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Revision 8763

Added by ben leinfelder over 10 years ago

simplify lookup for classes and orcid. remove the "random" annotation code branches -- just too confusing to look at those bogus classes especially now that we have "real" generated annotations.

     //		suite.addTest(new DatapackageSummarizerTest("testGenerateAnnotation"));
     //		suite.addTest(new DatapackageSummarizerTest("testStandaloneAnnotation"));
     		suite.addTest(new DatapackageSummarizerTest("testIndexAnnotations"));
     //		suite.addTest(new DatapackageSummarizerTest("testGenerateRandomAnnotation"));
     		return suite;
+    	}
-...
     	 * @throws Exception
     	 */
     	public void testGenerateAnnotation() throws Exception {
     		this.testGenerateAnnotation_base(false);
+    	}
     	/**
     	 * Generate a bunch of random annotations
     	 * @throws Exception
     	 */
     	public void testGenerateRandomAnnotation() throws Exception {
     		for (int i = 0; i < 5; i++) {
     			this.testGenerateAnnotation_base(true);
+    		}
+    	}
     	private void testGenerateAnnotation_base(boolean randomize) throws Exception {
     		Identifier metadataPid = new Identifier();
     		metadataPid.setValue("testAnnotation.eml." + System.currentTimeMillis());
     		Session session = getTestSession();
-...
     		// generate the annotation for the metadata
     		DatapackageSummarizer ds = new DatapackageSummarizer();
     		ds.randomize = randomize;
     		String rdfContent = ds.generateAnnotation(metadataPid);
     		// save the annotation

     import org.apache.log4j.Logger;
     import org.w3c.dom.Node;
     import edu.ucsb.nceas.metacat.replication.ReplicationService;
     import edu.ucsb.nceas.utilities.XMLUtilities;
     public class OrcidService {
-...
     			String url = REST_URL + "?q=" + urlParameters + "&rows=1";
     			URL restURL = new URL(url);
     			//InputStream is = restURL.openStream();
     			InputStream is = ReplicationService.getURLStream(restURL);
     			InputStream is = restURL.openStream();
     			String results = IOUtils.toString(is);
     			logMetacat.debug("RESULTS: " + results);
     			Node doc = XMLUtilities.getXMLReaderAsDOMTreeRootNode(new StringReader(results));

