      }

      KuabaRepository repo = new OwlApiKuabaRepository(inst, manager.getOWLDataFactory());
      repoMap.put(inst.getOntologyID().getOntologyIRI(), repo);
      fileMap.put(repo, f);
      return repo;
    } catch (OWLOntologyAlreadyExistsException ex) {
      OWLOntologyID id = ex.getOntologyID();
      //            System.err.println("Ontologia "+id.getOntologyIRI().toString()+" já está
      // carregada, esta será retornada.");
      return repoMap.get(id.getOntologyIRI());

    } catch (OWLOntologyCreationException ex) {
      throw new RepositoryLoadException(url, "Invalid Location.");
      //            Logger.getLogger(OwlApiFileGateway.class.getName()).log(Level.SEVERE, null, ex);
    }
  }
 public DLOntology_withMaps preprocessAndClausify(OWLOntology rootOntology) {
   OWLDataFactory factory = rootOntology.getOWLOntologyManager().getOWLDataFactory();
   String ontologyIRI =
       rootOntology.getOntologyID().getDefaultDocumentIRI() == null
           ? "urn:hermit:kb"
           : rootOntology.getOntologyID().getDefaultDocumentIRI().toString();
   Collection<OWLOntology> importClosure = rootOntology.getImportsClosure();
   OWLAxioms_withMaps axioms = new OWLAxioms_withMaps();
   OWLNormalization_withMaps normalization =
       new OWLNormalization_withMaps(factory, axioms, 0, m_datatypeManager);
   for (OWLOntology ontology : importClosure) normalization.processOntology(ontology);
   BuiltInPropertyManager_withMaps builtInPropertyManager =
       new BuiltInPropertyManager_withMaps(factory);
   builtInPropertyManager.axiomatizeBuiltInPropertiesAsNeeded(axioms);
   ObjectPropertyInclusionManager_withMaps objectPropertyInclusionManager =
       new ObjectPropertyInclusionManager_withMaps(axioms);
   // now object property inclusion manager added all non-simple properties to
   // axioms.m_complexObjectPropertyExpressions
   // now that we know which roles are non-simple, we can decide which negative object property
   // assertions have to be
   // expressed as concept assertions so that transitivity rewriting applies properly.
   objectPropertyInclusionManager.rewriteNegativeObjectPropertyAssertions(
       factory, axioms, normalization.getDefinitions().size());
   objectPropertyInclusionManager.rewriteAxioms(factory, axioms, 0);
   OWLAxiomsExpressivity_withMaps axiomsExpressivity = new OWLAxiomsExpressivity_withMaps(axioms);
   DLOntology_withMaps dlOntology =
       clausify_withMaps(factory, ontologyIRI, axioms, axiomsExpressivity);
   return dlOntology;
 }
 public OWLOntology getMergedOntology() {
   final IRI mergedOntologyIRI =
       IRI.create(queryOntology.getOntologyID().getDefaultDocumentIRI() + "-merged");
   final OWLOntologyManager mm = controller.getOWLOntologyManager();
   if (mm.contains(mergedOntologyIRI)) {
     return mm.getOntology(mergedOntologyIRI);
   } else {
     try {
       final OWLOntology mergedOntology = mm.createOntology(mergedOntologyIRI);
       mm.setOntologyFormat(mergedOntology, new RDFXMLOntologyFormat());
       final String mergedOntologyFileName =
           mergedOntologyIRI
                   .toURI()
                   .toString()
                   .substring(mergedOntologyIRI.toURI().toString().lastIndexOf("/") + 1)
               + ".owl";
       mm.setOntologyDocumentIRI(
           mergedOntology,
           IRI.create(
               controller.getRuleSpec().getOutputDir().toURI() + "/" + mergedOntologyFileName));
       mm.applyChange(
           new AddImport(
