@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();
}
}
/**
* Tests whether a query gives the same results when run both with and without a given optimizer
*
* @param queryStr Query
* @param ds Dataset
* @param opt Optimizer
* @param expected Expected number of results
*/
public static void test(String queryStr, Dataset ds, Symbol opt, int expected) {
Query q = QueryFactory.create(queryStr);
if (!q.isSelectType()) Assert.fail("Only SELECT queries are testable with this method");
Op op = Algebra.compile(q);
// Track current state
boolean isEnabled = ARQ.isTrue(opt);
boolean isDisabled = ARQ.isFalse(opt);
try {
// Run first without optimization
ARQ.set(opt, false);
ResultSetRewindable rs;
try (QueryExecution qe = QueryExecutionFactory.create(q, ds)) {
rs = ResultSetFactory.makeRewindable(qe.execSelect());
if (expected != rs.size()) {
System.err.println("Non-optimized results not as expected");
TextOutput output = new TextOutput((SerializationContext) null);
output.format(System.out, rs);
rs.reset();
}
Assert.assertEquals(expected, rs.size());
}
// Run with optimization
ARQ.set(opt, true);
ResultSetRewindable rsOpt;
try (QueryExecution qeOpt = QueryExecutionFactory.create(q, ds)) {
rsOpt = ResultSetFactory.makeRewindable(qeOpt.execSelect());
if (expected != rsOpt.size()) {
System.err.println("Optimized results not as expected");
TextOutput output = new TextOutput((SerializationContext) null);
output.format(System.out, rsOpt);
rsOpt.reset();
}
Assert.assertEquals(expected, rsOpt.size());
}
Assert.assertTrue(ResultSetCompare.isomorphic(rs, rsOpt));
} finally {
// Restore previous state
if (isEnabled) {
ARQ.set(opt, true);
} else if (isDisabled) {
ARQ.set(opt, false);
} else {
ARQ.unset(opt);
}
}
}
@Override
protected QueryExecution createQueryExecution(Query q) throws SQLException {
if (this.remoteConn.getQueryEndpoint() == null)
throw new SQLException(
"This statement is backed by a write-only connection, read operations are not supported");
// Create basic execution
QueryEngineHTTP exec =
(QueryEngineHTTP)
QueryExecutionFactory.sparqlService(this.remoteConn.getQueryEndpoint(), q);
// Apply HTTP settings
if (this.client != null) {
exec.setClient(this.client);
}
// Apply default and named graphs if appropriate
if (this.remoteConn.getDefaultGraphURIs() != null) {
exec.setDefaultGraphURIs(this.remoteConn.getDefaultGraphURIs());
}
if (this.remoteConn.getNamedGraphURIs() != null) {
exec.setNamedGraphURIs(this.remoteConn.getNamedGraphURIs());
}
// Set result types
if (this.remoteConn.getSelectResultsType() != null) {
exec.setSelectContentType(this.remoteConn.getSelectResultsType());
}
if (this.remoteConn.getModelResultsType() != null) {
exec.setModelContentType(this.remoteConn.getModelResultsType());
}
// Return execution
return exec;
}
public BedStats findAvailableBedsByClinic(Integer clinicId) {
ClassLoader classLoader = getClass().getClassLoader();
File file = new File(classLoader.getResource("sparqlQueries/BedsAvailabilityQuery").getFile());
try {
queryTemplate = FileUtils.readFileToString(file);
List<String> params = new ArrayList<String>();
params.add(clinicId.toString());
String sparqlQuery = prepareQuery(queryTemplate, params);
Query query = QueryFactory.create(sparqlQuery);
QueryExecution qexec = QueryExecutionFactory.sparqlService(endpoint, query);
System.out.println(sparqlQuery);
ResultSet results = qexec.execSelect();
if (results.hasNext()) {
QuerySolution soln = results.nextSolution();
Literal l = soln.getLiteral("bedsAvailable"); // Get a result variable - must be a literal
BedStats bedStats = new BedStats();
bedStats.setClinicId(clinicId);
bedStats.setAvailabeBeds(l.getInt());
return bedStats;
} else {
return null;
}
} catch (IOException e) {
e.printStackTrace();
return null;
}
}
@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();
}
}
@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();
}
@Override
public QueryExecution createQueryExecution(Query query) {
// Plan plan = QueryExecutionFactory.createPlan(query, dataset, input, context);
// plan.
