@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();
}
}
@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();
}
}
/**
* 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);
}
/**
* 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;
}