               mergedOntology,
               mm.getOWLDataFactory()
                   .getOWLImportsDeclaration(
                       queryOntology.getOntologyID().getDefaultDocumentIRI())));
       return mergedOntology;
     } catch (OWLOntologyCreationException e) {
       // TODO Auto-generated catch block
       e.printStackTrace();
       return null;
     }
   }
 }
 public void writeOntologyHeader(OWLOntology ontology) {
   event = new RendererEvent(this, ontology);
   fireFrameRenderingPrepared(ONTOLOGY.toString());
   write(ONTOLOGY.toString());
   write(":");
   writeSpace();
   if (!ontology.isAnonymous()) {
     int indent = getIndent();
     writeFullURI(ontology.getOntologyID().getOntologyIRI().toString());
     writeNewLine();
     pushTab(indent);
     if (ontology.getOntologyID().getVersionIRI() != null) {
       writeFullURI(ontology.getOntologyID().getVersionIRI().toString());
     }
     popTab();
   }
   fireFrameRenderingStarted(ONTOLOGY.toString());
   writeNewLine();
   for (OWLImportsDeclaration decl : ontology.getImportsDeclarations()) {
     fireSectionItemPrepared(IMPORT.toString());
     write(IMPORT.toString());
     write(":");
     writeSpace();
     fireSectionRenderingStarted(IMPORT.toString());
     writeFullURI(decl.getURI().toString());
     writeNewLine();
     fireSectionRenderingFinished(IMPORT.toString());
   }
   writeNewLine();
   writeSection(ANNOTATIONS, ontology.getAnnotations(), ",", true);
   fireFrameRenderingFinished(ONTOLOGY.toString());
 }
 @Test
 public void testCreateAnonymousOntology() throws Exception {
   OWLOntologyManager manager = Factory.getManager();
   OWLOntology ontology = manager.createOntology();
   assertNotNull("ontology should not be null", ontology);
   assertNotNull("ontology id should not be null", ontology.getOntologyID());
   assertNull(ontology.getOntologyID().getDefaultDocumentIRI());
   assertNull(ontology.getOntologyID().getOntologyIRI());
   assertNull(ontology.getOntologyID().getVersionIRI());
   assertNotNull("iri should not be null", manager.getOntologyDocumentIRI(ontology));
 }
 @Test
 public void testCreateOntologyWithIRI() throws Exception {
   OWLOntologyManager manager = Factory.getManager();
   IRI ontologyIRI = IRI("http://www.semanticweb.org/ontologies/ontology");
   OWLOntology ontology = manager.createOntology(ontologyIRI);
   assertNotNull("ontology should not be null", ontology);
   assertNotNull("ontology id should not be null", ontology.getOntologyID());
   assertEquals(ontologyIRI, ontology.getOntologyID().getDefaultDocumentIRI());
   assertEquals(ontologyIRI, ontology.getOntologyID().getOntologyIRI());
   assertNull(ontology.getOntologyID().getVersionIRI());
   assertEquals(ontologyIRI, manager.getOntologyDocumentIRI(ontology));
 }
Пример #7
0
  /**
   * This method makes sure is used to setup a new/fresh OBDA model. This is done by replacing the
   * instance this.obdacontroller (the OBDA model) with a new object. On creation listeners for the
   * datasources, mappings and queries are setup so that changes in these trigger and ontology
   * change.
   *
   * <p>Additionally, this method configures all available OBDAOWLReasonerFacotry objects to have a
   * reference to the newly created OBDA model and to the global preference object. This is
   * necessary so that the factories are able to pass the OBDA model to the reasoner instances when
   * they are created.
   */
  private void setupNewOBDAModel() {
    OBDAModel activeOBDAModel = getActiveOBDAModel();

