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

Example 26 with OWLOntologyManager

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

the class TestOntologyReconciliation method versioned.

/*
     * Two versioned ontologies that share their ontology IRI are stored with separate public keys that manage
     * their full ontology IDs.
     */
@Test
public void versioned() throws Exception {
    OWLOntologyManager onMgr = OWLManager.createOWLOntologyManager();
    // Load the first ontology
    String location = "/ontologies/versiontest_v1.owl";
    InputStream in = getClass().getResourceAsStream(location);
    in.mark(Integer.MAX_VALUE);
    // Keep tack of the original in a separate ontology.
    OWLOntology o1 = onMgr.loadOntologyFromOntologyDocument(in);
    assertFalse(o1.isAnonymous());
    OWLOntologyID id1 = o1.getOntologyID();
    in.reset();
    // in = getClass().getResourceAsStream(location); // use if stream cannot be reset
    OWLOntologyID key = ontologyProvider.loadInStore(in, RDF_XML, false);
    assertNotNull(key);
    assertFalse(key.isAnonymous());
    log.info("Named ontology loaded with public key {}", key);
    assertEquals(id1, key);
    log.info(" -- (matches actual ontology ID).");
    // The unversioned ID should return no match...
    OWLOntologyID unversioned = new OWLOntologyID(key.getOntologyIRI());
    assertSame(Status.NO_MATCH, ontologyProvider.getStatus(unversioned));
    // ...but a query on the available versions should return only the public key.
    Set<OWLOntologyID> versions = ontologyProvider.listVersions(key.getOntologyIRI());
    assertFalse(versions.isEmpty());
    assertSame(1, versions.size());
    assertTrue(versions.contains(id1));
    // Now load the second version.
    location = "/ontologies/versiontest_v2.owl";
    in = getClass().getResourceAsStream(location);
    in.mark(Integer.MAX_VALUE);
    // Keep tack of the original in a separate ontology.
    OWLOntology o2 = onMgr.loadOntologyFromOntologyDocument(in);
    assertFalse(o2.isAnonymous());
    OWLOntologyID id2 = o2.getOntologyID();
    in.reset();
    // in = getClass().getResourceAsStream(location); // use if stream cannot be reset
    key = ontologyProvider.loadInStore(in, RDF_XML, false);
    assertNotNull(key);
    assertFalse(key.isAnonymous());
    log.info("Named ontology loaded with public key {}", key);
    assertEquals(id2, key);
    log.info(" -- (matches actual ontology ID).");
    // The unversioned ID should still return no match...
    assertSame(Status.NO_MATCH, ontologyProvider.getStatus(unversioned));
    // ...but a query on the available versions should return both public keys now.
    versions = ontologyProvider.listVersions(key.getOntologyIRI());
    assertFalse(versions.isEmpty());
    assertSame(2, versions.size());
    assertTrue(versions.contains(id1));
    assertTrue(versions.contains(id2));
    // Check that axioms match for version 1
    log.info("Version 1:");
    OWLOntology o1_1 = ontologyProvider.getStoredOntology(id1, OWLOntology.class, false);
    assertFalse(o1_1.isAnonymous());
    // Cannot equal OWLOntology objects
    assertEquals(o1.getOntologyID(), o1_1.getOntologyID());
    log.warn("Plain OWL API seems to be failing to preserve owl:versionInfo. Will test non-annotation axioms only.");
    assertEquals(o1.getTBoxAxioms(false), o1_1.getTBoxAxioms(false));
    log.info(" -- TBox axiom check successful.");
    assertEquals(o1.getABoxAxioms(false), o1_1.getABoxAxioms(false));
    log.info(" -- ABox axiom check successful.");
    // Check that axioms match for version 2 (therefore differ from each other)
    log.info("Version 2:");
    OWLOntology o2_1 = ontologyProvider.getStoredOntology(id2, OWLOntology.class, false);
    assertFalse(o2_1.isAnonymous());
    // Cannot equal OWLOntology objects
    assertEquals(o2.getOntologyID(), o2_1.getOntologyID());
    log.warn("Plain OWL API seems to be failing to preserve owl:versionInfo. Will test non-annotation axioms only.");
    assertEquals(o2.getTBoxAxioms(false), o2_1.getTBoxAxioms(false));
    log.info(" -- TBox axiom check successful.");
    assertEquals(o2.getABoxAxioms(false), o2_1.getABoxAxioms(false));
    log.info(" -- ABox axiom check successful.");
    // There should be no aliases.
    assertSame(0, ontologyProvider.listAliases(unversioned).size());
    assertSame(0, ontologyProvider.listAliases(id1).size());
    assertSame(0, ontologyProvider.listAliases(id2).size());
}

Example 27 with OWLOntologyManager

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

the class TestOntologyReconciliation method versionedOnlyFromStream.

