Examples of org.apache.stanbol.commons.indexedgraph.IndexedMGraph

Package org.apache.stanbol.commons.indexedgraph

Examples of org.apache.stanbol.commons.indexedgraph.IndexedMGraph

org.apache.stanbol.commons.indexedgraph.IndexedMGraph

                        }
                        //the metadata may define the ID for the contentItem
                        if(fis.getName() != null && !fis.getName().isEmpty()){
                            contentItemId = fis.getName();
                        }
                        metadata = new IndexedMGraph();
                        try {
                            getParser().parse(metadata, fis.openStream(), fis.getContentType());
                        } catch (Exception e) {
                            throw new WebApplicationException(e, 
                                Response.status(Response.Status.BAD_REQUEST)
                                .entity(String.format("Unable to parse Metadata " +
                                    "from Multipart MIME part '%s' (" +
                                    "contentItem: %s| contentType: %s)",
                                    fis.getFieldName(),fis.getName(),fis.getContentType()))
                                .build());
                        }
                    } else if(fis.getFieldName().equals("content")){
                        contentItem = createContentItem(contentItemId, metadata, fis, parsedContentIds);
                    } else if(fis.getFieldName().equals("properties") ||
                            fis.getFieldName().equals(ENHANCEMENT_PROPERTIES_URI.getUnicodeString())){
                        //parse the enhancementProperties
                        if(contentItem == null){
                            throw new WebApplicationException(
                                Response.status(Response.Status.BAD_REQUEST)
                                .entity("Multipart MIME parts for " +
                                    "EnhancementProperties MUST BE after the " +
                                    "MIME parts for 'metadata' AND 'content'")
                                .build());
                        }
                        MediaType propMediaType = MediaType.valueOf(fis.getContentType());
                        if(!APPLICATION_JSON_TYPE.isCompatible(propMediaType)){
                            throw new WebApplicationException(
                                Response.status(Response.Status.BAD_REQUEST)
                                .entity("EnhancementProperties (Multipart MIME parts" +
                                    "with the name '"+fis.getFieldName()+"') MUST " +
                                    "BE encoded as 'appicaltion/json' (encountered: '" +
                                    fis.getContentType()+"')!")
                                .build());
                        }
                        String propCharset = propMediaType.getParameters().get("charset");
                        if(propCharset == null){
                            propCharset = "UTF-8";
                        }
                        Map<String,Object> enhancementProperties = getEnhancementProperties(contentItem); 
                        try {
                            enhancementProperties.putAll(toMap(new JSONObject(
                                IOUtils.toString(fis.openStream(),propCharset))));
                        } catch (JSONException e) {
                            throw new WebApplicationException(e,
                                Response.status(Response.Status.BAD_REQUEST)
                                .entity("Unable to parse EnhancementProperties from" +
                                    "Multipart MIME parts with the name 'properties'!")
                                .build());
                        }
                        
                    } else { //additional metadata as serialised RDF
                        if(contentItem == null){
                            throw new WebApplicationException(
                                Response.status(Response.Status.BAD_REQUEST)
                                .entity("Multipart MIME parts for additional " +
                                    "contentParts MUST BE after the MIME " +
                                    "parts for 'metadata' AND 'content'")
                                .build());
                        }
                        if(fis.getFieldName() == null || fis.getFieldName().isEmpty()){
                            throw new WebApplicationException(
                                Response.status(Response.Status.BAD_REQUEST)
                                .entity("Multipart MIME parts representing " +
                                    "ContentParts for additional RDF metadata" +
                                    "MUST define the contentParts URI as" +
                                    "'name' of the MIME part!").build());
                        }
                        MGraph graph = new IndexedMGraph();
                        try {
                            getParser().parse(graph, fis.openStream(), fis.getContentType());
                        } catch (Exception e) {
                            throw new WebApplicationException(e, 
                                Response.status(Response.Status.BAD_REQUEST)

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    protected InMemoryContentItem(String uriString, Blob blob, MGraph metadata) {
        this(uriString != null ? new UriRef(uriString) : null, blob, metadata);
    }
    protected InMemoryContentItem(UriRef uri, Blob blob, MGraph metadata) {
        super(uri == null ? ContentItemHelper.makeDefaultUrn(blob): uri,blob,
                metadata == null ? new IndexedMGraph() : metadata);
    }

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                OWLOntology o = OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(graph, mgr);
                return o;
            }


            // FIXME when there's more than one ontology, this way of merging them seems inefficient...
            TripleCollection tempGraph = new IndexedMGraph();
            // The set of triples that will be excluded from the merge
            Set<Triple> exclusions = new HashSet<Triple>();
            // Examine all reverse imports
            for (UriRef ref : revImps)
                if (!loaded.contains(ref)) {
                    // Get the triples
                    TripleCollection imported = store.getTriples(ref);
                    // For each owl:Ontology
                    Iterator<Triple> remove = imported.filter(null, RDF.type, OWL.Ontology);
                    while (remove.hasNext()) {
                        NonLiteral 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);
                }
            // Since they are all merged and import statements removed, there should be no risk of going

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                    log.warn("The content of library " + smallest + " could not be accessed.", e);
                }
            }
        }


        if (oTemp != null) o = new IndexedMGraph(oTemp);


        if (o == null) {
            log.debug("Ontology {} not found in any ontology provider or library.", iri);
            return Response.status(NOT_FOUND).build();
        }

