Examples with IndexedGraph org.apache.stanbol.commons.indexedgraph.IndexedGraph used on opensource projects

Example 6 with IndexedGraph

use of org.apache.stanbol.commons.indexedgraph.IndexedGraph in project stanbol by apache.

the class ReferencedSiteRootResource method executeLDPathQuery.

/**
     * Execute a Query that uses LDPath to process results.
     * @param query the query
     * @param mediaType the mediaType for the response
     * @param headers the http headers of the request
     * @return the response
     */
private Response executeLDPathQuery(Site site, FieldQuery query, String ldpathProgramString, MediaType mediaType, HttpHeaders headers) {
    QueryResultList<Representation> result;
    ValueFactory vf = new RdfValueFactory(new IndexedGraph());
    SiteBackend backend = new SiteBackend(site, vf);
    EntityhubLDPath ldPath = new EntityhubLDPath(backend, vf);
    //copy the selected fields, because we might need to delete some during
    //the preparation phase
    Set<String> selectedFields = new HashSet<String>(query.getSelectedFields());
    //first prepare (only execute the query if the parameters are valid)
    Program<Object> program;
    try {
        program = prepareQueryLDPathProgram(ldpathProgramString, selectedFields, backend, ldPath);
    } catch (LDPathParseException e) {
        log.warn("Unable to parse LDPath program used as select for Query:");
        log.warn("FieldQuery: \n {}", query);
        log.warn("LDPath: \n {}", ((LDPathSelect) query).getLDPathSelect());
        log.warn("Exception:", e);
        return Response.status(Status.BAD_REQUEST).entity(("Unable to parse LDPath program (Messages: " + getLDPathParseExceptionMessage(e) + ")!\n")).header(HttpHeaders.ACCEPT, mediaType).build();
    } catch (IllegalStateException e) {
        log.warn("parsed LDPath program is not compatible with parsed Query!", e);
        return Response.status(Status.BAD_REQUEST).entity(e.getMessage()).header(HttpHeaders.ACCEPT, mediaType).build();
    }
    //2. execute the query
    Iterator<Representation> resultIt;
    try {
        // we need to adapt from Entity to Representation
        resultIt = new AdaptingIterator<Entity, Representation>(site.findEntities(query).iterator(), new AdaptingIterator.Adapter<Entity, Representation>() {

            @Override
            public Representation adapt(Entity value, Class<Representation> type) {
                return value.getRepresentation();
            }
        }, Representation.class);
    } catch (SiteException e) {
        String message = String.format("Unable to Query Site '%s' (message: %s)", site.getId(), e.getMessage());
        log.error(message, e);
        return Response.status(Status.INTERNAL_SERVER_ERROR).entity(message).header(HttpHeaders.ACCEPT, mediaType).build();
    }
    //process the results
    Collection<Representation> transformedResults = transformQueryResults(resultIt, program, selectedFields, ldPath, backend, vf);
    result = new QueryResultListImpl<Representation>(query, transformedResults, Representation.class);
    ResponseBuilder rb = Response.ok(result);
    rb.header(HttpHeaders.CONTENT_TYPE, mediaType + "; charset=utf-8");
    //addCORSOrigin(servletContext, rb, headers);
    return rb.build();
}

Example 7 with IndexedGraph

use of org.apache.stanbol.commons.indexedgraph.IndexedGraph in project stanbol by apache.

the class EntityhubRootResource method executeLDPathQuery.

