--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/MergeImportedOntologies.java	Sat Oct 06 21:50:39 2012 +0200
@@ -0,0 +1,39 @@
+package es.upm.cbgp.opplquery.oppl.galaxy;
+
+import java.io.IOException;
+
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+
+import es.upm.fi.dia.oeg.oppl.galaxy.GalaxyOWLAPI;
+
+public class MergeImportedOntologies {
+
+	/**
+	 * @param args
+	 * @throws OWLOntologyCreationException 
+	 * @throws IOException 
+	 * @throws OWLOntologyStorageException 
+	 */
+	public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException {
+		String OWLFilePath = args [0]; 
+		String MergedOntologyNewURI = args [1]; 
+//		String OWLFilePath = "/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/ontology/imports/merge_test.owl";
+//		String MergedOntologyNewURI = "http://cbgp.upm.es/merged.owl"; 
+		
+		// Create the manager
+		GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
+				
+		// Load the main ontology and hope for the imported URIs to be resolvable		
+		galaxyowlapi.loadMainOntology(OWLFilePath);
+		
+		// Merge and save
+		
+		if(MergedOntologyNewURI.isEmpty()){
+			MergedOntologyNewURI = "http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl";
+		}
+		
+		galaxyowlapi.merge(MergedOntologyNewURI);	
+		galaxyowlapi.saveOntology(true);			
+	}
+}