/*
 * 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 java.util.ArrayList;
import java.util.List;

import org.erasmusmc.ontology.Ontology;
import org.erasmusmc.ontology.OntologyFileLoader;
import org.erasmusmc.ontology.OntologyManager;
import org.erasmusmc.ontology.OntologyStore;
import org.erasmusmc.ontology.ontologyutilities.OntologyCurator;
import org.erasmusmc.utilities.StringUtilities;
import org.erasmusmc.utilities.TextFileUtilities;

public class UMLS2008Loader {
	//This file will contain the rewritten terms
	public static String rewrittenMRCONSOfile = "/home/khettne/UMLS/2008AB/MRCONSO2008AB_060209_rewrittenAndSuppressed_test.RRF";

	//Rewrite and suppress log
	public static String rewriteAndSuppressLog = "/home/khettne/UMLS/2008AB/UMLS2008AB_060209_rewriting_log_test.log";

//	This file contains concept IDs, terms, and vocabularies
	public static String MRCONSOfile = "/home/public/thesauri/UMLS2008AB/META/MRCONSO.RRF";

	//This file contains semantic types for a concept
	public static String MRSTYfile = "/home/public/thesauri/UMLS2008AB/META/MRSTY.RRF";
	public static String SRDEFfile = "/home/public/thesauri/UMLS2008AB/NET/SRDEF";

//	This file contains abbreviations
	public static String LRABRfile = "/home/public/thesauri/UMLS2008AB/LEX/LRABR";

	//This file contains the concept definitions
	public static String MRDEFfile = "/home/public/thesauri/UMLS2008AB/META/MRDEF.RRF";

	//Create loading log
	public static List<String> log_output = new ArrayList<String>();
	public static String logname = "/home/khettne/UMLS/2008AB/UMLS2008AB_loading_log_test.log";

	//Curation file 
	public static String curationFilePath = "/home/public/thesauri/UMLS2008AB/UMLS_curation_file_updatedFor2008AB.txt";

	//Name of the ontology
	public static String ontologyName = "UMLS2008AB_060209";
	public static String ontologyPath = "/home/khettne/UMLS/2008AB/UMLS2008AB_060209.ontology";


	public static void main(String[] args) {

		System.out.println("Starting script: "+StringUtilities.now());


		Ontology newOntology = new OntologyStore();
		newOntology.setName(ontologyName);    

		//Filter the UMLS
		System.out.println("Rewriting and suppressing MRCONSO... "+StringUtilities.now());
		RewriteAndSuppressUMLSusingCasper rewriteAndSuppress = new RewriteAndSuppressUMLSusingCasper();
		rewriteAndSuppress.run(MRCONSOfile, MRSTYfile, rewrittenMRCONSOfile, rewriteAndSuppressLog);

		//Fill the ontology
		System.out.println("Executing MRCONSOLoader... "+StringUtilities.now());
		RewrittenMRCONSOLoader.loadFromRewrittenMRCONSO(newOntology, rewrittenMRCONSOfile, log_output, LRABRfile);

		System.out.println("Executing MRSTYLoader... "+StringUtilities.now());
		MRSTYLoader.addSemanticType(newOntology, MRSTYfile, SRDEFfile);

		System.out.println("Executing MRDEFLoader... "+StringUtilities.now());
		MRDEFLoader.addDefinition(newOntology, MRDEFfile, log_output);

//		Save to log
		System.out.println("Saving to log file "+StringUtilities.now());
		TextFileUtilities.saveToFile(log_output, logname);

		System.out.println("Formatting UMLS database IDs: "+StringUtilities.now());
		newOntology = AddUMLSidAsDatabaseID.addUMLSid(newOntology);

		System.out.println("Mapping ontology: "+StringUtilities.now());		
		newOntology = MapGoAndOmimToOntology.mapGoAndOMIMFromMRCONSOtoOntology(newOntology, MRCONSOfile);

		//Curate
		OntologyCurator curator = new OntologyCurator(curationFilePath);
		curator.curateAndPrepare(newOntology);

//		Save ontology
		OntologyFileLoader loader = new OntologyFileLoader();
		loader.save((OntologyStore)newOntology, ontologyPath);

//		Load ontology into database
		OntologyManager ontologyManager = new OntologyManager();
		ontologyManager.dumpStoreInDatabase((OntologyStore)newOntology);  


	}

}