/**
* Leo Bard spotted a problem whereby removing a reified statement from a model with style
* Standard didn't leave the model empty. Here's a test for it.
*/
public void testLeosBug() {
Model A = getModel();
Statement st = statement(A, "pigs fly south");
ReifiedStatement rst = st.createReifiedStatement("eh:pointer");
A.removeReification(rst);
assertIsoModels(ModelFactory.createDefaultModel(), A);
}
/**
* 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 testCalendarLiterals() {
Calendar now = Calendar.getInstance();
Literal A = ModelFactory.createDefaultModel().createTypedLiteral(now);
Literal B = ResourceFactory.createTypedLiteral(now);
assertEquals(A, B);
}
/** Load the premises or conclusions for the test. */
public Model getDoc(Resource test, Property docType) throws IOException {
Model result = ModelFactory.createDefaultModel();
StmtIterator si = test.listProperties(docType);
while (si.hasNext()) {
String fname = si.nextStatement().getObject().toString() + ".rdf";
loadFile(fname, result);
}
return result;
}
/**
* Answer a new model which is the aggregation of
*
* <ul>
* <li>the statements of <code>model</code>
* <li>the non-bnode subclass statements of <code>schema</code>
* <li>the subclass closure of those statements
* <li>the rdf:type statements implied by the rdfs:domain statements of <code>schema</code> and
* the <code>model</code> statements using that statements property
* <li>similarly for rdfs:range
* <li>the rdf:type statements implied by the subclass closure
* </ul>
*/
public static Model withSchema(Model model, Model schema) {
Model result = ModelFactory.createDefaultModel().add(model);
addSubclassesFrom(result, schema);
addSubClassClosure(result);
addDomainTypes(result, schema);
addRangeTypes(result, schema);
addIntersections(result, schema);
addSupertypes(result);
return result;
}
/** Run a single test of any sort, return true if the test succeeds. */
public boolean doRunTest(Resource test) throws IOException {
if (test.hasProperty(RDF.type, OWLTest.PositiveEntailmentTest)
|| test.hasProperty(RDF.type, OWLTest.NegativeEntailmentTest)
|| test.hasProperty(RDF.type, OWLTest.OWLforOWLTest)
|| test.hasProperty(RDF.type, OWLTest.ImportEntailmentTest)
|| test.hasProperty(RDF.type, OWLTest.TrueTest)) {
// Entailment tests
boolean processImports = test.hasProperty(RDF.type, OWLTest.ImportEntailmentTest);
Model premises = getDoc(test, RDFTest.premiseDocument, processImports);
Model conclusions = getDoc(test, RDFTest.conclusionDocument);
comprehensionAxioms(premises, conclusions);
long t1 = System.currentTimeMillis();
InfGraph graph = reasoner.bind(premises.getGraph());
if (printProfile) {
((FBRuleInfGraph) graph).resetLPProfile(true);
}
Model result = ModelFactory.createModelForGraph(graph);
boolean correct = WGReasonerTester.testConclusions(conclusions.getGraph(), result.getGraph());
long t2 = System.currentTimeMillis();
lastTestDuration = t2 - t1;
if (printProfile) {
((FBRuleInfGraph) graph).printLPProfile();
}
if (test.hasProperty(RDF.type, OWLTest.NegativeEntailmentTest)) {
correct = !correct;
}
return correct;
} else if (test.hasProperty(RDF.type, OWLTest.InconsistencyTest)) {
// System.out.println("Starting: " + test);
Model input = getDoc(test, RDFTest.inputDocument);
long t1 = System.currentTimeMillis();
InfGraph graph = reasoner.bind(input.getGraph());
boolean correct = !graph.validate().isValid();
long t2 = System.currentTimeMillis();
lastTestDuration = t2 - t1;
return correct;
} else if (test.hasProperty(RDF.type, OWLTest.ConsistencyTest)) {
// Not used normally becase we are not complete enough to prove consistency
