changeset 13:5a3a1c7fa3a8

organized imports

changed finalModelFileName to "src/rdf/finalSiaModel" (to distinguish from finalSiaTecModel)

removed select query

changed one of the sparql construct query filenames from construct_vector_table_bnodes to construct_sia_vector_table_bnodes

moved public static String SIA_NS_URI to the (new) "Namespaces" class

moved sparql-related methods to (new) class "SparqlWrapperMethods"

now use the newly-created "SiaVectorTableElementFactory.createV" method instead of the old "SiaVectorTableElementFactory.create" method for creating specifically the Vector Table V (as opposed to W) described in the paper

removed unnecessary code

moved display code to the "Display" class

--- a/src/org/qmul/eecs/c4dm/sia/SiaMain.java	Tue Jan 08 18:06:02 2013 +0000
+++ b/src/org/qmul/eecs/c4dm/sia/SiaMain.java	Tue Jan 08 18:15:46 2013 +0000
@@ -1,11 +1,3 @@
-// Copyright (c) 2006 - 2008, Clark & Parsia, LLC. <http://www.clarkparsia.com>
-// This source code is available under the terms of the Affero General Public
-// License v3.
-//
-// Please see LICENSE.txt for full license terms, including the availability of
-// proprietary exceptions.
-// Questions, comments, or requests for clarification: [e-mail]
-
 package org.qmul.eecs.c4dm.sia;
 
 import java.io.File;
@@ -16,31 +8,23 @@
 import java.util.List;
 
 import org.mindswap.pellet.jena.PelletReasonerFactory;
-import org.qmul.eecs.c4dm.sia.exceptions.DimensionException;
 import org.qmul.eecs.c4dm.sia.model.Datapoint;
-import org.qmul.eecs.c4dm.sia.model.NDimensionalObject;
+import org.qmul.eecs.c4dm.sia.model.VectorTable;
 import org.qmul.eecs.c4dm.sia.model.VectorTableElement;
+import org.qmul.eecs.c4dm.sia.rdf.Namespaces;
+import org.qmul.eecs.c4dm.sia.utilities.Display;
+import org.qmul.eecs.c4dm.sparql.utilities.SparqlWrapperMethods;
 
-import com.clarkparsia.pellet.sparqldl.jena.SparqlDLExecutionFactory;
 import com.hp.hpl.jena.ontology.OntModel;
-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.query.Syntax;
 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;
 
 /**
  * <p>
  * Title: SiaMain
  * </p>
  * <p>
- * Description: An RDF/OWL/Java implementation of the sia pattern discovery algorithm.
+ * Description: An RDF/OWL/Java implementation of the SIA pattern discovery algorithm.
  * </p>
  * 
  * @author Steve Hargreaves, C4DM, Queen Mary University of London
@@ -51,17 +35,18 @@
 	private static final String ontology = "file:src/rdf/siaDatapointOntology.n3";
 
 	// The final output file
-	private static final String finalModelFileName = "src/rdf/finalModel";
+	private static final String finalModelFileName = "src/rdf/finalSiaModel";
 
 	// SPARQL queries
 	private static final String[] selectQueries = new String[] {
 		// A SPARQL-DL query
+		"file:src/sparql/select_all.sparql"
 	};
 
 	// CONSTRUCT queries
 	private static final String[] constructQueries = new String[] {
 		// A SPARQL-DL CONSTRUCT query
-		"file:src/sparql/construct_vector_table_bnodes.sparql",
+		"file:src/sparql/construct_sia_vector_table_bnodes.sparql",
 		"file:src/sparql/construct_vector_table_details.sparql" };
 
 	// ASK queries
@@ -69,8 +54,6 @@
 		// A SPARQL-DL ASK query
 		};
 	
-	public static String SIA_NS_URI = null;
-
 	public void run() {
 
 		// First create a Jena ontology model backed by the Pellet reasoner
@@ -83,34 +66,34 @@
 		
 		// Set the value of SIA_NS_URI as the namespace for 'sia' found in
 		// the ontology
-		SIA_NS_URI = ontModel.getNsPrefixURI("sia");
+		Namespaces.SIA_NS_URI = ontModel.getNsPrefixURI("sia");
 
 		// Create custom sia Datapoint objects
 		List<Datapoint> datapoints = SiaDatapointFactory.create(ontModel);
 		
-		// Order the datapoints
+		// STEP 1 - Order the datapoints
 		Collections.sort(datapoints);
 
 		// Add datapoint order info to model
 		SiaDatapointFactory.assertOrder(ontModel, datapoints);
 		
+		// STEP 2 - Compute the vector table
 		// Run all the CONSTRUCT queries
 		for (int i = 0; i < constructQueries.length; i++) {
 			String constructQuery = constructQueries[i];
 
-			Model newModel = executeConstructQuery(constructQuery, ontModel);
+			Model newModel = SparqlWrapperMethods.executeConstructQuery(constructQuery, ontModel);
 
 			// Add new triples to the current model
 			ontModel.add(newModel);
 		}
 
 		// Create custom sia VectorTableElement objects
-		List<VectorTableElement> vteList = SiaVectorTableElementFactory.create(ontModel, datapoints);
-		Iterator<VectorTableElement> vteIter = vteList.iterator();
+		VectorTable vectorTableV = SiaVectorTableElementFactory.createV(ontModel, datapoints);
+		List<VectorTableElement> vteList = vectorTableV.getVteList();
 
