Examples with OWLOntologyManager org.semanticweb.owlapi.model.OWLOntologyManager used on opensource projects

Example 6 with OWLOntologyManager

use of org.semanticweb.owlapi.model.OWLOntologyManager in project stanbol by apache.

the class RecipeWriter method writeTo.

@Override
public void writeTo(Recipe recipe, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    log.debug("Rendering the list of recipes.");
    if (mediaType.toString().equals(MediaType.TEXT_PLAIN)) {
        String recipeString = recipe.toString();
        out.write(recipeString.getBytes());
    } else if (mediaType.toString().equals(MediaType.TEXT_HTML)) {
        String recipeString = recipe.toString();
        out.write(recipeString.getBytes());
    } else {
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLDataFactory factory = OWLManager.getOWLDataFactory();
        OWLOntology ontology;
        try {
            ontology = manager.createOntology();
            RuleList rules = recipe.getRuleList();
            IRI recipeID = recipe.getRecipeID();
            String recipeURI = recipeID.toString().replace("<", "").replace(">", "");
            org.semanticweb.owlapi.model.IRI recipeIRI = org.semanticweb.owlapi.model.IRI.create(recipeURI);
            OWLIndividual recipeIndividual = factory.getOWLNamedIndividual(recipeIRI);
            String descriptionURI = Symbols.description.toString().replace("<", "").replace(">", "");
            org.semanticweb.owlapi.model.IRI descriptionIRI = org.semanticweb.owlapi.model.IRI.create(descriptionURI);
            OWLDataProperty descriptionProperty = factory.getOWLDataProperty(descriptionIRI);
            OWLAxiom axiom;
            String recipeDescription = recipe.getRecipeDescription();
            if (recipeDescription != null) {
                axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, recipeIndividual, recipeDescription);
                manager.addAxiom(ontology, axiom);
            }
            if (rules != null) {
                for (Rule rule : rules) {
                    IRI ruleID = rule.getRuleID();
                    String ruleName = rule.getRuleName();
                    String ruleDescription = rule.getDescription();
                    String ruleURI = ruleID.toString().replace("<", "").replace(">", "");
                    String ruleNameURI = Symbols.ruleName.toString().replace("<", "").replace(">", "");
                    String ruleBodyURI = Symbols.ruleBody.toString().replace("<", "").replace(">", "");
                    String ruleHeadURI = Symbols.ruleHead.toString().replace("<", "").replace(">", "");
                    String hasRuleURI = Symbols.hasRule.toString().replace("<", "").replace(">", "");
                    String ruleContent = rule.toString();
                    String[] ruleParts = ruleContent.split("\\->");
                    org.semanticweb.owlapi.model.IRI ruleIRI = org.semanticweb.owlapi.model.IRI.create(ruleURI);
                    org.semanticweb.owlapi.model.IRI ruleNameIRI = org.semanticweb.owlapi.model.IRI.create(ruleNameURI);
                    org.semanticweb.owlapi.model.IRI ruleBodyIRI = org.semanticweb.owlapi.model.IRI.create(ruleBodyURI);
                    org.semanticweb.owlapi.model.IRI ruleHeadIRI = org.semanticweb.owlapi.model.IRI.create(ruleHeadURI);
                    org.semanticweb.owlapi.model.IRI hasRuleIRI = org.semanticweb.owlapi.model.IRI.create(hasRuleURI);
                    OWLIndividual ruleIndividual = factory.getOWLNamedIndividual(ruleIRI);
                    OWLObjectProperty hasRule = factory.getOWLObjectProperty(hasRuleIRI);
                    OWLDataProperty nameProperty = factory.getOWLDataProperty(ruleNameIRI);
                    OWLDataProperty ruleBodyProperty = factory.getOWLDataProperty(ruleBodyIRI);
                    OWLDataProperty ruleHeadProperty = factory.getOWLDataProperty(ruleHeadIRI);
                    // add the name to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(nameProperty, ruleIndividual, ruleName);
                    manager.addAxiom(ontology, axiom);
                    // add the description to the rule individual
                    if (ruleDescription != null) {
                        axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, ruleIndividual, ruleDescription);
                        manager.addAxiom(ontology, axiom);
                    }
                    // add the rule body to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(ruleBodyProperty, ruleIndividual, ruleParts[0]);
                    manager.addAxiom(ontology, axiom);
                    // add the rule head to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(ruleHeadProperty, ruleIndividual, ruleParts[1]);
                    manager.addAxiom(ontology, axiom);
                    // bind the rule to the recipe
                    axiom = factory.getOWLObjectPropertyAssertionAxiom(hasRule, recipeIndividual, ruleIndividual);
                    manager.addAxiom(ontology, axiom);
                }
            }
            if (mediaType.toString().equals(KRFormat.RDF_XML)) {
                try {
                    manager.saveOntology(ontology, new RDFXMLOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.OWL_XML)) {
                try {
                    manager.saveOntology(ontology, new OWLXMLOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.MANCHESTER_OWL)) {
                try {
                    manager.saveOntology(ontology, new ManchesterOWLSyntaxOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.FUNCTIONAL_OWL)) {
                try {
                    manager.saveOntology(ontology, new OWLFunctionalSyntaxOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.TURTLE)) {
                try {
                    manager.saveOntology(ontology, new TurtleOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.RDF_JSON)) {
                Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
                RdfJsonSerializingProvider provider = new RdfJsonSerializingProvider();
                provider.serialize(out, mGraph, SupportedFormat.RDF_JSON);
            }
        } catch (OWLOntologyCreationException e1) {
            log.error("An error occurred.", e1);
        }
    }
    out.flush();
}

