Mercurial > hg > semantic-sia

changeset 70:fe08d8cdd150

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new
author stevenh
date Fri, 02 Aug 2013 15:01:59 +0100
parents 94e6592eb106
children 39106212a3c6
files src/org/qmul/eecs/c4dm/sia/N3ToRdf.java src/org/qmul/eecs/c4dm/sia/SiaSemWeb.java
diffstat 2 files changed, 293 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/org/qmul/eecs/c4dm/sia/N3ToRdf.java	Fri Aug 02 15:01:59 2013 +0100
@@ -0,0 +1,68 @@
+package org.qmul.eecs.c4dm.sia;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+
+import org.apache.jena.web.DatasetGraphAccessorHTTP;
+import org.mindswap.pellet.jena.PelletReasonerFactory;
+import org.qmul.eecs.c4dm.sparql.utilities.SparqlWrapperMethods;
+
+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.DatasetAccessor;
+import com.hp.hpl.jena.query.DatasetAccessorFactory;
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+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;
+
+/**
+ * @author stevenh
+ * Utility class which converts an N3 file to RDF/XML
+ */
+public class N3ToRdf {
+	
+	// Ontology N3 file
+	private static final String n3ontology = "file:src/rdf/siaTestDatapointOntology.n3";
+//	private static final String n3ontology = "file:src/rdf/midiModel.n3";
+
+	// The RDF output file
+	private static final String rdfFileName = "/Volumes/USB_DISK/mercurial/SiaSesame/ontology/siaTestDatapointOntology";
+	
+	/**
+	 * @param args
+	 */
+	public static void main(String[] args) {
+		
+		// Create an ontology model
+		OntModel ontModel = ModelFactory
+				.createOntologyModel();
+		
+		// Read the ontology and data from the file into the ontology model
+		ontModel.read(n3ontology, "N3");
+		
+		// Write the model to a file
+		File outFileRdf = new File(rdfFileName  + ".rdf");
+		FileOutputStream outFileOutputStreamRdf;
+
+		// RDF/XML version
+		try {
+			outFileOutputStreamRdf = new FileOutputStream(outFileRdf);
+			ontModel.writeAll(outFileOutputStreamRdf, "RDF/XML", null);
+		} catch (FileNotFoundException e) {
+			System.out.println("Unable to write to file: "
+					+ outFileRdf.getAbsolutePath());
+			e.printStackTrace();
+			System.exit(1);
+		}
+
+		System.out.println("Model written to file: "
+				+ outFileRdf.getAbsolutePath());
+
+	}
+
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/org/qmul/eecs/c4dm/sia/SiaSemWeb.java	Fri Aug 02 15:01:59 2013 +0100
@@ -0,0 +1,225 @@
+package org.qmul.eecs.c4dm.sia;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+
+import org.apache.jena.web.DatasetGraphAccessorHTTP;
+import org.mindswap.pellet.jena.PelletReasonerFactory;
+import org.qmul.eecs.c4dm.sparql.utilities.SparqlWrapperMethods;
+
+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.DatasetAccessor;
+import com.hp.hpl.jena.query.DatasetAccessorFactory;
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+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;
+
+public class SiaSemWeb {
+
+	private static final String selectOrderedVteInfoQuery = "file:src/sparql/select_ordered_vte_info.sparql";
+	private static final String selectAllQuery = "file:src/sparql/select_all.sparql";
+	private static final String selectEqualVtesQuery = "file:src/sparql/select_equal_vtes.sparql";
+	private static final String selectVectorTableDetailsQuery = "file:src/sparql/select_vector_table_details.sparql";
+	private static final String selectPartialQuery = "file:src/sparql/partial.sparql";
+	private static final String selectVteEquivalenceQuery = "file:src/sparql/select_vte_equivalence.sparql";
+	private static final String selectMtpsQuery = "file:src/sparql/select_mtps.sparql";
+	private static final String selectNewVectorsQuery = "file:src/sparql/select_new_vectors.sparql";
+	private static final String selectExistingVectorsQuery = "file:src/sparql/select_existing_vectors.sparql";
+
+	// SPARQL updates
+	private static final String insertDatapointOrderBarOneSparql = "file:src/sparql/insert_datapoint_order_bar_one.sparql";
+	private static final String insertDatapointOrderLastOneSparql = "file:src/sparql/insert_datapoint_order_last_one.sparql";
+	private static final String insertSiatecVectorTableBNodesSparql = "file:src/sparql/insert_siatec_vector_table_bnodes.sparql";
+	private static final String insertSetVClassificationSparql = "file:src/sparql/insert_set_v_classification.sparql";