    if (activeOBDAModel != null) {
      return;
    }
    activeOBDAModel = dfac.getOBDAModel();

    activeOBDAModel.addSourcesListener(dlistener);
    activeOBDAModel.addMappingsListener(mlistener);
    queryController.addListener(qlistener);

    OWLModelManager mmgr = owlEditorKit.getOWLWorkspace().getOWLModelManager();

    Set<OWLOntology> ontologies = mmgr.getOntologies();
    for (OWLOntology ontology : ontologies) {
      // Setup the entity declarations
      for (OWLClass c : ontology.getClassesInSignature()) {
        OClass pred = ofac.createClass(c.getIRI().toString());
        activeOBDAModel.declareClass(pred);
      }
      for (OWLObjectProperty r : ontology.getObjectPropertiesInSignature()) {
        ObjectPropertyExpression pred = ofac.createObjectProperty(r.getIRI().toString());
        activeOBDAModel.declareObjectProperty(pred);
      }
      for (OWLDataProperty p : ontology.getDataPropertiesInSignature()) {
        DataPropertyExpression pred = ofac.createDataProperty(p.getIRI().toString());
        activeOBDAModel.declareDataProperty(pred);
      }
    }

    // Setup the prefixes
    PrefixOWLOntologyFormat prefixManager =
        PrefixUtilities.getPrefixOWLOntologyFormat(mmgr.getActiveOntology());
    //		addOBDACommonPrefixes(prefixManager);

    PrefixManagerWrapper prefixwrapper = new PrefixManagerWrapper(prefixManager);
    activeOBDAModel.setPrefixManager(prefixwrapper);

    OWLOntology activeOntology = mmgr.getActiveOntology();

    String defaultPrefix = prefixManager.getDefaultPrefix();
    if (defaultPrefix == null) {
      OWLOntologyID ontologyID = activeOntology.getOntologyID();
      defaultPrefix = ontologyID.getOntologyIRI().toURI().toString();
    }
    activeOBDAModel.getPrefixManager().addPrefix(PrefixManager.DEFAULT_PREFIX, defaultPrefix);

    // Add the model
    URI modelUri = activeOntology.getOntologyID().getOntologyIRI().toURI();
    obdamodels.put(modelUri, activeOBDAModel);
  }
 public boolean assertDataPropertyInstance(String ind, String prop, int value) {
   OWLDataProperty dataProp =
       OWLFactory.getOWLDataProperty(
           IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + prop));
   OWLDataPropertyAssertionAxiom tmpAx =
       OWLFactory.getOWLDataPropertyAssertionAxiom(
           dataProp,
           OWLFactory.getOWLNamedIndividual(
               IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + ind)),
           OWLFactory.getOWLLiteral(value));
   manager.addAxiom(topIxOnt, tmpAx);
   return true;
 }
  ////////////////////////////////
  // INDIVIDUAL ASSERTION METHODS//
  ////////////////////////////////
  public boolean assertSiteIndividual(String siteNameHash, String siteNameAnnotation) {
    OWLClassExpression tmpCE = OWLFactory.getOWLClass(":Site", topIxPrefixManager);
    OWLIndividual tmpInd = OWLFactory.getOWLNamedIndividual(':' + siteNameHash, topIxPrefixManager);

    manager.addAxiom(topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tmpCE, tmpInd));
    manager.addAxiom(
        topIxOnt,
        OWLFactory.getOWLAnnotationAssertionAxiom(
            OWLFactory.getOWLAnnotationProperty(
                IRI.create(
                    topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
            IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + siteNameHash),
            OWLFactory.getOWLLiteral(siteNameAnnotation)));
    return true;
  }
Пример #10
0
  public KuabaRepository createNewRepository(String url, File destination) {
    IRI iri;
    if (url == null) iri = IRI.generateDocumentIRI();
    else iri = IRI.create(url);

    try {
      OWLOntology inst = manager.createOntology(iri);
      OWLImportsDeclaration imp =
          manager.getOWLDataFactory().getOWLImportsDeclaration(IRI.create(ONTOLOGY_URL));
      AddImport addi = new AddImport(inst, imp);
      manager.applyChange(addi);
      KuabaRepository repo = new OwlApiKuabaRepository(inst, manager.getOWLDataFactory());
      repoMap.put(inst.getOntologyID().getOntologyIRI(), repo);
      fileMap.put(repo, destination);

