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

Example 41 with OWLOntologyManager

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

the class HermitReasoningServiceTest method testEnrichWithRules.

private void testEnrichWithRules(String testID, String rulesID, String testExpectedID) {
    log.info("Testing the task ENRICH with rules");
    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);
        OWLImportsDeclaration importTest = TestData.factory.getOWLImportsDeclaration(IRI.create(testID));
        manager.applyChange(new AddImport(testOntology, importTest));
        Set<SWRLRule> rules = manager.getOntology(IRI.create(rulesID)).getAxioms(AxiomType.SWRL_RULE);
        // Maybe we want to see the list of rules
        if (log.isDebugEnabled()) {
            log.debug("List of {} rules: ", rules.size());
            TestUtils.debug(rules, log);
        }
        log.debug("We add the rules to the ontology");
        manager.addAxioms(manager.getOntology(testOntologyID), rules);
        // Maybe we want to see what is in before
        if (log.isDebugEnabled())
            log.debug("Content of the input is:");
        TestUtils.debug(manager.getOntology(testOntologyID), log);
        // Now we test the method
        log.debug("Running HermiT");
        Set<OWLAxiom> inferred = this.theinstance.runTask(ReasoningService.Tasks.ENRICH, manager.getOntology(testOntologyID));
        // Maybe we want to see the inferred axiom list
        if (log.isDebugEnabled()) {
            log.debug("{} inferred axioms:", inferred.size());
            TestUtils.debug(inferred, log);
        }
        Set<OWLLogicalAxiom> expectedAxioms = manager.getOntology(IRI.create(testExpectedID)).getLogicalAxioms();
        Set<OWLAxiom> missing = new HashSet<OWLAxiom>();
        for (OWLAxiom expected : expectedAxioms) {
            // We consider here all kind of axioms
            if (!inferred.contains(expected)) {
                log.error("missing expected axiom: {}", expected);
                missing.add(expected);
            }
        }
        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 (ReasoningServiceException e) {
        log.error("An {} have been thrown while executing the reasoning", e.getClass());
        assertTrue(false);
    } catch (InconsistentInputException e) {
        log.error("An {} have been thrown while executing the reasoning", e.getClass());
        assertTrue(false);
    } catch (UnsupportedTaskException e) {
        log.error("An {} have been thrown while executing the reasoning", e.getClass());
        assertTrue(false);
    }
}

Example 42 with OWLOntologyManager

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

the class RegistryManagerImpl method activate.

protected void activate(Dictionary<String, Object> configuration) {
    // Parse configuration.
    try {
        lazyLoading = (Boolean) (configuration.get(RegistryManager.LAZY_LOADING));
    } catch (Exception ex) {
        lazyLoading = _LAZY_LOADING_DEFAULT;
    }
    try {
        retainIncomplete = (Boolean) (configuration.get(RegistryManager.RETAIN_INCOMPLETE));
    } catch (Exception ex) {
        retainIncomplete = _RETAIN_INCOMPLETE_DEFAULT;
    }
    Object obj = configuration.get(RegistryManager.REGISTRY_LOCATIONS);
    if (obj instanceof String[])
        locations = (String[]) obj;
    else if (obj instanceof String)
        locations = new String[] { (String) obj };
    if (locations == null)
        locations = new String[] { "stanbol_network.owl" };
    Object cachingPolicy = configuration.get(RegistryManager.CACHING_POLICY);
    if (cachingPolicy == null) {
        this.cachingPolicyString = _CACHING_POLICY_DEFAULT.name();
    } else {
        this.cachingPolicyString = cachingPolicy.toString();
    }
    final IRI[] offlineResources;
    if (this.offline != null) {
        List<IRI> paths = offline.getOntologySourceLocations();
        if (paths != null)
            offlineResources = paths.toArray(new IRI[0]);
        else
            // There are no offline paths.
            offlineResources = new IRI[0];
    } else
        // There's no offline configuration at all.
        offlineResources = new IRI[0];
    // Used only for creating the registry model, do not use for caching.
    OWLOntologyManager mgr = OWLOntologyManagerFactory.createOWLOntologyManager(offlineResources);
    OWLOntologyLoaderConfiguration conf = new OWLOntologyLoaderConfiguration();
    // If we are retaining incomplete registries, do not throw exceptions if imports fail.
    conf.setSilentMissingImportsHandling(retainIncomplete);
    // Load registries
    Set<OWLOntology> regOnts = new HashSet<OWLOntology>();
    for (String loc : locations) {
        try {
            IRI iri = IRI.create(loc);
            OWLOntologyDocumentSource src = null;
            OWLOntology o = null;
            if (iri.isAbsolute())
                src = new IRIDocumentSource(iri);
            else {
                // Relative IRI : use data file provider
                log.debug("Found relative IRI {} . Will try to retrieve from data file providers.", iri);
                Map<String, String> info = new HashMap<String, String>();
                if (dataFileProvider != null && dataFileProvider.isAvailable(null, loc, info))
                    src = new StreamDocumentSource(dataFileProvider.getInputStream(null, loc, info));
            }
            if (src != null)
                o = mgr.loadOntologyFromOntologyDocument(src, conf);
            if (o != null)
                regOnts.add(o);
            else
                log.warn("Failed to obtain OWL ontology from resource {}", loc);
        } catch (OWLOntologyAlreadyExistsException e) {
            log.info("Skipping cached ontology {}.", e.getOntologyID());
            continue;
        } catch (OWLOntologyCreationException e) {
            log.warn("Failed to load ontology " + loc + " - Skipping...", e);
            continue;
        } catch (Exception e) {
            log.warn("Invalid registry configuration " + loc + " - Skipping...", e);
            continue;
        }
    }
    // Create and set the cache.
    if (cachingPolicyString.equals(CachingPolicy.CENTRALISED.name())) {
        // this.cache = OWLOntologyManagerFactory.createOWLOntologyManager(offlineResources);
        if (cache == null) {
            log.warn("Caching policy is set as Centralised, but no ontology provider is supplied. Will use new in-memory tcProvider.");
            cache = new ClerezzaOntologyProvider(TcManager.getInstance(), offline, Parser.getInstance());
        }
    // else sta bene cosi'
    } else if (cachingPolicyString.equals(CachingPolicy.DISTRIBUTED.name())) {
        this.cache = null;
    }
    riFactory = new RegistryItemFactoryImpl(cache);
    // Build the model.
    createModel(regOnts);
    // Set the cache on libraries.
    Set<RegistryItem> visited = new HashSet<RegistryItem>();
    for (Registry reg : getRegistries()) for (RegistryItem child : reg.getChildren()) if (!visited.contains(child)) {
        if (child instanceof Library) {
            if (this.cache != null)
                ((Library) child).setCache(this.cache);
            else
                ((Library) child).setCache(new ClerezzaOntologyProvider(TcManager.getInstance(), offline, Parser.getInstance()));
        }
        visited.add(child);
    }
    if (isLazyLoading()) {
    // Nothing to do about it at the moment.
    } else {
        loadEager();
    }
}