/*
     * If an ontology has no ontology IRI but does have a version IRI, it should still be possible to load it,
     * but the version IRI must be erased.
     */
@Test
public void versionedOnlyFromStream() throws Exception {
    String location = "/ontologies/naming/versionedonly.owl";
    InputStream in = getClass().getResourceAsStream(location);
    in.mark(Integer.MAX_VALUE);
    OWLOntologyManager onMgr = OWLManager.createOWLOntologyManager();
    OWLOntology o1 = onMgr.loadOntologyFromOntologyDocument(in);
    // Ensure that the OWL API erases the version IRI.
    assertTrue(o1.isAnonymous());
    assertNull(o1.getOntologyID().getVersionIRI());
    in.reset();
    // in = getClass().getResourceAsStream(location); // use if stream cannot be reset
    // The public key must be non-anonymous nonetheless.
    OWLOntologyID key = ontologyProvider.loadInStore(in, RDF_XML, false);
    assertNotNull(key);
    assertFalse(key.isAnonymous());
    assertNull(key.getVersionIRI());
    log.info("Wrongly versioned ontology loaded with public key {}", key);
    assertFalse(o1.equals(key));
    OWLOntology o1_1 = ontologyProvider.getStoredOntology(key, OWLOntology.class, false);
    assertNotNull(o1_1);
    assertTrue(o1_1.isAnonymous());
    assertNull(o1_1.getOntologyID().getVersionIRI());
    // Cannot equal two OWLOntology objects, especially if anonymous.
    // Check that they match axiom-wise.
    log.warn("Plain OWL API seems to be failing to preserve owl:versionInfo. Will test non-annotation axioms only.");
    assertEquals(o1.getTBoxAxioms(false), o1_1.getTBoxAxioms(false));
    log.info(" -- TBox axiom check successful.");
    assertEquals(o1.getABoxAxioms(false), o1_1.getABoxAxioms(false));
    log.info(" -- ABox axiom check successful.");
    // No aliases should have been created.
    assertSame(0, ontologyProvider.listAliases(key).size());
}

Example 28 with OWLOntologyManager

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

the class ScopeManagerImpl method activate.

/**
 * Called within both OSGi and non-OSGi environments.
 *
 * @param configuration
 * @throws IOException
 */
protected void activate(Dictionary<String, Object> configuration) throws IOException {
    long before = System.currentTimeMillis();
    // Assign singleton instance
    me = this;
    // Parse configuration
    if (offline != null)
        ontonetNS = offline.getDefaultOntologyNetworkNamespace();
    scopeRegistryId = (String) configuration.get(ScopeManager.ID_SCOPE_REGISTRY);
    if (scopeRegistryId == null)
        scopeRegistryId = _ID_SCOPE_REGISTRY_DEFAULT;
    configPath = (String) configuration.get(ScopeManager.CONFIG_ONTOLOGY_PATH);
    if (configPath == null)
        configPath = _CONFIG_ONTOLOGY_PATH_DEFAULT;
    // Bind components, starting with the local directories.
    List<String> dirs = new ArrayList<String>();
    try {
        for (IRI iri : offline.getOntologySourceLocations()) dirs.add(iri.toString());
    } catch (NullPointerException ex) {
    // Ok, go empty
    }
    bindResources();
    // String tfile = (String) configuration.get(CONFIG_FILE_PATH);
    // if (tfile != null) this.configPath = tfile;
    // String tns = (String) configuration.get(KRES_NAMESPACE);
    // if (tns != null) this.kresNs = tns;
    // configPath = (String) configuration.get(CONFIG_FILE_PATH);
    // If there is no configuration file, just start with an empty scope set
    Object connectivityPolicy = configuration.get(ScopeManager.CONNECTIVITY_POLICY);
    if (connectivityPolicy == null) {
        this.connectivityPolicyString = _CONNECTIVITY_POLICY_DEFAULT;
    } else {
        this.connectivityPolicyString = connectivityPolicy.toString();
    }
    String configPath = getOntologyNetworkConfigurationPath();
    if (configPath != null && !configPath.trim().isEmpty()) {
        OWLOntology oConf = null;
        OWLOntologyManager tempMgr = OWLOntologyManagerFactory.createOWLOntologyManager(offline.getOntologySourceLocations().toArray(new IRI[0]));
        OWLOntologyDocumentSource oConfSrc = null;
        try {
            log.debug("Try to load the configuration ontology from a local bundle relative path");
            InputStream is = this.getClass().getResourceAsStream(configPath);
            oConfSrc = new StreamDocumentSource(is);
        } catch (Exception e1) {
            try {
                log.debug("Cannot load from a local bundle relative path", e1);
                log.debug("Try to load the configuration ontology resolving the given IRI");
                IRI iri = IRI.create(configPath);
                if (!iri.isAbsolute())
                    throw new Exception("IRI seems to be not absolute! value was: " + iri.toQuotedString());
                oConfSrc = new IRIDocumentSource(iri);
            } catch (Exception e) {
                try {
                    log.debug("Cannot load from the web", e1);
                    log.debug("Try to load the configuration ontology as full local file path");
                    oConfSrc = new FileDocumentSource(new File(configPath));
                } catch (Exception e2) {
                    log.error("Cannot load the configuration ontology from parameter value: " + configPath, e2);
                }
            }
        }
        if (oConfSrc == null) {
            log.warn("No ONM configuration file found at path " + configPath + ". Starting with blank scope set.");
        } else {
            try {
                oConf = tempMgr.loadOntologyFromOntologyDocument(oConfSrc);
            } catch (OWLOntologyCreationException e) {
                log.error("Cannot create the configuration ontology", e);
            }
        }
        // Create and populate the scopes from the config ontology.
        bootstrapOntologyNetwork(oConf);
    } else {
        // No ontology supplied. Access the local graph
        rebuildScopes();
    }
    log.debug(ScopeManager.class + " activated. Time : {} ms.", System.currentTimeMillis() - before);
}

