/** @inheritDoc */
@SuppressWarnings("unchecked")
public <T> T merge(final T theT) {
assertStateOk(theT);
Graph aExistingData = null;
if (theT instanceof EmpireGenerated) {
aExistingData = ((EmpireGenerated) theT).getInstanceTriples();
}
if (aExistingData == null || aExistingData.isEmpty()) {
try {
aExistingData = assertContainsAndDescribe(theT);
} catch (IllegalArgumentException e) {
// it doesnt exist, so really, nothing to delete
aExistingData = new GraphImpl();
}
}
try {
preUpdate(theT);
Graph aData = RdfGenerator.asRdf(theT);
boolean isTopOperation = (mOp == null);
DataSourceOperation aOp = new DataSourceOperation();
if (doesSupportNamedGraphs() && EmpireUtil.hasNamedGraphSpecified(theT)) {
java.net.URI aGraphURI = EmpireUtil.getNamedGraph(theT);
aOp.remove(aGraphURI, aExistingData);
aOp.add(aGraphURI, aData);
} else {
aOp.remove(aExistingData);
aOp.add(aData);
}
joinCurrentDataSourceOperation(aOp);
// cascade the merge
cascadeOperation(theT, new IsMergeCascade(), new MergeCascade());
finishCurrentDataSourceOperation(isTopOperation);
postUpdate(theT);
return theT;
} catch (DataSourceException ex) {
throw new PersistenceException(ex);
} catch (InvalidRdfException ex) {
throw new IllegalStateException(ex);
}
}
/**
* Add this graph to the set of data to be added, to the specified named graph, when this
* operation is executed
*
* @param theGraphURI the named graph the data should be added to
* @param theGraph the data to add
*/
public void add(java.net.URI theGraphURI, Graph theGraph) {
Graph aGraph = mAdd.get(theGraphURI);
if (aGraph == null) {
aGraph = new ExtGraph();
}
aGraph.addAll(theGraph);
mAdd.put(theGraphURI, aGraph);
}
/**
* Add this graph to the set of data to be removed, from the specified named graph, when this
* operation is executed
*
* @param theGraphURI the named graph the data should be removed from
* @param theGraph the data to remove
*/
public void remove(java.net.URI theGraphURI, Graph theGraph) {
Graph aGraph = mRemove.get(theGraphURI);
if (aGraph == null) {
aGraph = new ExtGraph();
}
aGraph.addAll(theGraph);
mRemove.put(theGraphURI, aGraph);
}
/**
* call this method if you need the RDF Graph that represents the R2RML mappings
*
* @return an RDF Graph
*/
@Deprecated
public Graph getGraph() {
OBDAMappingTransformer transformer = new OBDAMappingTransformer();
transformer.setOntology(ontology);
List<Statement> statements = new ArrayList<Statement>();
for (OBDAMappingAxiom axiom : this.mappings) {
List<Statement> statements2 = transformer.getStatements(axiom, prefixmng);
statements.addAll(statements2);
}
@SuppressWarnings("deprecation")
Graph g = new GraphImpl();
g.addAll(statements);
return g;
}
/**
* @param g Where to assemble the description.
* @param tripleStore The KB instance to be described.
* @param serviceURI The SPARQL service end point.
* @param aDefaultDataset The data set identifier that will be used on the description (the
* bigdata namespace of the dataset is obtained from the <i>tripleStore</i>).
*/
public VoID(
final Graph g,
final AbstractTripleStore tripleStore,
final String[] serviceURI,
final Resource aDataset) {
if (g == null) throw new IllegalArgumentException();
if (tripleStore == null) throw new IllegalArgumentException();
if (serviceURI == null) throw new IllegalArgumentException();
if (serviceURI.length == 0) throw new IllegalArgumentException();
for (String s : serviceURI) if (s == null) throw new IllegalArgumentException();
if (aDataset == null) throw new IllegalArgumentException();
this.g = g;
this.tripleStore = tripleStore;
this.serviceURI = serviceURI;
this.f = g.getValueFactory();
this.aDataset = aDataset;
this.aDefaultGraph = f.createBNode("defaultGraph");
}
/**
* Describe the vocabularies which are in use in the KB based on the predicate partition
* statistics.