     import com.hp.hpl.jena.rdf.model.Property;
     import com.hp.hpl.jena.rdf.model.Resource;
     import com.hp.hpl.jena.tdb.TDBFactory;
     import com.hp.hpl.jena.util.iterator.ExtendedIterator;
     import edu.ucsb.nceas.metacat.DBUtil;
     import edu.ucsb.nceas.metacat.DocumentImpl;
-...
     	public static String OBOE_SBC = "OBOE-SBC";
         // package visibility for testing only
         boolean randomize = false;
         public void indexEphemeralAnnotation(Identifier metadataPid) throws Exception {
         	// generate an annotation for the metadata given
-...
         	// read the annotation into the triplestore
     		InputStream source = IOUtils.toInputStream(rdfContent, "UTF-8");
         	String name = "http://annotation";
         	String name = "http://annotation/" + metadataPid.getValue();
         	boolean loaded = dataset.containsNamedModel(name);
         	if (loaded) {
         		dataset.removeNamedModel(name);
-...
             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#> "
             List<String> queries = new ArrayList<String>();
             queries.add("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 "
     			+ "SELECT ?standard_sm ?pid "
     			+ "FROM <$GRAPH_NAME> "
     			+ "WHERE { "
     			+ "		?measurement rdf:type oboe-core:Measurement . "
-...
     			+ "		?annotation oa:hasBody ?measurement . "
     			+ "		?annotation oa:hasTarget ?target . "
     			+ "		?target oa:hasSource ?metadata . "
     			+ "		?metadata dcterms:identifier ?id . "
     			+ "}";
             q = q.replaceAll("\\$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());
     			+ "		?metadata dcterms:identifier ?pid . "
     			+ "}");
             queries.add("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 ?characteristic_sm ?pid "
         		+ "FROM <$GRAPH_NAME>"
         		+ "WHERE { "
         		+ "		?measurement rdf:type oboe-core:Measurement . "
         		+ "		?measurement rdf:type ?restriction . "
     			+ "		?restriction owl:onProperty oboe-core:ofCharacteristic . "
     			+ "		?restriction owl:allValuesFrom ?characteristic . "
     			+ "		?characteristic rdfs:subClassOf+ ?characteristic_sm . "
     			+ "		?characteristic_sm rdfs:subClassOf oboe-core:Characteristic . "
     			+ "		?annotation oa:hasBody ?measurement .	"
     			+ "		?annotation oa:hasTarget ?target . "
     			+ "		?target oa:hasSource ?metadata . "
     			+ "		?metadata dcterms:identifier ?pid . "
     			+ "}");
             for (String q: queries) {
     	        q = q.replaceAll("\\$GRAPH_NAME", name);
     			Query query = QueryFactory.create(q);
     			QueryExecution qexec = QueryExecutionFactory.create(query, dataset);
     			ResultSet results = qexec.execSelect();
     			// 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;
+    				}
     			while (results.hasNext()) {
     				QuerySolution solution = results.next();
     				System.out.println(solution.toString());
+    			}
     			// 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;
     				// find the index document we are trying to augment with the annotation
     				if (solution.contains("pid")) {
     					String id = solution.getLiteral("pid").getString();
     					if (!id.equals(metadataPid.getValue())) {
     						// skip any solution that does not annotate the given pid
     						continue;
+    					}
+    				}
     				String value = solution.get(key).toString();
     				List<Object> values = fields.get(key);
     				if (values  == null) {
     					values = new ArrayList<Object>();
     				// 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("pid")) {
     						// 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);
+    				}
     				values.add(value);
     				fields.put(key, values);
+    			}
+    		}
+            }
     		// clean up the triple store
     		TDBFactory.release(dataset);
-...
     	private Resource lookupStandard(OntClass standardClass, Attribute attribute) {
     		// what's our unit?
     		String unit = attribute.getUnit().toLowerCase();
     		/*
     		boolean found = false;
     		List<String> tokens = Arrays.asList(unit.split(" "));
     		boolean found = false;
     		ExtendedIterator iter = standardClass.listSubClasses(false);
     		if (randomize) {
     			List subclasses = iter.toList();
     			int size = subclasses.size();
     			Long index = new Long(Math.round(Math.floor((Math.random() * (size-1)))));
     			OntClass subclass = (OntClass) subclasses.get( index.intValue() );
     			return subclass;
+    		}
     		while (iter.hasNext()) {
     			OntClass subclass = (OntClass) iter.next();
     			String subclassName = subclass.getLocalName().toLowerCase();
-...
     				return subclass;
+    			}
+    		}
     		*/
     		// try to look it up if we got this far
     		return BioPortalService.lookupAnnotationClass(standardClass, unit, OBOE_SBC);
+    	}
     	private Resource lookupCharacteristic(OntClass characteristicClass, Attribute attribute) {
     		// what's our label?
     		// what are we looking for?
     		String label = attribute.getLabel().toLowerCase();
     		List<String> tokens = Arrays.asList(label.split(" "));
     		String definition = attribute.getDefinition();
     		String text = label + " " + definition;
     		/*
     		// find something that matches
     		boolean found = false;
     		// find something that matches
     		List<String> tokens = Arrays.asList(label.split(" "));
     		ExtendedIterator iter = characteristicClass.listSubClasses();
     		if (randomize) {
     			List subclasses = iter.toList();
     			int size = subclasses.size();
     			Long index = new Long(Math.round(Math.floor((Math.random() * (size-1)))));
     			OntClass subclass = (OntClass) subclasses.get( index.intValue() );
     			return subclass;
+    		}
     		while (iter.hasNext()) {
     			OntClass subclass = (OntClass) iter.next();
     			String subclassName = subclass.getLocalName().toLowerCase();
-...
     				return subclass;
+    			}
+    		}
     		*/
     		// try to look it up if we got this far
     		return BioPortalService.lookupAnnotationClass(characteristicClass, attribute.getDefinition(), OBOE_SBC);
     		// try to look it up from the service
     		return BioPortalService.lookupAnnotationClass(characteristicClass, text, OBOE_SBC);
+    	}

     import com.hp.hpl.jena.ontology.OntClass;
     import com.hp.hpl.jena.rdf.model.Resource;
     import edu.ucsb.nceas.metacat.replication.ReplicationService;
     import edu.ucsb.nceas.utilities.XMLUtilities;
     public class BioPortalService {
-...
     			String url = REST_URL + "/annotator?" + urlParameters ;
     			URL restURL = new URL(url);
     			InputStream is = ReplicationService.getURLStream(restURL);
     			InputStream is = restURL.openStream();
     			Document doc = XMLUtilities.getXMLReaderAsDOMDocument(new InputStreamReader(is, "UTF-8"));
     			NodeList classNodeList = XMLUtilities.getNodeListWithXPath(doc, "//annotation/annotatedClass/id");
     			if (classNodeList != null && classNodeList.getLength() > 0) {

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Revision 8763

Added by ben leinfelder over 10 years ago