litvinovg/vitro
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

development

Browse source
This commit is contained in:
stellamit 2012-05-10 20:41:49 +00:00
parent 423ec922d8
commit 0219f927ba
4 changed files with 561 additions and 10 deletions
Download patch file Download diff file Expand all files Collapse all files

2
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/ModelChange.java
View file

@ -15,7 +15,7 @@ public interface ModelChange {
ADD, REMOVE ADD, REMOVE
} }
abstract InputStream getSerializedModel(); public InputStream getSerializedModel();
public void setSerializedModel(InputStream serializedModel); public void setSerializedModel(InputStream serializedModel);

53
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/RDFService.java
View file

@ -3,6 +3,7 @@
package edu.cornell.mannlib.vitro.webapp.rdfservice; package edu.cornell.mannlib.vitro.webapp.rdfservice;
import java.io.InputStream; import java.io.InputStream;
import java.io.OutputStream;
import java.util.List; import java.util.List;
/* /*
@ -22,13 +23,16 @@ public interface RDFService {
/** /**
* Perform a series of additions to and or removals from specified graphs * Perform a series of additions to and or removals from specified graphs
* in the RDF store. For each change preConditionSparql will be executed * in the RDF store. preConditionSparql will be executed against the
* before the update is made and if it returns a non-empty result, no updates * union of all the graphs in the knowledge base before any updates are made.
* will be made. The same preConditionSparql is used for each change/graph pair. * If the precondition query returns a non-empty result, no updates
* will be made.
* *
* @param ChangeSet - a set of changes to be performed on the RDF store. * @param ChangeSet - a set of changes to be performed on the RDF store.
*
* @return boolean - indicates whether the precondition was satisfied
*/ */
public void changeSetUpdate(ChangeSet changeSet) throws RDFServiceException; public boolean changeSetUpdate(ChangeSet changeSet) throws RDFServiceException;
/** /**
* If the given individual already exists in the default graph, throws an * If the given individual already exists in the default graph, throws an
@ -52,16 +56,49 @@ public interface RDFService {
public void newIndividual(String individualURI, String individualTypeURI, String graphURI) throws RDFServiceException; public void newIndividual(String individualURI, String individualTypeURI, String graphURI) throws RDFServiceException;
/** /**
* Performs a SPARQL query against the knowledge base. The query may have * Performs a SPARQL construct query against the knowledge base. The query may have
* an embedded graph identifier.
*
* @param String query - the SPARQL query to be executed against the RDF store
* @param RDFService.ModelSerializationFormat resultFormat - type of serialization for RDF result of the SPARQL query
* @param OutputStream outputStream - the result of the query
*
*/
public InputStream sparqlConstructQuery(String query, RDFService.ModelSerializationFormat resultFormat) throws RDFServiceException;
/**
* Performs a SPARQL describe query against the knowledge base. The query may have
* an embedded graph identifier. * an embedded graph identifier.
* *
* @param String query - the SPARQL query to be executed against the RDF store * @param String query - the SPARQL query to be executed against the RDF store
* @param RDFService.SPARQLQueryType queryType - the type of SPARQL query (SELECT, CONSTRUCT, DESCRIBE, ASK)
* @param RDFService.ModelSerializationFormat resultFormat - type of serialization for RDF result of the SPARQL query * @param RDFService.ModelSerializationFormat resultFormat - type of serialization for RDF result of the SPARQL query
* *
* @return InputStream - the result of the SPARQL query * @return InputStream - the result of the query
*
*/ */
public InputStream sparqlConstructQuery(String query, RDFService.SPARQLQueryType queryType, RDFService.ModelSerializationFormat resultFormat) throws RDFServiceException; public InputStream sparqlDescribeQuery(String query, RDFService.ModelSerializationFormat resultFormat) throws RDFServiceException;
/**
* Performs a SPARQL select query against the knowledge base. The query may have
* an embedded graph identifier.
*
* @param String query - the SPARQL query to be executed against the RDF store
*
* @return InputStream - the result of the query
*
*/
public InputStream sparqlSelectQuery(String query) throws RDFServiceException;
/**
* Performs a SPARQL ASK query against the knowledge base. The query may have
* an embedded graph identifier.
*
* @param String query - the SPARQL query to be executed against the RDF store
*
* @return boolean - the result of the SPARQL query
*/
public boolean sparqlAskQuery(String query) throws RDFServiceException;
/** /**
* Get a list of all the graph URIs in the RDF store. * Get a list of all the graph URIs in the RDF store.

