/**
* Self configuration Properties(target) - Properties(source) Find properties in target which are
* not in source
*
* @param source
* @param target
* @return Map of (key, value) pairs of self configured parameters
* @author sherif
*/
public Map<String, String> selfConfig(Model source, Model target) {
Map<String, String> parameters = new HashMap<String, String>();
Set<Property> properties = getPropertyDifference(source, target);
int propertyNr = 1;
for (Property p : properties) {
parameters.put(INPUT_PROPERTY + propertyNr, p.toString());
parameters.put(OUTPUT_PROPERTY + propertyNr, p.toString());
propertyNr++;
}
// logger.info("Self configuration: " + parameters);
if (parameters.size() == 0) {
return null;
}
return parameters;
}
/**
* Index all the resources in a Jena Model to ES
*
* @param model the model to index
* @param bulkRequest a BulkRequestBuilder
* @param getPropLabel if set to true all URI property values will be indexed as their label. The
* label is taken as the value of one of the properties set in {@link #uriDescriptionList}.
*/
private void addModelToES(Model model, BulkRequestBuilder bulkRequest, boolean getPropLabel) {
long startTime = System.currentTimeMillis();
long bulkLength = 0;
HashSet<Property> properties = new HashSet<Property>();
StmtIterator it = model.listStatements();
while (it.hasNext()) {
Statement st = it.nextStatement();
Property prop = st.getPredicate();
String property = prop.toString();
if (rdfPropList.isEmpty()
|| (isWhitePropList && rdfPropList.contains(property))
|| (!isWhitePropList && !rdfPropList.contains(property))
|| (normalizeProp.containsKey(property))) {
properties.add(prop);
}
}
ResIterator resIt = model.listSubjects();
while (resIt.hasNext()) {
Resource rs = resIt.nextResource();
Map<String, ArrayList<String>> jsonMap = getJsonMap(rs, properties, model, getPropLabel);
bulkRequest.add(
client.prepareIndex(indexName, typeName, rs.toString()).setSource(mapToString(jsonMap)));
bulkLength++;
// We want to execute the bulk for every DEFAULT_BULK_SIZE requests
if (bulkLength % EEASettings.DEFAULT_BULK_SIZE == 0) {
BulkResponse bulkResponse = bulkRequest.execute().actionGet();
// After executing, flush the BulkRequestBuilder.
bulkRequest = client.prepareBulk();
if (bulkResponse.hasFailures()) {
processBulkResponseFailure(bulkResponse);
}
}
}
// Execute remaining requests
if (bulkRequest.numberOfActions() > 0) {
BulkResponse response = bulkRequest.execute().actionGet();
// Handle failure by iterating through each bulk response item
if (response.hasFailures()) {
processBulkResponseFailure(response);
}
}
// Show time taken to index the documents
logger.info(
"Indexed {} documents on {}/{} in {} seconds",
bulkLength,
indexName,
typeName,
(System.currentTimeMillis() - startTime) / 1000.0);
}
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() ;
} */
}
/**
* @param uri : the URI to be dereferenced
* @param predicates : targeted predicates to be added to enrich the model
* @return This method retrieves list of values for targeted predicates for a URI-typed object for
* each URI-typed object, through content negotiation an open connection is done retrieving
* its predicates/values. An iteration is made over targeted predicates. For each predicate
* list of statements with the targeted predicate is retrieved and extracting its value in
* order to be added to hashmap<predicate,Value>
*/
@SuppressWarnings("unchecked")
private static HashMap<Property, List<RDFNode>> getURIInfo(RDFNode p) {
String uri = p.asResource().getURI();
// to store each predicate and its value
HashMap<Property, List<RDFNode>> resourceFocusedInfo = new HashMap<Property, List<RDFNode>>();
if (demo) { // Deserialize the results if exists (For Demo purpose)
if (useCache) {
try {
HashMap<String, List<String>> ser = new HashMap<String, List<String>>();
File file = new File("resourceFocusedInfo.ser");
if (file.exists()) {
ObjectInputStream in = new ObjectInputStream(new FileInputStream(file));
ser = (HashMap<String, List<String>>) in.readObject();
in.close();
// convert every object back from string
for (String prop : ser.keySet()) {
List<String> l = ser.get(prop);
List<RDFNode> nodes = new ArrayList<RDFNode>();
for (String n : l) {
nodes.add(ResourceFactory.createResource(n));
}
resourceFocusedInfo.put(ResourceFactory.createProperty(prop), nodes);
}
return resourceFocusedInfo;
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