      TemplateGenerator.generateRootQuestion(repo);

      if (destination != null) this.save(repo);
      return repo;
    } catch (OWLOntologyCreationException ex) {
      Logger.getLogger(OwlApiFileGateway.class.getName()).log(Level.SEVERE, null, ex);
    }

    return null;
  }
 @Test
 public void testCreateOntologyWithIRIAndVersionIRIWithMapper() throws Exception {
   OWLOntologyManager manager = Factory.getManager();
   IRI ontologyIRI = IRI("http://www.semanticweb.org/ontologies/ontology");
   IRI versionIRI = IRI("http://www.semanticweb.org/ontologies/ontology/version");
   IRI documentIRI = IRI("file:documentIRI");
   SimpleIRIMapper mapper = new SimpleIRIMapper(versionIRI, documentIRI);
   manager.addIRIMapper(mapper);
   OWLOntology ontology = manager.createOntology(new OWLOntologyID(ontologyIRI, versionIRI));
   assertNotNull("ontology should not be null", ontology);
   assertNotNull("ontology id should not be null", ontology.getOntologyID());
   assertEquals(versionIRI, ontology.getOntologyID().getDefaultDocumentIRI());
   assertEquals(ontologyIRI, ontology.getOntologyID().getOntologyIRI());
   assertEquals(versionIRI, ontology.getOntologyID().getVersionIRI());
   assertEquals(documentIRI, manager.getOntologyDocumentIRI(ontology));
 }
Пример #12
0
 OntologyDataProperty(
     OWLOntologyManager manager, OWLOntology localContext, OntologyChangeManager changeManager) {
   this.manager = manager;
   this.localContext = localContext;
   this.changeManager = changeManager;
   prefix = localContext.getOntologyID().getOntologyIRI() + "#";
 }
Пример #13
0
 public void classifyOntology(OWLOntology ontology, OWLReasonerFactory factory) {
   ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
   OWLReasoner reasoner = factory.createNonBufferingReasoner(ontology);
   // reasoner.precomputeInferences(InferenceType.values());
   long time = System.currentTimeMillis();
   boolean isConsistent = reasoner.isConsistent();
   int numOfUnsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size();
   time = System.currentTimeMillis() - time;
   DLExpressivityChecker checker = new DLExpressivityChecker(Collections.singleton(ontology));
   String e = checker.getDescriptionLogicName();
   String name = ontology.getOntologyID().getOntologyIRI().getFragment();
   logger.info(
       "ontology: "
           + name
           + ", reasoner: "
           + factory.getReasonerName()
           + ", expressivity: "
           + e
           + ", consistent: "
           + isConsistent
           + ", unsat classes: "
           + numOfUnsatClasses
           + ", time: "
           + time);
 }
Пример #14
0
 @Deprecated
 protected boolean isInternal(OWLEntity ent) {
   return ent.getIRI()
       .toURI()
       .getPath()
       .equals(_ontology.getOntologyID().getOntologyIRI().get().toURI().getPath());
 }
Пример #15
0
  public static Map<EdamUri, Concept> load(String edamPath) throws OWLOntologyCreationException {

    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLOntology ontology = manager.loadOntologyFromOntologyDocument(new File(edamPath));

    String prefix = ontology.getOntologyID().getOntologyIRI().get().toString();