4
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/RDFServiceException.java
View file

@ -6,4 +6,8 @@ public class RDFServiceException extends Exception {
super(); super();
} }
public RDFServiceException(String message) {
super(message);
}
} }

510
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceImpl.java Normal file
View file

@ -0,0 +1,510 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.rdfservice.impl;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.InputStream;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.openrdf.query.MalformedQueryException;
import org.openrdf.query.QueryLanguage;
import org.openrdf.query.Update;
import org.openrdf.query.UpdateExecutionException;
import org.openrdf.repository.Repository;
import org.openrdf.repository.RepositoryConnection;
import org.openrdf.repository.RepositoryException;
import org.openrdf.repository.http.HTTPRepository;
import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.graph.Triple;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
/*
* API to write, read, and update Vitro's RDF store, with support
* to allow listening, logging and auditing.
*/
public class RDFServiceImpl implements RDFService {
private static final Log log = LogFactory.getLog(RDFServiceImpl.class);
private String endpointURI;
private Repository repository;
/**
* Returns an RDFService for a remote repository
* @param endpointURI
*/
public RDFServiceImpl(String endpointURI) {
this.endpointURI = endpointURI;
this.repository = new HTTPRepository(endpointURI);
}
/**
* Perform a series of additions to and or removals from specified graphs
* in the RDF store. preConditionSparql will be executed against the
* union of all the graphs in the knowledge base before any updates are made.
* If the precondition query returns a non-empty result, no updates
* will be made.
*
* @param ChangeSet - a set of changes to be performed on the RDF store.
*
* @return boolean - indicates whether the precondition was satisfied
*/
@Override
public boolean changeSetUpdate(ChangeSet changeSet) throws RDFServiceException {
if (!isPreconditionSatisfied(changeSet.getPreconditionQuery(), changeSet.getPreconditionQueryType())) {
return false;
}
Iterator<ModelChange> csIt = changeSet.getModelChanges().iterator();
while (csIt.hasNext()) {
ModelChange modelChange = csIt.next();
if (modelChange.getOperation() == ModelChange.Operation.ADD) {
performAdd(modelChange);
} else if (modelChange.getOperation() == ModelChange.Operation.REMOVE) {
performRemove(modelChange);
} else {
log.error("unrecognized operation type");
}
}
return true;
}
/**
* If the given individual already exists in the default graph, throws an
* RDFServiceException, otherwise adds one type assertion to the default
* graph.
*
* @param String individualURI - URI of the individual to be added
* @param String individualTypeURI - URI of the type for the individual
*/
@Override
public void newIndividual(String individualURI,
String individualTypeURI) throws RDFServiceException {
}
/**
* If the given individual already exists in the given graph, throws an
* RDFServiceException, otherwise adds one type assertion to the given
* graph.
*
* @param String individualURI - URI of the individual to be added
* @param String individualTypeURI - URI of the type for the individual
* @param String graphURI - URI of the graph to which to add the individual
*/
@Override
public void newIndividual(String individualURI,
String individualTypeURI,
String graphURI) throws RDFServiceException {
}
/**
* Performs a SPARQL construct query against the knowledge base. The query may have
* an embedded graph identifier.
*
* @param String query - the SPARQL query to be executed against the RDF store
* @param RDFService.ModelSerializationFormat resultFormat - type of serialization for RDF result of the SPARQL query
* @param OutputStream outputStream - the result of the query
*
*/
@Override
public InputStream sparqlConstructQuery(String queryStr,
RDFServiceImpl.ModelSerializationFormat resultFormat) throws RDFServiceException {
Model model = ModelFactory.createDefaultModel();
Query query = QueryFactory.create(queryStr);
QueryExecution qe = QueryExecutionFactory.sparqlService(endpointURI, query);
try {
qe.execConstruct(model);
} finally {
qe.close();
}
ByteArrayOutputStream serializedModel = new ByteArrayOutputStream();
model.write(serializedModel,getSerializationFormatString(resultFormat));
InputStream result = new ByteArrayInputStream(serializedModel.toByteArray());
return result;
}
/**
* Performs a SPARQL describe query against the knowledge base. The query may have
