/*
 * Copyright (C) 2011 SeqWare
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
package net.sourceforge.seqware.pipeline.plugins;

import java.util.Arrays;
import net.sourceforge.seqware.common.hibernate.CheckForCycles;
import net.sourceforge.seqware.common.module.ReturnValue;
import net.sourceforge.seqware.pipeline.plugin.Plugin;
import net.sourceforge.seqware.pipeline.plugin.PluginInterface;
import org.openide.util.lookup.ServiceProvider;

/**
 * <p>
 * CycleChecker class.
 * </p>
 * 
 * @author mtaschuk
 * @version $Id: $Id
 */
@ServiceProvider(service = PluginInterface.class)
public class CycleChecker extends Plugin {

    ReturnValue ret = new ReturnValue();

    /**
     * <p>
     * Constructor for CycleChecker.
     * </p>
     */
    public CycleChecker() {
        super();
        parser.acceptsAll(Arrays.asList("study-accession"), "The SeqWare accession of the study you want to check").withRequiredArg();
        ret.setExitStatus(ReturnValue.SUCCESS);
    }

    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue init() {
        return ret;
    }

    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue do_test() {
        return ret;
    }

    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue do_run() {

        if (options.has("study-accession")) {
            Integer study = Integer.parseInt((String) options.valueOf("study"));
            CheckForCycles cfc = new CheckForCycles();
            println(cfc.checkStudy(study));
        } else {
            println("Combination of parameters not recognized!");
            println(this.get_syntax());
            ret.setExitStatus(ReturnValue.INVALIDPARAMETERS);
        }

        return ret;
    }

    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue clean_up() {
        return ret;
    }

    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public String get_description() {
        return "Checks for cycles in the sample hierarchy and processing hierarchy of a particular study and prints some information about the study";
    }

}