Java class to export Protege 3 database backend.

gistfile1.java

package ncbo.proto;

import java.io.FileInputStream;
import java.net.URI;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Properties;

import edu.stanford.smi.protegex.owl.database.creator.OwlDatabaseCreator;
import edu.stanford.smi.protegex.owl.model.OWLModel;
import edu.stanford.smi.protegex.owl.writer.rdfxml.rdfwriter.OWLModelAllTripleStoresWriter;
/**
 * 
 * @author manuelso@stanford.edu
 * 
 * Sample code to export a protege 3 database backend programatically. 
 * References:
 * http://protegewiki.stanford.edu/wiki/LoadOWLOntologyFromDB (method 2)
 * http://smi-protege.stanford.edu/svn/owl/trunk/src/edu/stanford/smi/protegex/owl/jena/export/JenaExportPlugin.java?view=markup
 *
 */
public class MetadataExport {

	public static void main(String[] args) throws Exception {
	    if (args.length < 1) {
	       System.out.println("use: java ncbo.proto.MetadataExport <file_to_export>");
	       System.out.println("make sure that MetadataExport.properties contains the database configuration");
	       return;
	    }
            URI fileURI = new URI("file://"+(new File(args[0])).getAbsolutePath());

            Properties properties = new Properties();
	    properties.load(new FileInputStream("MetadataExport.properties"));
		
	    Collection<String> errors = new ArrayList<String>();
	    //the "false" argument means that it won't overide the existing table <--- IMPORTANT otherwise will destroy existing database.
	    OwlDatabaseCreator creator = new OwlDatabaseCreator(false);
	    creator.setDriver(properties.getProperty("jdbcDriver"));
	    creator.setURL(properties.getProperty("protegeJdbcUrl"));
	    creator.setUsername(properties.getProperty("protegeJdbcUsername"));
	    creator.setPassword(properties.getProperty("protegeJdbcPassword"));
	    creator.setTable(properties.getProperty("tableName"));
            creator.create(errors);
            if (errors.size() > 0) {
        	System.out.println("Errors opening database ...\n" + StringUtils.join(errors,"\n"));
            }

            OWLModel owlModel = creator.getOwlModel();
      
            try {
		OWLModelAllTripleStoresWriter writer = new OWLModelAllTripleStoresWriter(owlModel, fileURI, true);
		writer.write();
            }
     	    catch (Exception ex) {
		String message = "Failed to save file " + fileURI;
		System.out.println(message);
		throw ex;
  	    }
	}
}