QueryExecution result = QueryExecutionFactory.create(query, model);
// QueryExecution result = QueryExecutionWrapper.wrap(tmp);
return result;
}
@Test
public void testReconnectWorks() {
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("ASK { ?s ?p ?o }", ds);
assertTrue("Querying still works", !qe.execAsk());
// Haha! Say goodbye!
toQuery.getDatasetGraph().getStore().getConnection().close();
qe = QueryExecutionFactory.create("ASK { ?s ?p ?o }", ds);
assertTrue("Reconnected query still works", !qe.execAsk());
qe = QueryExecutionFactory.create("ASK { ?s ?p ?o }", ds);
assertTrue("Reconnected query works with test", !qe.execAsk());
}
public ResultSet executeQuery(String queryStr, String dialect) {
// System.out.println(queryStr);
Query query = QueryFactory.create(queryStr);
QueryExecution qe = QueryExecutionFactory.create(query, mapping);
this.dialect = dialect;
ResultSet rs = ConvertResults(qe.execSelect());
qe.close();
return rs;
}
@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"));
}
}
/** @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse response) */
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
/** Check for the input parameter and redirect. */
PrintWriter writer = response.getWriter();
response.setContentType("text/html");
if (request.getParameter("input") != null && request.getParameter("input") != "") {
String wikiDataQuery =
"PREFIX p: <http://www.wikidata.org/prop/>\r\n"
+ "PREFIX wdt: <http://www.wikidata.org/prop/direct/>\r\n"
+ "PREFIX wd: <http://www.wikidata.org/entity/>\r\n"
+ "PREFIX wikibase: <http://wikiba.se/ontology#>\n"
+ "PREFIX bd: <http://www.bigdata.com/rdf#>\n"
+ "\r\n"
+ "SELECT ?musician ?musicianLabel ?genre ?genreLabel WHERE {\r\n"
+ " {\r\n"
+ " ?musician wdt:P106 wd:Q639669.\r\n"
+ " ?musician wdt:P136 ?genre .\r\n"
+ " }\r\n"
+ " SERVICE wikibase:label { bd:serviceParam wikibase:language \"en\". }\r\n"
+ "}\r\n"
+ "ORDER BY DESC(?musician)";
Query rawQuery = QueryFactory.create(wikiDataQuery);
QueryExecution execute =
QueryExecutionFactory.sparqlService("https://query.wikidata.org/sparql", rawQuery);
ResultSet wikiDataResults = execute.execSelect();
/*try
{
insertRawDataToDB(wikiDataResults);
}
catch (ClassNotFoundException e)
{
e.printStackTrace();
}*/
createResultTable(wikiDataResults, writer, request.getParameter("input"));
} else if (request.getParameter("check") != null) {
insertSelectedValuesToDB(request);
response.sendRedirect("/TestWebProject/umut-dabager.jsp");
} else if (request.getParameter("retrieve") != null) {
writer.println(retrieveSavedResults());
} else if (request.getParameter("clear") != null) {
clearSavedResults();
response.sendRedirect("/TestWebProject/umut-dabager.jsp");
} else {
response.sendRedirect("/TestWebProject/umut-dabager.jsp");
}
}
public BedStats findHospitalAvailableBedsAllClinics(String hospital) {
ApplicationContext appContext = new ClassPathXmlApplicationContext();
org.springframework.core.io.Resource resource =
appContext.getResource("classpath:sparqlQueries/BedsAvailabilityQuery");
try {
InputStream is = resource.getInputStream();
BufferedReader br = new BufferedReader(new InputStreamReader(is));
String line;
queryTemplate = "";
while ((line = br.readLine()) != null) {
queryTemplate += line + "\n";
}
br.close();
} catch (IOException e1) {
e1.printStackTrace();
return null;
}
List<String> params = new ArrayList<String>();
params.add(hospital);
params.add(hospital);
String sparqlQuery = prepareQuery(queryTemplate, params);
System.out.println(sparqlQuery);
Query query = QueryFactory.create(sparqlQuery);