-		// Order the VectorTableElement objects
+		// STEP 3 - Order the VectorTableElement objects
 		Collections.sort(vteList);
-		vteIter = vteList.iterator();
 
 		// Add vector table element order info to model
 		SiaVectorTableElementFactory.assertOrder(ontModel, vteList);
@@ -119,7 +102,7 @@
 		for (int i = 0; i < selectQueries.length; i++) {
 
 			String selectQuery = selectQueries[i];
-			queryTheModel(selectQuery, ontModel);
+			SparqlWrapperMethods.queryTheModel(selectQuery, ontModel);
 
 		}
 
@@ -127,7 +110,7 @@
 		for (int i = 0; i < askQueries.length; i++) {
 
 			String askQuery = askQueries[i];
-			askTheModel(askQuery, ontModel);
+			SparqlWrapperMethods.askTheModel(askQuery, ontModel);
 
 		}
 
@@ -162,7 +145,7 @@
 		System.out.println("Model written to files: "
 				+ outFileRdf.getAbsolutePath() + " and " + outFileN3.getAbsolutePath());
 		
-		// Display the results
+		// STEP 4 - Display the results
 		displaySiaResults(vteList);
 	}
 
@@ -179,15 +162,15 @@
 		while (i < m)
 		{
 			System.out.print("<");
-			printVector(vteList.get(i));
+			Display.printVector(vteList.get(i));
 			System.out.print(",{");
-			printVector(vteList.get(i).getFromDatapoint());
+			Display.printVector(vteList.get(i).getFromDatapoint());
 			int j = i + 1;
 						
 			while (j < m && (vteList.get(i).compareToIgnoreDatapoints(vteList.get(j)) == 0))
 			{
 				System.out.print(",");
-				printVector(vteList.get(j).getFromDatapoint());
+				Display.printVector(vteList.get(j).getFromDatapoint());
 				j++;
 			}
 			System.out.print("}>");
@@ -230,134 +213,6 @@
 	}
 
 	/**
-	 * @param vector
-	 */
-	private void printVector(NDimensionalObject vector) {
-		System.out.print("<");
-		
-		int maxDimension = vector.getDimensionValues().size();
-		
-		for (int dim = 1; dim <= maxDimension; dim++)
-		{
-			try {
-				double value = vector.getDimensionValue(dim);
-				System.out.print(value + (dim == maxDimension ? "" : ","));
-			} catch (DimensionException e) {
-				e.printStackTrace();
-				System.exit(1);
-			}
-		}
-		System.out.print(">");
-		
-	}
-
-	/**
-	 * @param query
-	 * @param m
-	 * @return
-	 */
-	private Model executeConstructQuery(String query, Model m) {
-
-		// Now read the query file into a query object
-		Query q = QueryFactory.read(query, Syntax.syntaxARQ); // only required
-																// if using
-																// (e.g.) LET in
-																// SPARQL
-
-		QueryExecution qe = QueryExecutionFactory.create(q, m);
-
-		// We want to execute a CONSTRUCT query, do it, and return the new
-		// triples
-		Model newModel = qe.execConstruct();
-
-		// Print the query for better understanding
-		System.out.println(q.toString());
-
-		// Print the new triples
-		StmtIterator iter = newModel.listStatements();
-		printStmts(iter);
-
-		return newModel;
-	}
-
-	/**
-	 * @param iter
-	 */
-	private void printStmts(StmtIterator iter) {
-		Statement statement;
-
-		while (iter.hasNext()) {
-			statement = iter.nextStatement();
-			System.out.println(" | <" + statement.getSubject() + "> | <"
-					+ statement.getPredicate() + "> | <"
-					+ statement.getObject() + "> | ");
-		}
-
-		// And an empty line to make it pretty
-		System.out.println();
-	}
-
-	/**
-	 * @param query
-	 * @param m
-	 */
-	private void queryTheModel(String query, Model m) {
-
-		// Now read the query file into a query object
-		Query q = QueryFactory.read(query, Syntax.syntaxARQ); // only required
-																// if using
-																// (e.g.) LET in
-																// SPARQL
-
-		// Create a SPARQL-DL query execution for the given query and
-		// ontology model
-		QueryExecution qe = SparqlDLExecutionFactory.create(q, m);
-
-		// We want to execute a SELECT query, do it, and return the result set
-		ResultSet rs = qe.execSelect();
-
-		// Print the query for better understanding
-		System.out.println(q.toString());
-
-		// There are different things we can do with the result set, for
-		// instance iterate over it and process the query solutions or, what we
-		// do here, just print out the results
-		ResultSetFormatter.out(rs);
-
-		// And an empty line to make it pretty
-		System.out.println();
-	}
-
-	/**
-	 * @param query
-	 * @param m
-	 */
-	private void askTheModel(String query, Model m) {
-
-		// Now read the query file into a query object
-		Query q = QueryFactory.read(query);
-
-		// Create a SPARQL-DL query execution for the given query and
-		// ontology model
-		QueryExecution qe = SparqlDLExecutionFactory.create(q, m);
-
-		// We want to execute a SELECT query, do it, and return the result set
-		boolean result = qe.execAsk();
-
-		// Print the query for better understanding
-		System.out.println(q.toString());
-
-		// Print the result
-		System.out.println("Result: " + result);
-
-		// And an empty line to make it pretty
-		System.out.println();
-	}
-
-	/**
-	 * @param args
-	 */
-	/**
 	 * @param args
 	 */
 	public static void main(String[] args) {