// System.out.println("Starting: " + test);
Model input = getDoc(test, RDFTest.inputDocument);
long t1 = System.currentTimeMillis();
InfGraph graph = reasoner.bind(input.getGraph());
boolean correct = graph.validate().isValid();
long t2 = System.currentTimeMillis();
lastTestDuration = t2 - t1;
return correct;
} else {
for (StmtIterator i = test.listProperties(RDF.type); i.hasNext(); ) {
System.out.println("Test type = " + i.nextStatement().getObject());
}
throw new ReasonerException("Unknown test type");
}
}
protected static void addRangeTypes(Model result, Model schema) {
Model toAdd = ModelFactory.createDefaultModel();
for (StmtIterator it = schema.listStatements(ANY, RDFS.range, ANY); it.hasNext(); ) {
Statement s = it.nextStatement();
RDFNode type = s.getObject();
Property property = s.getSubject().as(Property.class);
for (StmtIterator x = result.listStatements(ANY, property, ANY); x.hasNext(); ) {
RDFNode ob = x.nextStatement().getObject();
if (ob.isResource()) toAdd.add((Resource) ob, RDF.type, type);
}
}
result.add(toAdd);
}
/** Load the premises or conclusions for the test, optional performing import processing. */
public Model getDoc(Resource test, Property docType, boolean processImports) throws IOException {
if (processImports) {
Model result = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, null);
StmtIterator si = test.listProperties(docType);
while (si.hasNext()) {
String fname = si.nextStatement().getObject().toString() + ".rdf";
loadFile(fname, result);
}
return result;
} else {
return getDoc(test, docType);
}
}
/** Initialize the result model. */
public void initResults() {
testResults = ModelFactory.createDefaultModel();
jena2 = testResults.createResource(BASE_RESULTS_URI + "#jena2");
jena2.addProperty(
RDFS.comment,
testResults.createLiteral(
"<a xmlns=\"http://www.w3.org/1999/xhtml\" href=\"http://jena.sourceforce.net/\">Jena2</a> includes a rule-based inference engine for RDF processing, "
+ "supporting both forward and backward chaining rules. Its OWL rule set is designed to provide sound "
+ "but not complete instance resasoning for that fragment of OWL/Full limited to the OWL/lite vocabulary. In"
+ "particular it does not support unionOf/complementOf.",
true));
jena2.addProperty(RDFS.label, "Jena2");
testResults.setNsPrefix("results", OWLResults.NS);
}
protected static void addSupertypes(Model result) {
Model temp = ModelFactory.createDefaultModel();
for (StmtIterator it = result.listStatements(ANY, RDF.type, ANY); it.hasNext(); ) {
Statement s = it.nextStatement();
Resource c = AssemblerHelp.getResource(s);
for (StmtIterator subclasses = result.listStatements(c, RDFS.subClassOf, ANY);
subclasses.hasNext(); ) {
RDFNode type = subclasses.nextStatement().getObject();
// System.err.println( ">> adding super type: subject " + s.getSubject() + ", type " + type
// );
temp.add(s.getSubject(), RDF.type, type);
}
}
result.add(temp);
}
private static ResultSetRewindable unique(ResultSetRewindable results) {
// VERY crude. Utilises the fact that bindings have value equality.
List<Binding> x = new ArrayList<Binding>();
Set<Binding> seen = new HashSet<Binding>();
for (; results.hasNext(); ) {
Binding b = results.nextBinding();
if (seen.contains(b)) continue;
seen.add(b);
x.add(b);
}
QueryIterator qIter = new QueryIterPlainWrapper(x.iterator());
ResultSet rs =
new ResultSetStream(results.getResultVars(), ModelFactory.createDefaultModel(), qIter);
return ResultSetFactory.makeRewindable(rs);
}
/**
* Check that a predicate for which no shortnames are defined in name map still gets a term
* binding in the metadata.
