--- a/OPPL/Tool.java	Wed Sep 14 19:52:06 2011 +0200
+++ b/OPPL/Tool.java	Sat Sep 17 13:41:28 2011 +0200
@@ -47,8 +47,10 @@
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.model.OWLAxiomChange;
+import org.semanticweb.owlapi.model.OWLDataFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
 import org.semanticweb.owlapi.reasoner.InferenceType;
@@ -57,33 +59,62 @@
 import org.semanticweb.owlapi.util.InferredAxiomGenerator;
 import org.semanticweb.owlapi.util.InferredOntologyGenerator;
 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
+import org.semanticweb.owlapi.util.SimpleIRIMapper;
 
 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
 
-
 /**
  * @author Mikel Egaña Aranguren
- *
  */
 public class Tool {
 
 	/**
-	 * @param OWL file 
-	 * @param OPPL script 
 	 * @throws FileNotFoundException 
 	 * @throws OWLOntologyCreationException 
 	 * @throws OWLOntologyStorageException 
 	 */
-	public static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException {
-		 		
+	public static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException {		
 		// Get the arguments from command-line
 		String OWLFilePath = args [0]; 
 		String OPPL_script_file = args [1];
-		String Output_format = args [2];
-		String Add_inferred = args [3];
-		String OPPL_script_source = "";
+		String Output_format = args [2]; // OWL|OBO
+		String Add_inferred = args [3]; // Add_inferred|Whatever
+		String imports_file_path = args [4]; // Flat tab delimited file: URI	Document URI
+		
+		// Load the main ontology		
+		File owl_file = new File(OWLFilePath);
+		OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); 
+		
+		// Load the imports if any
+		if(!imports_file_path.equals("NoImports")){
+			File imports_file = new File(imports_file_path);
+			Scanner imports_input = new Scanner(imports_file);
+			while(imports_input.hasNext()){
+			    String nextLine = imports_input.nextLine();
+			    if(!nextLine.startsWith("#")){
+				    String [] URI_documentURI = nextLine.split("\t");
+		//		    System.out.println(URI_documentURI[0]);
+		//		    System.out.println(URI_documentURI[1]);
+		//			IRI ontology_IRI = IRI.create("http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology");
+		//			IRI document_IRI = IRI.create("file://" + "/home/pik/UPM/OPPL_galaxy/SWAT4LS_2011/GONG/chebi.owl");		
+				    IRI ontology_IRI = IRI.create(URI_documentURI[0]);
+					IRI document_IRI = IRI.create("file://" + URI_documentURI[1]);	
+					OWLOntologyIRIMapper iriMapper = new SimpleIRIMapper(ontology_IRI,document_IRI);
+					manager.addIRIMapper(iriMapper);
+				}
+			}
+			imports_input.close();
+		}
+		OWLDataFactory factory = manager.getOWLDataFactory();
+		OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file);
+		
+		// Reasoner
+		OWLReasonerFactory reasonerFactory = new PelletReasonerFactory(); 
+		OWLReasoner reasoner = reasonerFactory.createReasoner(OWL_ontology);
+		reasoner.isConsistent();
 		
 		// Load the 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()) {
@@ -91,15 +122,6 @@
 		    OPPL_script_source = OPPL_script_source + " " + nextToken;
 		}
 		input.close();
-		
-		// Load the OWL ontology		
-		File owl_file = new File(OWLFilePath);
-		OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); 
-		OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file);
-		
-		// Sync reasoner and check consistency
-		OWLReasonerFactory reasonerFactory = new PelletReasonerFactory(); 
-		OWLReasoner reasoner = reasonerFactory.createReasoner(OWL_ontology);
 	
 		// Parse the OPPL script
 		ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner);