private boolean isObsolete(Resource ctx) throws SailException {
CloseableIteration<? extends Statement, SailException> stmts;
stmts = super.getStatements(null, null, null, true, ctx);
try {
while (stmts.hasNext()) {
Statement st = stmts.next();
URI pred = st.getPredicate();
Value obj = st.getObject();
String ns = pred.getNamespace();
if (Audit.NAMESPACE.equals(ns) || PROV.equals(ns) || AUDIT_2012.equals(ns)) continue;
if (RDF.SUBJECT.equals(pred) || RDF.PREDICATE.equals(pred) || RDF.OBJECT.equals(pred))
continue;
if (RDF.TYPE.equals(pred) && obj instanceof URI) {
ns = ((URI) obj).getNamespace();
if (Audit.NAMESPACE.equals(ns)
|| PROV.equals(ns)
|| AUDIT_2012.equals(ns)
|| RDF.NAMESPACE.equals(ns)) continue;
}
return false;
}
} finally {
stmts.close();
}
return true;
}
/**
* find properties with no domain or range defined and also add some generic elements like label
* or type
*
* @return
*/
List<OntologyElement> findHangingElements() throws Exception {
List<OntologyElement> elements = new ArrayList<OntologyElement>();
Set<String> properties = new HashSet<String>();
properties.add(RDFS.LABEL.toString());
properties.add(RDF.TYPE.toString());
String table = suggestionsHelper.getDatatypePropertiesNoDomain();
properties.addAll(StringUtil.fromStringToSet(table));
String thingUri = "http://www.w3.org/2002/07/owl#Thing";
properties.addAll(
luceneAnnotator.getDefinedPropertiesWhereClassIsADomain(thingUri, forceSuperClasses));
properties.addAll(
luceneAnnotator.getDefinedPropertiesWhereClassIsARange(thingUri, forceSuperClasses));
elements.addAll(returnPropertyElements(properties));
logger.info("Adding:" + properties.size() + " hanging properties");
Set<String> classes = new HashSet<String>();
classes.add(thingUri);
elements.addAll(returnClassElements(classes));
return elements;
}
/**
* Asynchronously explains why {@code instance} is an instance of {@code cl}
*
* @param instance The instance
* @param cl The class
* @param callback The {@link Callback} to execute after the explanation is done
*/
public void instance(Resource instance, Resource cl, Callback<Graph> callback) {
String query = selectQuery(instance.toString(), RDF.TYPE.stringValue(), cl.stringValue());
query(query, callback);
}
/**
* Explains why {@code instance} is an instance of {@code cl}
*
* @param instance The instance
* @param cl The class
* @return The explanation {@link org.openrdf.model.Graph Graph}
* @throws PelletClientException If there is an error or the {@code instance} is not an instance
* of {@code cl}
*/
public Graph instance(Resource instance, Resource cl) throws PelletClientException {
String query = selectQuery(instance.toString(), RDF.TYPE.stringValue(), cl.stringValue());
return query(query);
}
public class SesameDataSet {
// Log
private static Log log = LogFactory.getLog(SesameDataSet.class);
private Repository currentRepository = null;
// useful -local- constants
static RDFFormat NTRIPLES = RDFFormat.NTRIPLES;
static RDFFormat N3 = RDFFormat.N3;
static RDFFormat RDFXML = RDFFormat.RDFXML;
static String RDFTYPE = RDF.TYPE.toString();
/** In memory Sesame repository without inferencing */
public SesameDataSet() {
this(false);
}
/**
* In memory Sesame repository with optional inferencing
*
* @param inferencing
*/
public SesameDataSet(boolean inferencing) {
try {
if (inferencing) {
currentRepository =
new SailRepository(new ForwardChainingRDFSInferencer(new MemoryStore()));
} else {
currentRepository = new SailRepository(new MemoryStore());
}
currentRepository.initialize();
} catch (RepositoryException e) {
e.printStackTrace();
}
}
public SesameDataSet(String pathToDir, boolean inferencing) {
File f = new File(pathToDir);
try {
if (inferencing) {
currentRepository =
new SailRepository(new ForwardChainingRDFSInferencer(new NativeStore(f)));
} else {
currentRepository = new SailRepository(new NativeStore(f));
}
currentRepository.initialize();
} catch (RepositoryException e) {
e.printStackTrace();
}
}
public SesameDataSet(String sesameServer, String repositoryID) {
currentRepository = new HTTPRepository(sesameServer, repositoryID);
try {
currentRepository.initialize();
} catch (RepositoryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
/**
* Load data in specified graph (use default graph if contexts is null)
*
* @param filePath
* @param format
* @param contexts
*/
public void loadDataFromFile(String filePath, RDFFormat format, Resource... contexts) {
RepositoryConnection con;
try {
con = currentRepository.getConnection();
try {
// upload a file
File f = new File(filePath);
con.add(f, null, format, contexts);
} catch (RDFParseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (RepositoryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} finally {
try {
con.close();