*
* @param predicateParitionCounts The predicate partition statistics.
*/
protected void describeVocabularies(final IVCount[] predicatePartitionCounts) {
// Find the distinct vocabularies in use.
final Set<String> namespaces = new LinkedHashSet<String>();
{
// property partitions.
for (IVCount tmp : predicatePartitionCounts) {
final URI p = (URI) tmp.getValue();
String namespace = p.getNamespace();
if (namespace.endsWith("#")) {
// Strip trailing '#' per VoID specification.
namespace = namespace.substring(0, namespace.length() - 1);
}
namespaces.add(namespace);
}
}
// Sort into dictionary order.
final String[] a = namespaces.toArray(new String[namespaces.size()]);
Arrays.sort(a);
for (String namespace : a) {
g.add(aDataset, VoidVocabularyDecl.vocabulary, f.createURI(namespace));
}
}
/**
* Describe a named or default graph.
*
* @param graph The named graph.
* @param predicatePartitionCounts The predicate partition statistics for that graph.
* @param classPartitionCounts The class partition statistics for that graph.
*/
protected void describeGraph(
final Resource graph,
final IVCount[] predicatePartitionCounts,
final IVCount[] classPartitionCounts) {
// The graph is a Graph.
g.add(graph, RDF.TYPE, SD.Graph);
// #of triples in the default graph
g.add(graph, VoidVocabularyDecl.triples, f.createLiteral(tripleStore.getStatementCount()));
// #of entities in the default graph.
g.add(graph, VoidVocabularyDecl.entities, f.createLiteral(tripleStore.getURICount()));
// #of distinct predicates in the default graph.
g.add(graph, VoidVocabularyDecl.properties, f.createLiteral(predicatePartitionCounts.length));
// #of distinct classes in the default graph.
g.add(graph, VoidVocabularyDecl.classes, f.createLiteral(classPartitionCounts.length));
// property partition statistics.
for (IVCount tmp : predicatePartitionCounts) {
final BNode propertyPartition = f.createBNode();
final URI p = (URI) tmp.getValue();
g.add(graph, VoidVocabularyDecl.propertyPartition, propertyPartition);
g.add(propertyPartition, VoidVocabularyDecl.property, p);
g.add(propertyPartition, VoidVocabularyDecl.triples, f.createLiteral(tmp.count));
}
// class partition statistics.
{
// per class partition statistics.
for (IVCount tmp : classPartitionCounts) {
final BNode classPartition = f.createBNode();
final BigdataValue cls = tmp.getValue();
g.add(graph, VoidVocabularyDecl.classPartition, classPartition);
g.add(classPartition, VoidVocabularyDecl.class_, cls);
g.add(classPartition, VoidVocabularyDecl.triples, f.createLiteral(tmp.count));
}
} // end class partition statistics.
}
/**
* Describe the default data set (the one identified by the namespace associated with the {@link
* AbstractTripleStore}.
*
* @param describeStatistics When <code>true</code>, the VoID description will include the {@link
* VoidVocabularyDecl#vocabulary} declarations, the property partition statistics, and the
* class partition statistics.
* @param describeNamedGraphs When <code>true</code>, each named graph will also be described in
* in the same level of detail as the default graph. Otherwise only the default graph will be
* described.
*/
public void describeDataSet(final boolean describeStatistics, final boolean describeNamedGraphs) {
final String namespace = tripleStore.getNamespace();
// This is a VoID data set.
g.add(aDataset, RDF.TYPE, VoidVocabularyDecl.Dataset);
// The namespace is used as a title for the data set.
g.add(aDataset, DCTermsVocabularyDecl.title, f.createLiteral(namespace));
// Also present the namespace in an unambiguous manner.
g.add(aDataset, SD.KB_NAMESPACE, f.createLiteral(namespace));
/**
* Service end point for this namespace.