    return ontology
        .classesInSignature()
        .filter(c -> EdamUri.isEdamUri(c.getIRI().toString(), prefix))
        .collect(
            Collectors.toMap(
                c -> new EdamUri(c.getIRI().toString(), prefix),
                c -> {
                  Concept concept = new Concept();
                  EntitySearcher.getAnnotations(c, ontology)
                      .forEachOrdered(
                          a -> {
                            if (a.getProperty().isLabel())
                              concept.setLabel(a.getValue().asLiteral().get().getLiteral());
                            else if (a.getProperty().isDeprecated()) concept.setObsolete(true);
                            else if (a.getProperty()
                                    .toStringID()
                                    .equals(
                                        "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym")
                                && a.getValue().asLiteral().isPresent())
                              concept.addExactSynonym(a.getValue().asLiteral().get().getLiteral());
                            else if (a.getProperty()
                                    .toStringID()
                                    .equals(
                                        "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym")
                                && a.getValue().asLiteral().isPresent())
                              concept.addNarrowSynonym(a.getValue().asLiteral().get().getLiteral());
                            else if (a.getProperty()
                                    .toStringID()
                                    .equals(
                                        "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym")
                                && a.getValue().asLiteral().isPresent())
                              concept.addBroadSynonym(a.getValue().asLiteral().get().getLiteral());
                            else if (a.getProperty()
                                    .toStringID()
                                    .equals(
                                        "http://www.geneontology.org/formats/oboInOwl#hasDefinition")
                                && a.getValue().asLiteral().isPresent())
                              concept.setDefinition(a.getValue().asLiteral().get().getLiteral());
                            else if (a.getProperty().isComment()
                                && a.getValue().asLiteral().isPresent())
                              concept.setComment(a.getValue().asLiteral().get().getLiteral());
                          });
                  if (concept.getLabel().isEmpty())
                    throw new IllegalStateException(
                        String.format("Label of concept %s is empty", c.getIRI()));
                  return concept;
                },
                (u, v) -> {
                  throw new IllegalStateException(String.format("Duplicate key %s", u));
                },
                LinkedHashMap::new));
  }
Пример #16
0
 private OWLOntology findOntology(List<OWLOntology> loadedOntologies, IRI documentIRI) {
   for (OWLOntology o : loadedOntologies) {
     if (documentIRI.equals(o.getOntologyID().getOntologyIRI())) {
       return o;
     }
   }
   return null;
 }
  public boolean assertHouseIndividual(String houseEntryHash, String houseEntryAnnotation) {
    OWLClassExpression tempClassExpression = OWLFactory.getOWLClass(":House", topIxPrefixManager);
    OWLIndividual tempIndividual =
        OWLFactory.getOWLNamedIndividual(':' + houseEntryHash, topIxPrefixManager);

    manager.addAxiom(
        topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tempClassExpression, tempIndividual));
    manager.addAxiom(
        topIxOnt,
        OWLFactory.getOWLAnnotationAssertionAxiom(
            OWLFactory.getOWLAnnotationProperty(
                IRI.create(
                    topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
            IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + houseEntryHash),
            OWLFactory.getOWLLiteral(houseEntryAnnotation)));
    return true;
  }
Пример #18
0
  /**
   * Initialization consists of:
   *
   * <ul>
   *   <li>Setting aboxOntology, if not set - defaults to a new ontology using tbox.IRI as base.
   *       Adds import to tbox.
   *   <li>Setting queryOntology, if not set. Adds abox imports queryOntology declaration
   * </ul>
   *
   * @throws OWLOntologyCreationException
   */
  private void init() throws OWLOntologyCreationException {
    // reasoner -> query -> abox -> tbox
    if (aboxOntology == null) {
      LOG.debug("Creating abox ontology. mgr = " + getOWLOntologyManager());
      IRI ontologyIRI = IRI.create(tboxOntology.getOntologyID().getOntologyIRI() + "__abox");
      aboxOntology = getOWLOntologyManager().getOntology(ontologyIRI);
      if (aboxOntology != null) {
        LOG.warn("Clearing existing abox ontology");
        getOWLOntologyManager().removeOntology(aboxOntology);
      }
      aboxOntology = getOWLOntologyManager().createOntology(ontologyIRI);
      AddImport ai =
          new AddImport(
              aboxOntology,
              getOWLDataFactory()
                  .getOWLImportsDeclaration(tboxOntology.getOntologyID().getOntologyIRI()));
      getOWLOntologyManager().applyChange(ai);
    }
    // add listener to abox to set modified flag
    OWLOntologyChangeBroadcastStrategy strategy =
        new SpecificOntologyChangeBroadcastStrategy(aboxOntology);
    OWLOntologyChangeListener listener =
        new OWLOntologyChangeListener() {

          @Override
          public void ontologiesChanged(List<? extends OWLOntologyChange> changes)
              throws OWLException {
            for (OWLOntologyChange owlOntologyChange : changes) {
              if (aboxOntology.equals(owlOntologyChange.getOntology())) {
                setAboxModified(true);
              }
            }
          }
        };
    aboxOntology.getOWLOntologyManager().addOntologyChangeListener(listener, strategy);
    if (queryOntology == null) {
      // Imports: {q imports a, a imports t}
      LOG.debug("Creating query ontology");