*/
@Test
public void testTermBindingsCoverAllPredicates() throws URISyntaxException {
Resource thisPage = ResourceFactory.createResource("elda:thisPage");
String pageNumber = "1";
Bindings cc = new Bindings();
URI reqURI = new URI("");
//
EndpointDetails spec =
new EndpointDetails() {
@Override
public boolean isListEndpoint() {
return true;
}
@Override
public boolean hasParameterBasedContentNegotiation() {
return false;
}
};
EndpointMetadata em = new EndpointMetadata(spec, thisPage, pageNumber, cc, reqURI);
//
PrefixMapping pm =
PrefixMapping.Factory.create().setNsPrefix("this", "http://example.com/root#");
Model toScan = ModelIOUtils.modelFromTurtle(":a <http://example.com/root#predicate> :b.");
toScan.setNsPrefixes(pm);
Resource predicate = toScan.createProperty("http://example.com/root#predicate");
Model meta = ModelFactory.createDefaultModel();
Resource exec = meta.createResource("fake:exec");
ShortnameService sns = new StandardShortnameService();
// APIEndpoint.Request r = new APIEndpoint.Request( new Controls(), reqURI, cc );
CompleteContext c =
new CompleteContext(CompleteContext.Mode.PreferPrefixes, sns.asContext(), pm)
.include(toScan);
em.addTermBindings(toScan, meta, exec, c);
@SuppressWarnings("unused")
Map<String, String> termBindings = c.Do();
Resource tb = meta.listStatements(null, API.termBinding, Any).nextStatement().getResource();
assertTrue(meta.contains(tb, API.label, "this_predicate"));
assertTrue(meta.contains(tb, API.property, predicate));
}
/** Harvests all the triplets from each URI in the @rdfUris list */
private void harvestFromDumps() {
for (String uri : rdfUris) {
if (uri.isEmpty()) continue;
logger.info("Harvesting uri [{}]", uri);
Model model = ModelFactory.createDefaultModel();
try {
RDFDataMgr.read(model, uri.trim(), RDFLanguages.RDFXML);
BulkRequestBuilder bulkRequest = client.prepareBulk();
addModelToES(model, bulkRequest, true);
} catch (RiotException re) {
logger.error("Illegal xml character [{}]", re.getLocalizedMessage());
} catch (Exception e) {
logger.error(
"Exception when harvesting url: {}. Details: {}", uri, e.getLocalizedMessage());
}
}
}
/** Load all of the known manifest files into a single model */
public static Model loadAllTestDefinitions() {
System.out.print("Loading manifests ");
System.out.flush();
Model testDefs = ModelFactory.createDefaultModel();
int count = 0;
for (String TEST_DIR : TEST_DIRS) {
File dir = new File(BASE_TESTDIR + TEST_DIR);
String[] manifests =
dir.list(
new FilenameFilter() {
@Override
public boolean accept(File df, String name) {
if (name.startsWith("Manifest") && name.endsWith(".rdf")) {
return includeModified || !name.endsWith("-mod.rdf");
} else {
return false;
}
}
});
for (String manifest : manifests) {
File mf = new File(dir, manifest);
try {
testDefs.read(new FileInputStream(mf), "file:" + mf);
count++;
if (count % 8 == 0) {
System.out.print(".");
System.out.flush();
}
} catch (FileNotFoundException e) {
System.out.println("File not readable - " + e);
}
}
}
System.out.println("loaded");
return testDefs;
}
@Test
public void testInfoStamp() {
String versionString = "E3.14159", commentString = "gloopSmurfale";
String resourceString =
"_x eye:assumed 'ABC'; _x eye:checked 'DEF'; _x eye:version '%v'; _x eye:comment '%c'"
.replaceAll("%v", versionString)
.replaceAll("%c", commentString);
InfoStamp i = new InfoStamp(resourceInModel(resourceString));
Calendar now = Calendar.getInstance();
Resource root = i.stamp(now);
Model stamp = root.getModel();
Literal dateLiteral = ModelFactory.createDefaultModel().createTypedLiteral(now);
String dateString = "'" + dateLiteral.getLexicalForm() + "'" + dateLiteral.getDatatypeURI();
String expectedFormat =
"[eye:assumed 'ABC' & eye:checked 'DEF' & eye:dated <date>"
+ " & eye:comment '<comment>' & eye:version '<version>']";
String expectedString =
expectedFormat
.replaceAll("<date>", dateString)
.replaceAll("<version>", versionString)
.replaceAll("<comment>", commentString);
Model expected = model(expectedString);
assertIsoModels(expected, stamp);
}
/**
* This section is written to handle the inheritance between the interfaces. The models supports
* multiple inheritance.
*
* @param type The given {@link Model} interface.
* @parma impl The {@link ModelProxy} is the proxy implementation for <code>type</code>. It will
* be modified after the execution of <code>initSupers</code>.