*
* @see <a href="https://sourceforge.net/apps/trac/bigdata/ticket/689" > Missing URL encoding in
* RemoteRepositoryManager </a>
*/
for (String uri : serviceURI) {
g.add(
aDataset,
VoidVocabularyDecl.sparqlEndpoint,
f.createURI(uri + "/" + ConnectOptions.urlEncode(namespace) + "/sparql"));
}
// any URI is considered to be an entity.
g.add(aDataset, VoidVocabularyDecl.uriRegexPattern, f.createLiteral("^.*"));
if (!describeStatistics) {
// No statistics.
return;
}
// Frequency count of the predicates in the default graph.
final IVCount[] predicatePartitionCounts = predicateUsage(tripleStore);
// Frequency count of the classes in the default graph.
final IVCount[] classPartitionCounts = classUsage(tripleStore);
// Describe vocabularies based on the predicate partitions.
describeVocabularies(predicatePartitionCounts);
// defaultGraph description.
{
// Default graph in the default data set.
g.add(aDataset, SD.defaultGraph, aDefaultGraph);
// Describe the default graph using statistics.
describeGraph(aDefaultGraph, predicatePartitionCounts, classPartitionCounts);
} // end defaultGraph
// sb.append("termCount\t = " + tripleStore.getTermCount() + "\n");
//
// sb.append("uriCount\t = " + tripleStore.getURICount() + "\n");
//
// sb.append("literalCount\t = " + tripleStore.getLiteralCount() +
// "\n");
//
// /*
// * Note: The blank node count is only available when using the told
// * bnodes mode.
// */
// sb
// .append("bnodeCount\t = "
// + (tripleStore.getLexiconRelation()
// .isStoreBlankNodes() ? ""
// + tripleStore.getBNodeCount() : "N/A")
// + "\n");
/*
* Report for each named graph.
*/
if (describeNamedGraphs && tripleStore.isQuads()) {
final SPORelation r = tripleStore.getSPORelation();
// the index to use for distinct term scan.
final SPOKeyOrder keyOrder = SPOKeyOrder.CSPO;
// visit distinct IVs for context position on that index.
@SuppressWarnings("rawtypes")
final IChunkedIterator<IV> itr = r.distinctTermScan(keyOrder);
// resolve IVs to terms efficiently during iteration.
final BigdataValueIterator itr2 =
new BigdataValueIteratorImpl(tripleStore /* resolveTerms */, itr);
try {
while (itr2.hasNext()) {
/*
* Describe this named graph.
*
* Note: This is using the predicate and class partition
* statistics from the default graph (RDF merge) to identify
* the set of all possible predicates and classes within
* each named graph. It then tests each predicate and class
* partition against the named graph and ignores those which
* are not present in a given named graph. This is being
* done because we do not have a CPxx index.
*/
final BigdataResource graph = (BigdataResource) itr2.next();
final IVCount[] predicatePartitionCounts2 =
predicateUsage(tripleStore, graph.getIV(), predicatePartitionCounts);
final IVCount[] classPartitionCounts2 =
classUsage(tripleStore, graph.getIV(), classPartitionCounts);
final BNode aNamedGraph = f.createBNode();
// Named graph in the default data set.
g.add(aDataset, SD.namedGraph, aNamedGraph);
// The name of that named graph.
g.add(aNamedGraph, SD.name, graph);
// Describe the named graph.
describeGraph(aNamedGraph, predicatePartitionCounts2, classPartitionCounts2);
}
} finally {
itr2.close();
}
}
}
/**
* Implementation using the json.org API.
*
* @param json The RDF/JSON string to be parsed and converted into a Sesame Graph.
* @return A Sesame Graph if successful, otherwise null.
