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();
}
}
/*
* Originally written as a utility function by Atakan Guney.
* Modified by Umut Dabager.
*/
public void createResultTable(ResultSet results, PrintWriter writer, String searchQuery) {
String table = "<form name=\"ftable\" method=\"post\" action=\"/TestWebProject/umut-dabager\">";
table +=
"<table border=\"1\" style=\"width:100%\">\n"
+ "<tr>\n"
+ "<th>Select</th>"
+ "<th>Musician</th>\n"
+ "<th>Genre</th>\n"
+ "</tr>\n";
while (results.hasNext()) {
QuerySolution currentSolution = results.nextSolution();
String musicianName =
currentSolution.getLiteral("?musicianLabel").toString().replace("@en", "");
String musicianURI = currentSolution.getResource("?musician").toString();
String genreName = currentSolution.getLiteral("?genreLabel").toString().replace("@en", "");
String genreURI = currentSolution.getResource("?genre").toString();
if (musicianName.toLowerCase().contains(searchQuery.toLowerCase())
|| genreName.toLowerCase().contains(searchQuery.toLowerCase())) {
table +=
"<tr>\n"
+ "<td>\n"
+ "<input type=\"checkbox\" name=\"check\" value=\""
+ musicianURI
+ valueSeperatorChar
+ musicianName
+ valueSeperatorChar
+ genreURI
+ valueSeperatorChar
+ genreName
+ "\"/>"
+ "</td>\n"
+ "<td>\n";
table +=
"<a href=\""
+ musicianURI
+ "\">"
+ musicianName
+ "</td>\n"
+ "<td>\n"
+ "<a href=\""
+ genreURI
+ "\">"
+ genreName;
}
}
table += "</table>";
table +=
"<table><tr><td><input id=\"submit\" name=\"submit\" type=\"submit\" value=\"Save the selected results.\"/></td></tr></table>";
table += "</form>";
writer.println(table);
}
@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"));
}
}
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 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();
}
@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();
}
}
public static void BoxActivite() { // method
String rol = "";
String p = "";
try {
// OntModel model = OpenOWL.OpenConnectOWL();
System.out.println("Avoir les activités"); // get the activity from my File OWL
String queryString;
queryString =
"PREFIX saidi:<http://www.owl-ontologies.com/Ontology1364995044.owl#> "
+ "SELECT (str(?x) as ?xs) "
+ "where { ?y saidi:hasnameactivite ?x."
+ " ?y saidi:avoirrole ?ro. "
+ " ?y saidi:Activitepour ?p. "
+ "?ro saidi:hasnamerole ?nr."
+ " FILTER (?p ='"
+ p
+ "') "
+ "FILTER (?nr ='"
+ rol
+ "') }";
// call method ExecSparQl from class OpenOWL
// ExecSparQl return a Resultset
ResultSet results = OpenOWL.ExecSparQl(queryString);
while (results.hasNext()) {
QuerySolution soln = results.nextSolution();
String nomactiviter = soln.getLiteral("xs").getString();
// test --
System.out.println("nomactiviter " + nomactiviter.toString());
// public ArrayList<String> ListActivite = new ArrayList<String>();
// ListActivite.add(nomactiviter.toString());
System.out.println("ListActivity: " + nomactiviter.toString());
}
// Jcombobox (ac = new javax.swing.JComboBox();)
} catch (Exception ex) {
System.err.println(ex);
}
} // end first method
/**
* Textual representation : layout using given separator. Ensure the PrintWriter can handle UTF-8.
*
* @param pw PrintWriter
* @param colSep Column separator
*/
public void write(
PrintWriter pw, ResultSet resultSet, String colStart, String colSep, String colEnd) {
if (resultSet.getResultVars().size() == 0) {
pw.println("==== No variables ====");
// return ;
}
ResultSetRewindable resultSetRewindable = ResultSetFactory.makeRewindable(resultSet);
int numCols = resultSetRewindable.getResultVars().size();
int[] colWidths = colWidths(resultSetRewindable);
String row[] = new String[numCols];
int lineWidth = 0;
for (int col = 0; col < numCols; col++) {
String rVar = resultSet.getResultVars().get(col);
row[col] = rVar;
lineWidth += colWidths[col];
if (col > 0) lineWidth += colSep.length();
}
if (colStart != null) lineWidth += colStart.length();
if (colEnd != null) lineWidth += colEnd.length();
for (int i = 0; i < lineWidth; i++) pw.print('-');
pw.println();
printRow(pw, row, colWidths, colStart, colSep, colEnd);
for (int i = 0; i < lineWidth; i++) pw.print('=');
pw.println();
for (; resultSetRewindable.hasNext(); ) {
QuerySolution rBind = resultSetRewindable.nextSolution();
for (int col = 0; col < numCols; col++) {
String rVar = resultSet.getResultVars().get(col);
row[col] = this.getVarValueAsString(rBind, rVar);
}
printRow(pw, row, colWidths, colStart, colSep, colEnd);
}
for (int i = 0; i < lineWidth; i++) pw.print('-');
pw.println();
resultSetRewindable = null;
}
/*
* Inserts raw data into database.
* @param results Retrieved results from wikiData
*
* UPDATE !! Tried to insert all the raw data into db and pulling data from there.
* Insert is taking too long for big data. ABANDONED!
