/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
 *
 * This library 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.  The software and
 * documentation provided hereunder is on an "as is" basis, and
 * Memorial Sloan-Kettering Cancer Center 
 * has no obligations to provide maintenance, support,
 * updates, enhancements or modifications.  In no event shall
 * Memorial Sloan-Kettering Cancer Center
 * be liable to any party for direct, indirect, special,
 * incidental or consequential damages, including lost profits, arising
 * out of the use of this software and its documentation, even if
 * Memorial Sloan-Kettering Cancer Center 
 * has been advised of the possibility of such damage.
*/

package org.mskcc.cbio.portal.scripts;

import org.mskcc.cbio.portal.dao.DaoException;
import org.mskcc.cbio.portal.dao.DaoTypeOfCancer;
import org.mskcc.cbio.portal.model.TypeOfCancer;
import org.mskcc.cbio.portal.util.ConsoleUtil;
import org.mskcc.cbio.portal.util.ProgressMonitor;

import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Iterator;
import java.util.Properties;
import java.util.Scanner;

/**
 * Load all the types of cancer and their names from a file.
 *
 * @author Arthur Goldberg goldberg@cbio.mskcc.org
 */
public class ImportTypesOfCancers {
    public static void main(String[] args) throws IOException, DaoException {
        if (args.length != 1) {
            System.out.println("command line usage: importTypesOfCancer.pl <types_of_cancer.txt>");
            return;
        }

        ProgressMonitor pMonitor = new ProgressMonitor();
        pMonitor.setConsoleMode(true);

        File file = new File(args[0]);
        load(pMonitor, file, true);
    }

    public static void load(ProgressMonitor pMonitor, File file) throws IOException, DaoException {
        ImportTypesOfCancers.load(pMonitor, file, true);
    }

    public static void load(ProgressMonitor pMonitor, File file, boolean clobber) throws IOException, DaoException {
        if (clobber) DaoTypeOfCancer.deleteAllRecords();
        TypeOfCancer aTypeOfCancer = new TypeOfCancer();
        Scanner scanner = new Scanner(file);

        while(scanner.hasNextLine()) {
            String[] tokens = scanner.nextLine().split("\t", -1);
            assert tokens.length == 5;

            String typeOfCancerId = tokens[0].trim().toLowerCase();
            aTypeOfCancer.setTypeOfCancerId(typeOfCancerId);
            aTypeOfCancer.setName(tokens[1].trim());
            aTypeOfCancer.setClinicalTrialKeywords(tokens[2].trim().toLowerCase());
            aTypeOfCancer.setDedicatedColor(tokens[3].trim());
            aTypeOfCancer.setParentTypeOfCancerId(tokens[4].trim());
            DaoTypeOfCancer.addTypeOfCancer(aTypeOfCancer);
        }
        pMonitor.setCurrentMessage("Loaded " + DaoTypeOfCancer.getCount() + " TypesOfCancers.");
        ConsoleUtil.showWarnings(pMonitor);
    }

}

@@ -2496,30 +2496,16 @@
 %5D.trim()
-.toLowerCase()
 ;%0A      
@@ -2556,16 +2556,30 @@
 CancerId
+.toLowerCase()
 );%0A     
@@ -2765,32 +2765,88 @@
 ens%5B3%5D.trim());%0A
+            aTypeOfCancer.setShortName(typeOfCancerId);%0A
             aTyp

set short name