view src/org/qmul/eecs/c4dm/sia/SiaMain.java @ 43:f3f6ef9bd5bd

organised imports

changed various public/private static final Strings

no longer uses Pellet - now uses a basic jena ontology model

reads/writes model to/from an external TDB dataset instead of flat files

performs sparql updates (inserts) when creating the vector table instead of sparql constructs followed by adding new triples to the model

removed unnecessary sparql select and ask queries

the whole procedure is now timed

package org.qmul.eecs.c4dm.sia;

import java.util.Collections;
import java.util.Iterator;
import java.util.List;

import org.qmul.eecs.c4dm.sia.model.Datapoint;
import org.qmul.eecs.c4dm.sia.model.VectorTable;
import org.qmul.eecs.c4dm.sia.model.VectorTableElement;
import org.qmul.eecs.c4dm.sia.utilities.Display;

import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.ReadWrite;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.tdb.TDBFactory;
import com.hp.hpl.jena.update.UpdateAction;

/**
 * <p>
 * Title: SiaMain
 * </p>
 * <p>
 * Description: An RDF/OWL/Java implementation of the SIA pattern discovery algorithm.
 * </p>
 * 
 * @author Steve Hargreaves, C4DM, Queen Mary University of London
 */
public class SiaMain {
	
	// The location of the TDB database
	public static final String assemblerFile = "src/assemblers/tdb-assembler.ttl";
	
	// The name of the graph used in the dataset
	public static final String graph = "http://localhost:3030/siaGraph";

	// SPARQL queries
	private static final String selectAllQuery = "file:src/sparql/select_all.sparql";

	// UPDATE queries
	private static final String insertSiaVectorTableBNodesQuery = "file:src/sparql/insert_sia_vector_table_bnodes.sparql";
	private static final String insertVectorTableDetailsQuery = "file:src/sparql/insert_vector_table_details.sparql";

	public void run() {

		// Obtain a dataset context
		Dataset dataset = TDBFactory.assembleDataset(assemblerFile);

		// Get the sia graph, as a model, from the dataset
		Model siaModel = dataset.getNamedModel(graph);
		
		OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, siaModel);
				
		// Create custom sia Datapoint objects
		List<Datapoint> datapoints = SiaDatapointFactory.create(ontModel);
		
		// 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 UPDATE queries
    	UpdateAction.readExecute(insertSiaVectorTableBNodesQuery, ontModel);
    	UpdateAction.readExecute(insertVectorTableDetailsQuery, ontModel);
		
		// Create custom sia VectorTableElement objects
		VectorTable vectorTableV = SiaVectorTableElementFactory.createV(ontModel, datapoints);
		List<VectorTableElement> vteList = vectorTableV.getVteList();

		// STEP 3 - Order the VectorTableElement objects
		Collections.sort(vteList);

		// Add vector table element order info to model
		SiaVectorTableElementFactory.assertOrder(ontModel, vteList);

		// STEP 4 - Display the results
		displaySiaResults(vteList);

		// Write the model to the TDB dataset
        dataset.begin(ReadWrite.WRITE) ;
        try {
        	dataset.replaceNamedModel(graph, ontModel);
        	dataset.commit();
        	System.out.println("dataset.commit() done");
        } finally {
        	dataset.end();
        	System.out.println("dataset.end() done");
        }

		dataset.close();
    	System.out.println("dataset.close() done");
		
	}

	/**
	 * @param vteList
	 */
	public void displaySiaResults(List<VectorTableElement> vteList) {
		int m = vteList.size();
		int i = 0;
		
		System.out.println();
		System.out.print("{");
		
		while (i < m)
		{
			System.out.print("<");
			Display.printVector(vteList.get(i));
			System.out.print(",{");
			Display.printVector(vteList.get(i).getFromDatapoint());
			int j = i + 1;
						
			while (j < m && (vteList.get(i).compareToIgnoreDatapoints(vteList.get(j)) == 0))
			{
				System.out.print(",");
				Display.printVector(vteList.get(j).getFromDatapoint());
				j++;
			}
			System.out.print("}>");
			if (j < m)
			{
				System.out.print(",");
				System.out.println();
			}
			i = j;
		}
		System.out.println("}");
	}

	/**
	 * @param vteIter
	 * @param message
	 */
	public void displayNDimensionalObjects(Iterator<VectorTableElement> vteIter, String message) {
		System.out.println(message);
		System.out.println("----------");
		while (vteIter.hasNext())
		{
			VectorTableElement vte = vteIter.next();
			System.out.println("from: " + vte.getFromDatapoint().getResource().getLocalName() + " to: " + vte.getToDatapoint().getResource().getLocalName());			
		}
	}

	/**
	 * @param datapointIter
	 * @param message
	 */
	public void displayDatapoints(Iterator<Datapoint> datapointIter, String message) {
		System.out.println(message);
		System.out.println("----------");
		while (datapointIter.hasNext())
		{
			Datapoint datapoint = datapointIter.next();
			System.out.println( datapoint.getResource().getLocalName());			
		}
	}

	/**
	 * @param args
	 */
	public static void main(String[] args) {
		long startTime = System.currentTimeMillis();
		SiaMain app = new SiaMain();
		app.run();
		long endTime = System.currentTimeMillis();
		long elapsedTime = endTime - startTime;
		System.out.println("Completed in " + elapsedTime + " ms");
	}

}