      IRI ontologyIRI = IRI.create(tboxOntology.getOntologyID().getOntologyIRI() + "__query");
      queryOntology = getOWLOntologyManager().getOntology(ontologyIRI);
      if (queryOntology == null) {
        queryOntology = getOWLOntologyManager().createOntology(ontologyIRI);
      }
      AddImport ai =
          new AddImport(
              queryOntology,
              getOWLDataFactory()
                  .getOWLImportsDeclaration(aboxOntology.getOntologyID().getOntologyIRI()));
      getOWLOntologyManager().applyChange(ai);
    }
    if (LOG.isDebugEnabled()) {
      LOG.debug(modelId + " manager(T) = " + tboxOntology.getOWLOntologyManager());
      LOG.debug(modelId + " manager(A) = " + aboxOntology.getOWLOntologyManager());
      LOG.debug(modelId + " manager(Q) = " + queryOntology.getOWLOntologyManager());
      LOG.debug(modelId + " id(T) = " + tboxOntology.getOntologyID().getOntologyIRI());
      LOG.debug(modelId + " id(A) = " + aboxOntology.getOntologyID().getOntologyIRI());
      LOG.debug(modelId + " id(Q) = " + queryOntology.getOntologyID().getOntologyIRI());
    }
  }
Пример #19
0
 @Override
 protected Set<? extends OWLAxiom> createAxioms() {
   OWLOntology ont = getOWLOntology("Ont");
   OWLClass cls =
       getFactory().getOWLClass(IRI.create(ont.getOntologyID().getOntologyIRI() + "/Office"));
   Set<OWLAxiom> axs = new HashSet<OWLAxiom>();
   axs.add(getFactory().getOWLDeclarationAxiom(cls));
   return axs;
 }
Пример #20
0
  public void mergeOntologies() {
    List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
    for (OWLOntology ont : ontologies) {
      if (!ont.equals(targetOntology)) {

        // move the axioms
        for (OWLAxiom ax : ont.getAxioms()) {
          changes.add(new AddAxiom(targetOntology, ax));
        }

        // move ontology annotations
        for (OWLAnnotation annot : ont.getAnnotations()) {
          changes.add(new AddOntologyAnnotation(targetOntology, annot));
        }

        if (!targetOntology.getOntologyID().isAnonymous()) {
          // move ontology imports
          for (OWLImportsDeclaration decl : ont.getImportsDeclarations()) {
            if (ontologies.contains(ont.getOWLOntologyManager().getImportedOntology(decl))) {
              continue;
            }
            Optional<IRI> defaultDocumentIRI =
                targetOntology.getOntologyID().getDefaultDocumentIRI();
            if (defaultDocumentIRI.isPresent() && !decl.getIRI().equals(defaultDocumentIRI.get())) {
              changes.add(new AddImport(targetOntology, decl));
            } else {
              logger.warn(
                  "Merge: ignoring import declaration for ontology "
                      + targetOntology.getOntologyID()
                      + " (would result in target ontology importing itself).");
            }
          }
        }
      }
    }
    try {
      owlOntologyManager.applyChanges(changes);
    } catch (OWLOntologyChangeException e) {
      ErrorLogPanel.showErrorDialog(e);
    }
  }
 // asserts a hasHouse property instance between a house and its corresponding
 // site
 public boolean assertHasHousePropertyInstance(String houseEntryHash, String siteNameHash) {
   OWLObjectProperty objProp =
       OWLFactory.getOWLObjectProperty(
           IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasHouse"));
   OWLIndividual houseIndividual =
       OWLFactory.getOWLNamedIndividual(':' + houseEntryHash, topIxPrefixManager);
   OWLIndividual siteIndividual =
       OWLFactory.getOWLNamedIndividual(':' + siteNameHash, topIxPrefixManager);
   manager.addAxiom(
       topIxOnt,
       OWLFactory.getOWLObjectPropertyAssertionAxiom(objProp, siteIndividual, houseIndividual));
   return true;
 }
Пример #22
0
  public KuabaRepository copy(KuabaRepository kr, String url, File destination) {
    IRI iri;
    if (url == null) iri = IRI.generateDocumentIRI();
    else iri = IRI.create(url);

    try {
      OWLOntology model = (OWLOntology) kr.getModel();
      OWLOntology inst = manager.createOntology(iri);

