/*
 * Concept profile generation tool suite
 * Copyright (C) 2015 Biosemantics Group, Erasmus University Medical Center,
 *  Rotterdam, The Netherlands
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero 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 Affero General Public License for more details.
 * 
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>
 */

package org.erasmusmc.dataimport.UMLS;

import org.erasmusmc.ontology.Ontology;
import org.erasmusmc.ontology.OntologyFileLoader;
import org.erasmusmc.ontology.OntologyStore;
import org.erasmusmc.utilities.StringUtilities;

public class GoAndOmimMapping {

	public static String inFilename = "/home/public/thesauri/UMLS2010AB/META/MRCONSO.RRF";
	public static String ontologyInfile = "/home/khettne/Projects/UMLS/UMLS2010AB_medlinefilter.ontology";
	public static String onotologyOutfile = "/home/khettne/Projects/UMLS/UMLS2010AB_medlinefilter_final.ontology";
	public static void main(String[] args) {
		System.out.println("Starting script: "+StringUtilities.now());

		OntologyFileLoader loader = new OntologyFileLoader();
		Ontology ontology = loader.load(ontologyInfile);
		//OntologyManager manager = new OntologyManager();
		System.out.println("Loading ontology: "+StringUtilities.now());
		//Ontology ontology = manager.fetchClient("UMLS2008ABHomologeneChemToxV1_4");

		System.out.println("Mapping ontology: "+StringUtilities.now());		
		ontology = MapGoAndOmimToOntology.mapGoAndOMIMFromMRCONSOtoOntology(ontology, inFilename);
		loader.save((OntologyStore)ontology, onotologyOutfile);
		
//		System.out.println("Dumping ontology into database: "+StringUtilities.now());
//		ontology.setName("UMLS2008ABHomologeneChemToxV1_5");
//		manager.dumpStoreInDatabase(ontology);

		System.out.println("Done! "+StringUtilities.now());
	}
}