steve@0: package org.qmul.eecs.c4dm.sia;
steve@0: 
steve@0: import java.util.ArrayList;
steve@0: import java.util.Iterator;
steve@0: import java.util.List;
steve@0: import java.util.Vector;
steve@0: 
stevenh@16: import org.qmul.eecs.c4dm.sia.exceptions.DimensionException;
steve@0: import org.qmul.eecs.c4dm.sia.model.Datapoint;
steve@0: import org.qmul.eecs.c4dm.sia.model.DimensionValue;
steve@0: import org.qmul.eecs.c4dm.sia.model.DirectlyFollows;
steve@0: import org.qmul.eecs.c4dm.sia.model.FromDatapoint;
steve@0: import org.qmul.eecs.c4dm.sia.model.MemberOfOrderedSet;
steve@0: import org.qmul.eecs.c4dm.sia.model.OrderedIndex;
steve@0: import org.qmul.eecs.c4dm.sia.model.OrderedSet;
steve@0: import org.qmul.eecs.c4dm.sia.model.ToDatapoint;
stevenh@16: import org.qmul.eecs.c4dm.sia.model.VectorTable;
steve@0: import org.qmul.eecs.c4dm.sia.model.VectorTableElement;
steve@0: 
steve@0: import com.hp.hpl.jena.ontology.OntClass;
steve@0: import com.hp.hpl.jena.ontology.OntModel;
stevenh@45: import com.hp.hpl.jena.ontology.OntResource;
steve@0: import com.hp.hpl.jena.rdf.model.AnonId;
stevenh@45: import com.hp.hpl.jena.rdf.model.ModelFactory;
stevenh@45: import com.hp.hpl.jena.rdf.model.NodeIterator;
steve@0: import com.hp.hpl.jena.rdf.model.Property;
steve@0: import com.hp.hpl.jena.rdf.model.RDFNode;
steve@0: import com.hp.hpl.jena.rdf.model.Resource;
steve@0: import com.hp.hpl.jena.rdf.model.Statement;
steve@0: import com.hp.hpl.jena.rdf.model.StmtIterator;
steve@0: import com.hp.hpl.jena.util.iterator.ExtendedIterator;
steve@0: import com.hp.hpl.jena.vocabulary.RDF;
steve@0: 
steve@0: public class SiaVectorTableElementFactory {
steve@0: 
stevenh@16: 	/**
stevenh@16: 	 * @param datapoints
stevenh@16: 	 * @return
stevenh@90: 	 * @throws DimensionException 
stevenh@16: 	 */
stevenh@90: 	public static VectorTable createV(List<Datapoint> datapoints) throws DimensionException {
stevenh@90: 		return create(datapoints, false);
stevenh@16: 	}
stevenh@16: 	
stevenh@16: 	/**
stevenh@16: 	 * @param datapoints
stevenh@16: 	 * @return
stevenh@90: 	 * @throws DimensionException 
stevenh@16: 	 */
stevenh@90: 	public static VectorTable createW(List<Datapoint> datapoints) throws DimensionException {
stevenh@90: 		return create(datapoints, true);
stevenh@16: 	}
stevenh@16: 
stevenh@16: 	/**
stevenh@16: 	 * @param datapoints
stevenh@16: 	 * @param returnWResults
stevenh@16: 	 * @return
stevenh@90: 	 * @throws DimensionException 
stevenh@16: 	 */
stevenh@90: 	public static VectorTable create(List<Datapoint> datapoints, boolean returnWResults) throws DimensionException {
steve@0: 		
stevenh@45: 		VectorTable vectorTable = new VectorTable();
stevenh@90: 		
stevenh@90: 		List<Datapoint> fromDatapoints = datapoints;
stevenh@90: 		Iterator<Datapoint> fromDatapointsIter = fromDatapoints.iterator();
stevenh@45: 		
steve@0: 		List<VectorTableElement> vteList = new ArrayList<VectorTableElement>();
steve@0: 		VectorTableElement vte;
stevenh@90: 		while (fromDatapointsIter.hasNext())
stevenh@90: 		{
stevenh@90: 			Datapoint fromDatapoint = fromDatapointsIter.next();
stevenh@90: 
stevenh@90: 			List<Datapoint> toDatapoints = datapoints;
stevenh@90: 			Iterator<Datapoint> toDatapointsIter = toDatapoints.iterator();
stevenh@90: 
stevenh@90: 			while (toDatapointsIter.hasNext())
stevenh@90: 			{
stevenh@90: 				Datapoint toDatapoint = toDatapointsIter.next();
stevenh@45: 				
stevenh@90: 				vte = new VectorTableElement();
stevenh@16: 				vte.setFromDatapoint(fromDatapoint);
