@Test public void testSelectAllType() { eval = new MockSecurityEvaluator(true, true, true, true, true, true) { @Override public boolean evaluate( final Object principal, final Action action, final Node graphIRI, final Triple triple) { if (triple.getSubject().isURI() && triple.getSubject().getURI().equals("http://example.com/resource/1")) { return false; } return super.evaluate(principal, action, graphIRI, triple); } }; setup(); try { String query = "SELECT ?s ?p ?o WHERE " + " { ?s ?p ?o } "; QueryExecution qexec = QueryExecutionFactory.create(query, dataset); try { final ResultSet results = qexec.execSelect(); int count = 0; for (; results.hasNext(); ) { count++; results.nextSolution(); } // 2x 3 values + type triple Assert.assertEquals(8, count); } finally { qexec.close(); } query = "SELECT ?g ?s ?p ?o WHERE " + " { GRAPH ?g {?s ?p ?o } }"; qexec = QueryExecutionFactory.create(query, dataset); try { final ResultSet results = qexec.execSelect(); int count = 0; for (; results.hasNext(); ) { count++; results.nextSolution(); } // 2x 3 values + type triple // all are in the base graph so no named graphs Assert.assertEquals(0, count); } finally { qexec.close(); } } finally { dataset.close(); } }
@Test public void testOpenQueryType() { eval = new MockSecurityEvaluator(true, true, true, true, true, true); setup(); try { final String query = "prefix fn: <http://www.w3.org/2005/xpath-functions#> " + " SELECT ?foo ?bar WHERE " + " { ?foo a <http://example.com/class> ; " + "?bar [] ." + " } "; final QueryExecution qexec = QueryExecutionFactory.create(query, dataset); try { final ResultSet results = qexec.execSelect(); int count = 0; for (; results.hasNext(); ) { count++; results.nextSolution(); } Assert.assertEquals(8, count); } finally { qexec.close(); } } finally { dataset.close(); } }
/** * Query SPARQL endpoint with a SELECT query * * @param qExec QueryExecution encapsulating the query * @return model retrieved by querying the endpoint */ private Model getSelectModel(QueryExecution qExec) { Model model = ModelFactory.createDefaultModel(); Graph graph = model.getGraph(); ResultSet results = qExec.execSelect(); while (results.hasNext()) { QuerySolution sol = results.next(); String subject; String predicate; RDFNode object; try { subject = sol.getResource("s").toString(); predicate = sol.getResource("p").toString(); object = sol.get("o"); } catch (NoSuchElementException e) { logger.error("SELECT query does not return a (?s ?p ?o) Triple"); continue; } Node objNode; if (object.isLiteral()) { Literal obj = object.asLiteral(); objNode = NodeFactory.createLiteral(obj.getString(), obj.getDatatype()); } else { objNode = NodeFactory.createLiteral(object.toString()); } graph.add( new Triple(NodeFactory.createURI(subject), NodeFactory.createURI(predicate), objNode)); } return model; }
@Test public void testFullQueryWorks() { ReconnectingDatasetGraph toQuery = (ReconnectingDatasetGraph) ((Dataset) AssemblerUtils.build("basic.ttl", SDBConnect.TYPE)).asDatasetGraph(); toQuery.getDatasetGraph().getStore().getTableFormatter().format(); Dataset ds = DatasetImpl.wrap(toQuery); // Dataset ds = new DatasetImpl(toQuery); QueryExecution qe = QueryExecutionFactory.create("SELECT * { ?s ?p ?o }", ds); ResultSet r = qe.execSelect(); assertTrue("Querying works", !r.hasNext()); qe.close(); qe = QueryExecutionFactory.create("SELECT * { graph ?g { ?s ?p ?o } }", ds); r = qe.execSelect(); assertTrue("Querying with named graphs works", !r.hasNext()); qe.close(); }
public String GetResult() { String result_s = ""; while (results.hasNext()) { QuerySolution row = results.next(); // RDFNode thing= row.get("rule"); // result_s = row.getLiteral("id").getString(); result_s = result_s + row.getLiteral("id").getString() + ","; } if (!result_s.equals("")) { result_s = result_s.substring(0, result_s.length() - 1); } return result_s; }