} catch (RepositoryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
} catch (RepositoryException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
}
public void loadDataFromURL(String stringURL) {
RepositoryConnection con;
try {
con = currentRepository.getConnection();
try {
// upload a URL
URL url = new URL(stringURL);
con.add(url, null, RDFFormat.RDFXML);
} catch (RDFParseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (RepositoryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} finally {
try {
con.close();
} catch (RepositoryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
} catch (RepositoryException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
}
/**
* Literal factory
*
* @param s the literal value
* @param typeuri uri representing the type (generally xsd)
* @return
*/
public org.openrdf.model.Literal Literal(String s, URI typeuri) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
ValueFactory vf = con.getValueFactory();
if (typeuri == null) {
return vf.createLiteral(s);
} else {
return vf.createLiteral(s, typeuri);
}
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
return null;
}
}
/**
* Untyped Literal factory
*
* @param s the literal
* @return
*/
public org.openrdf.model.Literal Literal(String s) {
return Literal(s, null);
}
/**
* URIref factory
*
* @param uri
* @return
*/
public URI URIref(String uri) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
ValueFactory vf = con.getValueFactory();
return vf.createURI(uri);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
return null;
}
}
/**
* BNode factory
*
* @return
*/
public BNode bnode() {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
ValueFactory vf = con.getValueFactory();
return vf.createBNode();
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
return null;
}
}
/**
* Insert Triple/Statement into graph
*
* @param s subject uriref
* @param p predicate uriref
* @param o value object (URIref or Literal)
* @param contexts varArgs context objects (use default graph if null)
*/
public void add(Resource s, URI p, Value o, Resource... contexts) {
if (log.isDebugEnabled())
log.debug(
"[SesameDataSet:add] Add triple ("
+ s.stringValue()
+ ", "
+ p.stringValue()
+ ", "
+ o.stringValue()
+ ").");
try {
RepositoryConnection con = currentRepository.getConnection();
try {
ValueFactory myFactory = con.getValueFactory();
Statement st = myFactory.createStatement((Resource) s, p, (Value) o);
con.add(st, contexts);
con.commit();
} catch (Exception e) {
e.printStackTrace();
} finally {
con.close();
}
} catch (Exception e) {
// handle exception
}
}
public void remove(Resource s, URI p, Value o, Resource... context) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
ValueFactory myFactory = con.getValueFactory();
Statement st = myFactory.createStatement((Resource) s, p, (Value) o);
con.remove(st, context);
} finally {
con.close();
}
} catch (Exception e) {
// handle exception
}
}
/**
* Import RDF data from a string
*
* @param rdfstring string with RDF data
* @param format RDF format of the string (used to select parser)
*/
public void addString(String rdfstring, RDFFormat format) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
StringReader sr = new StringReader(rdfstring);
con.add(sr, "", format);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Import RDF data from a file
*
* @param location of file (/path/file) with RDF data
* @param format RDF format of the string (used to select parser)
*/
public void addFile(String filepath, RDFFormat format) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
con.add(new File(filepath), "", format);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Import data from URI source Request is made with proper HTTP ACCEPT header and will follow
* redirects for proper LOD source negotiation
*
* @param urlstring absolute URI of the data source
* @param format RDF format to request/parse from data source
*/
public void addURI(String urlstring, RDFFormat format) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
URL url = new URL(urlstring);
URLConnection uricon = (URLConnection) url.openConnection();
uricon.addRequestProperty("accept", format.getDefaultMIMEType());
InputStream instream = uricon.getInputStream();
con.add(instream, urlstring, format);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Dump RDF graph
*
* @param out output stream for the serialization
* @param outform the RDF serialization format for the dump
* @return
*/
public void dumpRDF(OutputStream out, RDFFormat outform) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
RDFWriter w = Rio.createWriter(outform, out);
con.export(w);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* dump RDF graph
*
* @param filePath destination file for the serialization
* @param outform the RDF serialization format for the dump
* @return
*/
public void dumpRDF(String filePath, RDFFormat outform) {
OutputStream output;
try {
output = new FileOutputStream(filePath);
dumpRDF(output, outform);
try {
output.close();
} catch (IOException e) {
e.printStackTrace();
}
} catch (FileNotFoundException e) {
e.printStackTrace();
}
}
public String printRDF(RDFFormat outform) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
ByteArrayOutputStream out = new ByteArrayOutputStream();
RDFWriter w = Rio.createWriter(outform, out);
con.export(w);
String result = new String(out.toByteArray(), "UTF-8");
return result;
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
/**
* Convenience URI import for RDF/XML sources
*
* @param urlstring absolute URI of the data source
*/
public void addURI(String urlstring) {
addURI(urlstring, RDFFormat.RDFXML);
}
/**
* Tuple pattern query - find all statements with the pattern, where null is a wildcard
*
* @param s subject (null for wildcard)
* @param p predicate (null for wildcard)
* @param o object (null for wildcard)
* @param contexts varArgs contexts (use default graph if null)
* @return serialized graph of results
*/
public List<Statement> tuplePattern(Resource s, URI p, Value o, Resource... contexts) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
RepositoryResult<Statement> repres = con.getStatements(s, p, o, true, contexts);
ArrayList<Statement> reslist = new ArrayList<Statement>();
while (repres.hasNext()) {
reslist.add(repres.next());
}
return reslist;
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
/**
* Execute a CONSTRUCT/DESCRIBE SPARQL query against the graphs
*
* @param qs CONSTRUCT or DESCRIBE SPARQL query
* @param format the serialization format for the returned graph
* @return serialized graph of results
*/
public String runSPARQL(String qs, RDFFormat format) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
GraphQuery query = con.prepareGraphQuery(org.openrdf.query.QueryLanguage.SPARQL, qs);
StringWriter stringout = new StringWriter();
RDFWriter w = Rio.createWriter(format, stringout);
query.evaluate(w);
return stringout.toString();
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
/**
* Execute a SELECT SPARQL query against the graphs
*
* @param qs SELECT SPARQL query
* @return list of solutions, each containing a hashmap of bindings
*/
public List<HashMap<String, Value>> runSPARQL(String qs) {
try {
RepositoryConnection con = currentRepository.getConnection();
try {
TupleQuery query = con.prepareTupleQuery(org.openrdf.query.QueryLanguage.SPARQL, qs);
TupleQueryResult qres = query.evaluate();
ArrayList<HashMap<String, Value>> reslist = new ArrayList<HashMap<String, Value>>();
while (qres.hasNext()) {
BindingSet b = qres.next();
Set<String> names = b.getBindingNames();
HashMap<String, Value> hm = new HashMap<String, Value>();
for (String n : names) {
hm.put(n, b.getValue(n));
}
reslist.add(hm);
}
return reslist;
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
/**
* Execute CONSTRUCT/DESCRIBE SPARQL queries against the graph from a SPARQL request file. This
* file contains only one request. // TODO : up this limit
*
* @param pathToFile path to SPARQL request file
* @return list of solutions, each containing a hashmap of bindings
*/
public String runSPARQLFromFile(String pathToSPARQLFile, RDFFormat format) {
// Read SPARQL request
String s = null;
StringBuffer sb = new StringBuffer();
try {
FileReader fr = new FileReader(new File(pathToSPARQLFile));
// be sure to not have line starting with "--" or "/*" or any other
// non aplhabetical character
BufferedReader br = new BufferedReader(fr);
while ((s = br.readLine()) != null) {
sb.append(s);
}
br.close();
} catch (Exception e) {
e.printStackTrace();
}
if (log.isDebugEnabled())
log.debug("[Graph:runSPARQLFromFile] SPARQL query : " + sb.toString());
return runSPARQL(sb.toString(), format);
}
/**
* Execute SELECT SPARQL queries against the graph from a SPARQL request file. This file contains
* only one request. // TODO : up this limit
*
* @param pathToFile path to SPARQL request file
* @return list of solutions, each containing a hashmap of bindings
*/
public List<HashMap<String, Value>> runSPARQLFromFile(String pathToSPARQLFile) {
// Read SPARQL request
String s = null;
StringBuffer sb = new StringBuffer();
try {
FileReader fr = new FileReader(new File(pathToSPARQLFile));
// be sure to not have line starting with "--" or "/*" or any other
// non aplhabetical character
BufferedReader br = new BufferedReader(fr);
while ((s = br.readLine()) != null) {
sb.append(s);
}
br.close();
} catch (Exception e) {
e.printStackTrace();
}
if (log.isDebugEnabled())
log.debug("[Graph:runSPARQLFromFile] SPARQL query : " + sb.toString());
return runSPARQL(sb.toString());
}
/**
* Close current repository.