stevenh@16: 				vte.setToDatapoint(toDatapoint);
stevenh@90: 					
stevenh@90: 				// Only add VectorTableElements whose 'from' ordered index is less than the 'to' ordered index
stevenh@90: 				if (returnWResults || vte.getFromDatapoint().getOrderedIndex() < vte.getToDatapoint().getOrderedIndex())
stevenh@90: 				{
stevenh@90: 					// Find all dimensionValues for this VectorTableElement
stevenh@90: 					Vector<DimensionValue> dimensionValues = SiaDimensionValueFactory.getDimensionValuesForVectorTableElement(vte);
stevenh@90: 					vte.setDimensionValues(dimensionValues);
stevenh@90: 					vteList.add(vte);
stevenh@90: 				}
stevenh@16: 			}
steve@0: 		}
stevenh@90: 
stevenh@16: 		vectorTable.setVteList(vteList);
stevenh@16: 		vectorTable.setNumDatapoints(datapoints.size());
stevenh@16: 		return vectorTable;
steve@0: 	}
steve@0: 
stevenh@45: 	/**
stevenh@45: 	 * Java version of the two sparql construct queries
stevenh@45: 	 * <i>construct_sia(tec)_vector_table_bnodes.sparql</i> and 
stevenh@45: 	 * <i>construct_vector_table_details.sparql</i>
stevenh@45: 	 * for execution time comparison purposes.
stevenh@45: 	 * 
stevenh@45: 	 * @param ontModel
stevenh@45: 	 * @param addWResults
stevenh@45: 	 */
stevenh@45: 	public static void addToModel(OntModel ontModel, boolean addWResults) {
stevenh@45: 		// Replacement code for "construct_sia(tec)_vector_table_bnodes.sparql" start
stevenh@45: 		
stevenh@45: 		long startTime = System.currentTimeMillis();
stevenh@45: 
stevenh@45: 		// (note - we could do this by working exclusively with our OntModel, or we could
stevenh@45: 		// create separate java objects (as we already have done with Datapoint, VectorTable etc.)
stevenh@45: 		// as a first attempt, we'll use OntModel in order to avoid too much data model duplication, 
stevenh@45: 		// but if performance is poor then we should try java objects
stevenh@45: 		
stevenh@45: 		// Find all instances of sia:OrderedSet
stevenh@45: 		OntModel vteTempOntModel = ModelFactory
stevenh@45: 				.createOntologyModel(); // OntModelSpec.OWL_MEM
stevenh@45: 		OntClass orderedSetClass = ontModel.getOntClass(OrderedSet.RESOURCE_URI);
stevenh@45: 		ExtendedIterator<? extends OntResource> orderedSetIter = orderedSetClass.listInstances();
stevenh@45: 		Property memberOfOrderedSetProperty = ontModel.getOntProperty(MemberOfOrderedSet.PROPERTY_URI);
stevenh@45: 		Property fromDatapointProperty = ontModel.getOntProperty(FromDatapoint.PROPERTY_URI);
stevenh@45: 		Property toDatapointProperty = ontModel.getOntProperty(ToDatapoint.PROPERTY_URI);
stevenh@45: 		Property orderedIndexProperty = ontModel.getOntProperty(OrderedIndex.PROPERTY_URI);
stevenh@45: 		Property dimensionValueProperty = ontModel.getOntProperty(DimensionValue.PROPERTY_URI);
stevenh@45: 		Property dimensionProperty = ontModel.getOntProperty(DimensionValue.DIMENSION_URI);
stevenh@45: 		Property valueProperty = ontModel.getOntProperty(DimensionValue.VALUE_URI);
stevenh@45: 		Resource vectorTableElementResource = ontModel.createResource(VectorTableElement.RESOURCE_URI);
stevenh@45: 		
stevenh@45: 		// For each sia:OrderedSet, find every sia:Datapoint (which has property sia:memberOfOrderedSet object sia:OrderedSet)
stevenh@45: 		// Make two copies of the list of sia:datapoints
stevenh@45: 		
stevenh@45: 		OntResource orderedSet;
stevenh@45: 		StmtIterator datapoint1StmtIter;
stevenh@45: 		StmtIterator datapoint2StmtIter;
stevenh@45: 		while (orderedSetIter.hasNext())
stevenh@45: 		{
stevenh@45: 			orderedSet = orderedSetIter.next();