* an embedded graph identifier.
*
* @param String query - the SPARQL query to be executed against the RDF store
* @param RDFService.ModelSerializationFormat resultFormat - type of serialization for RDF result of the SPARQL query
*
* @return InputStream - the result of the query
*
*/
@Override
public InputStream sparqlDescribeQuery(String queryStr,
RDFServiceImpl.ModelSerializationFormat resultFormat) throws RDFServiceException {
Model model = ModelFactory.createDefaultModel();
Query query = QueryFactory.create(queryStr);
QueryExecution qe = QueryExecutionFactory.sparqlService(endpointURI, query);
try {
qe.execDescribe(model);
} finally {
qe.close();
}
ByteArrayOutputStream serializedModel = new ByteArrayOutputStream();
model.write(serializedModel,getSerializationFormatString(resultFormat));
InputStream result = new ByteArrayInputStream(serializedModel.toByteArray());
return result;
}
/**
* Performs a SPARQL select query against the knowledge base. The query may have
* an embedded graph identifier.
*
* @param String query - the SPARQL query to be executed against the RDF store
*
* @return InputStream - the result of the query
*
*/
@Override
public InputStream sparqlSelectQuery(String queryStr) throws RDFServiceException {
Query query = QueryFactory.create(queryStr);
QueryExecution qe = QueryExecutionFactory.sparqlService(endpointURI, query);
try {
ResultSet resultSet = qe.execSelect();
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
ResultSetFormatter.out(outputStream,resultSet);
InputStream result = new ByteArrayInputStream(outputStream.toByteArray());
return result;
} finally {
qe.close();
}
}
/**
* Performs a SPARQL ASK query against the knowledge base. The query may have
* an embedded graph identifier.
*
* @param String query - the SPARQL query to be executed against the RDF store
*
* @return boolean - the result of the SPARQL query
*/
@Override
public boolean sparqlAskQuery(String queryStr) throws RDFServiceException {
Query query = QueryFactory.create(queryStr);
QueryExecution qe = QueryExecutionFactory.sparqlService(endpointURI, query);
try {
return qe.execAsk();
} finally {
qe.close();
}
}
/**
* Get a list of all the graph URIs in the RDF store.
*
* @return List<String> - list of all the graph URIs in the RDF store
*/
@Override
public List<String> getGraphURIs() throws RDFServiceException {
List<String> list = null;
return list;
}
/**
* TODO - what is the definition of this method?
* @return
*/
@Override
public void getGraphMetadata() throws RDFServiceException {
}
/**
* Get the URI of the default write graph
*
* @return String URI of default write graph
*/
@Override
public String getDefaultWriteGraphURI() throws RDFServiceException {
String graphURI = null;
return graphURI;
}
/**
* Get the URI of the default read graph
*
* @return String URI of default read graph
*/
@Override
public String getDefaultReadGraphURI() throws RDFServiceException {
String graphURI = null;
return graphURI;
}
/**
* Register a listener to listen to changes in any graph in
* the RDF store.
*
* @return String URI of default read graph
*/
@Override
public void registerListener(ChangeListener changeListener) throws RDFServiceException {
}
/**
* Unregister a listener to listen to changes in any graph in
* the RDF store.
*
* @return String URI of default read graph
*/
@Override
public void unregisterListener(ChangeListener changeListener) throws RDFServiceException {
}
/**
* Create a ChangeSet object
*
* @return a ChangeSet object
*/
@Override
public ChangeSet manufactureChangeSet() {
return new ChangeSetImpl();
}
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// Non override methods below
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
protected String getEndpointURI() {
return endpointURI;
}
protected RepositoryConnection getConnection() {
try {
return this.repository.getConnection();
} catch (RepositoryException e) {
throw new RuntimeException(e);
}
}
protected void executeUpdate(String updateString) {
try {
RepositoryConnection conn = getConnection();
try {
Update u = conn.prepareUpdate(QueryLanguage.SPARQL, updateString);
u.execute();
} catch (MalformedQueryException e) {
throw new RuntimeException(e);
} catch (UpdateExecutionException e) {
log.error(e,e);
log.error("Update command: \n" + updateString);
throw new RuntimeException(e);
} finally {
conn.close();
}
} catch (RepositoryException re) {
throw new RuntimeException(re);
}
}
protected void addTriple(Triple t, String graphURI) {
//log.info("adding " + t);
String updateString = "INSERT DATA { " + ((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "" )