/**
     * Execute a Query that uses LDPath to process results.
     * @param query the query
     * @param mediaType the mediaType for the response
     * @param headers the http headers of the request
     * @return the response
     */
private Response executeLDPathQuery(Entityhub entityhub, FieldQuery query, String ldpathProgramString, MediaType mediaType, HttpHeaders headers) {
    QueryResultList<Representation> result;
    ValueFactory vf = new RdfValueFactory(new IndexedGraph());
    EntityhubBackend backend = new EntityhubBackend(entityhub);
    EntityhubLDPath ldPath = new EntityhubLDPath(backend, vf);
    //copy the selected fields, because we might need to delete some during
    //the preparation phase
    Set<String> selectedFields = new HashSet<String>(query.getSelectedFields());
    //first prepare (only execute the query if the parameters are valid)
    Program<Object> program;
    try {
        program = prepareQueryLDPathProgram(ldpathProgramString, selectedFields, backend, ldPath);
    } catch (LDPathParseException e) {
        log.warn("Unable to parse LDPath program used as select for Query:");
        log.warn("FieldQuery: \n {}", query);
        log.warn("LDPath: \n {}", ((LDPathSelect) query).getLDPathSelect());
        log.warn("Exception:", e);
        return Response.status(Status.BAD_REQUEST).entity(("Unable to parse LDPath program (Messages: " + getLDPathParseExceptionMessage(e) + ")!\n")).header(HttpHeaders.ACCEPT, mediaType).build();
    } catch (IllegalStateException e) {
        log.warn("parsed LDPath program is not compatible with parsed Query!", e);
        return Response.status(Status.BAD_REQUEST).entity(e.getMessage()).header(HttpHeaders.ACCEPT, mediaType).build();
    }
    //2. execute the query
    Iterator<Representation> resultIt;
    try {
        // go directly to the yard and query there for Representations
        resultIt = entityhub.getYard().findRepresentation(query).iterator();
    } catch (EntityhubException e) {
        String message = String.format("Exception while performing the " + "FieldQuery on the EntityHub (message: %s)", e.getMessage());
        log.error(message, e);
        return Response.status(Status.INTERNAL_SERVER_ERROR).entity(message).header(HttpHeaders.ACCEPT, mediaType).build();
    }
    //process the results
    Collection<Representation> transformedResults = transformQueryResults(resultIt, program, selectedFields, ldPath, backend, vf);
    result = new QueryResultListImpl<Representation>(query, transformedResults, Representation.class);
    ResponseBuilder rb = Response.ok(result);
    rb.header(HttpHeaders.CONTENT_TYPE, mediaType + "; charset=utf-8");
    //addCORSOrigin(servletContext, rb, headers);
    return rb.build();
}

Example 8 with IndexedGraph

use of org.apache.stanbol.commons.indexedgraph.IndexedGraph in project stanbol by apache.

the class EnhancementEngineHelperTest method testTextAnnotationNewModel.

@Test
public void testTextAnnotationNewModel() {
    String content = "The Stanbol Enhancer can extract Entities form parsed Text.";
    Language lang = new Language("en");
    int start = content.indexOf("Stanbol");
    int end = start + "Stanbol Enhancer".length();
    IRI ciUri = new IRI("http://www.example.org/contentItem#1");
    Graph metadata = new IndexedGraph();
    IRI ta = EnhancementEngineHelper.createTextEnhancement(metadata, dummyEngine, ciUri);
    EnhancementEngineHelper.setOccurrence(metadata, ta, content, start, end, lang, -1, true);
    Assert.assertEquals("The ", EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTION_PREFIX));
    Assert.assertEquals("Stanbol Enhancer", EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTED_TEXT));
    Assert.assertEquals(" can extra", EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTION_SUFFIX));
    Assert.assertEquals(Integer.valueOf(start), EnhancementEngineHelper.get(metadata, ta, Properties.ENHANCER_START, Integer.class, lf));
    Assert.assertEquals(Integer.valueOf(end), EnhancementEngineHelper.get(metadata, ta, Properties.ENHANCER_END, Integer.class, lf));
    //head and tail should be null
    Assert.assertNull(EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTION_HEAD));
    Assert.assertNull(EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTION_TAIL));
    content = "Ich habe den Schlüssel fürs Donaudampfschiffahrtsgesellschaftskapitänskajütenschloss verlohren.";
    start = content.indexOf("Donaudampfschi");
    end = content.indexOf(" verlohren");
    ta = EnhancementEngineHelper.createTextEnhancement(metadata, dummyEngine, ciUri);
    EnhancementEngineHelper.setOccurrence(metadata, ta, content, start, end, lang, -1, true);
    Assert.assertEquals("ssel fürs ", EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTION_PREFIX));
    Assert.assertEquals(" verlohren", EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTION_SUFFIX));
    Assert.assertEquals(Integer.valueOf(start), EnhancementEngineHelper.get(metadata, ta, Properties.ENHANCER_START, Integer.class, lf));
    Assert.assertEquals(Integer.valueOf(end), EnhancementEngineHelper.get(metadata, ta, Properties.ENHANCER_END, Integer.class, lf));
    //selected text is expected to be null
    Assert.assertNull(EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTED_TEXT));
    //tail and head should be present
    Assert.assertEquals("Donaudampf", EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTION_HEAD));
    Assert.assertEquals("tenschloss", EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTION_TAIL));
    //finally the same but deactivating head/tail
    ta = EnhancementEngineHelper.createTextEnhancement(metadata, dummyEngine, ciUri);
    EnhancementEngineHelper.setOccurrence(metadata, ta, content, start, end, lang, -1, false);
    Assert.assertEquals("Donaudampfschiffahrtsgesellschaftskapitänskajütenschloss", EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTED_TEXT));
    Assert.assertNull(EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTION_HEAD));
    Assert.assertNull(EnhancementEngineHelper.getString(metadata, ta, Properties.ENHANCER_SELECTION_TAIL));
}

Example 9 with IndexedGraph

use of org.apache.stanbol.commons.indexedgraph.IndexedGraph in project stanbol by apache.

the class EntityLinkingEngineTest method setUpServices.