Example 43 with OWLOntologyManager

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

the class SessionImpl method attachScopeImportsOwlApi.

private void attachScopeImportsOwlApi(OWLOntology target, org.semanticweb.owlapi.model.IRI prefix) {
    if (!attachedScopes.isEmpty()) {
        String scopePrefix = prefix.toString();
        scopePrefix = scopePrefix.substring(0, scopePrefix.lastIndexOf("/" + shortName + "/")) + "/ontology/";
        List<OWLOntologyChange> changes = new LinkedList<OWLOntologyChange>();
        OWLOntologyManager ontologyManager = target.getOWLOntologyManager();
        OWLDataFactory df = ontologyManager.getOWLDataFactory();
        // Add import declarations for attached scopes.
        for (String scopeID : attachedScopes) {
            org.semanticweb.owlapi.model.IRI physIRI = org.semanticweb.owlapi.model.IRI.create(scopePrefix + scopeID);
            changes.add(new AddImport(target, df.getOWLImportsDeclaration(physIRI)));
        }
        // Commit
        ontologyManager.applyChanges(changes);
    }
}

Example 44 with OWLOntologyManager

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

the class TestOntologyCollectors method spacePreservesImports.

@Test
public void spacePreservesImports() throws Exception {
    InputStream content = getClass().getResourceAsStream("/ontologies/characters_all.owl");
    URL url = getClass().getResource("/ontologies/characters_all.owl");
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    mgr.addOntologyLoaderListener(new OWLOntologyLoaderListener() {

        @Override
        public void startedLoadingOntology(LoadingStartedEvent arg0) {
        }

        @Override
        public void finishedLoadingOntology(LoadingFinishedEvent arg0) {
            log.info((arg0.isSuccessful() ? "Loaded" : "Failed") + (arg0.isImported() ? " imported " : " ") + "ontology " + arg0.getDocumentIRI());
        }
    });
    mgr.addIRIMapper(new PhonyIRIMapper(null));
    File f = new File(url.toURI());
    OntologyInputSource<OWLOntology> src = new ParentPathInputSource(f, mgr);
    // OntologyInputSource<OWLOntology> src = new RootOntologyIRISource(IRI.create(f), mgr);
    // OntologyInputSource<OWLOntology> src = new OntologyContentInputSource(content,mgr);
    OWLOntology original = src.getRootOntology();
    Assert.assertNotNull(original);
    OntologySpace spc = new CustomSpaceImpl("Test", scopeNs, ontologyProvider);
    spc.addOntology(src);
}

Example 45 with OWLOntologyManager

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

the class TestOntologyReconciliation method anonymousFromURL.

/*
     * Anonymous ontologies loaded from a URL must reconcile with a public key that matches the resource URL
     * in its ontology IRI.
     */
@Test
public void anonymousFromURL() throws Exception {
    URL in = getClass().getResource(location_nameless);
    OWLOntologyManager onMgr = OWLManager.createOWLOntologyManager();
    OWLOntology o1 = onMgr.loadOntologyFromOntologyDocument(IRI.create(in));
    assertTrue(o1.isAnonymous());
    // in = getClass().getResourceAsStream(location); // use if stream cannot be reset
    OWLOntologyID key = ontologyProvider.loadInStore(IRI.create(in), RDF_XML, false);
    assertNotNull(key);
    assertFalse(key.isAnonymous());
    log.info("Anonymous ontology loaded with non-anonymous public key {}", key);
    OWLOntology o2 = ontologyProvider.getStoredOntology(key, OWLOntology.class, false);
    assertTrue(o2.isAnonymous());
    // Cannot equal OWLOntology objects
    assertEquals(o1.getAxioms(), o2.getAxioms());
}