Example 7 with OWLOntologyManager

use of org.semanticweb.owlapi.model.OWLOntologyManager in project stanbol by apache.

the class RecipeListWriter method writeTo.

@Override
public void writeTo(RecipeList recipeList, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    log.debug("Rendering the list of recipes.");
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLDataFactory factory = OWLManager.getOWLDataFactory();
    OWLOntology ontology;
    try {
        ontology = manager.createOntology();
        String recipeClassURI = Symbols.Recipe.toString().replace("<", "").replace(">", "");
        IRI recipeClassIRI = IRI.create(recipeClassURI);
        OWLClass owlRecipeClass = factory.getOWLClass(recipeClassIRI);
        String descriptionURI = Symbols.description.toString().replace("<", "").replace(">", "");
        IRI descriptionIRI = IRI.create(descriptionURI);
        OWLDataProperty descriptionProperty = factory.getOWLDataProperty(descriptionIRI);
        if (recipeList != null) {
            log.info("Converting the recipe list to OWL.");
            for (Recipe recipe : recipeList) {
                String recipeURI = recipe.getRecipeID().toString().replace("<", "").replace(">", "");
                IRI recipeIRI = IRI.create(recipeURI);
                OWLIndividual recipeIndividual = factory.getOWLNamedIndividual(recipeIRI);
                OWLAxiom axiom = factory.getOWLClassAssertionAxiom(owlRecipeClass, recipeIndividual);
                manager.addAxiom(ontology, axiom);
                String description = recipe.getRecipeDescription();
                if (description != null) {
                    axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, recipeIndividual, description);
                    manager.addAxiom(ontology, axiom);
                }
            }
        }
        if (mediaType.toString().equals(KRFormat.RDF_XML)) {
            try {
                manager.saveOntology(ontology, new RDFXMLOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.OWL_XML)) {
            try {
                manager.saveOntology(ontology, new OWLXMLOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.MANCHESTER_OWL)) {
            try {
                manager.saveOntology(ontology, new ManchesterOWLSyntaxOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.FUNCTIONAL_OWL)) {
            try {
                manager.saveOntology(ontology, new OWLFunctionalSyntaxOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.TURTLE)) {
            try {
                manager.saveOntology(ontology, new TurtleOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.RDF_JSON)) {
            Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
            RdfJsonSerializingProvider provider = new RdfJsonSerializingProvider();
            provider.serialize(out, mGraph, SupportedFormat.RDF_JSON);
        }
    } catch (OWLOntologyCreationException e1) {
        log.error("An error occurred.", e1);
    }
    out.flush();
}

Example 8 with OWLOntologyManager

use of org.semanticweb.owlapi.model.OWLOntologyManager in project stanbol by apache.

the class RefactorResource method doRefactoring.

/**
 * Utility method that groups all calls to the refactorer.
 *
 * @param input
 * @param recipe
 * @return
 * @throws OWLOntologyCreationException
 * @throws RefactoringException
 */
private OWLOntology doRefactoring(InputStream input, KB kb) throws OWLOntologyCreationException, RefactoringException {
    if (kb == null)
        return null;
    RuleList ruleList = kb.getRuleList();
    if (ruleList == null)
        return null;
    Recipe actualRecipe = new RecipeImpl(null, null, ruleList);
    // Parse the input ontology
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLOntology inputOntology = manager.loadOntologyFromOntologyDocument(input);
    Graph tripleCollection = refactorer.graphRefactoring(OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(inputOntology), actualRecipe);
    // Refactor
    return OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(tripleCollection);
}

Example 9 with OWLOntologyManager

use of org.semanticweb.owlapi.model.OWLOntologyManager in project stanbol by apache.

the class RefactorResource method performRefactoring.