View Full Code Here

        else formats = Collections.singleton(formatIdentifier);
        TripleCollection graph = null;
        if (tcProvider != null) {
            UriRef name = new UriRef(getClass().getCanonicalName() + "-" + System.currentTimeMillis());
            graph = tcProvider.createMGraph(name);
        } else graph = new IndexedMGraph();
        for (String format : formats) {
            try {
                parser.parse((MGraph) graph, content, format);
                loaded = true;
                break;

View Full Code Here

     * @param headers the http headers of the request
     * @return the response
     */
    private Response executeLDPathQuery(FieldQuery query, String ldpathProgramString, MediaType mediaType, HttpHeaders headers) {
        QueryResultList<Representation> result;
        ValueFactory vf = new RdfValueFactory(new IndexedMGraph());
        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());

View Full Code Here


    static MGraph toRDF(QueryResultList<?> resultList) {
        final MGraph resultGraph;
        Class<?> type = resultList.getType();
        if (String.class.isAssignableFrom(type)) {
            resultGraph = new IndexedMGraph(); //create a new Graph
            for (Object result : resultList) {
                //add a triple to each reference in the result set
                resultGraph.add(new TripleImpl(QUERY_RESULT_LIST, QUERY_RESULT, new UriRef(result.toString())));
            }
        } else {
            //first determine the type of the resultList
            final boolean isSignType;
            if (Representation.class.isAssignableFrom(type)) {
                isSignType = false;
            } else if (Representation.class.isAssignableFrom(type)) {
                isSignType = true;
            } else {
                //incompatible type -> throw an Exception
                throw new IllegalArgumentException("Parsed type " + type + " is not supported");
            }
            //special treatment for RdfQueryResultList for increased performance
            if (resultList instanceof RdfQueryResultList) {
                resultGraph = ((RdfQueryResultList) resultList).getResultGraph();
                if (isSignType) { //if we build a ResultList for Signs, that we need to do more things
                    //first remove all triples representing results
                    Iterator<Triple> resultTripleIt = resultGraph.filter(QUERY_RESULT_LIST, QUERY_RESULT, null);
                    while (resultTripleIt.hasNext()) {
                        resultTripleIt.next();
                        resultTripleIt.remove();
                    }
                    //now add the Sign specific triples and add result triples
                    //to the Sign IDs
                    for (Object result : resultList) {
                        UriRef signId = new UriRef(((Entity) result).getId());
                        EntityToRDF.addEntityTriplesToGraph(resultGraph, (Entity) result);
                        resultGraph.add(new TripleImpl(QUERY_RESULT_LIST, QUERY_RESULT, signId));
                    }
                }
            } else { //any other implementation of the QueryResultList interface
                resultGraph = new IndexedMGraph(); //create a new graph
                if (Representation.class.isAssignableFrom(type)) {
                    for (Object result : resultList) {
                        UriRef resultId;
                        if (!isSignType) {
                            EntityToRDF.addRDFTo(resultGraph, (Representation) result);

View Full Code Here

     * @param parser
     * @return
     * @throws IOException
     */
    protected static MGraph parseRdfData(ParsingProvider parser,String name) throws IOException {
        MGraph rdfData = new IndexedMGraph();
        InputStream in = getTestResource(name);
        assertNotNull("File '"+name+"' not found",in);
        ZipInputStream zipIn = new ZipInputStream(new BufferedInputStream(in));
        InputStream uncloseable = new UncloseableStream(zipIn);
        ZipEntry entry;
        while((entry = zipIn.getNextEntry()) != null){
            if(entry.getName().endsWith(".rdf")){
                parser.parse(rdfData,uncloseable, SupportedFormat.RDF_XML,null);
            }
        }
        assertTrue(rdfData.size() > 0);
        zipIn.close();
        return rdfData;
    }

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    @BeforeClass
    public static void setUpServices() throws IOException {
        searcher = new TestSearcherImpl(TEST_REFERENCED_SITE_NAME,NAME,new SimpleLabelTokenizer());
        //add some terms to the searcher
        MGraph graph = new IndexedMGraph();
        UriRef uri = new UriRef("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 UriRef("urn:test:Geologist");
        graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("Geologist")));
        graph.add(new TripleImpl(uri, TYPE, new UriRef(NamespaceEnum.skos+"Concept")));
        graph.add(new TripleImpl(uri, REDIRECT, new UriRef("urn:test:redirect:Geologist")));
        searcher.addEntity(new Entity(uri, graph));
        //a redirect
        uri = new UriRef("urn:test:redirect:Geologist");
        graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("Geologe (redirect)")));
        graph.add(new TripleImpl(uri, TYPE, new UriRef(NamespaceEnum.skos+"Concept")));
        searcher.addEntity(new Entity(uri, graph));


        uri = new UriRef("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 UriRef("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 UriRef("urn:test:University");
        graph.add(new TripleImpl(uri, NAME, new PlainLiteralImpl("University")));
        graph.add(new TripleImpl(uri, TYPE, new UriRef(NamespaceEnum.skos+"Concept")));
        searcher.addEntity(new Entity(uri, graph));


        uri = new UriRef("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 UriRef("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 UriRef("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));
        
        Value<PhraseTag> nounPhrase = Value.value(new PhraseTag("NP",LexicalCategory.Noun),1d);
        TEST_ANALYSED_TEXT = AnalysedTextFactory.getDefaultInstance().createAnalysedText(
                ciFactory.createBlob(new StringSource(TEST_TEXT)));

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