*
* @throws RepositoryException
*/
public void closeRepository() throws RepositoryException {
currentRepository.shutDown();
}
/** Return the number of triples in the repository. */
public int getSize() {
return tuplePattern(null, null, null).size();
}
public String toString() {
String result = "{[SimpleGraph:toString] triples = ";
List<Statement> triples = tuplePattern(null, null, null);
for (Object o : triples) result += o + System.getProperty("line.separator");
result += "}";
return result;
}
}
public class SimpleSesameGraph {
Repository therepository = null;
// useful -local- constants
static RDFFormat NTRIPLES = RDFFormat.NTRIPLES;
static RDFFormat N3 = RDFFormat.N3;
static RDFFormat RDFXML = RDFFormat.RDFXML;
static String RDFTYPE = RDF.TYPE.toString();
/** In memory Sesame repository without type inferencing */
public SimpleSesameGraph() {
this(false);
}
/**
* In memory Sesame Repository with optional inferencing
*
* @param inferencing determines whether we load the inferencer or not
*/
public SimpleSesameGraph(boolean inferencing) {
try {
if (inferencing) {
therepository = new SailRepository(new ForwardChainingRDFSInferencer(new MemoryStore()));
} else {
therepository = new SailRepository(new MemoryStore());
}
therepository.initialize();
} catch (RepositoryException e) {
e.printStackTrace();
}
}
/**
* Literal factory
*
* @param s the literal value
* @param typeuri uri representing the type (generally xsd)
* @return Literal type
*/
public org.openrdf.model.Literal Literal(String s, URI typeuri) {
try {
RepositoryConnection con = therepository.getConnection();
try {
ValueFactory vf = con.getValueFactory();
if (typeuri == null) {
return vf.createLiteral(s);
} else {
return vf.createLiteral(s, typeuri);
}
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
return null;
}
}
/**
* Untyped Literal factory
*
* @param s the literal
* @return Literal value
*/
public org.openrdf.model.Literal Literal(String s) {
return Literal(s, null);
}
/**
* UR Iref factory
*
* @param uri to build
* @return URI resource
*/
public URI URIref(String uri) {
try {
RepositoryConnection con = therepository.getConnection();
try {
ValueFactory vf = con.getValueFactory();
return vf.createURI(uri);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
return null;
}
}
/**
* BNode factory
*
* @return BNode a blank node
*/
public BNode bnode() {
try {
RepositoryConnection con = therepository.getConnection();
try {
ValueFactory vf = con.getValueFactory();
return vf.createBNode();
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
return null;
}
}
/**
* dump RDF graph
*
* @param out output stream for the serialization
* @param outform the RDF serialization format for the dump
*/
public void dumpRDF(OutputStream out, RDFFormat outform) {
try {
RepositoryConnection con = therepository.getConnection();
try {
RDFWriter w = Rio.createWriter(outform, out);
con.export(w);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Convenience URI import for RDF/XML sources
*
* @param urlstring absolute URI of the data source
*/
public void addURI(String urlstring) {
addURI(urlstring, RDFFormat.RDFXML);
}
/**
* Import data from URI source Request is made with proper HTTP ACCEPT header and will follow
* redirects for proper LOD source negotiation
*
* @param urlstring absolute URI of the data source
* @param format RDF format to request/parse from data source
*/
public void addURI(String urlstring, RDFFormat format) {
try {
RepositoryConnection con = therepository.getConnection();
try {
URL url = new URL(urlstring);
URLConnection uricon = url.openConnection();
uricon.addRequestProperty("accept", format.getDefaultMIMEType());
InputStream instream = uricon.getInputStream();
con.add(instream, urlstring, format);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Import RDF data from a string
*
* @param rdfstring string with RDF data
* @param format RDF format of the string (used to select parser)
*/
public void addString(String rdfstring, RDFFormat format) {
try {
RepositoryConnection con = therepository.getConnection();