      OntologyMigrator migrator = new OntologyMigrator(manager, model, inst);
      migrator.performMigration();

      EntityFindAndReplaceURIRenamer renamer =
          new EntityFindAndReplaceURIRenamer(
              manager,
              inst.getSignature(false),
              Collections.singleton(inst),
              model.getOntologyID().getOntologyIRI().toString(),
              iri.toString());

      if (renamer.hasErrors()) System.err.println("ERRO durante a cópia - rename");

      manager.applyChanges(renamer.getChanges());

      KuabaRepository repo = new OwlApiKuabaRepository(inst, manager.getOWLDataFactory());
      repoMap.put(inst.getOntologyID().getOntologyIRI(), repo);
      fileMap.put(repo, destination);

      return repo;

    } catch (OWLOntologyCreationException ex) {
      System.err.println("ERRO em copy");
      Logger.getLogger(OwlApiFileGateway.class.getName()).log(Level.SEVERE, null, ex);
    }

    return null;
  }
 public void executeRuleSpec(final RuleSpec r) {
   this.controller.clearResults();
   IRI id = queryOntology.getOntologyID().getDefaultDocumentIRI();
   int i = 0;
   for (final Rule rule : r.getRuleList()) {
     if (rule.isActive()) {
       if (rule.getException() != null) {
         log.info("The query " + rule.getName() + " is not valid, execution cancelled.");
         controller.setStatus(rule.getException().getMessage());
         return;
       }
       id = executeRule(rule, id);
     }
   }
 }
 public boolean assertHasRoomPropertyInstance(
     String houseIndividualHash, String roomIndividualHash) {
   OWLObjectProperty tempOWLbjectProperty =
       OWLFactory.getOWLObjectProperty(
           IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasRoom"));
   OWLIndividual houseIndividual =
       OWLFactory.getOWLNamedIndividual(':' + houseIndividualHash, topIxPrefixManager);
   OWLIndividual roomIndividual =
       OWLFactory.getOWLNamedIndividual(':' + roomIndividualHash, topIxPrefixManager);
   manager.addAxiom(
       topIxOnt,
       OWLFactory.getOWLObjectPropertyAssertionAxiom(
           tempOWLbjectProperty, houseIndividual, roomIndividual));
   return true;
 }
  public boolean assertRoomIndividual(
      String roomName, String roomIndividualHash, String roomIndividualAnnotation) {
    OWLClassExpression tempClassExpression =
        OWLFactory.getOWLClass(
            IRI.create(
                roomToIRI.get(
                    roomName))); // retrieves the Room Class IRI fron the roomToIRI map, using
                                 // roomID as a key.
    OWLIndividual tempIndividual =
        OWLFactory.getOWLNamedIndividual(':' + roomIndividualHash, topIxPrefixManager);

