fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction.java Source code

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Here is the source code for fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction.java

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/*
 *                  Eoulsan development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public License version 2.1 or
 * later and CeCILL-C. This should be distributed with the code.
 * If you do not have a copy, see:
 *
 *      http://www.gnu.org/licenses/lgpl-2.1.txt
 *      http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
 *
 * Copyright for this code is held jointly by the Genomic platform
 * of the Institut de Biologie de l'cole normale suprieure and
 * the individual authors. These should be listed in @author doc
 * comments.
 *
 * For more information on the Eoulsan project and its aims,
 * or to join the Eoulsan Google group, visit the home page
 * at:
 *
 *      http://outils.genomique.biologie.ens.fr/eoulsan
 *
 */

package fr.ens.biologie.genomique.eoulsan.actions;

import static com.google.common.base.Preconditions.checkNotNull;

import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.List;

import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.GnuParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;

import fr.ens.biologie.genomique.eoulsan.Common;
import fr.ens.biologie.genomique.eoulsan.EoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException;
import fr.ens.biologie.genomique.eoulsan.Globals;
import fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode;
import fr.ens.biologie.genomique.eoulsan.core.workflow.TaskSerializationUtils;
import fr.ens.biologie.genomique.eoulsan.data.DataFile;

/**
 * This class define a action to launch a task on a cluster.
 * @author Laurent Jourdren
 * @since 2.0
 */
public class ClusterTaskAction extends AbstractAction {

    /** Name of this action. */
    public static final String ACTION_NAME = "clustertask";

    @Override
    public String getName() {

        return ACTION_NAME;
    }

    @Override
    public String getDescription() {

        return "Execute a cluster task";
    }

    @Override
    public void action(final List<String> arguments) {

        final Options options = makeOptions();
        final CommandLineParser parser = new GnuParser();

        int argsOptions = 0;

        try {

            // parse the command line arguments
            final CommandLine line = parser.parse(options, arguments.toArray(new String[arguments.size()]), true);

            // Help option
            if (line.hasOption("help")) {
                help(options);
            }

        } catch (ParseException e) {
            Common.errorExit(e, "Error while parsing parameter file: " + e.getMessage());
        }

        if (arguments.size() != argsOptions + 1) {
            help(options);
        }

        final DataFile contextFile = new DataFile(arguments.get(0));

        // Execute task
        run(contextFile);
    }

    //
    // Command line parsing
    //

    /**
     * Create options for command line
     * @return an Options object
     */
    private Options makeOptions() {

        // create Options object
        final Options options = new Options();

        // Help option
        options.addOption("h", "help", false, "display this help");

        return options;
    }

    /**
     * Show command line help.
     * @param options Options of the software
     */
    private void help(final Options options) {

        // Show help message
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(Globals.APP_NAME_LOWER_CASE + ".sh " + getName() + " [options] stepcontext.context",
                options);

        Common.exit(0);
    }

    //
    // Execution
    //

    /**
     * Execute the task.
     * @param taskContextFile context file
     */
    private static void run(final DataFile taskContextFile) {

        checkNotNull(taskContextFile, "contextFile is null");

        // Get Eoulsan runtime
        final LocalEoulsanRuntime localRuntime = (LocalEoulsanRuntime) EoulsanRuntime.getRuntime();

        // Set the cluster task mode
        localRuntime.setMode(EoulsanExecMode.CLUSTER_TASK);

        try {

            // Execute the task
            TaskSerializationUtils.execute(taskContextFile);

        } catch (FileNotFoundException e) {
            Common.errorExit(e, "File not found: " + e.getMessage());
        } catch (IOException e) {
            Common.errorExit(e, "IOException: " + e.getMessage());
        } catch (EoulsanRuntimeException e) {
            Common.errorExit(e, "Error while executing " + Globals.APP_NAME_LOWER_CASE + ": " + e.getMessage());
        } catch (Throwable t) {
            t.printStackTrace();
        }
    }

}