@POST
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces(value = { TURTLE, RDF_XML, MANCHESTER_OWL, FUNCTIONAL_OWL, OWL_XML, RDF_JSON, X_TURTLE })
public Response performRefactoring(MultiPartBody data, @Context HttpHeaders headers) {
    String recipe = null;
    InputStream input = null;
    if (data.getTextParameterValues("recipe") != null) {
        recipe = data.getTextParameterValues("recipe")[0];
    }
    if (data.getFormFileParameterValues("input") != null) {
        input = new ByteArrayInputStream(data.getFormFileParameterValues("input")[0].getContent());
    }
    if (recipe == null || input == null) {
        throw new WebApplicationException(BAD_REQUEST);
    }
    // Refactorer semionRefactorer = semionManager.getRegisteredRefactorer();
    ResponseBuilder rb;
    Recipe rcp;
    try {
        URI uri = new URI(recipe);
        if (uri != null && uri.getScheme() == null) {
            recipe = "urn:" + recipe;
            log.info("The recipe ID is a URI without scheme. The ID is set to " + recipe);
        }
        IRI recipeID = new IRI(recipe);
        rcp = ruleStore.getRecipe(recipeID);
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLOntology inputOntology = manager.loadOntologyFromOntologyDocument(input);
        Graph tripleCollection = refactorer.graphRefactoring(OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(inputOntology), rcp);
        OWLOntology outputOntology = OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(tripleCollection);
        rb = Response.ok(outputOntology);
        MediaType mediaType = MediaTypeUtil.getAcceptableMediaType(headers, null);
        if (mediaType != null)
            rb.header(HttpHeaders.CONTENT_TYPE, mediaType);
    } catch (NoSuchRecipeException e) {
        rb = Response.status(NOT_FOUND);
        log.error(e.getMessage(), e);
    } catch (RecipeConstructionException e) {
        rb = Response.status(NO_CONTENT);
        log.error(e.getMessage(), e);
    } catch (OWLOntologyCreationException e) {
        rb = Response.status(PRECONDITION_FAILED);
        log.error(e.getMessage(), e);
    } catch (RefactoringException e) {
        rb = Response.status(INTERNAL_SERVER_ERROR);
        log.error(e.getMessage(), e);
    } catch (URISyntaxException e) {
        rb = Response.status(NOT_ACCEPTABLE);
        log.error(e.getMessage(), e);
    }
    // addCORSOrigin(servletContext, rb, headers);
    return rb.build();
}

Example 10 with OWLOntologyManager

use of org.semanticweb.owlapi.model.OWLOntologyManager in project stanbol by apache.

the class HermitReasoningServiceTest method testRun.

private void testRun(String testID, String expectedID) {
    log.info("Testing the run() method");
    OWLOntologyManager manager = TestData.manager;
    // We prepare the input ontology
    try {
        OWLOntology testOntology = manager.createOntology();
        OWLOntologyID testOntologyID = testOntology.getOntologyID();
        log.debug("Created test ontology with ID: {}", testOntologyID);
        AddImport addImport = new AddImport(testOntology, TestData.factory.getOWLImportsDeclaration(IRI.create(testID)));
        manager.applyChange(addImport);
        // We just test class assertions
        List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
        gens.add(new InferredClassAssertionAxiomGenerator());
        // Maybe we want to see what is in before
        if (log.isDebugEnabled())
            TestUtils.debug(manager.getOntology(testOntologyID), log);
        // Now we test the method
        log.debug("Running HermiT");
        Set<OWLAxiom> inferred = this.theinstance.run(manager.getOntology(testOntologyID), gens);
        // Maybe we want to see the inferred axiom list
        if (log.isDebugEnabled()) {
            TestUtils.debug(inferred, log);
        }
        // These are the set of expected axioms
        Set<OWLLogicalAxiom> expectedAxioms = manager.getOntology(IRI.create(expectedID)).getLogicalAxioms();
        Set<OWLAxiom> missing = new HashSet<OWLAxiom>();
        for (OWLAxiom expected : expectedAxioms) {
            if (!inferred.contains(expected)) {
                log.error("missing expected axiom: {}", expected);
                missing.add(expected);
            }
        }
        log.info("Are all expected axioms in the result (true)? {}", missing.isEmpty());
        assertTrue(missing.isEmpty());
        // We want to remove the ontology from the manager
        manager.removeOntology(testOntology);
    } catch (OWLOntologyCreationException e) {
        log.error("An {} have been thrown while creating the input ontology for test", e.getClass());
        assertTrue(false);
    } catch (org.apache.stanbol.reasoners.servicesapi.ReasoningServiceException e) {
        log.error("An {} have been thrown while executing the reasoning", e.getClass());
        assertTrue(false);
    } catch (org.apache.stanbol.reasoners.servicesapi.InconsistentInputException e) {
        log.error("An {} have been thrown while executing the reasoning", e.getClass());
        assertTrue(false);
    }
}