@BeforeClass
public static void setUpServices() throws IOException {
    searcher = new TestSearcherImpl(TEST_REFERENCED_SITE_NAME, NAME, new SimpleLabelTokenizer());
    //add some terms to the searcher
    Graph graph = new IndexedGraph();
    IRI uri = new IRI("urn:test:PatrickMarshall");
    graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("Patrick Marshall")));
    graph.add(new TripleImpl(uri, TYPE, OntologicalClasses.DBPEDIA_PERSON));
    searcher.addEntity(new Entity(uri, graph));
    uri = new IRI("urn:test:Geologist");
    graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("Geologist")));
    graph.add(new TripleImpl(uri, TYPE, new IRI(NamespaceEnum.skos + "Concept")));
    graph.add(new TripleImpl(uri, REDIRECT, new IRI("urn:test:redirect:Geologist")));
    searcher.addEntity(new Entity(uri, graph));
    //a redirect
    uri = new IRI("urn:test:redirect:Geologist");
    graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("Geologe (redirect)")));
    graph.add(new TripleImpl(uri, TYPE, new IRI(NamespaceEnum.skos + "Concept")));
    searcher.addEntity(new Entity(uri, graph));
    uri = new IRI("urn:test:NewZealand");
    graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("New Zealand")));
    graph.add(new TripleImpl(uri, TYPE, OntologicalClasses.DBPEDIA_PLACE));
    searcher.addEntity(new Entity(uri, graph));
    uri = new IRI("urn:test:UniversityOfOtago");
    graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("University of Otago")));
    graph.add(new TripleImpl(uri, TYPE, OntologicalClasses.DBPEDIA_ORGANISATION));
    searcher.addEntity(new Entity(uri, graph));
    uri = new IRI("urn:test:University");
    graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("University")));
    graph.add(new TripleImpl(uri, TYPE, new IRI(NamespaceEnum.skos + "Concept")));
    searcher.addEntity(new Entity(uri, graph));
    uri = new IRI("urn:test:Otago");
    graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("Otago")));
    graph.add(new TripleImpl(uri, TYPE, OntologicalClasses.DBPEDIA_PLACE));
    searcher.addEntity(new Entity(uri, graph));
    //add a 2nd Otago (Place and University
    uri = new IRI("urn:test:Otago_Texas");
    graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("Otago (Texas)")));
    graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("Otago")));
    graph.add(new TripleImpl(uri, TYPE, OntologicalClasses.DBPEDIA_PLACE));
    searcher.addEntity(new Entity(uri, graph));
    uri = new IRI("urn:test:UniversityOfOtago_Texas");
    graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("University of Otago (Texas)")));
    graph.add(new TripleImpl(uri, TYPE, OntologicalClasses.DBPEDIA_ORGANISATION));
    searcher.addEntity(new Entity(uri, graph));
    TEST_ANALYSED_TEXT = AnalysedTextFactory.getDefaultInstance().createAnalysedText(ciFactory.createBlob(new StringSource(TEST_TEXT)));
    TEST_ANALYSED_TEXT_WO = AnalysedTextFactory.getDefaultInstance().createAnalysedText(ciFactory.createBlob(new StringSource(TEST_TEXT_WO)));
    initAnalyzedText(TEST_ANALYSED_TEXT);
    TEST_ANALYSED_TEXT.addChunk(0, "Dr. Patrick Marshall".length()).addAnnotation(PHRASE_ANNOTATION, NOUN_PHRASE);
    TEST_ANALYSED_TEXT.addToken(4, 11).addAnnotation(POS_ANNOTATION, Value.value(new PosTag("NP", Pos.ProperNoun), 1d));
    TEST_ANALYSED_TEXT.addToken(12, 20).addAnnotation(POS_ANNOTATION, Value.value(new PosTag("NP", Pos.ProperNoun), 1d));
    initAnalyzedText(TEST_ANALYSED_TEXT_WO);
    TEST_ANALYSED_TEXT_WO.addChunk(0, "Dr. Marshall Patrick".length()).addAnnotation(PHRASE_ANNOTATION, NOUN_PHRASE);
    TEST_ANALYSED_TEXT_WO.addToken(4, 12).addAnnotation(POS_ANNOTATION, Value.value(new PosTag("NP", Pos.ProperNoun), 1d));
    TEST_ANALYSED_TEXT_WO.addToken(13, 20).addAnnotation(POS_ANNOTATION, Value.value(new PosTag("NP", Pos.ProperNoun), 1d));
}

Example 10 with IndexedGraph

use of org.apache.stanbol.commons.indexedgraph.IndexedGraph in project stanbol by apache.

the class ClerezzaOntologyProvider method toOWLOntology.

