rfe8812: Jena Graph compliance tests

Added AGGraphTest to exercise 57 tests for Jena Graph compliance,
along with supporting code changes that allow 55 of them to pass.
The remaining 2 tests will be addressed in a future commit.

Tests added for:  AGGraphTest for rfe8812
make test-suite run? no
make prepush run? yes (in agraph-java-client)

src/com/franz/agraph/jena/AGBulkUpdateHandler.java

@@ -17,6 +17,7 @@
 
 import com.franz.agraph.repository.AGValueFactory;
 import com.hp.hpl.jena.graph.BulkUpdateHandler;
+import com.hp.hpl.jena.graph.Graph;
 import com.hp.hpl.jena.graph.Triple;
 import com.hp.hpl.jena.graph.impl.SimpleBulkUpdateHandler;
 
@@ -63,4 +64,14 @@ protected void delete(List<Triple> triples, boolean notify) {
 		if (notify)
 			manager.notifyDeleteList(graph, triples);
 	}
+
+	@Override
+	public void removeAll() {
+		try {
+			graph.getConnection().clear(graph.getGraphContext());
+			notifyRemoveAll(); 
+		} catch (RepositoryException e) {
+			throw new RuntimeException(e);
+		}
+	}
 }

src/com/franz/agraph/jena/AGCapabilities.java

@@ -0,0 +1,12 @@
+package com.franz.agraph.jena;
+
+import com.hp.hpl.jena.graph.Capabilities;
+import com.hp.hpl.jena.graph.impl.AllCapabilities;
+
+public class AGCapabilities extends AllCapabilities implements Capabilities {
+
+	@Override
+	// TODO: "true" would require support for D-entailment 
+    public boolean handlesLiteralTyping() { return false; }
+
+}

src/com/franz/agraph/jena/AGGraph.java

@@ -8,6 +8,8 @@
 
 package com.franz.agraph.jena;
 
+import java.util.ArrayList;
+
 import org.openrdf.http.protocol.UnauthorizedException;
 import org.openrdf.model.Resource;
 import org.openrdf.model.Statement;
@@ -21,7 +23,9 @@
 import com.franz.agraph.repository.AGValueFactory;
 import com.franz.util.Closeable;
 import com.hp.hpl.jena.graph.BulkUpdateHandler;
+import com.hp.hpl.jena.graph.Capabilities;
 import com.hp.hpl.jena.graph.Graph;
+import com.hp.hpl.jena.graph.GraphUtil;
 import com.hp.hpl.jena.graph.Node;
 import com.hp.hpl.jena.graph.TransactionHandler;
 import com.hp.hpl.jena.graph.Triple;
@@ -30,6 +34,7 @@
 import com.hp.hpl.jena.shared.AddDeniedException;
 import com.hp.hpl.jena.shared.DeleteDeniedException;
 import com.hp.hpl.jena.shared.PrefixMapping;
+import com.hp.hpl.jena.util.iterator.ClosableIterator;
 import com.hp.hpl.jena.util.iterator.ExtendedIterator;
 
 public class AGGraph extends GraphBase implements Graph, Closeable {
@@ -59,6 +64,12 @@ Node getGraphNode() {
 		return graphNode;
 	}
 
+	public String getGraphName() {
+		if (graphNode == null)
+			return "default-graph";
+		return graphNode.toString();
+	}
+
 	Resource getGraphContext() {
 		return context;
 	}
@@ -67,15 +78,22 @@ AGRepositoryConnection getConnection() {
 		return conn;
 	}
 
-	@Override
-	public void close() {
-	}
+	//@Override
+	//public void close() {
+	//}
 
 	@Override
 	public BulkUpdateHandler getBulkUpdateHandler() {
 		return new AGBulkUpdateHandler(this);
 	}
 
+    @Override
+    public Capabilities getCapabilities()
+    { 
+    	if (capabilities == null) capabilities = new AGCapabilities();
+    	return capabilities;
+    }
+
 	@Override
 	public PrefixMapping getPrefixMapping() {
 		return new AGPrefixMapping(this);
@@ -86,12 +104,38 @@ public TransactionHandler getTransactionHandler() {
 		return new AGTransactionHandler(this);
 	}
 
-	@Override
+	/*@Override
 	public String toString() {
 		if (graphNode == null)
 			return "default-graph";
 		return graphNode.toString();
-	}
+	}*/
+	@Override
+    public String toString() 
+        { return toString(getGraphName()+(closed ? " (closed) " : " (size: " + graphBaseSize() + ")."),this); }
+
+    /**
+    Answer a human-consumable representation of <code>that</code>. The 
+    string <code>prefix</code> will appear near the beginning of the string. Nodes
+    may be prefix-compressed using <code>that</code>'s prefix-mapping. This
+    default implementation will display all the triples exposed by the graph (ie
+    including reification triples if it is Standard).
+*/
+public static String toString( String prefix, Graph that )
+   {
+   //PrefixMapping pm = that.getPrefixMapping();
+	StringBuffer b = new StringBuffer( prefix + " {" );
+	String gap = "";
+	ClosableIterator<Triple> it = GraphUtil.findAll( that );
+	while (it.hasNext()) 
+       {
+		b.append( gap );
+		gap = "; ";
+		b.append( it.next().toString() );
+	    } 
+	b.append( "}" );
+	return b.toString();
+  }
 