@Test public void testSelectToWurcsSparql() throws SparqlException, UnsupportedEncodingException { GlycoSequenceToWurcsSelectSparql s = new GlycoSequenceToWurcsSelectSparql("glycoct"); SparqlEntity se = new SparqlEntity(); se.setValue( GlycoSequenceToWurcsSelectSparql.FromSequence, "RES\n1b:a-dgal-HEX-1:5\n2s:n-acetyl\n3b:b-dgal-HEX-1:5\n4b:b-dglc-HEX-1:5\n5s:n-acetyl\n6b:b-dgal-HEX-1:5\n7b:a-lgal-HEX-1:5|6:d\n8b:b-dglc-HEX-1:5\n9s:n-acetyl\n10b:b-dglc-HEX-1:5\n11s:n-acetyl\n12b:b-dgal-HEX-1:5\n13b:a-lgal-HEX-1:5|6:d\nLIN\n1:1d(2+1)2n\n2:1o(3+1)3d\n3:3o(3+1)4d\n4:4d(2+1)5n\n5:4o(4+1)6d\n6:6o(2+1)7d\n7:3o(6+1)8d\n8:8d(2+1)9n\n9:1o(6+1)10d\n10:10d(2+1)11n\n11:10o(4+1)12d\n12:12o(2+1)13d" .replaceAll("\n", "\\\\n")); s.setSparqlEntity(se); logger.debug(s.getSparql()); Query query = QueryFactory.create(s.getSparql().replaceAll("null", "").replace("?Sequence", "")); // QueryExecution qe = // QueryExecutionFactory.sparqlService("http://localhost:3030/glycobase/query",query); QueryExecution qe = QueryExecutionFactory.sparqlService("http://test.ts.glytoucan.org/sparql", query); ResultSet rs = qe.execSelect(); List<SparqlEntity> results = new ArrayList<SparqlEntity>(); while (rs.hasNext()) { QuerySolution row = rs.next(); Iterator<String> columns = row.varNames(); SparqlEntity se2 = new SparqlEntity(); while (columns.hasNext()) { String column = columns.next(); RDFNode cell = row.get(column); if (cell.isResource()) { Resource resource = cell.asResource(); // do something maybe with the OntModel??? if (resource.isLiteral()) se.setValue(column, resource.asLiteral().getString()); else se.setValue(column, resource.toString()); } else if (cell.isLiteral()) { se.setValue(column, cell.asLiteral().getString()); } else if (cell.isAnon()) { se.setValue(column, "anon"); } else { se.setValue(column, cell.toString()); } } results.add(se); } for (SparqlEntity entity : results) { System.out.println("results: " + entity.getValue("PrimaryId")); } }
@Test public void testRestrictedQueryType() { eval = new MockSecurityEvaluator(true, true, true, true, true, true) { @Override public boolean evaluate( final Object principal, final Action action, final Node graphIRI, final Triple triple) { if (triple.getSubject().isURI() && triple.getSubject().getURI().equals("http://example.com/resource/1")) { return false; } return super.evaluate(principal, action, graphIRI, triple); } }; setup(); try { final String query = "prefix fn: <http://www.w3.org/2005/xpath-functions#> " + " SELECT ?foo ?bar WHERE " + " { ?foo a <http://example.com/class> ; " + "?bar [] ." + " } "; final QueryExecution qexec = QueryExecutionFactory.create(query, dataset); try { final ResultSet results = qexec.execSelect(); int count = 0; for (; results.hasNext(); ) { count++; results.nextSolution(); } Assert.assertEquals(4, count); } finally { qexec.close(); } } finally { dataset.close(); } }
/** * Perform the {@link QueryExecution} once. * * @param action * @param queryExecution * @param query * @param queryStringLog Informational string created from the initial query. * @return */ protected SPARQLResult executeQuery( HttpAction action, QueryExecution queryExecution, Query query, String queryStringLog) { setAnyTimeouts(queryExecution, action); if (query.isSelectType()) { ResultSet rs = queryExecution.execSelect(); // Force some query execution now. // If the timeout-first-row goes off, the output stream has not // been started so the HTTP error code is sent. rs.hasNext(); // If we wanted perfect query time cancellation, we could consume // the result now to see if the timeout-end-of-query goes off. // rs = ResultSetFactory.copyResults(rs) ; // action.log.info(format("[%d] exec/select", action.id)) ; return new SPARQLResult(rs); } if (query.isConstructType()) { Dataset dataset = queryExecution.execConstructDataset(); // action.log.info(format("[%d] exec/construct", action.id)); return new SPARQLResult(dataset); } if (query.isDescribeType()) { Model model = queryExecution.execDescribe(); // action.log.info(format("[%d] exec/describe", action.id)) ; return new SPARQLResult(model); } if (query.isAskType()) { boolean b = queryExecution.execAsk(); // action.log.info(format("[%d] exec/ask", action.id)) ; return new SPARQLResult(b); } ServletOps.errorBadRequest("Unknown query type - " + queryStringLog); return null; }