    manager.addAxiom(
        topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tempClassExpression, tempIndividual));
    manager.addAxiom(
        topIxOnt,
        OWLFactory.getOWLAnnotationAssertionAxiom(
            OWLFactory.getOWLAnnotationProperty(
                IRI.create(
                    topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
            IRI.create(
                topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + roomIndividualHash),
            OWLFactory.getOWLLiteral(String.format(roomIndividualAnnotation))));
    return true;
  }
Пример #26
0
 public OBDAModel getActiveOBDAModel() {
   OWLOntology ontology = owlEditorKit.getOWLModelManager().getActiveOntology();
   if (ontology != null) {
     OWLOntologyID ontologyID = ontology.getOntologyID();
     IRI ontologyIRI = ontologyID.getOntologyIRI();
     URI uri = null;
     if (ontologyIRI != null) {
       uri = ontologyIRI.toURI();
     } else {
       uri = URI.create(ontologyID.toString());
     }
     return obdamodels.get(uri);
   }
   return null;
 }
 @Test
 public void testNamedOntologyToString() throws Exception {
   OWLOntologyManager man = Factory.getManager();
   IRI ontIRI = IRI("http://owlapi.sourceforge.net/ont");
   OWLOntology ont = man.createOntology(ontIRI);
   String s = ont.toString();
   String expected =
       "Ontology("
           + ont.getOntologyID().toString()
           + ") [Axioms: "
           + ont.getAxiomCount()
           + " Logical Axioms: "
           + ont.getLogicalAxiomCount()
           + "]";
   assertEquals(expected, s);
 }
Пример #28
0
 public TurtleRenderer(
     OWLOntology ontology, OWLOntologyManager manager, Writer writer, OWLOntologyFormat format) {
   super(ontology, manager, format);
   this.writer = new PrintWriter(writer);
   pending = new HashSet<RDFResourceNode>();
   pm = new DefaultPrefixManager();
   if (!ontology.isAnonymous()) {
     pm.setDefaultPrefix(ontology.getOntologyID().getOntologyIRI() + "#");
   }
   if (format instanceof PrefixOWLOntologyFormat) {
     PrefixOWLOntologyFormat prefixFormat = (PrefixOWLOntologyFormat) format;
     for (String prefixName : prefixFormat.getPrefixNames()) {
       pm.setPrefix(prefixName, prefixFormat.getPrefix(prefixName));
     }
   }
   base = "";
 }
 public HGDBOntology createOntologyInDatabase(IRI ontologyIRI)
     throws OWLOntologyCreationException {
   try {
     HGDBOntologyFormat format = new HGDBOntologyFormat();
     IRI hgdbDocumentIRI = HGDBOntologyFormat.convertToHGDBDocumentIRI(ontologyIRI);
     OWLOntology o = super.createOntology(ontologyIRI);
     setOntologyFormat(o, format);
     setOntologyDocumentIRI(o, hgdbDocumentIRI);
     saveOntology(o, format, hgdbDocumentIRI);
     HGDBOntology result = ontologyRepository.getOntologyByDocumentIRI(hgdbDocumentIRI);
     result.setOWLOntologyManager(this);
     this.ontologiesByID.put(o.getOntologyID(), result);
     return result;
   } catch (Exception ex) {
     throw new RuntimeException(ex);
   }
 }
  public void loadOntology() {
    try {
      /*
       * --apaitoymena vimata gia th dhmioyrgia mapped ontologias:
       * 1.dhmioyrgoyme ena toBeMappedIRI me skopo toy thn antistoixish me
       * to local File. 2.dhmioyrgoyme ena File me th dieythynsh ths
       * ontologias sto topiko apothikeytiko meso. 3.dhmioyrgoyme enan
       * SimpleIRIMapper kai ton prosthetoyme mesw toy manager. o
       * SimpleIRIMapper syndeei to toBeMappedIRI poy dwsame arxika, me
       * thn fysikh topothesia ths ontologias sto topiko apothikeytiko
       * meso. 4.dhmioyrgoyme ena ontologyIRI me akrivws thn idia arxiki
       * timh me to toBeMappedIRI to opoio tha einai to IRI ths ontologias
       * mas 5.dhmioyrgoyme thn ontologia mas xrhsimopoiwntas to
       * manager.loadOntology(ontologyIRI);
       */
      String sep = File.separator;

      manager = OWLManager.createOWLOntologyManager();
      toBeMappedIRI =
          IRI.create(
              "http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl");
      // ontFile = new File("../src/ontologyresources/ptyxiaki_v0.8.owl");
      ontFile = new File("src/ontologyresources/ptyxiaki_v0.8.owl");
      // in case of alternative location on load time when the application is jar'ed!
      if (!ontFile.canRead()) {
        ontFile = new File("ontologyresources/ptyxiaki_v0.8.owl");
      }
      manager.addIRIMapper(new SimpleIRIMapper(toBeMappedIRI, IRI.create(ontFile)));
      ontologyIRI =
          IRI.create(
              "http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl");
      topIxOnt = manager.loadOntology(ontologyIRI);
      OWLFactory = manager.getOWLDataFactory();
      topIxFormat = manager.getOntologyFormat(topIxOnt);
      topIxPrefixManager =
          new DefaultPrefixManager(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#');

      System.out.println("loaded ontology: " + this.topIxOnt);
      System.out.println("from: " + this.manager.getOntologyDocumentIRI(this.topIxOnt));

    } catch (OWLException oex) {
      logger.info(oex.getMessage());
    }
  }