+	private static final String insertSetWClassificationSparql = "file:src/sparql/insert_set_w_classification.sparql";
+	private static final String insertNewDimValsForVectorTableSparql = "file:src/sparql/insert_new_dimVals_for_vector_table.sparql";
+	private static final String insertVectorTableDetailsSparql = "file:src/sparql/insert_vector_table_details.sparql";
+	private static final String insertVteOrderBarOneSparql = "file:src/sparql/insert_vte_order_bar_one.sparql";
+	private static final String insertVteOrderLastOneSparql = "file:src/sparql/insert_vte_order_last_one.sparql";
+	private static final String insertDimensionEquivalenceSparql = "file:src/sparql/insert_dimension_equivalence.sparql";
+	private static final String insertVteEquivalenceSparql = "file:src/sparql/insert_vte_equivalence.sparql";
+	private static final String insertTecsSparql = "file:src/sparql/insert_tecs.sparql";
+	private static final String insertTranslatedTecBnodesSparql = "file:src/sparql/insert_translated_tec_bnodes.sparql";
+	private static final String insertCORRECTEquivalentTecDetailsSparql = "file:src/sparql/insert_correct_equivalent_tec_details.sparql";
+	private static final String insertNewVectorsSparql = "file:src/sparql/insert_new_vectors.sparql";
+	private static final String insertEqualVteSuperclassesSparql = "file:src/sparql/insert_equal_vte_superclasses.sparql";
+
+	// Ontology file
+	private static final String ontology = "file:src/rdf/siaTestDatapointOntology.n3";
+//	private static final String ontology = "file:src/rdf/midiModel.n3";
+
+	// The final output file
+	private static final String finalModelFileName = "src/rdf/finalSiaModel";
+	
+	// The HTTP sparql (sesame) services
+	private static final String sparqlQueryService = "http://localhost:8080/openrdf-workbench/repositories/sia4/query";
+	private static final String sparqlUpdateService = "http://localhost:8080/openrdf-workbench/repositories/sia4/update";
+	private static final String sparqlAddService = "http://localhost:8080/openrdf-workbench/repositories/sia4/add";
+	private static final String sparqlRemoveService = "http://localhost:8080/openrdf-workbench/repositories/sia4/remove";
+	private static final String sparqlClearService = "http://localhost:8080/openrdf-workbench/repositories/sia4/clear";
+
+	/**
+	 * @param args
+	 */
+	public static void main(String[] args) {
+		
+		// Create a pellet ontology model
+		OntModel ontModel = ModelFactory
+				.createOntologyModel(PelletReasonerFactory.THE_SPEC);
+		
+//		// Create a jena ontology model
+//		OntModel ontModel = ModelFactory
+//				.createOntologyModel();
+
+		// Read the ontology and data from the file into the ontology model
+		ontModel.read(ontology, "N3");
+		
+		//TODO Should probably check for and deal with duplicate vectors here
+		// (vectors must be unique - datapoints don't have to be)
+				
+//		DatasetAccessor sparqlAdd = DatasetAccessorFactory.createHTTP(sparqlAddService);
+		
+//		DatasetGraphAccessorHTTP datasetGraphAccessorHTTP = new DatasetGraphAccessorHTTP(sparqlAddService);
+		
+//		System.out.println("Load the model...");
+////		sparqlAdd.add(ontModel);
+//		datasetGraphAccessorHTTP.httpPut(ontModel.getGraph());
+//
+//		System.out.println("Final model...");
+//		ResultSet rs = SparqlWrapperMethods.querySparqlService(selectAllQuery, sparqlQueryService);
+//		
+//		while (rs.hasNext())
+//		{
+//			QuerySolution soln = rs.next();
+//			System.out.println(soln.toString());
+//		}
+//		
+//		System.exit(0);
+
+		// Perform SPARQL inserts
+    	System.out.println("Performing step 1...");
+    	UpdateAction.readExecute(insertDatapointOrderBarOneSparql, ontModel);
+    			
+    	System.out.println("Performing step 2...");
+		UpdateAction.readExecute(insertDatapointOrderLastOneSparql, ontModel);
+		
+		System.out.println("Performing step 3...");
+    	UpdateAction.readExecute(insertSiatecVectorTableBNodesSparql, ontModel);
+
+    	System.out.println("Performing step 3a...");
+    	UpdateAction.readExecute(insertSetVClassificationSparql, ontModel);
+    	
+    	System.out.println("Performing step 3b...");
+    	UpdateAction.readExecute(insertSetWClassificationSparql, ontModel);
+    	
+		System.out.println("Performing step (pre) 4...");