/** * Returns the string value of the first of the properties in the uriDescriptionList for the given * resource (as an URI). In case the resource does not have any of the properties mentioned, its * URI is returned. The value is obtained by querying the endpoint and the endpoint is queried * repeatedly until it gives a response (value or the lack of it) * * <p>It is highly recommended that the list contains properties like labels or titles, with test * values. * * @param uri - the URI for which a label is required * @return a String value, either a label for the parameter or its value if no label is obtained * from the endpoint */ private String getLabelForUri(String uri) { String result; if (uriLabelCache.containsKey(uri)) { return uriLabelCache.get(uri); } for (String prop : uriDescriptionList) { String innerQuery = "SELECT ?r WHERE {<" + uri + "> <" + prop + "> ?r } LIMIT 1"; try { Query query = QueryFactory.create(innerQuery); QueryExecution qExec = QueryExecutionFactory.sparqlService(rdfEndpoint, query); boolean keepTrying = true; while (keepTrying) { keepTrying = false; try { ResultSet results = qExec.execSelect(); if (results.hasNext()) { QuerySolution sol = results.nextSolution(); result = EEASettings.parseForJson(sol.getLiteral("r").getLexicalForm()); if (!result.isEmpty()) { uriLabelCache.put(uri, result); return result; } } } catch (Exception e) { keepTrying = true; logger.warn("Could not get label for uri {}. Retrying.", uri); } finally { qExec.close(); } } } catch (QueryParseException qpe) { logger.error("Exception for query {}. The label cannot be obtained", innerQuery); } } return uri; }
/** * Get a set of unique queryObjName returned from a select query * * <p>Used to retrieve sets of modified objects used in sync * * @param rdfQuery query to execute * @param queryObjName name of the object returned * @return set of values for queryObjectName in the rdfQuery result */ HashSet<String> executeSyncQuery(String rdfQuery, String queryObjName) { HashSet<String> rdfUrls = new HashSet<String>(); Query query; try { query = QueryFactory.create(rdfQuery); } catch (QueryParseException qpe) { logger.warn( "Could not parse [{}]. Please provide a relevant query. {}", rdfQuery, qpe.getLocalizedMessage()); return null; } QueryExecution qExec = QueryExecutionFactory.sparqlService(rdfEndpoint, query); try { ResultSet results = qExec.execSelect(); while (results.hasNext()) { QuerySolution sol = results.nextSolution(); try { String value = sol.getResource(queryObjName).toString(); rdfUrls.add(value); } catch (NoSuchElementException e) { logger.error("Encountered a NoSuchElementException: " + e.getLocalizedMessage()); return null; } } } catch (Exception e) { logger.error( "Encountered a [{}] while querying the endpoint for sync", e.getLocalizedMessage()); return null; } finally { qExec.close(); } return rdfUrls; }
@Test public void testDO() { String doid = "1485"; String queryString = "prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n" + "prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n" + "prefix owl: <http://www.w3.org/2002/07/owl#>\n" + "\n" + "select ?s ?p ?o \n" + "from <http://purl.obolibrary.org/obo/merged/DOID>\n" + "\n" + "WHERE {\n" + " <http://purl.obolibrary.org/obo/DOID_" + doid + "> ?p ?o\n" + "}"; Query query = QueryFactory.create(queryString); QueryExecution qExe = QueryExecutionFactory.sparqlService("http://sparql.hegroup.org/sparql/", query); ResultSet results = qExe.execSelect(); ResultSetFormatter.out(System.out, results, query); assertNotNull(results); /*Model model = ModelFactory.createDefaultModel(); Selector selector = new SimpleSelector(null, model.getProperty("<http://www.geneontology.org/formats/oboInOwl#hasDbXref>"), (RDFNode) null); // you need to cast the last null as otherwise the method is ambigious */ List<String> dbXref = new ArrayList<>(); List<String> iao = new ArrayList<>(); List<String> exactSynonym = new