 	public Dataset getDataset() {
 		DatasetImpl dataset = new DatasetImpl();
@@ -114,13 +158,22 @@ public Dataset getDataset() {
 	protected ExtendedIterator<Triple> graphBaseFind(TripleMatch m) {
 		RepositoryResult<Statement> result;
 		try {
-			result = conn.getStatements(vf.asResource(m.getMatchSubject()), vf
-					.asURI(m.getMatchPredicate()), vf.asValue(m
+			// TODO: allow arbitrary values in subject and predicate positions? 
+			Node s = m.getMatchSubject();
+			Node p = m.getMatchPredicate();
+			// quickly return no results if RDF constraints for subject and predicate
+			// are violated, as occurs in the Jena test suite for Graph. 
+			if ((s!=null && s.isLiteral()) || 
+					(p!=null && (p.isLiteral() || p.isBlank()))) {
+				result = conn.createRepositoryResult(new ArrayList<Statement>());
+			} else {
+				result = conn.getStatements(vf.asResource(s), vf.asURI(p), vf.asValue(m
 					.getMatchObject()), inferred, context);
+			}
 		} catch (RepositoryException e) {
 			throw new RuntimeException(e);
 		}
-		return new AGTripleIterator(result);
+		return new AGTripleIterator(this, result);
 	}
 
 	@Override

src/com/franz/agraph/jena/AGTransactionHandler.java

@@ -4,6 +4,7 @@
 
 import com.hp.hpl.jena.graph.TransactionHandler;
 import com.hp.hpl.jena.shared.Command;
+import com.hp.hpl.jena.shared.JenaException;
 
 public class AGTransactionHandler implements TransactionHandler {
 
@@ -48,7 +49,17 @@ public void commit() {
 
 	@Override
 	public Object executeInTransaction(Command c) {
-		throw new UnsupportedOperationException(AGUnsupportedOperation.message);
+		try {
+			begin();
+			c.execute();
+			commit();
+		} catch (Throwable e) {
+			throw new JenaException(e);
+		}
+
+		// TODO determine what object to return here, currently the 
+		// command is executed for side effects rather than a result.
+		return null;
 	}
 
 	@Override

src/com/franz/agraph/jena/AGTripleIterator.java

@@ -19,9 +19,12 @@
 public class AGTripleIterator extends NiceIterator<Triple>
 implements Closeable {
 
-	private RepositoryResult<Statement> result;
+	private final AGGraph graph;
+	private final RepositoryResult<Statement> result;
+	private Statement current = null;
 
-	AGTripleIterator(RepositoryResult<Statement> result) {
+	AGTripleIterator(AGGraph graph, RepositoryResult<Statement> result) {
+		this.graph = graph;
 		this.result = result;
 	}
 
@@ -47,7 +50,8 @@ public boolean hasNext() {
 	public Triple next() {
 		Triple tr;
 		try {
-			tr = AGNodeFactory.asTriple(result.next());
+			current = result.next();
+			tr = AGNodeFactory.asTriple(current);
 		} catch (RepositoryException e) {
 			throw new RuntimeException(e);		
 		}
@@ -56,10 +60,13 @@ public Triple next() {
 
 	@Override
 	public void remove() {
-		try {
-			result.remove();
-		} catch (RepositoryException e) {
-			throw new RuntimeException(e);		
+		if (current != null) {
+			Triple tr = AGNodeFactory.asTriple(current);
+			graph.delete(tr);
+			// TODO the following only removes triples from the underlying
+			// collection (in memory), rather than from the store.   
+			//result.remove();
+			current = null;
 		}
 	}
 }

src/com/franz/agraph/repository/AGRepositoryConnection.java

@@ -260,7 +260,7 @@ public RepositoryResult<Resource> getContextIDs()
 	/**
 	 * Creates a RepositoryResult for the supplied element set.
 	 */
-	protected <E> RepositoryResult<E> createRepositoryResult(
+	public <E> RepositoryResult<E> createRepositoryResult(
 			Iterable<? extends E> elements) {
 		return new RepositoryResult<E>(
 				new CloseableIteratorIteration<E, RepositoryException>(elements

src/com/franz/agraph/repository/AGValueFactory.java

@@ -102,7 +102,7 @@ public Value asValue(Node node) {
 			if (node.getLiteralDatatypeURI()!=null) {
 				URI datatype = createURI(node.getLiteralDatatypeURI());
 				val = createLiteral(node.getLiteralLexicalForm(), datatype);
-			} else if (lang!=null && lang!="") {
+			} else if (lang!=null && !lang.equals("")) {
 				val = createLiteral(node.getLiteralLexicalForm(),lang);
 			} else {
 				// TODO
@@ -134,6 +134,10 @@ public URI asURI(Node node) {
 			uri = null;
 		} else if (node.isURI()) {
 			uri = createURI(node.getURI());
+		} else if (node.isBlank()) {
+			// TODO: research this more, seems to be needed for the test 
+			// suite, as blank nodes appear in the predicate position
+			uri = createURI("http://anon/" + node.getBlankNodeLabel());
 		} else {
 			throw new IllegalArgumentException("Cannot convert Node to URI: " + node);
 		}

src/test/AGAbstractTest.java

@@ -72,13 +72,13 @@ private static String findServerUrl1() {
 
 		if ((host == null || host.equals("localhost")) && port == null) {
 			File portFile = new File("../agraph/lisp/agraph.port");
-			System.out.println("Reading agraph.port: " + portFile.getAbsolutePath());
 			try {
+				host = "localhost";
 				if (portFile.exists()) {
+					System.out.println("Reading agraph.port: " + portFile.getAbsolutePath());
 					port = readLines(portFile).get(0);
-					host = "localhost";
 				} else {
-					throw new RuntimeException("PortFile not found.");
+					port = "10035";
 				}
 			} catch (Exception e) {
 				throw new RuntimeException("Trying to read PortFile: " + portFile.getAbsolutePath(), e);