+    	UpdateAction.readExecute(insertNewDimValsForVectorTableSparql, ontModel);
+    	
+//		System.out.println("Inserting new Vectors...");
+//    	UpdateAction.readExecute(insertNewVectorsSparql, ontModel);
+//
+		System.out.println("Performing step 4...");
+    	UpdateAction.readExecute(insertVectorTableDetailsSparql, ontModel);
+
+    	System.out.println("Performing step 5...");
+    	long startTime = System.currentTimeMillis();
+    	UpdateAction.readExecute(insertVteOrderBarOneSparql, ontModel);
+    	long endTime = System.currentTimeMillis();
+    	long elapsedTime = endTime - startTime;
+    	System.out.println("Step 5 took " + elapsedTime + " ms");
+
+    	System.out.println("Performing step 6...");
+    	UpdateAction.readExecute(insertVteOrderLastOneSparql, ontModel);
+
+//    	// Perform insertVectorTableDetailsSparql using the raw model, because
+//    	// the pellet ontology model adds superfluous typed/untyped literals
+//    	Model rawModel = ontModel.getRawModel();
+//
+//    	System.out.println("Model after step 6...");
+////		SparqlWrapperMethods.queryOntModel(selectAllQuery, ontModel);
+////		SparqlWrapperMethods.queryTheModel(selectAllQuery, rawModel);
+//		
+		System.out.println("Ordered vtes:");
+		SparqlWrapperMethods.queryOntModel(selectOrderedVteInfoQuery, ontModel);
+////		SparqlWrapperMethods.queryTheModel(selectOrderedVteInfoQuery, rawModel);
+////
+////
+//////    	// Now recreate the pellet version of the model
+//////    	ontModel = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC, rawModel);
+////
+//////    	System.out.println("Performing step 7...");
+//////    	UpdateAction.readExecute(insertDimensionEquivalenceSparql, ontModel);
+////
+//////    	System.out.println("Final model...");
+//////		SparqlWrapperMethods.queryOntModel(selectAllQuery, ontModel);
+////
+////		System.out.println("equivalent vtes...");
+////		SparqlWrapperMethods.queryOntModel(selectVteEquivalenceQuery, ontModel);		
+		System.out.println("Performing step 7...");
+		UpdateAction.readExecute(insertVteEquivalenceSparql, ontModel);
+
+		System.out.println("Performing insertTecs...");
+		UpdateAction.readExecute(insertTecsSparql, ontModel);
+		
+		System.out.println("Performing insertTranslatedTecBnodes...");
+		UpdateAction.readExecute(insertTranslatedTecBnodesSparql, ontModel);
+		
+		System.out.println("Performing insertCORRECTEquivalentTecDetails...");
+		UpdateAction.readExecute(insertCORRECTEquivalentTecDetailsSparql, ontModel);
+		
+//
+//		System.out.println("Performing step 8...");
+//		UpdateAction.readExecute(insertEqualVteSuperclassesSparql, ontModel);
+//
+//		System.out.println("Final model...");
+//		SparqlWrapperMethods.queryOntModel(selectAllQuery, ontModel);
+////		System.out.println("ordered vtes...");
+////		SparqlWrapperMethods.queryOntModel(selectOrderedVteInfoQuery, ontModel);
+//
+		System.out.println("Equal vtes...");
+		SparqlWrapperMethods.queryOntModel(selectEqualVtesQuery, ontModel);
+////		System.out.println("MTPs...");
+////		SparqlWrapperMethods.queryOntModel(selectMtpsQuery, ontModel);
+		System.out.println("Final model...");
+		SparqlWrapperMethods.queryOntModel(selectAllQuery, ontModel);
+
+//		// Write the model to a file
+//		File outFileRdf = new File(finalModelFileName  + ".rdf");
+//		File outFileN3 = new File(finalModelFileName + ".n3");
+//		FileOutputStream outFileOutputStreamRdf;
+//		FileOutputStream outFileOutputStreamN3;
+//
+//		// RDF/XML version
+//		try {
+//			outFileOutputStreamRdf = new FileOutputStream(outFileRdf);
+//			ontModel.writeAll(outFileOutputStreamRdf, "RDF/XML", null);
+//		} catch (FileNotFoundException e) {
+//			System.out.println("Unable to write to file: "
+//					+ outFileRdf.getAbsolutePath());
+//			e.printStackTrace();
+//			System.exit(1);
+//		}
+//
+//		// N3 version
+//		try {
+//			outFileOutputStreamN3 = new FileOutputStream(outFileN3);
+//			ontModel.writeAll(outFileOutputStreamN3, "N3", null);
+//		} catch (FileNotFoundException e) {
+//			System.out.println("Unable to write to file: "
+//					+ outFileN3.getAbsolutePath());
+//			e.printStackTrace();
+//			System.exit(1);
+//		}
+//
+//		System.out.println("Model written to files: "
+//				+ outFileRdf.getAbsolutePath() + " and " + outFileN3.getAbsolutePath());
+//
+	}
+
+}