org.obiba.genobyte.cli.InconsistenciesCommand.java Source code

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Here is the source code for org.obiba.genobyte.cli.InconsistenciesCommand.java

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/*******************************************************************************
 * Copyright 2007(c) Gnome Qubec. All rights reserved.
 * 
 * This file is part of GenoByte.
 * 
 * GenoByte 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.
 * 
 * GenoByte 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 org.obiba.genobyte.cli;

import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.ParseException;

/**
 * Launches the inconsistencies calculation.
 */
public class InconsistenciesCommand implements CliCommand {

    public boolean requiresOpenStore() {
        return true;
    }

    public boolean execute(Option opt, CliContext context) throws ParseException {
        context.getOutput().println("Computing inconsistencies...");
        try {
            context.getStore().startTransaction();
            context.getOutput().println("Computing sample reproducibility errors.");
            context.getStore().reproDna();
            context.getOutput().println("Computing assay reproducibility errors.");
            context.getStore().reproAssay();
            context.getOutput().println("Computing mendelian errors.");
            context.getStore().mendel();
            context.getStore().commitTransaction();
        } catch (RuntimeException e) {
            context.getOutput().println("An error occured during the inconsistencies computation.");
        } finally {
            context.getStore().endTransaction();
        }
        context.getOutput().println("All done.");
        return false;
    }

    public Option getOption() {
        return OptionBuilder.withDescription("compute the store's inconsistencies").withLongOpt("inconsistencies")
                .create('i');
    }
}