AddGenome.java

package org.seqcode.data.core.tools;

import org.seqcode.genome.Genome;
import org.seqcode.genome.Species;
import org.seqcode.gseutils.Args;
import org.seqcode.gseutils.NotFoundException;

/**
 * AddGenome --species "mus musculus" --genome "mm22"
 */

public class AddGenome {

    public static void main(String args[]) throws Exception {
        String species = Args.parseString(args,"species",null);
        String genome = Args.parseString(args,"genome",null);
        if (species == null) {
            System.err.println("Must supply --species");
            System.exit(1);
        }
        if (genome == null) {
            System.err.println("Must supply --genome");
            System.exit(1);
        }
        try {
            Species o = new Species(species);
            try {
                Genome g = new Genome(o, genome);
                System.err.println("Genome " + genome + " already exists.");
                System.exit(2);
            } catch (NotFoundException e) {
                Genome.insertGenome(o, genome);
            }
        } catch (NotFoundException e) {
            System.err.println("Species " + species + " doesn't exist.  Please create with AddSpecies");
            System.exit(2);
        }


    }

}