stevenh@45: 			datapoint1StmtIter = ontModel.listStatements((Resource)null, memberOfOrderedSetProperty, orderedSet);
stevenh@45: 
stevenh@45: 			// For every pair of sia:Datapoints datapoint1 and datapoint2 (one taken from each list), create a sia:VectorTableElement
stevenh@45: 			while (datapoint1StmtIter.hasNext())
stevenh@45: 			{
stevenh@45: 				Statement datapoint1Stmt = datapoint1StmtIter.next();
stevenh@45: 				datapoint2StmtIter = ontModel.listStatements((Resource)null, memberOfOrderedSetProperty, orderedSet);
stevenh@45: 				
stevenh@45: 				while (datapoint2StmtIter.hasNext())
stevenh@45: 				{
stevenh@45: 					// Assert that the sia:VectorTableElement has sia:fromDatapoint ?datapoint1 and sia:toDatapoint ?datapoint2
stevenh@45: 					// (in the case where we're creating the 'V' vector table (i.e. returnWResults == false), only make this assertion
stevenh@45: 					// if ((?datapoint1 != ?datapoint2) && (?i1 < ?i2)) where ?datapoint1 sia:orderedIndex ?i1 and ?datapoint2 sia:orderedIndex ?i2
stevenh@45: 					Statement datapoint2Stmt = datapoint2StmtIter.next();
stevenh@45: 					Resource fromDatapoint = datapoint1Stmt.getSubject();
stevenh@45: 					Resource toDatapoint = datapoint2Stmt.getSubject();
stevenh@45: 					
stevenh@45: 					Statement i1Stmt = ontModel.getProperty(fromDatapoint, orderedIndexProperty);
stevenh@45: 					Statement i2Stmt = ontModel.getProperty(toDatapoint, orderedIndexProperty);
stevenh@45: 					int i1 = i1Stmt.getInt();
stevenh@45: 					int i2 = i2Stmt.getInt();
stevenh@45: 										
stevenh@45: 					if (addWResults || i1 < i2)
stevenh@45: 					{
stevenh@45: 						Resource vteBnode = ontModel.createResource(AnonId.create());
stevenh@45: 						vteTempOntModel.add(vteBnode, RDF.type, vectorTableElementResource);
stevenh@45: 						vteTempOntModel.add(vteBnode, fromDatapointProperty, fromDatapoint);
stevenh@45: 						vteTempOntModel.add(vteBnode, toDatapointProperty, toDatapoint);					
stevenh@45: 
stevenh@45: 						// Replacement code for "construct_sia(tec)_vector_table_bnodes.sparql" end
stevenh@45: 
stevenh@45: 						// Replacement code for "construct_vector_table_details.sparql" start
stevenh@45: 						NodeIterator fromDimValIter = ontModel.listObjectsOfProperty(fromDatapoint, dimensionValueProperty);
stevenh@45: 						while (fromDimValIter.hasNext())
stevenh@45: 						{
stevenh@45: 							RDFNode fromDimValNode = fromDimValIter.next();
stevenh@45: 							Statement fromDimensionStmt = ontModel.getProperty(fromDimValNode.asResource(), dimensionProperty);
stevenh@45: 							Statement fromValueStmt = ontModel.getProperty(fromDimValNode.asResource(), valueProperty);
stevenh@45: 							
stevenh@45: 							int fromDimension = fromDimensionStmt.getInt();
stevenh@45: 							double fromValue = fromValueStmt.getDouble();
stevenh@45: 							
stevenh@45: 							NodeIterator toDimValIter = ontModel.listObjectsOfProperty(toDatapoint, dimensionValueProperty);
stevenh@45: 							while (toDimValIter.hasNext())
stevenh@45: 							{
stevenh@45: 								RDFNode toDimValNode = toDimValIter.next();
stevenh@45: 								Statement toDimensionStmt = ontModel.getProperty(toDimValNode.asResource(), dimensionProperty);
stevenh@45: 								
stevenh@45: 								int toDimension = toDimensionStmt.getInt();
stevenh@45: 								
stevenh@45: 								if (fromDimension == toDimension)
stevenh@45: 								{
stevenh@45: 									Statement toValueStmt = ontModel.getProperty(toDimValNode.asResource(), valueProperty);