/**
     * 
     * @param graphName
     * @param forceMerge
     *            if set to false, the selected import management policy will be applied.
     * @return
     * @throws OWLOntologyCreationException
     */
protected OWLOntology toOWLOntology(IRI graphName, boolean forceMerge) throws OWLOntologyCreationException {
    log.debug("Exporting graph to OWLOntology");
    log.debug(" -- ImmutableGraph name : {}", graphName);
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    // Never try to import
    mgr.addIRIMapper(new PhonyIRIMapper(Collections.<org.semanticweb.owlapi.model.IRI>emptySet()));
    Set<OWLOntologyID> loaded = new HashSet<OWLOntologyID>();
    Graph graph = store.getGraph(graphName);
    IRI ontologyId = null;
    // Get the id of this ontology.
    Iterator<Triple> itt = graph.filter(null, RDF.type, OWL.Ontology);
    if (itt.hasNext()) {
        BlankNodeOrIRI nl = itt.next().getSubject();
        if (nl instanceof IRI)
            ontologyId = (IRI) nl;
    }
    List<OWLOntologyID> revImps = new Stack<OWLOntologyID>();
    List<OWLOntologyID> lvl1 = new Stack<OWLOntologyID>();
    fillImportsReverse(keymap.getReverseMapping(graphName), revImps, lvl1);
    // If not set to merge (either by policy of by force), adopt the set import policy.
    if (!forceMerge && !ImportManagementPolicy.MERGE.equals(getImportManagementPolicy())) {
        OWLOntology o = OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(graph, mgr);
        // TODO make it not flat.
        // Examining the reverse imports stack will flatten all imports.
        List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
        OWLDataFactory df = OWLManager.getOWLDataFactory();
        List<OWLOntologyID> listToUse;
        switch(getImportManagementPolicy()) {
            case FLATTEN:
                listToUse = revImps;
                break;
            case PRESERVE:
                listToUse = lvl1;
                break;
            default:
                listToUse = lvl1;
                break;
        }
        for (OWLOntologyID ref : listToUse) if (!loaded.contains(ref) && !ref.equals(keymap.getReverseMapping(graphName))) {
            changes.add(new AddImport(o, df.getOWLImportsDeclaration(ref.getOntologyIRI())));
            loaded.add(ref);
        }
        o.getOWLOntologyManager().applyChanges(changes);
        return o;
    } else {
        // If there is just the root ontology, convert it straight away.
        if (revImps.size() == 1 && revImps.contains(graphName)) {
            OWLOntology o = OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(graph, mgr);
            return o;
        }
        // FIXME when there's more than one ontology, this way of merging them seems inefficient...
        Graph tempGraph = new IndexedGraph();
        // The set of triples that will be excluded from the merge
        Set<Triple> exclusions = new HashSet<Triple>();
        // Examine all reverse imports
        for (OWLOntologyID ref : revImps) if (!loaded.contains(ref)) {
            // Get the triples
            Graph imported = // store.getTriples(ref);
            getStoredOntology(getKey(ref), Graph.class, false);
            // For each owl:Ontology
            Iterator<Triple> remove = imported.filter(null, RDF.type, OWL.Ontology);
            while (remove.hasNext()) {
                BlankNodeOrIRI subj = remove.next().getSubject();
                /*
                         * If it's not the root ontology, trash all its triples. If the root ontology is
                         * anonymous, all ontology annotations are to be trashed without distinction.
                         */
                if (ontologyId == null || !subj.equals(ontologyId)) {
                    Iterator<Triple> it = imported.filter(subj, null, null);
                    while (it.hasNext()) {
                        Triple t = it.next();
                        exclusions.add(t);
                    }
                }
            }
            Iterator<Triple> it = imported.iterator();
            while (it.hasNext()) {
                Triple t = it.next();
                if (!exclusions.contains(t))
                    tempGraph.add(t);
            }
            loaded.add(ref);
        }
        // online.
        return OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(tempGraph, mgr);
    }
}