QueryExecution qexec = QueryExecutionFactory.sparqlService(endpoint, query);
ResultSet results = qexec.execSelect();
if (results.hasNext()) {
QuerySolution soln = results.next();
Literal available = soln.getLiteral("available"); // Get a result variable - must be a literal
Literal deployed = soln.getLiteral("deployed");
Literal supplementary = soln.getLiteral("supplementary");
// Literal lastDate = soln.getLiteral("maxDate");
BedStats bedStats = new BedStats();
bedStats.setHospitalName(params.get(0));
bedStats.setAvailabeBeds(available.getInt());
bedStats.setDeployedBeds(deployed.getInt());
bedStats.setSupplementaryBeds(supplementary.getInt());
// bedStats.setLastDate(lastDate.getShort());
return bedStats;
} else {
return null;
}
}
@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();
}
}
@Test
public void testUnionWorks() {
Dataset ds = (Dataset) AssemblerUtils.build("union.ttl", SDBConnect.TYPE);
ReconnectingDatasetGraph toQuery = (ReconnectingDatasetGraph) ds.asDatasetGraph();
toQuery.getDatasetGraph().getStore().getTableFormatter().format();
UpdateRequest ur =
UpdateFactory.create(
"insert data {"
+ "graph <http://example.com/a> { <http://example.com/1> <http://example.com/prop> 1 }"
+ "graph <http://example.com/b> { <http://example.com/2> <http://example.com/prop> 2 }"
+ "}");
UpdateProcessor u = UpdateExecutionFactory.create(ur, toQuery);
u.execute();
QueryExecution qe = QueryExecutionFactory.create("SELECT * { ?s ?p ?o }", ds);
ResultSetRewindable r = ResultSetFactory.makeRewindable(qe.execSelect());
assertEquals("We have a union!", 2, r.size());
}
@Test
public void testSparql() {
String queryStr = "select distinct ?Concept where {[] a ?Concept} LIMIT 10";
Query query = QueryFactory.create(queryStr);
// Remote execution.
try (QueryExecution qexec =
QueryExecutionFactory.sparqlService("http://dbpedia.org/sparql", query)) {
// Set the DBpedia specific timeout.
((QueryEngineHTTP) qexec).addParam("timeout", "10000");
// Execute.
ResultSet rs = qexec.execSelect();
ResultSetFormatter.out(System.out, rs, query);
} catch (Exception e) {
e.printStackTrace();
}
}
public static List<String> listThingDescriptions(String query) {
List<String> tds = new ArrayList<>();
Dataset dataset = Repository.get().dataset;
dataset.begin(ReadWrite.READ);
try {
String q = "SELECT DISTINCT ?g WHERE { GRAPH ?g { " + query + " }}";
try (QueryExecution qexec = QueryExecutionFactory.create(q, dataset)) {
ResultSet result = qexec.execSelect();
while (result.hasNext()) {
tds.add(result.next().get("g").asResource().getURI());
}
}
} finally {
dataset.end();
}
return tds;
}
public static void outputInfo(Model model, String var) {
// compose the query
String sparql =
"BASE <http://example.org/inst/>"
+ "CONSTRUCT { <"
+ var
+ "> ?P ?O } "
+ "WHERE { <"
+ var
+ "> ?P ?O }";
// carry out the query
Query query = QueryFactory.create(sparql);
QueryExecution qe = QueryExecutionFactory.create(query, model);
Model results = qe.execConstruct();
// print inferred triples
System.out.println();
System.out.println(var + ":");
RDFDataMgr.write(System.out, results, RDFLanguages.NT);
}
public static ResultSet sparql(InstrumentosBean instrumentos, int acao) throws IOException {
InputStream input =
new FileInputStream(
new File("C:/Users/nilso/workspace/InstrumentosIA/instrumentos_novo.rdf"));
Model model = ModelFactory.createDefaultModel();
model.read(input, null, "RDF/XML");
input.close();
String queryStr =
" PREFIX rdf: <http://www.semanticweb.org/renan/ontologies/2015/7/untitled-ontology-2#>"
+ " SELECT ?rdf ?tipoInstrumento ?feitoDe ?numeroCordas ?temPes ?mediaPreco WHERE {"
+ " ?rdf rdf:feitoDe ?feitoDe ."