*/
public static Graph rdfJsonToGraph(String json) {
Graph result = new GraphImpl();
ValueFactory vf = result.getValueFactory();
try {
JSONObject input = new JSONObject(json);
Iterator<String> subjects = input.keys();
while (subjects.hasNext()) {
String subjStr = subjects.next();
Resource subject = null;
subject =
subjStr.startsWith("_:") ? vf.createBNode(subjStr.substring(2)) : vf.createURI(subjStr);
JSONObject pObj = input.getJSONObject(subjStr);
Iterator<String> predicates = pObj.keys();
while (predicates.hasNext()) {
String predStr = predicates.next();
URI predicate = vf.createURI(predStr);
JSONArray predArr = pObj.getJSONArray(predStr);
for (int i = 0; i < predArr.length(); i++) {
Value object = null;
JSONObject obj = predArr.getJSONObject(i);
if (!obj.has("value")) {
continue;
}
String value = obj.getString("value");
if (!obj.has("type")) {
continue;
}
String type = obj.getString("type");
String lang = null;
if (obj.has("lang")) {
lang = obj.getString("lang");
}
String datatype = null;
if (obj.has("datatype")) {
datatype = obj.getString("datatype");
}
if ("literal".equals(type)) {
if (lang != null) {
object = vf.createLiteral(value, lang);
} else if (datatype != null) {
object = vf.createLiteral(value, vf.createURI(datatype));
} else {
object = vf.createLiteral(value);
}
} else if ("bnode".equals(type)) {
object = vf.createBNode(value.substring(2));
} else if ("uri".equals(type)) {
object = vf.createURI(value);
}
if (obj.has("graphs")) {
JSONArray a = obj.getJSONArray("graphs");
// System.out.println("a.length() = " + a.length());
for (int j = 0; j < a.length(); j++) {
// Note: any nulls here will result in statements in the default context.
String s = a.getString(j);
Resource context = s.equals("null") ? null : vf.createURI(s);
// System.out.println("context = " + context);
result.add(subject, predicate, object, context);
}
} else {
result.add(subject, predicate, object);
}
}
}
}
} catch (JSONException e) {
log.error(e.getMessage(), e);
return null;
}
return result;
}
/**
* Implementation using the org.json API.
*
* @param graph A Sesame Graph.
* @return An RDF/JSON string if successful, otherwise null.
*/
public static String graphToRdfJson(Graph graph) {
JSONObject result = new JSONObject();
try {
Set<Resource> subjects = new HashSet<Resource>();
for (Statement s1 : graph) {
subjects.add(s1.getSubject());
}
for (Resource subject : subjects) {
JSONObject predicateObj = new JSONObject();
Set<URI> predicates = new HashSet<URI>();
Iterator<Statement> s2 = graph.match(subject, null, null);
while (s2.hasNext()) {
predicates.add(s2.next().getPredicate());
}
for (URI predicate : predicates) {
JSONArray valueArray = new JSONArray();
Iterator<Statement> stmnts = graph.match(subject, predicate, null);
Set<Value> objects = new HashSet<Value>();
while (stmnts.hasNext()) {
objects.add(stmnts.next().getObject());
}
for (Value object : objects) {
Iterator<Statement> stmnts2 = graph.match(subject, predicate, object);
JSONArray contexts = new JSONArray();
int i = 0;
boolean nonDefaultContext = false;
while (stmnts2.hasNext()) {
Resource context = stmnts2.next().getContext();
contexts.put(i, null == context ? null : context.toString());
if (null != context) {
nonDefaultContext = true;
}
i++;
}
JSONObject valueObj = new JSONObject();
valueObj.put("value", object.stringValue());
if (object instanceof Literal) {
valueObj.put("type", "literal");
Literal l = (Literal) object;
if (l.getLanguage() != null) {
valueObj.put("lang", l.getLanguage());
} else if (l.getDatatype() != null) {
valueObj.put("datatype", l.getDatatype().stringValue());
}
} else if (object instanceof BNode) {
valueObj.put("type", "bnode");
} else if (object instanceof URI) {
valueObj.put("type", "uri");
}
if (nonDefaultContext) {
valueObj.put("graphs", contexts);
}
valueArray.put(valueObj);
}
predicateObj.put(predicate.stringValue(), valueArray);
}
result.put(subject.stringValue(), predicateObj);
}
return result.toString(2);
} catch (JSONException e) {
log.error(e.getMessage(), e);
}
return null;
}