*/
protected void initSupers(Class type, ModelProxy imp) {
List<Class> sC = getSupers(type);
/* Creates the superclass instances */
for (Class i : sC) if (!imp.supers.containsKey(i)) imp.supers.put(i, owner.create(i));
}
private Resource createMetadata(final boolean isListEndpoint, Integer totalResults)
throws URISyntaxException {
Model objectModel = ModelFactory.createDefaultModel();
MergedModels mergedModels = new MergedModels(objectModel);
//
Model meta = mergedModels.getMetaModel();
//
Resource thisMetaPage = meta.createResource("eh:/thisMetaPage");
Resource SEP = meta.createResource("eh:/sparqlEndpoint");
thisMetaPage.addProperty(API.sparqlEndpoint, SEP);
Bindings bindings = new Bindings();
URI ru = new URI(thisMetaPage.getURI());
Resource uriForDefinition = objectModel.createResource(thisMetaPage.getURI());
boolean suppressIPTO = true;
int page = 1, perPage = 10;
boolean hasMorePages = true;
Context context = new Context();
CompleteContext cc = new CompleteContext(Mode.PreferLocalnames, context, objectModel);
//
SetsMetadata setsMeta =
new SetsMetadata() {
@Override
public void setMetadata(String type, Model meta) {}
};
WantsMetadata wantsMeta =
new WantsMetadata() {
@Override
public boolean wantsMetadata(String name) {
return true;
}
};
//
Map<String, View> views = new HashMap<String, View>();
Set<FormatNameAndType> formats = new HashSet<FormatNameAndType>();
//
EndpointDetails details =
new EndpointDetails() {
@Override
public boolean isListEndpoint() {
return isListEndpoint;
}
@Override
public boolean hasParameterBasedContentNegotiation() {
return false;
}
};
//
EndpointMetadata.addAllMetadata(
mergedModels,
ru,
uriForDefinition,
bindings,
cc,
suppressIPTO,
thisMetaPage,
page,
perPage,
totalResults,
hasMorePages,
CollectionUtils.list(objectModel.createResource("eh:/item/_1")),
setsMeta,
wantsMeta,
"SELECT",
"VIEW",
new TestCaches.FakeSource("Nemos"),
views,
formats,
details);
return thisMetaPage;
}
/**
* Starts a harvester with predefined queries to synchronize with the changes from the SPARQL
* endpoint
*/
public boolean sync() {
logger.info("Sync resources newer than {}", startTime);
String rdfQueryTemplate =
"PREFIX xsd:<http://www.w3.org/2001/XMLSchema#> "
+ "SELECT DISTINCT ?resource WHERE { "
+ " GRAPH ?graph { %s }"
+ " ?graph <%s> ?time . %s "
+ " FILTER (?time > xsd:dateTime(\"%s\")) }";
String queryStr =
String.format(
rdfQueryTemplate, syncConditions, syncTimeProp, graphSyncConditions, startTime);
Set<String> syncUris = executeSyncQuery(queryStr, "resource");
if (syncUris == null) {
logger.error("Errors occurred during sync procedure. Aborting!");
return false;
}
/**
* If desired, query for old data that has the sync conditions modified
*
* <p>This option is useful in the case in which the application indexes resources that match
* some conditions. In this case, if they are modified and no longer match the initial
* conditions, they will not be synchronized. When syncOldData is True, the modified resources
* that no longer match the conditions are deleted.