// define local model to have the data of the URI and extract focused info through built sparql
// query
List<RDFNode> values = new ArrayList<RDFNode>();
try {
URLConnection conn = new URL(uri).openConnection();
conn.setRequestProperty("Accept", "application/rdf+xml");
conn.setRequestProperty("Accept-Language", "en");
Model model = ModelFactory.createDefaultModel();
InputStream in = conn.getInputStream();
model.read(in, null);
for (Property inputProperty : inputProperties) {
for (Statement st :
model.listStatements(model.getResource(uri), inputProperty, (RDFNode) null).toList()) {
RDFNode value = st.getObject();
if (value.isLiteral()) {
if (value.asLiteral().getLanguage().toLowerCase().equals("en")
|| value.asLiteral().getLanguage().toLowerCase().equals("")) {
values.add(value);
}
} else {
values.add(value);
}
}
resourceFocusedInfo.put(inputProperty, values);
values = new ArrayList<RDFNode>(); // create new list for new predicate
}
} catch (Exception e) {
e.printStackTrace();
}
if (demo) { // serialize the output (for Demo purpose)
try {
HashMap<String, List<String>> ser = new HashMap<String, List<String>>();
FileOutputStream fileOut = new FileOutputStream("resourceFocusedInfo.ser");
ObjectOutputStream out = new ObjectOutputStream(fileOut);
// convert to Serializabe Strings
for (Property prop : resourceFocusedInfo.keySet()) {
List<String> l = new ArrayList<String>();
for (RDFNode n : resourceFocusedInfo.get(prop)) {
l.add(n.toString());
}
ser.put(prop.toString(), l);
}
out.writeObject(ser);
out.close();
} catch (Exception e2) {
e2.printStackTrace();
}
}
return resourceFocusedInfo;
}
/**
* Get JSON map for a given resource by applying the river settings
*
* @param rs resource being processed
* @param properties properties to be indexed
* @param model model returned by the indexing query
* @param getPropLabel if set to true all URI property values will be indexed as their label. The
* label is taken as the value of one of the properties set in {@link #uriDescriptionList}.
* @return map of properties to be indexed for res
*/
private Map<String, ArrayList<String>> getJsonMap(
Resource rs, Set<Property> properties, Model model, boolean getPropLabel) {
Map<String, ArrayList<String>> jsonMap = new HashMap<String, ArrayList<String>>();
ArrayList<String> results = new ArrayList<String>();
if (addUriForResource) {
results.add("\"" + rs.toString() + "\"");
jsonMap.put("http://www.w3.org/1999/02/22-rdf-syntax-ns#about", results);
}
Set<String> rdfLanguages = new HashSet<String>();
for (Property prop : properties) {
NodeIterator niter = model.listObjectsOfProperty(rs, prop);
String property = prop.toString();
results = new ArrayList<String>();
String lang;
String currValue;
while (niter.hasNext()) {
RDFNode node = niter.next();
currValue = getStringForResult(node, getPropLabel);
if (addLanguage) {
if (node.isLiteral()) {
lang = node.asLiteral().getLanguage();
if (!lang.isEmpty()) {
rdfLanguages.add("\"" + lang + "\"");
}
}
}
String shortValue = currValue;
int currLen = currValue.length();
// Unquote string
if (currLen > 1) shortValue = currValue.substring(1, currLen - 1);
// If either whiteMap does contains shortValue
// or blackMap contains the value
// skip adding it to the index
boolean whiteMapCond =
whiteMap.containsKey(property) && !whiteMap.get(property).contains(shortValue);
boolean blackMapCond =
blackMap.containsKey(property) && blackMap.get(property).contains(shortValue);
if (whiteMapCond || blackMapCond) {
continue;
}
if (normalizeObj.containsKey(shortValue)) {
results.add("\"" + normalizeObj.get(shortValue) + "\"");
} else {
results.add(currValue);
}
}
// Do not index empty properties
if (results.isEmpty()) continue;
if (normalizeProp.containsKey(property)) {
property = normalizeProp.get(property);
if (jsonMap.containsKey(property)) {
jsonMap.get(property).addAll(results);
} else {
jsonMap.put(property, results);
}
} else {
jsonMap.put(property, results);
}
}
if (addLanguage) {
if (rdfLanguages.isEmpty() && !language.isEmpty()) rdfLanguages.add(language);
if (!rdfLanguages.isEmpty()) jsonMap.put("language", new ArrayList<String>(rdfLanguages));
}
for (Map.Entry<String, String> it : normalizeMissing.entrySet()) {
if (!jsonMap.containsKey(it.getKey())) {
ArrayList<String> res = new ArrayList<String>();
res.add("\"" + it.getValue() + "\"");
jsonMap.put(it.getKey(), res);
}
}
return jsonMap;
}