--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/OPPLGalaxy.java	Sat Oct 06 21:50:39 2012 +0200
@@ -0,0 +1,121 @@
+/**
+ * 
+ */
+package es.upm.fi.dia.oeg.oppl.galaxy;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Scanner;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+//import org.apache.log4j.Level;
+import org.coode.oppl.ChangeExtractor;
+import org.coode.oppl.OPPLParser;
+import org.coode.oppl.OPPLScript;
+import org.coode.oppl.ParserFactory;
+import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
+import org.coode.oppl.log.Logging;
+import org.coode.parsers.ErrorListener;
+import org.coode.parsers.LoggerErrorListener;
+import org.semanticweb.owlapi.model.OWLAxiomChange;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+
+
+
+
+/**
+ * @author Mikel Ega��a Aranguren
+ *
+ */
+public class OPPLGalaxy {
+
+	/**
+	 * @param args
+	 * @throws OWLOntologyCreationException 
+	 * @throws OWLOntologyStorageException 
+	 * @throws IOException 
+	 */
+	public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException {
+		// Get the arguments from command-line
+		String OWLFilePath = args [0];
+		String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|Elk|HermiT
+		
+		String OPPL_script_file = args [2];
+		String OWL = args [3]; // OWL|OBO
+		
+		// Create the manager
+		GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
+				
+		// Load the main ontology and hope for the imported URIs to be resolvable		
+		galaxyowlapi.loadMainOntology(OWLFilePath);
+				
+		// Set the reasoner
+		
+		// Pellet
+		if(reasoner_type.equals("Pellet")){
+			galaxyowlapi.setReasonerPellet();
+		}
+		// FaCTPlusPlus
+		else if (reasoner_type.equals("FaCTPlusPlus")){
+			galaxyowlapi.setReasonerFaCT();
+		}
+		// Elk
+		else if (reasoner_type.equals("Elk")){
+			galaxyowlapi.setReasonerElk();
+		}
+		// HermiT
+		else{
+			galaxyowlapi.setReasonerHermit();
+		}
+		
+		// Load the OPPL flat file with script in memory
+		String OPPL_script_source = "";
+		File file = new File(OPPL_script_file);
+		Scanner input = new Scanner(file);
+		while(input.hasNext()) {
+		    String nextToken = input.next();
+		    OPPL_script_source = OPPL_script_source + " " + nextToken;
+		}
+		input.close();
+	
+		OWLOntologyManager manager = galaxyowlapi.getOWLManager();
+		OWLOntology ontology = galaxyowlapi.getMainOntology();
+		OWLReasoner reasoner = galaxyowlapi.getReasoner();
+		
+		// Parse the OPPL script
+		ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner); 
+		Logger logger = Logger.getLogger(OPPLGalaxy.class.getName());
+//		logger.setLevel(Level.OFF);
+//		Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
+		
+		ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
+		OPPLParser opplparser = parserFactory.build(errorListener);
+		OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
+			
+		// Execute the script
+		ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true);
+		List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
+		manager.applyChanges(changes);
+		
+		galaxyowlapi.disposeReasoner();
+		
+		// Merge imported ontologies if requested
+//		if(merge.equals("Merge")){
+//			galaxyowlapi.merge();
+//		}
+		
+		// Save the ontology
+		if(OWL.equals("OWL")){
+			galaxyowlapi.saveOntology(true);
+		}
+		else{
+			galaxyowlapi.saveOntology(false);
+		}	
+	}
+}