Example 29 with OWLOntologyManager

use of org.semanticweb.owlapi.model.OWLOntologyManager in project webprotege by protegeproject.

the class RevisionManagerImpl method getOntologyManagerForRevision.

@Nonnull
@Override
public OWLOntologyManager getOntologyManagerForRevision(@Nonnull RevisionNumber revision) {
    try {
        OWLOntologyManager manager = WebProtegeOWLManager.createOWLOntologyManager();
        final OWLOntologyID singletonOntologyId = new OWLOntologyID();
        for (Revision rev : revisionStore.getRevisions()) {
            if (rev.getRevisionNumber().compareTo(revision) <= 0) {
                for (OWLOntologyChangeRecord record : rev) {
                    // Anonymous ontologies are not handled nicely at all.
                    OWLOntologyChangeRecord normalisedChangeRecord = normaliseChangeRecord(record, singletonOntologyId);
                    OWLOntologyID ontologyId = normalisedChangeRecord.getOntologyID();
                    if (!manager.contains(ontologyId)) {
                        manager.createOntology(ontologyId);
                    }
                    OWLOntologyChange change = normalisedChangeRecord.createOntologyChange(manager);
                    manager.applyChange(change);
                }
            }
        }
        if (manager.getOntologies().isEmpty()) {
            // No revisions exported.  Just create an empty ontology
            manager.createOntology();
        }
        return manager;
    } catch (OWLOntologyCreationException e) {
        throw new RuntimeException("Problem creating ontology: " + e);
    }
}

Example 30 with OWLOntologyManager

use of org.semanticweb.owlapi.model.OWLOntologyManager in project webprotege by protegeproject.

the class ProjectDownloader method exportProjectRevision.

private void exportProjectRevision(@Nonnull String projectDisplayName, @Nonnull RevisionNumber revisionNumber, @Nonnull OutputStream outputStream, @Nonnull DownloadFormat format) throws IOException, OWLOntologyStorageException {
    RevisionManager revisionManager = project.getRevisionManager();
    OWLOntologyManager manager = revisionManager.getOntologyManagerForRevision(revisionNumber);
    OWLOntologyID rootOntologyId = project.getRootOntology().getOntologyID();
    Optional<OWLOntology> revisionRootOntology = getOntologyFromManager(manager, rootOntologyId);
    if (revisionRootOntology.isPresent()) {
        saveImportsClosureToStream(projectDisplayName, revisionRootOntology.get(), format, outputStream, revisionNumber);
    } else {
        // An error - no flipping ontology!
        logger.info("Project download failed because the root ontology could not be retrived from the manager.  Project: ", project.getProjectId());
        throw new RuntimeException("The ontology could not be downloaded from " + applicationName + ".  Please contact the administrator.");
    }
}