stevenh@45: 									double toValue = toValueStmt.getDouble();
stevenh@45: 									double vteValue = toValue - fromValue;
stevenh@45: 
stevenh@45: 									Resource dimValBnode = ontModel.createResource(AnonId.create());
stevenh@45: 									vteTempOntModel.add(vteBnode, dimensionValueProperty, dimValBnode);
stevenh@45: 									vteTempOntModel.addLiteral(dimValBnode, dimensionProperty, toDimension);
stevenh@45: 									vteTempOntModel.addLiteral(dimValBnode, valueProperty, vteValue);
stevenh@45: 
stevenh@45: 									break;
stevenh@45: 								}
stevenh@45: 							}
stevenh@45: 						}												
stevenh@45: 					}					
stevenh@45: 				}
stevenh@45: 			}
stevenh@45: 		}
stevenh@45: 		
stevenh@45: 		ontModel.add(vteTempOntModel);
stevenh@45: 		long endTime = System.currentTimeMillis();
stevenh@45: 		long elapsedTime = endTime - startTime;
stevenh@45: 		System.out.println("Completed java replacement for all SPARQL CONSTRUCTs in " + elapsedTime + " ms");
stevenh@45: 		// Replacement code for "construct_vector_table_details.sparql" end
stevenh@45: 	}
stevenh@45: 
steve@0: 	public static Datapoint findDatapoint(OntModel ontModel, List<Datapoint> datapoints, Resource resource) {
steve@0: 		Iterator<Datapoint> datapointsIter = datapoints.iterator();
steve@0: 		Datapoint datapoint;
stevenh@16: 		
steve@0: 		while (datapointsIter.hasNext())
steve@0: 		{
steve@0: 			datapoint = datapointsIter.next();
stevenh@45: 			
stevenh@45: 			if (datapoint.getResource().toString().equals(resource.toString()))
steve@0: 				return datapoint;
steve@0: 		}
stevenh@16: 		
steve@0: 		datapoint = new Datapoint();
steve@0: 		datapoint.setResource(resource);
steve@0: 		Vector<DimensionValue> dimensionValues = SiaDimensionValueFactory.getDimensionValuesForResource(ontModel, resource);
steve@0: 		datapoint.setDimensionValues(dimensionValues);
steve@0: 		return datapoint;
steve@0: 	}
steve@0: 
steve@0: 	public static void assertOrder(OntModel ontModel, List<VectorTableElement> vteList) {
steve@0: 		
steve@0: 		Resource bnode = ontModel.createResource(AnonId.create());
steve@0: 		Resource siaOrderedSet = ontModel.createResource(OrderedSet.RESOURCE_URI);
steve@0: 		
steve@0: 		ontModel.add(bnode, RDF.type, siaOrderedSet);
steve@0: 		
steve@0: 		int numVectorTableElements = vteList.size();
steve@0: 
steve@0: 		VectorTableElement vte;
steve@0: 		for (int orderedIndex = 0; orderedIndex < numVectorTableElements; orderedIndex++)
steve@0: 		{
steve@0: 			// Assert <bnode, rdf:type, sia:OrderedSet>
steve@0: 			vte = vteList.get(orderedIndex);
steve@0: 			Property memberOfOrderedSetProperty = ontModel.getProperty(MemberOfOrderedSet.PROPERTY_URI);
steve@0: 			ontModel.add(vte.getResource(), memberOfOrderedSetProperty, bnode);
steve@0: 			
steve@0: 			if (orderedIndex < numVectorTableElements - 1)
steve@0: 			{
steve@0: 				// Assert <nextVectorTable, sia:directlyFollows, currentVectorTableElement>
steve@0: 				VectorTableElement nextVte = vteList.get(orderedIndex + 1);
steve@0: 				Property directlyFollowsProperty = ontModel.getProperty(DirectlyFollows.PROPERTY_URI);
steve@0: 				ontModel.add(nextVte.getResource(), directlyFollowsProperty, vte.getResource());
steve@0: 			}
steve@0: 			
steve@0: 			// Assert <currentVectorTableElement, sia:orderedIndex, orderedIndex>
steve@0: 			Property orderedIndexProperty = ontModel.getProperty(OrderedIndex.PROPERTY_URI);
steve@0: 			ontModel.addLiteral(vte.getResource(), orderedIndexProperty, orderedIndex);
steve@0: 			
steve@0: 		}
steve@0: 		
steve@0: 	}
steve@0: 
steve@0: }