try {
StringReader sr = new StringReader(rdfstring);
con.add(sr, "", format);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Import RDF data from a file
*
* @param filepath of file (/path/file) with RDF data
* @param format RDF format of the string (used to select parser)
*/
public void addFile(String filepath, RDFFormat format) {
try {
RepositoryConnection con = therepository.getConnection();
try {
con.add(new File(filepath), "", format);
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Insert Triple/Statement into graph
*
* @param s subject uriref
* @param p predicate uriref
* @param o value object (URIref or Literal)
*/
public void add(URI s, URI p, Value o) {
try {
RepositoryConnection con = therepository.getConnection();
try {
ValueFactory myFactory = con.getValueFactory();
Statement st = myFactory.createStatement(s, p, o);
con.add(st);
} finally {
con.close();
}
} catch (Exception e) {
// handle exception
}
}
/**
* Tuple pattern query - find all statements with the pattern, where null is a wild card
*
* @param s subject (null for wildcard)
* @param p predicate (null for wildcard)
* @param o object (null for wildcard)
* @return serialized graph of results
*/
public List<Statement> tuplePattern(URI s, URI p, Value o) {
try {
RepositoryConnection con = therepository.getConnection();
try {
RepositoryResult<Statement> repres = con.getStatements(s, p, o, true);
ArrayList<Statement> reslist = new ArrayList<Statement>();
while (repres.hasNext()) {
reslist.add(repres.next());
}
return reslist;
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
/**
* Execute a CONSTRUCT/DESCRIBE SPARQL query against the graph
*
* @param qs CONSTRUCT or DESCRIBE SPARQL query
* @param format the serialization format for the returned graph
* @return serialized graph of results
*/
public String runSPARQL(String qs, RDFFormat format) {
try {
RepositoryConnection con = therepository.getConnection();
try {
GraphQuery query = con.prepareGraphQuery(org.openrdf.query.QueryLanguage.SPARQL, qs);
StringWriter stringout = new StringWriter();
RDFWriter w = Rio.createWriter(format, stringout);
query.evaluate(w);
return stringout.toString();
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
/**
* Execute a SELECT SPARQL query against the graph
*
* @param qs SELECT SPARQL query
* @return list of solutions, each containing a hashmap of bindings
*/
public List<HashMap<Object, Value>> runSPARQL(String qs) {
try {
RepositoryConnection con = therepository.getConnection();
try {
TupleQuery query = con.prepareTupleQuery(org.openrdf.query.QueryLanguage.SPARQL, qs);
TupleQueryResult qres = query.evaluate();
ArrayList<HashMap<Object, Value>> reslist = new ArrayList<HashMap<Object, Value>>();
while (qres.hasNext()) {
BindingSet b = qres.next();
Set<String> names = b.getBindingNames();
HashMap<Object, Value> hm = new HashMap<Object, Value>();
for (Object n : names) {
hm.put(n, b.getValue((String) n));
}
reslist.add(hm);
}
return reslist;
} finally {
con.close();
}
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
public static void main(String[] args) {
// create a graph with type inferencing
SimpleSesameGraph g = new SimpleSesameGraph(true);
// //load the film schema and the example data
// g.addFile("../roadstead_ontologies/film-ontology.owl", SimpleSesameGraph.RDFXML);
// try loading the geopolitical ontology
g.addURI("http://aims.fao.org/aos/geopolitical.owl");
// List<HashMap<Object, Value>> solutions = g.runSPARQL("SELECT ?who WHERE { " +
// "?who <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
// <http://roadstead.org/film#Person> ." +
// "}");
/*
Here we are looking for the names of all the things with a name
*/
List<HashMap<Object, Value>> solutions =
g.runSPARQL(
"SELECT ?name WHERE { "
+ "?what <http://aims.fao.org/aos/geopolitical.owl#territory> ?name ."
+ "?what <http://aims.fao.org/aos/geopolitical.owl#nameListEN> ?name ."
+ "}");
for (HashMap<Object, Value> object : solutions) {
for (Value value : object.values()) {
System.out.println("country: " + value.stringValue());
}
}
}
}