*/
private void insertRawDataToDB(ResultSet results) throws ClassNotFoundException {
Connection conn = null;
Statement statement = null;
String sqlInsertQuery = "TRUNCATE TABLE group5db.umut_rawData ";
try {
Class.forName("com.mysql.jdbc.Driver");
conn = DriverManager.getConnection(DB_URL, USER, PASS);
statement = conn.createStatement();
while (results.hasNext()) {
QuerySolution currentSolution = results.nextSolution();
String musicianName =
currentSolution.getLiteral("?musicianLabel").toString().replace("@en", "");
String musicianURI =
currentSolution
.getResource("?musician")
.toString()
.replace("http://www.wikidata.org/entity/", "");
String genreName = currentSolution.getLiteral("?genreLabel").toString().replace("@en", "");
String genreURI =
currentSolution
.getResource("?genre")
.toString()
.replace("http://www.wikidata.org/entity/", "");
sqlInsertQuery +=
"INSERT INTO group5db.umut_rawData "
+ "(musicianid,musician,genreid,genre) "
+ "VALUES ('"
+ musicianURI
+ "', '"
+ musicianName
+ "', '"
+ genreURI
+ "', '"
+ genreName
+ "') ";
}
statement.execute(sqlInsertQuery);
} catch (SQLException exc) {
exc.printStackTrace();
}
}
/**
* 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;
}
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;
}
private ResultSet ConvertResults(org.apache.jena.query.ResultSet results) {
ResultSet rs = new ResultSet();
while (results.hasNext()) {
Binding b = results.nextBinding();
Result result = new Result();
Iterator<Var> v = b.vars();
while (v.hasNext()) {
Var currentV = v.next();
Node val = b.get(currentV);
if (currentV.toString().contains("_info_")) {
String[] parts = val.getLiteral().getLexicalForm().toString().split("=");
if (parts.length > 1) {
for (int i = 0; i < parts.length; i++) {
String[] subParts = parts[i].split("\\.");
if (subParts.length > 1) {
if (!Character.isDigit(subParts[1].charAt(0))) result.addTable(subParts[0]);
}
}
}
result.addWhere(val.getLiteral().getLexicalForm());
} else {
if (val.isLiteral()) {
String value = val.getLiteral().getLexicalForm();
String datatype = val.getLiteralDatatypeURI();
if (datatype.equals(S2SML.LITERAL_MAP_IRI)) {
String[] parts = value.split("\\.");
if (parts.length > 1) {
if (!Character.isDigit(parts[1].charAt(0))) result.addTable(parts[0]);
}
}
}
// System.out.println(currentV.toString().replace("?", "") +" "+val);
result.addVarMapping(
currentV.toString().replace("?", ""), FormatUtil.processNode(val, dialect));
}
}
rs.add(result);
}
return rs;
}
@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 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);
}
}
/** {@inheritDoc} */
@Override
protected Collection<TestCaseResult> executeSingleTest(TestSource testSource, TestCase testCase)
throws TestCaseExecutionException {
Collection<TestCaseResult> testCaseResults = new ArrayList<>();
PropertyValuePairSet.PropertyValuePairSetBuilder annotationSetBuilder =
PropertyValuePairSet.builder();
try (QueryExecution qe =
testSource
.getExecutionFactory()
.createQueryExecution(queryGenerationFactory.getSparqlQuery(testCase))) {
ResultSet results = qe.execSelect();
ExtendedTestCaseResultImpl.Builder resultBuilder = null;
String prevResource = "";
while (results.hasNext()) {
QuerySolution qs = results.next();
String resource = qs.get("this").toString();
if (qs.get("this").isLiteral()) {
resource = StringUtils.getHashFromString(resource);
}
String message = testCase.getResultMessage();
if (qs.contains("message")) {
message = qs.get("message").toString();
}
RLOGLevel logLevel = testCase.getLogLevel();
// If resource != before
// we add the previous result in the list
if (!prevResource.equals(resource)) {
// The very first time we enter, result = null and we don't add any result
if (resultBuilder != null) {
testCaseResults.add(
resultBuilder
.setResultAnnotations(annotationSetBuilder.build().getAnnotations())
.build());
}
resultBuilder =
new ExtendedTestCaseResultImpl.Builder(
testCase.getTestURI(), logLevel, message, resource);
annotationSetBuilder = PropertyValuePairSet.builder(); // reset
// get static annotations for new test
for (ResultAnnotation resultAnnotation : testCase.getResultAnnotations()) {
// Get values
if (resultAnnotation.getAnnotationValue().isPresent()) {
annotationSetBuilder.annotation(
PropertyValuePair.create(
resultAnnotation.getAnnotationProperty(),
resultAnnotation.getAnnotationValue().get()));
}
}
}
// result must be initialized by now
checkNotNull(resultBuilder);
// get annotations from the SPARQL query
for (ResultAnnotation resultAnnotation : testCase.getVariableAnnotations()) {
// Get the variable name
if (resultAnnotation.getAnnotationVarName().isPresent()) {
String variable = resultAnnotation.getAnnotationVarName().get().trim();
// If it exists, add it in the Set
if (qs.contains(variable)) {
annotationSetBuilder.annotation(
PropertyValuePair.create(
resultAnnotation.getAnnotationProperty(), qs.get(variable)));
}
}
}
}
// Add last result (if query return any)
if (resultBuilder != null) {
testCaseResults.add(
resultBuilder
.setResultAnnotations(annotationSetBuilder.build().getAnnotations())
.build());
}
} catch (QueryExceptionHTTP e) {
checkQueryResultStatus(e);
}
return testCaseResults;
}
@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);
}