ArrayList<>(); List<String> alternativeId = new ArrayList<>(); String diseaseLabel; while (results.hasNext()) { QuerySolution querySolution = results.nextSolution(); if (querySolution.get("p").toString().matches("rdfs:label ")) { diseaseLabel = querySolution.get("o").toString(); } if (querySolution .get("p") .toString() .matches("http://www.geneontology.org/formats/oboInOwl#hasDbXref")) { System.out.println( querySolution.get("p").toString() + " " + querySolution.get("o").toString()); dbXref.add(querySolution.get("o").toString()); } if (querySolution.get("p").toString().matches("http://purl.obolibrary.org/obo/IAO_0000115")) { System.out.println( querySolution.get("p").toString() + " " + querySolution.get("o").toString()); iao.add(querySolution.get("o").toString()); } if (querySolution .get("p") .toString() .matches("http://www.geneontology.org/formats/oboInOwl#hasExactSynonym")) { System.out.println( querySolution.get("p").toString() + " " + querySolution.get("o").toString()); exactSynonym.add(querySolution.get("o").toString()); } if (querySolution .get("p") .toString() .matches("http://www.geneontology.org/formats/oboInOwl#hasAlternativeId")) { System.out.println( querySolution.get("p").toString() + " " + querySolution.get("o").toString()); alternativeId.add(querySolution.get("o").toString()); } } assertNotNull(dbXref); assertNotNull(iao); }
@Test public void testKBtoWurcsSparqlTranslation() throws SparqlException { List<Translation> translations = Ebean.find(Translation.class).findList(); HashSet<String> resultList = new HashSet<>(); String ct = ""; for (Translation translation : translations) { System.out.println("id check " + translation.id + " ct " + translation.ct); if (translation.ct == null) continue; if (translation.structure.id > 0) { ct = translation.ct; GlycoSequenceToWurcsSelectSparql s = new GlycoSequenceToWurcsSelectSparql("glycoct"); SparqlEntity se = new SparqlEntity(); ct = StringUtils.chomp(ct); System.out.println("ct on top: " + ct); if (ct != null) { se.setValue( GlycoSequenceToWurcsSelectSparql.FromSequence, ct.replaceAll("\n", "\\\\n") .replaceAll("x\\(", "u\\(") .replaceAll("\\)x", "\\)u") .trim()); s.setSparqlEntity(se); logger.debug(s.getSparql()); Query query = QueryFactory.create(s.getSparql().replaceAll("null", "").replace("?Sequence", "")); System.out.println( "Id " + translation.structure.id + " Query: " + s.getSparql().replaceAll("null", "").replace("?Sequence", "")); QueryExecution qe = QueryExecutionFactory.sparqlService("http://test.ts.glytoucan.org/sparql", query); ResultSet rs = qe.execSelect(); List<SparqlEntity> results = new ArrayList<>(); HashSet<String> resultsList = new HashSet<>(); while (rs.hasNext()) { QuerySolution row = rs.next(); Iterator<String> columns = row.varNames(); SparqlEntity se2 = new SparqlEntity(); while (columns.hasNext()) { String column = columns.next(); RDFNode cell = row.get(column); if (cell.isResource()) { Resource resource = cell.asResource(); // do something maybe with the OntModel??? if (resource.isLiteral()) se.setValue(column, resource.asLiteral().getString()); else se.setValue(column, resource.toString()); } else if (cell.isLiteral()) { se.setValue(column, cell.asLiteral().getString()); } else if (cell.isAnon()) { se.setValue(column, "anon"); } else { se.setValue(column, cell.toString()); } } results.add(se); } for (SparqlEntity entity : results) { // System.out.println("results: " + entity.getValue("PrimaryId")); resultList.add( translation.structure.id + "\t" + entity.getValue("PrimaryId").toString()); } } } } for (String c : resultList) { System.out.println(c); } }