+ " ?rdf rdf:mediaPreco ?mediaPreco ."
+ " ?rdf rdf:numeroCordas ?numeroCordas ."
+ " ?rdf rdf:temPes ?temPes ."
+ " ?rdf rdf:tipoInstrumento ?tipoInstrumento.";
if (Arrays.asList(1, 3, 5, 7, 9, 11, 13, 15).contains(acao))
queryStr += " FILTER regex(?tipoInstrumento,'" + instrumentos.getTipoInstrumento() + "')";
if (Arrays.asList(2, 3, 6, 7, 10, 11, 14, 15).contains(acao))
queryStr += " FILTER regex(?feitoDe,'" + instrumentos.getFeitoDe() + "')";
if (Arrays.asList(4, 5, 6, 7, 12, 13, 14, 15).contains(acao))
queryStr +=
" FILTER (?numeroCordas = " + String.valueOf(instrumentos.getNumeroCordas()) + ")";
if (Arrays.asList(8, 9, 10, 11, 12, 13, 14, 15).contains(acao)) {
queryStr +=
" FILTER (?mediaPreco <= "
+ String.valueOf(instrumentos.getMaxPreco())
+ ")"
+ " FILTER (?mediaPreco >= "
+ String.valueOf(instrumentos.getMinPreco())
+ ")";
}
queryStr = queryStr + " }";
Query query = QueryFactory.create(queryStr);
consulta = QueryExecutionFactory.create(query, model);
results = consulta.execSelect();
return results;
}
@Test
public void testDOQuery2() {
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 *\n"
+ "from <http://purl.obolibrary.org/obo/merged/DOID>\n"
+ "\n"
+ "WHERE {\n"
+ " <http://purl.obolibrary.org/obo/DOID_1485> <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?o\n"
+ "}";
Query query = QueryFactory.create(queryString);
System.out.println("String: " + queryString);
QueryExecution qExe =
QueryExecutionFactory.sparqlService("http://sparql.hegroup.org/sparql/", query);
ResultSet results = qExe.execSelect();
ResultSetFormatter.out(System.out, results, query);
}
@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);
}
/**
* Create the {@link QueryExecution} for this operation.
*
* @param query
* @param dataset
* @return QueryExecution
*/
protected QueryExecution createQueryExecution(Query query, Dataset dataset) {
return QueryExecutionFactory.create(query, dataset);
}
@Override
public EntityDefinition open(Assembler a, Resource root, Mode mode) {
String prologue = "PREFIX : <" + NS + "> PREFIX list: <http://jena.apache.org/ARQ/list#> ";
Model model = root.getModel();
String qs1 =
StrUtils.strjoinNL(
prologue,
"SELECT * {",
" ?eMap :entityField ?entityField ;",
" :map ?map ;",
" :defaultField ?dftField .",
" OPTIONAL {",
" ?eMap :graphField ?graphField",
" }",
" OPTIONAL {",
" ?eMap :langField ?langField",
" }",
" OPTIONAL {",
" ?eMap :uidField ?uidField",
" }",
"}");
ParameterizedSparqlString pss = new ParameterizedSparqlString(qs1);
pss.setIri("eMap", root.getURI());
Query query1 = QueryFactory.create(pss.toString());
QueryExecution qexec1 = QueryExecutionFactory.create(query1, model);
ResultSet rs1 = qexec1.execSelect();
List<QuerySolution> results = ResultSetFormatter.toList(rs1);
if (results.size() == 0) {
Log.warn(this, "Failed to find a valid EntityMap for : " + root);
throw new TextIndexException("Failed to find a valid EntityMap for : " + root);
}
if (results.size() != 1) {
Log.warn(this, "Multiple matches for EntityMap for : " + root);
throw new TextIndexException("Multiple matches for EntityMap for : " + root);
}
QuerySolution qsol1 = results.get(0);
String entityField = qsol1.getLiteral("entityField").getLexicalForm();
String graphField =
qsol1.contains("graphField") ? qsol1.getLiteral("graphField").getLexicalForm() : null;
String langField =
qsol1.contains("langField") ? qsol1.getLiteral("langField").getLexicalForm() : null;
String defaultField =
qsol1.contains("dftField") ? qsol1.getLiteral("dftField").getLexicalForm() : null;
String uniqueIdField =
qsol1.contains("uidField") ? qsol1.getLiteral("uidField").getLexicalForm() : null;
Multimap<String, Node> mapDefs = HashMultimap.create();
Map<String, Analyzer> analyzerDefs = new HashMap<>();
Statement listStmt = root.getProperty(TextVocab.pMap);
while (listStmt != null) {
RDFNode n = listStmt.getObject();
if (!n.isResource()) {
throw new TextIndexException("Text list node is not a resource : " + n);
}
Resource listResource = n.asResource();
if (listResource.equals(RDF.nil)) {
break; // end of the list
}
Statement listEntryStmt = listResource.getProperty(RDF.first);
if (listEntryStmt == null) {
throw new TextIndexException("Text map list is not well formed. No rdf:first property");
}
n = listEntryStmt.getObject();
if (!n.isResource()) {
throw new TextIndexException("Text map list entry is not a resource : " + n);
}
Resource listEntry = n.asResource();
Statement fieldStatement = listEntry.getProperty(TextVocab.pField);
if (fieldStatement == null) {
throw new TextIndexException("Text map entry has no field property");
}
n = fieldStatement.getObject();
if (!n.isLiteral()) {
throw new TextIndexException("Text map entry field property has no literal value : " + n);
}
String field = n.asLiteral().getLexicalForm();
Statement predicateStatement = listEntry.getProperty(TextVocab.pPredicate);
