annotate OPPL/Tool.java @ 3:5255f1333cc4

Version 1.0.1 Added output choice: OBO or OWL(RDF/XML)

/**
 * Copyright (C) 2011, Mikel Egaña Aranguren
 *
 *  This program is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation, either version 3 of the License, or
 *  (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package es.upm.fi.dia.oeg.oppl.galaxy;

import java.io.BufferedOutputStream;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FilterOutputStream;
import java.io.OutputStream;
import java.io.PipedOutputStream;
import java.io.PrintStream;
import java.util.List;
import java.util.Scanner;
import java.util.logging.Level;
import java.util.logging.Logger;

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.owlapi.obo.parser.OBOOntologyFormat;
import org.coode.parsers.ErrorListener;
import org.coode.parsers.LoggerErrorListener;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
import org.semanticweb.owlapi.model.IRI;
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;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;

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 {
		 		
		// Get the arguments from command-line
		String OWLFilePath = args [0]; 
		String OPPL_script_file = args [1];
		String Output_format = args [2];
		String OPPL_script_source = "";
		
		// Load the flat file with script in memory
		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();
		
		// 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); 
		Logger logger = Logger.getLogger(Tool.class.getName());
		Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy
		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);
		
		// Print the ontology to the standard output so other galaxy tools can operate on the output
		OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();
		
		if(Output_format.equals("OBO")){
			manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget());
		}
		else{
			manager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
		}

	}
}