@Test public void testKBtoWurcsSparql() throws SparqlException { List<Structure> structures = Ebean.find(Structure.class).findList(); HashSet<String> resultList = new HashSet<>(); String ct = ""; for (Structure structure : structures) { if (structure.id >= 7400) { if (structure.glycanst.startsWith("v--")) { structure.glycanst = structure.glycanst.replace("v--", "FreeEnd--"); } if (structure.glycanst.startsWith("FreenEnd")) { structure.glycanst = structure.glycanst.replace("FreenEnd", "FreeEnd"); } if (structure.glycanst.startsWith("FreeEnd?")) { structure.glycanst = structure.glycanst.replace("FreeEnd?", "FreeEnd--?"); } if (structure.glycanst.startsWith("<Gly") || structure.glycanst.contains("0.0000u")) { continue; } System.out.println(structure.getGlycanst()); BuilderWorkspace workspace = new BuilderWorkspace(new GlycanRendererAWT()); workspace.setNotation("cfg"); // cfgbw | uoxf | uoxfcol | text GlycanRenderer renderer = workspace.getGlycanRenderer(); org.eurocarbdb.application.glycanbuilder.Glycan glycan = org.eurocarbdb.application.glycanbuilder.Glycan.fromString(structure.glycanst.trim()); if (glycan != null) { ct = glycan.toGlycoCTCondensed(); System.out.println("this was the ct: " + ct); GlycoSequenceToWurcsSelectSparql s = new GlycoSequenceToWurcsSelectSparql("glycoct"); SparqlEntity se = new SparqlEntity(); ct = StringUtils.chomp(ct); se.setValue( GlycoSequenceToWurcsSelectSparql.FromSequence, ct.replaceAll("\n", "\\\\n") .replaceAll("x\\(", "u\\(") .replaceAll("\\)x", "\\)u") .trim()); s.setSparqlEntity(se); logger.debug(s.getSparql()); Query query = QueryFactory.create(s.getSparql().replaceAll("null", "").replace("?Sequence", "")); System.out.println( "Id " + structure.id + " Query: " + s.getSparql().replaceAll("null", "").replace("?Sequence", "")); QueryExecution qe = QueryExecutionFactory.sparqlService("http://test.ts.glytoucan.org/sparql", query); ResultSet rs = qe.execSelect(); List<SparqlEntity> results = new ArrayList<>(); HashSet<String> resultsList = new HashSet<>(); while (rs.hasNext()) { QuerySolution row = rs.next(); Iterator<String> columns = row.varNames(); SparqlEntity se2 = new SparqlEntity(); while (columns.hasNext()) { String column = columns.next(); RDFNode cell = row.get(column); if (cell.isResource()) { Resource resource = cell.asResource(); // do something maybe with the OntModel??? if (resource.isLiteral()) se.setValue(column, resource.asLiteral().getString()); else se.setValue(column, resource.toString()); } else if (cell.isLiteral()) { se.setValue(column, cell.asLiteral().getString()); } else if (cell.isAnon()) { se.setValue(column, "anon"); } else { se.setValue(column, cell.toString()); } } results.add(se); } for (SparqlEntity entity : results) { // System.out.println("results: " + entity.getValue("PrimaryId")); resultList.add(structure.id + "\t" + entity.getValue("PrimaryId").toString()); } } } } PrintWriter writer = null; try { writer = new PrintWriter( new OutputStreamWriter(new FileOutputStream("/tmp/HashSet.txt"), "UTF-8")); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } catch (FileNotFoundException e) { e.printStackTrace(); } for (String c : resultList) { System.out.println(c); writer.println(c); } }
/** * A method to build a collection of collaborator objects representing a network based on an * organisation * * @param id the id of the central organisation * @param radius the number of edges required from the central contributor * @return the collection of collaborator objects */ @SuppressWarnings("rawtypes") public TreeMap<Integer, Collaborator> getRawCollaboratorData_org(String id, int radius) { // check the parameters if (InputUtils.isValidInt(id) == false) { throw new IllegalArgumentException("Error: the id parameter is required"); } if (InputUtils.isValidInt(radius, ExportServlet.MIN_DEGREES, ExportServlet.MAX_DEGREES) == false) { throw new IllegalArgumentException( "Error: the radius parameter must be between " + ExportServlet.MIN_DEGREES + " and " + ExportServlet.MAX_DEGREES); } // define helper variables // collection of collaborators java.util.TreeMap<Integer, Collaborator> cId_cObj_map = new java.util.TreeMap<Integer, Collaborator>(); // set of collaborators that we've already processed java.util.TreeSet<Integer> foundCollaboratorsSet = new java.util.TreeSet<Integer>(); // define other helper variables String contributor_id = null; QuerySolution row = null; Collaborator collaborator = null; String sql = "SELECT DISTINCT b.eventid " + "FROM events a, orgevlink b " + "WHERE b.organisationid = ? " // +id + "AND a.eventid = b.eventid"; int[] param = {Integer.parseInt(id)}; java.sql.ResultSet resultSet = db.exePreparedStatement(sql, param); ArrayList<String> eventResults = new ArrayList<String>(); try { // check to see that data was returned if (!resultSet.last()) { db.tidyup(); return null; } else resultSet.beforeFirst(); // loop through the resultset while (resultSet.next() == true) { eventResults.add(resultSet.getString(1)); } } catch (java.sql.SQLException ex) { System.out.println("Exception: " + ex.getMessage()); resultSet = null; } db.tidyup(); // helper int first = 0; // define the query String sparqlQuery1 = "PREFIX foaf: <" + FOAF.NS + "> " + "PREFIX ausestage: <" + AuseStage.NS + "> " + "PREFIX event: <http://purl.org/NET/c4dm/event.owl#> " + "PREFIX dcterms: <http://purl.org/dc/terms/> " + "SELECT DISTINCT ?agent ?givenName ?familyName " + "WHERE { "; for (String event : eventResults) { if (first > 0) { sparqlQuery1 += "UNION "; } first++; sparqlQuery1 += "{<ausstage:e:" + event + "> a event:Event; " + " event:agent ?agent. " + " ?agent a foaf:Person; " + " foaf:givenName ?givenName; " + " foaf:familyName ?familyName. " + " } "; } sparqlQuery1 += " } "; // execute query ResultSet results = rdf.executeSparqlQuery(sparqlQuery1); // now we transfer the results to a TreeMap <Integer, while (results.hasNext()) { row = results.nextSolution(); contributor_id = AusStageURI.getId(row.get("agent").toString()); collaborator = new Collaborator(contributor_id); cId_cObj_map.put(Integer.parseInt(contributor_id), collaborator); foundCollaboratorsSet.add(Integer.parseInt(contributor_id)); } rdf.tidyUp(); return cId_cObj_map; } // end getRawCollaboratorData_org method
/* * add some of the additional required information for collaborator */ public ArrayList<Collaborator> getCollaborators( TreeMap<Integer, Collaborator> network, String id) { // declare helper variables java.util.ArrayList<Collaborator> collaborators = new java.util.ArrayList<Collaborator>(); // define a SPARQL query to get details about a collaborator String sparqlQuery = "PREFIX foaf: <" + FOAF.NS + ">" + "PREFIX ausestage: <" + AuseStage.NS + "> " + "SELECT ?collabName ?function ?gender ?nationality " + "WHERE { " + " @ a foaf:Person ; " + " foaf:name ?collabName. " + "OPTIONAL {@ ausestage:function ?function} " + "OPTIONAL {@ foaf:gender ?gender} " + "OPTIONAL {@ ausestage:nationality ?nationality} " + "} "; String queryToExecute = null; ResultSet results = null; QuerySolution row = null; Collaborator collaborator = null; // loop through the list of collaborators and get additional information Collection networkKeys = network.keySet(); Iterator networkKeyIterator = networkKeys.iterator(); Integer networkKey = null; Integer centreId = Integer.parseInt(id); // loop through the list of keys while (networkKeyIterator.hasNext()) { // get the key for this collaborator networkKey = (Integer) networkKeyIterator.next(); // create a new collaborator object collaborator = new Collaborator(networkKey.toString()); // build the query queryToExecute = sparqlQuery.replaceAll( "@", "<" + AusStageURI.getContributorURI(collaborator.getId()) + ">"); // execute the query results = rdf.executeSparqlQuery(queryToExecute); // add details to this contributor while (results.hasNext()) { // loop though the resulset // get a new row of data row = results.nextSolution(); // add the data to the collaborator collaborator.setName(row.get("collabName").toString()); if (row.get("function") != null) { collaborator.setFunction(row.get("function").toString()); } if (row.get("gender") != null) { collaborator.setGender(row.get("gender").toString()); } if (row.get("nationality") != null) { collaborator.setNationality(row.get("nationality").toString()); } collaborator.setUrl(AusStageURI.getContributorURL(collaborator.getId())); } // play nice and tidy rdf.tidyUp(); results = null; // add the collaborator to the list collaborators.add(collaborator); } return collaborators; }