if (predicateStatement == null) {
throw new TextIndexException("Text map entry has no predicate property");
}
n = predicateStatement.getObject();
if (!n.isURIResource()) {
throw new TextIndexException(
"Text map entry predicate property has non resource value : " + n);
}
mapDefs.put(field, n.asNode());
Statement analyzerStatement = listEntry.getProperty(TextVocab.pAnalyzer);
if (analyzerStatement != null) {
n = analyzerStatement.getObject();
if (!n.isResource()) {
throw new TextIndexException("Text map entry analyzer property is not a resource : " + n);
}
Resource analyzerResource = n.asResource();
Analyzer analyzer = (Analyzer) a.open(analyzerResource);
analyzerDefs.put(field, analyzer);
}
// move on to the next element in the list
listStmt = listResource.getProperty(RDF.rest);
}
// Primary field/predicate
if (defaultField != null) {
Collection<Node> c = mapDefs.get(defaultField);
if (c.isEmpty())
throw new TextIndexException("No definition of primary field '" + defaultField + "'");
}
EntityDefinition docDef = new EntityDefinition(entityField, defaultField);
docDef.setGraphField(graphField);
docDef.setLangField(langField);
docDef.setUidField(uniqueIdField);
for (String f : mapDefs.keys()) {
for (Node p : mapDefs.get(f)) docDef.set(f, p);
}
for (String f : analyzerDefs.keySet()) {
docDef.setAnalyzer(f, analyzerDefs.get(f));
}
return docDef;
}
@Test
public void testGlycotoucanCTSearch() {
List<Structure> structures = Ebean.find(Structure.class).findList();
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);
ct = glycan.toGlycoCTCondensed();
// System.out.println(ct);
// }
// }
/*String ct = "RES\\n" +
"1b:a-dgal-HEX-1:5\\n" +
"2s:n-acetyl\\n" +
"3b:b-dgal-HEX-1:5\\n" +
"4b:a-lgal-HEX-1:5|6:d\\n" +
"5b:a-dgal-HEX-1:5\\n" +
"6s:n-acetyl\\n" +
"7b:b-dglc-HEX-1:5\\n" +
"8s:n-acetyl\\n" +
"LIN\\n" +
"1:1d(2+1)2n\\n" +
"2:1o(3+1)3d\\n" +
"3:3o(2+1)4d\\n" +
"4:3o(3+1)5d\\n" +
"5:5d(2+1)6n\\n" +
"6:1o(6+1)7d\\n" +
"7:7d(2+1)8n";
ct = "RES\n" +
"1b:b-dglc-HEX-1:5\n" +
"2s:n-acetyl\n" +
"3b:b-dglc-HEX-1:5\n" +
"4s:n-acetyl\n" +
"5b:b-dman-HEX-1:5\n" +
"6b:a-dman-HEX-1:5\n" +
"7b:a-dman-HEX-1:5\n" +
"8b:a-lgal-HEX-1:5|6:d\n" +
"LIN\n" +
"1:1d(2+1)2n\n" +
"2:1o(4+1)3d\n" +
"3:3d(2+1)4n\n" +
"4:3o(4+1)5d\n" +
"5:5o(3+1)6d\n" +
"6:5o(6+1)7d\n" +
"7:1o(6+1)8d\n" +
"UND\n" +
"UND1:100.0:100.0\n" +
"ParentIDs:1|3|5|6|7|8\n" +
"SubtreeLinkageID1:x(-1+1)x\n" +
"RES\n" +
"9b:b-dglc-HEX-1:5\n" +
"10s:n-acetyl\n" +
"11b:a-lgal-HEX-1:5|6:d\n" +
"12b:b-dgal-HEX-1:5\n" +
"13b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d\n" +
"14s:n-acetyl\n" +
"LIN\n" +
"8:9d(2+1)10n\n" +
"9:9o(3+1)11d\n" +
"10:9o(4+1)12d\n" +
"11:12o(-1+2)13d\n" +
"12:13d(5+1)14n\n" +
"UND2:100.0:100.0\n" +
"ParentIDs:1|3|5|6|7|8\n" +
"SubtreeLinkageID1:x(-1+1)x\n" +
"RES\n" +
"15b:b-dglc-HEX-1:5\n" +
"16s:n-acetyl\n" +
"17b:a-lgal-HEX-1:5|6:d\n" +
"18b:b-dgal-HEX-1:5\n" +
"LIN\n" +
"13:15d(2+1)16n\n" +
"14:15o(3+1)17d\n" +
"15:15o(4+1)18d\n" +
"UND3:100.0:100.0\n" +
"ParentIDs:1|3|5|6|7|8\n" +
"SubtreeLinkageID1:x(-1+1)x\n" +
"RES\n" +
"19b:b-dglc-HEX-1:5\n" +
"20s:n-acetyl\n" +