+ sparqlNodeUpdate(t.getSubject(), "") + " "
+ sparqlNodeUpdate(t.getPredicate(), "") + " "
+ sparqlNodeUpdate(t.getObject(), "") + " } "
+ ((graphURI != null) ? " } " : "");
//log.info(updateString);
executeUpdate(updateString);
}
protected void removeTriple(Triple t, String graphURI) {
String updateString = "DELETE DATA { " + ((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "" )
+ sparqlNodeUpdate(t.getSubject(), "") + " "
+ sparqlNodeUpdate(t.getPredicate(), "") + " "
+ sparqlNodeUpdate(t.getObject(), "") + " } "
+ ((graphURI != null) ? " } " : "");
//log.info(updateString);
executeUpdate(updateString);
}
protected boolean isPreconditionSatisfied(String query,
RDFService.SPARQLQueryType queryType)
throws RDFServiceException {
Model model = ModelFactory.createDefaultModel();
switch (queryType) {
case DESCRIBE:
model.read(sparqlDescribeQuery(query,RDFService.ModelSerializationFormat.N3), null);
return !model.isEmpty();
case CONSTRUCT:
model.read(sparqlConstructQuery(query,RDFService.ModelSerializationFormat.N3), null);
return !model.isEmpty();
case SELECT:
return sparqlSelectQueryHasResults(query);
case ASK:
return sparqlAskQuery(query);
default:
throw new RDFServiceException("unrecognized SPARQL query type");
}
}
protected boolean sparqlSelectQueryHasResults(String queryStr) throws RDFServiceException {
Query query = QueryFactory.create(queryStr);
QueryExecution qe = QueryExecutionFactory.sparqlService(endpointURI, query);
try {
ResultSet resultSet = qe.execSelect();
return resultSet.hasNext();
} finally {
qe.close();
}
}
protected void performAdd(ModelChange modelChange) throws RDFServiceException {
Model model = ModelFactory.createDefaultModel();
model.read(modelChange.getSerializedModel(),getSerializationFormatString(modelChange.getSerializationFormat()));
StmtIterator stmtIt = model.listStatements();
while (stmtIt.hasNext()) {
Statement stmt = stmtIt.next();
Triple triple = new Triple(stmt.getSubject().asNode(), stmt.getPredicate().asNode(), stmt.getObject().asNode());
addTriple(triple, modelChange.getGraphURI());
}
}
protected void performRemove(ModelChange modelChange) throws RDFServiceException {
Model model = ModelFactory.createDefaultModel();
model.read(modelChange.getSerializedModel(),getSerializationFormatString(modelChange.getSerializationFormat()));
StmtIterator stmtIt = model.listStatements();
while (stmtIt.hasNext()) {
Statement stmt = stmtIt.next();
Triple triple = new Triple(stmt.getSubject().asNode(), stmt.getPredicate().asNode(), stmt.getObject().asNode());
removeTriple(triple, modelChange.getGraphURI());
}
}
protected static String getSerializationFormatString(RDFService.ModelSerializationFormat format) {
switch (format) {
case RDFXML:
return "RDFXML";
case N3:
return "N3";
default:
log.error("unexpected format in getFormatString");
return null;
}
}
protected static String sparqlNodeUpdate(Node node, String varName) {
if (node.isBlank()) {
return "_:" + node.getBlankNodeLabel().replaceAll("\\W", "");
} else {
return sparqlNode(node, varName);
}
}
protected static String sparqlNode(Node node, String varName) {
if (node == null || node.isVariable()) {
return varName;
} else if (node.isBlank()) {
return "<fake:blank>"; // or throw exception?
} else if (node.isURI()) {
StringBuffer uriBuff = new StringBuffer();
return uriBuff.append("<").append(node.getURI()).append(">").toString();
} else if (node.isLiteral()) {
StringBuffer literalBuff = new StringBuffer();
literalBuff.append("\"");
pyString(literalBuff, node.getLiteralLexicalForm());
literalBuff.append("\"");
if (node.getLiteralDatatypeURI() != null) {
literalBuff.append("^^<").append(node.getLiteralDatatypeURI()).append(">");
} else if (node.getLiteralLanguage() != null && node.getLiteralLanguage() != "") {
literalBuff.append("@").append(node.getLiteralLanguage());
}
return literalBuff.toString();
} else {
return varName;
}
}
// see http://www.python.org/doc/2.5.2/ref/strings.html
// or see jena's n3 grammar jena/src/com/hp/hpl/jena/n3/n3.g
protected static void pyString(StringBuffer sbuff, String s) {
for (int i = 0; i < s.length(); i++) {
char c = s.charAt(i);
// Escape escapes and quotes
if (c == '\\' || c == '"' )
{
sbuff.append('\\') ;
sbuff.append(c) ;
continue ;
}
// Whitespace
if (c == '\n'){ sbuff.append("\\n");continue; }
if (c == '\t'){ sbuff.append("\\t");continue; }
if (c == '\r'){ sbuff.append("\\r");continue; }
if (c == '\f'){ sbuff.append("\\f");continue; }
if (c == '\b'){ sbuff.append("\\b");continue; }
if( c == 7 ) { sbuff.append("\\a");continue; }
// Output as is (subject to UTF-8 encoding on output that is)
sbuff.append(c) ;
}
}
}