Metacat

//		suite.addTest(new DatapackageSummarizerTest("testGenerateAnnotation"));

		suite.addTest(new DatapackageSummarizerTest("testStandaloneAnnotation"));

	public void testStandaloneAnnotation() throws Exception {

		// insert the test document to sem-index

		Identifier metadataPid = new Identifier();

		metadataPid.setValue("testAnnotation.eml." + System.currentTimeMillis());

		Session session = getTestSession();

		try {

			InputStream object = new ByteArrayInputStream(this.getTestDocFromFile(ANNOTATION_TEST_DOC).getBytes("UTF-8"));

			SystemMetadata sysmeta = createSystemMetadata(metadataPid, session.getSubject(), object);

			ObjectFormatIdentifier formatId = new ObjectFormatIdentifier();

			formatId.setValue("eml://ecoinformatics.org/eml-2.0.0");

			sysmeta.setFormatId(formatId);

			Identifier pid = MNodeService.getInstance(request).create(session, metadataPid, object, sysmeta);

			assertEquals(metadataPid.getValue(), pid.getValue());

		} catch (Exception e) {

			e.printStackTrace();

			fail("Could not add metadata test file: " + e.getMessage());

		}

		// index it

		DatapackageSummarizer ds = new DatapackageSummarizer();

		ds.indexEphemeralAnnotation(metadataPid);

		// check it

	}

import java.util.HashMap;

import org.apache.commons.io.IOUtils;

import com.hp.hpl.jena.query.Dataset;

import com.hp.hpl.jena.query.Query;

import com.hp.hpl.jena.query.QueryExecution;

import com.hp.hpl.jena.query.QueryExecutionFactory;

import com.hp.hpl.jena.query.QueryFactory;

import com.hp.hpl.jena.query.QuerySolution;

import com.hp.hpl.jena.query.ResultSet;

import com.hp.hpl.jena.tdb.TDBFactory;

import edu.ucsb.nceas.metacat.index.MetacatSolrIndex;

    public void indexEphemeralAnnotation(Identifier metadataPid) throws Exception {

    	// generate an annotation for the metadata given

		String rdfContent = this.generateAnnotation(metadataPid);

		// load to triple store

		Dataset dataset = TDBFactory.createDataset("./tbd");

    	// read the annotation into the triplestore

		InputStream source = IOUtils.toInputStream(rdfContent, "UTF-8");

    	String name = "http://annotation";

    	boolean loaded = dataset.containsNamedModel(name);

    	if (loaded) {

    		dataset.removeNamedModel(name);

    		loaded = false;

    	}

		if (!loaded) {

			OntModel ontModel = ModelFactory.createOntologyModel();

			ontModel.read(source, name);

			dataset.addNamedModel(name, ontModel);

		}

		// query for fields to add to index

        Map<String, List<Object>> fields = new HashMap<String, List<Object>>();

        // TODO: look up the query to use (support multiple like in the indexing project)

        String q = null;

        q = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "

        	+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> "

        	+ "PREFIX owl: <http://www.w3.org/2002/07/owl#> " 

			+ "PREFIX oboe-core: <http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#> "

			+ "PREFIX oa: <http://www.w3.org/ns/oa#> "

			+ "PREFIX dcterms: <http://purl.org/dc/terms/> "

			+ "SELECT ?standard_sm ?id "

			+ "FROM <$GRAPH_NAME> "

			+ "WHERE { "

			+ "		?measurement rdf:type oboe-core:Measurement . "

			+ "		?measurement rdf:type ?restriction . "

			+ "		?restriction owl:onProperty oboe-core:usesStandard . "

			+ "		?restriction owl:allValuesFrom ?standard . "

			+ "		?standard rdfs:subClassOf+ ?standard_sm . "

			+ "		?standard_sm rdfs:subClassOf oboe-core:Standard . "				

			+ "		?annotation oa:hasBody ?measurement . "												

			+ "		?annotation oa:hasTarget ?target . "

			+ "		?target oa:hasSource ?metadata . "

			+ "		?metadata dcterms:identifier ?id . " 

			+ "}";

        q = q.replaceAll("\\$GRAPH_NAME", name);

		Query query = QueryFactory.create(q);

		QueryExecution qexec = QueryExecutionFactory.create(query, dataset);

		ResultSet results = qexec.execSelect();

		while (results.hasNext()) {

			QuerySolution solution = results.next();

			System.out.println(solution.toString());

			// find the index document we are trying to augment with the annotation

			if (solution.contains("id")) {

				String id = solution.getLiteral("id").getString();

				if (!id.equals(metadataPid.getValue())) {

					// skip any solution that does not annotate the given pid

					continue;

				}

			}

			// loop through the solution variables, add an index value for each

			Iterator<String> varNameIter = solution.varNames();

			while (varNameIter.hasNext()) {

				String key = varNameIter.next();

				if (key.equals("id")) {

					// don't include the id

					continue;

				}

				String value = solution.get(key).toString();

				List<Object> values = fields.get(key);

				if (values  == null) {

					values = new ArrayList<Object>();

				}

				values.add(value);

				fields.put(key, values);

			}

		}

		// clean up the triple store

		TDBFactory.release(dataset);

		// add to index

		MetacatSolrIndex.getInstance().submit(metadataPid, null, fields, true);

	}