"21b:b-dgal-HEX-1:5\n" +
"LIN\n" +
"16:19d(2+1)20n\n" +
"17:19o(4+1)21d";
*/
ct = ct.replaceAll("\n", "\\\\n").replaceAll("x\\(", "u\\(").replaceAll("\\)x", "\\)u");
System.out.println("new ct: " + ct);
String queryString =
"PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n"
+ "PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>\n"
+ "PREFIX wurcs: <http://www.glycoinfo.org/glyco/owl/wurcs#>\n"
+ "SELECT DISTINCT ?glycan ?c\n"
+ "# FROM <http://rdf.glycoinfo.org/wurcs/0.5.0>\n"
+ "# FROM <http://rdf.glycoinfo.org/wurcs/0.5.0/ms>\n"
+ "WHERE {\n"
+ " ?glycan a \tglycan:glycosequence ;\n"
+ "\tglycan:in_carbohydrate_format glycan:carbohydrate_format_glycoct ;\n"
+ "\tglycan:has_sequence\n"
+ "\t\t?c filter(contains(?c, \"RES\\n1b:b-dglc-HEX-1\")) .\n"
+
// "\t\t?c filter(contains(?c, \"" + ct + "\" )) .\n" +
"\n"
+ " }\n"
+ " ORDER BY ?glycan\n"
+ "limit 10";
System.out.println("String: " + queryString + "\t\tID: " + structure.id);
Query query = QueryFactory.create(queryString);
QueryExecution qExe =
QueryExecutionFactory.sparqlService("http://test.ts.glytoucan.org/sparql", query);
ResultSet results = qExe.execSelect();
ResultSetFormatter.out(System.out, results, query);
}
}
}
@Test
public void testWURCS() {
String ct =
"RES\n"
+ "1b:b-dglc-HEX-1:5\n"
+ "2s:n-acetyl\n"
+ "3b:b-dglc-HEX-1:5\n"
+ "4s:n-acetyl\n"
+ "5b:b-dman-HEX-1:5\n"
+ "6b:a-dman-HEX-1:5\n"
+ "7b:a-dman-HEX-1:5\n"
+ "8b:a-dman-HEX-1:5\n"
+ "9b:a-dman-HEX-1:5\n"
+ "10b:a-dman-HEX-1:5\n"
+ "LIN\n"
+ "1:1d(2+1)2n\n"
+ "2:1o(4+1)3d\n"
+ "3:3d(2+1)4n\n"
+ "4:3o(4+1)5d\n"
+ "5:5o(3+1)6d\n"
+ "6:6o(2+1)7d\n"
+ "7:5o(6+1)8d\n"
+ "8:8o(3+1)9d\n"
+ "9:8o(6+1)10d\n"
+ "UND\n"
+ "UND1:100.0:100.0\n"
+ "ParentIDs:7|9|10\n"
+ "SubtreeLinkageID1:o(2+1)d\n"
+ "RES\n"
+ "11b:a-dman-HEX-1:5";
ct = ct.replaceAll("\n", "\\\\n");
String queryString =
"PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>\n"
+ "PREFIX glytoucan: <http://www.glytoucan.org/glyco/owl/glytoucan#>\n"
+ "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n"
+ "\n"
+ "SELECT DISTINCT ?Sequence\n"
+ "FROM <http://rdf.glytoucan.org>\n"
+ "FROM <http://rdf.glytoucan.org/sequence/wurcs>\n"
+ "\n"
+ "WHERE {\n"
+ "?SaccharideURI a glycan:saccharide .\n"
+ "?SaccharideURI glycan:has_glycosequence ?GlycanSequenceURI .\n"
+ "?GlycanSequenceURI glycan:has_sequence ?Sequence .\n"
+ "?GlycanSequenceURI glycan:in_carbohydrate_format glycan:carbohydrate_format_wurcs .\n"
+ "?SaccharideURI glycan:has_glycosequence ?FormatGlycoSequenceURI .\n"
+ "?FormatGlycoSequenceURI glycan:in_carbohydrate_format glycan:carbohydrate_format_glycoct .\n"
+ "?FormatGlycoSequenceURI glycan:has_sequence"
+ " \""
+ ct
+ "\""
+ "^^xsd:string ."
+ "}";
System.out.println("String: " + queryString);
Query query = QueryFactory.create(queryString);
QueryExecution qExe =
QueryExecutionFactory.sparqlService("http://test.ts.glytoucan.org/sparql", query);
ResultSet results = qExe.execSelect();
ResultSetFormatter.out(System.out, results, query);
}
@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);
}
}
@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);
}
}