[VIVO-1240] Improve start up time with the graph equivalence test

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/RDFService.java

@@ -196,6 +196,17 @@ public interface RDFService {
 	public boolean isEquivalentGraph(String graphURI, InputStream serializedGraph, 
 			ModelSerializationFormat serializationFormat) throws RDFServiceException;
 
+	/**
+	 * Tests to see whether the supplied serialization is equivalent to the
+	 * named graph, as it exists in the store. Equivalence means that if this
+	 * serialization were written to the store, the resulting graph would be
+	 * isomorphic to the existing named graph.
+	 *
+	 * @param graphURI - the URI of the graph to test against. May not be null.
+	 * @param graph - the contents to be compared with the existing graph. May not be null.
+	 */
+	public boolean isEquivalentGraph(String graphURI, Model graph) throws RDFServiceException;
+
 	/**
 	 * Registers a listener to listen to changes in any graph in
 	 * the RDF store.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/filter/LanguageFilteringRDFService.java

@@ -431,7 +431,13 @@ public class LanguageFilteringRDFService implements RDFService {
 		return s.isEquivalentGraph(graphURI, serializedGraph, serializationFormat);
 	}
 
-	@Override
+    @Override
+    public boolean isEquivalentGraph(String graphURI,
+                                     Model graph) throws RDFServiceException {
+        return s.isEquivalentGraph(graphURI, graph);
+    }
+
+    @Override
     public void registerListener(ChangeListener changeListener)
             throws RDFServiceException {
         // TODO Auto-generated method stub

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/filter/SameAsFilteringRDFServiceFactory.java

@@ -289,6 +289,12 @@ public class SameAsFilteringRDFServiceFactory implements RDFServiceFactory {
     		return s.isEquivalentGraph(graphURI, serializedGraph, serializationFormat);
     	}
 
+        @Override
+        public boolean isEquivalentGraph(String graphURI,
+                                         Model graph) throws RDFServiceException {
+            return s.isEquivalentGraph(graphURI, graph);
+        }
+
         @Override
         public void close() {
             s.close();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceFactorySingle.java

@@ -145,7 +145,13 @@ public class RDFServiceFactorySingle implements RDFServiceFactory {
     		return s.isEquivalentGraph(graphURI, serializedGraph, serializationFormat);
     	}
 
-       @Override
+        @Override
+        public boolean isEquivalentGraph(String graphURI,
+                                         Model graph) throws RDFServiceException {
+            return s.isEquivalentGraph(graphURI, graph);
+        }
+
+        @Override
         public void registerListener(ChangeListener changeListener)
                 throws RDFServiceException {
             s.registerListener(changeListener);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java

@@ -607,7 +607,22 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
 		return fileModel.isIsomorphicWith(fromTripleStoreModel);
 	}
 
-	@Override
+    /**
+     * The basic version. Parse the model from the file, read the model from the
+     * tripleStore, and ask whether they are isomorphic.
+     */
+    @Override
+    public boolean isEquivalentGraph(String graphURI, Model graph) throws RDFServiceException {
+        // Retrieve the graph to compare
+        Model tripleStoreModel = new RDFServiceDataset(this).getNamedModel(graphURI);
+
+        // Load the entire graph into memory (faster comparison)
+        Model fromTripleStoreModel = ModelFactory.createDefaultModel().add(tripleStoreModel);
+
+        return graph.isIsomorphicWith(fromTripleStoreModel);
+    }
+
+    @Override
     public void close() {
         // nothing
     }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/tdb/RDFServiceTDB.java

@@ -3,6 +3,7 @@
 package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb;
 
 import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -211,6 +212,24 @@ public class RDFServiceTDB extends RDFServiceJena {
 				serializationFormat);
 	}
 
+	/**
+	 * TDB has a bug: if given a literal of type xsd:nonNegativeInteger, it
+	 * stores a literal of type xsd:integer.
+	 *
+	 * To determine whether this serialized graph is equivalent to what's in
+	 * TDB, we need to do the same.
+	 */
+	@Override
+	public boolean isEquivalentGraph(String graphURI,
+									 Model graph)
+			throws RDFServiceException {
+
+		ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+		graph.write(buffer, "N-TRIPLE");
+		InputStream inStream = new ByteArrayInputStream(buffer.toByteArray());
+		return isEquivalentGraph(graphURI, inStream, ModelSerializationFormat.NTRIPLE);
+	}
+
 	/**
 	 * Convert all of the references to "nonNegativeInteger" to "integer" in
 	 * this serialized graph.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/logging/LoggingRDFService.java

@@ -111,6 +111,15 @@ public class LoggingRDFService implements RDFService {
 		}
 	}
 
+	@Override
+	public boolean isEquivalentGraph(String graphURI,
+									 Model graph)
+			throws RDFServiceException {
+		try (RDFServiceLogger l = new RDFServiceLogger(graphURI)) {
+			return innerService.isEquivalentGraph(graphURI, graph);
+		}
+	}
+
 	// ----------------------------------------------------------------------
 	// Untimed methods
 	// ----------------------------------------------------------------------

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparql.java

@@ -929,6 +929,17 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 		return fileModel.isIsomorphicWith(fromTripleStoreModel);
 	}
 
+	/**
+	 * The basic version. Parse the model from the file, read the model from the
+	 * tripleStore, and ask whether they are isomorphic.
+	 */
+	@Override
+	public boolean isEquivalentGraph(String graphURI, Model graph) throws RDFServiceException {
+		Model tripleStoreModel = new RDFServiceDataset(this).getNamedModel(graphURI);
+		Model fromTripleStoreModel = ModelFactory.createDefaultModel().add(tripleStoreModel);
+		return graph.isIsomorphicWith(fromTripleStoreModel);
+	}
+
 	protected HttpContext getContext(HttpRequestBase request) {
 		UsernamePasswordCredentials credentials = getCredentials();
 		if (credentials != null) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/virtuoso/RDFServiceVirtuoso.java

@@ -3,6 +3,7 @@
 package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.virtuoso;
 
 import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.UnsupportedEncodingException;
@@ -247,6 +248,24 @@ public class RDFServiceVirtuoso extends RDFServiceSparql {
 		return true;
 	}
 
+	/**
+	 * TDB has a bug: if given a literal of type xsd:nonNegativeInteger, it
+	 * stores a literal of type xsd:integer.
+	 *
+	 * To determine whether this serialized graph is equivalent to what's in
+	 * TDB, we need to do the same.
+	 */
+	@Override
+	public boolean isEquivalentGraph(String graphURI,
+									 Model graph)
+			throws RDFServiceException {
+
+		ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+		graph.write(buffer, "N-TRIPLE");
+		InputStream inStream = new ByteArrayInputStream(buffer.toByteArray());
+		return isEquivalentGraph(graphURI, inStream, ModelSerializationFormat.NTRIPLE);
+	}
+
 	/**
 	 * Convert all of the references to "nonNegativeInteger" to "integer" in
 	 * this serialized graph.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/servlet/setup/FileGraphSetup.java

@@ -214,12 +214,9 @@ public class FileGraphSetup implements ServletContextListener {
     public boolean updateGraphInDB(RDFService rdfService, Model fileModel, String type, Path path) throws RDFServiceException {
         String graphURI = pathToURI(path,type);
         
-        ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+        if (rdfService.isEquivalentGraph(graphURI, fileModel)) {
-        fileModel.write(buffer, "N-TRIPLE");
+            return false;
-		InputStream inStream = new ByteArrayInputStream(buffer.toByteArray());
+        }
-		if (rdfService.isEquivalentGraph(graphURI, inStream, ModelSerializationFormat.NTRIPLE)) {
-			return false;
-		}
 
 		Model dbModel = new RDFServiceDataset(rdfService).getNamedModel(graphURI);
 		if (log.isDebugEnabled()) {