*/
int deleted = 0;
int count = 0;
if (this.syncOldData) {
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
queryStr =
String.format(
rdfQueryTemplate,
syncConditions,
syncTimeProp,
graphSyncConditions,
sdf.format(new Date(0)));
HashSet<String> allIndexURIs = executeSyncQuery(queryStr, "resource");
if (allIndexURIs == null) {
logger.error("Errors occurred during modified content sync query. Aborting!");
return false;
}
deleted = removeMissingUris(allIndexURIs);
}
/* Prepare a series of bulk uris to be described so we can make
* a smaller number of calls to the SPARQL endpoint. */
ArrayList<ArrayList<String>> bulks = new ArrayList<ArrayList<String>>();
ArrayList<String> currentBulk = new ArrayList<String>();
for (String uri : syncUris) {
currentBulk.add(uri);
if (currentBulk.size() == EEASettings.DEFAULT_BULK_SIZE) {
bulks.add(currentBulk);
currentBulk = new ArrayList<String>();
}
}
if (currentBulk.size() > 0) {
bulks.add(currentBulk);
}
/* Execute RDF queries for the resources in each bulk */
for (ArrayList<String> bulk : bulks) {
String syncQuery = getSyncQueryStr(bulk);
try {
Query query = QueryFactory.create(syncQuery);
QueryExecution qExec = QueryExecutionFactory.sparqlService(rdfEndpoint, query);
try {
Model constructModel = ModelFactory.createDefaultModel();
qExec.execConstruct(constructModel);
BulkRequestBuilder bulkRequest = client.prepareBulk();
/**
* When adding the model to ES do not use toDescribeURIs as the query already returned the
* correct labels.
*/
addModelToES(constructModel, bulkRequest, false);
count += bulk.size();
} catch (Exception e) {
logger.error("Error while querying for modified content. {}", e.getLocalizedMessage());
return false;
} finally {
qExec.close();
}
} catch (QueryParseException qpe) {
logger.warn(
"Could not parse Sync query. Please provide a relevant query. {}",
qpe.getLocalizedMessage());
return false;
}
}
logger.info(
"Finished synchronisation: Deleted {}, Updated {}/{}", deleted, count, syncUris.size());
return true;
}
/**
* Query SPARQL endpoint with a CONSTRUCT query
*
* @param qExec QueryExecution encapsulating the query
* @return model retrieved by querying the endpoint
*/
private Model getConstructModel(QueryExecution qExec) {
return qExec.execConstruct(ModelFactory.createDefaultModel());
}
/**
* Query SPARQL endpoint with a DESCRIBE query
*
* @param qExec QueryExecution encapsulating the query
* @return model retrieved by querying the endpoint
*/
private Model getDescribeModel(QueryExecution qExec) {
return qExec.execDescribe(ModelFactory.createDefaultModel());
}
public static void main(String[] args) {
List<String> obj = new ArrayList<String>();
Scanner input = new Scanner(System.in);
System.out.print("Enter URI: ");
String userIn = input.nextLine();
// create an empty Model
Model model = ModelFactory.createDefaultModel();
// read the RDF/XML file
model.read(userIn);
// write it to standard out
// model.write(System.out);
// list the statements in the Model
StmtIterator iter = model.listStatements();
System.out.println();
// print out the predicate, subject and object of each statement
while (iter.hasNext()) {
Statement stmt = iter.nextStatement(); // get next statement
Resource subject = stmt.getSubject(); // get the subject
Property predicate = stmt.getPredicate(); // get the predicate
RDFNode object = stmt.getObject(); // get the object
System.out.print(subject.toString());
System.out.print(" -> " + predicate.toString() + " -> ");
if (object instanceof Resource) {
System.out.print(object.toString() + "\n");
} else {
// object is a literal
System.out.print(" \"" + object.toString() + "\"\n");
}
}
/* for(int i = 0; i < (obj.size()); i++){
String sparqlQueryString1=
"SELECT ?s ?o "+
"WHERE {"+
"?s ?p ?o ."+
"?o <bif:contains> \""+obj.get(i)+"\" ."+
"}"+
"limit 10";
Query query = QueryFactory.create(sparqlQueryString1);
QueryExecution qexec = QueryExecutionFactory.sparqlService("http://pubmed.bio2rdf.org/sparql", query);
ResultSet results = qexec.execSelect();
System.out.println("Query: "+obj.get(i));
ResultSetFormatter.out(System.out, results, query);
qexec.close() ;
} */
}
public void testBulkByModel() {
testBulkByModel(ModelFactory.createDefaultModel());
}
public void testMBU() {
testMBU(ModelFactory.createDefaultModel());
}
/**
* To each subclass X of <code>parents.item</code> add as superclass all the classes between X and
* that item and all the items in the rest of <code>parents</code>.
*/
private static void addSuperClasses(Model m, LinkedSeq parents) {
Model toAdd = ModelFactory.createDefaultModel();
addSuperClasses(m, parents, toAdd);
m.add(toAdd);
}