Java tutorial
/* * 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 static fr.ens.biologie.genomique.eoulsan.EoulsanLogger.getLogger; import java.io.File; import java.io.IOException; import java.util.ArrayList; 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.OptionBuilder; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; import com.google.common.base.Joiner; import fr.ens.biologie.genomique.eoulsan.Common; import fr.ens.biologie.genomique.eoulsan.Globals; import fr.ens.biologie.genomique.eoulsan.Main; import fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJarRepackager; /** * This class launch Eoulsan in hadoop mode. * @since 1.0 * @author Laurent Jourdren */ public class HadoopExecAction extends AbstractAction { /** Name of this action. */ public static final String ACTION_NAME = "hadoopexec"; private static final String HADOOP_CLIENT_OPTS_ENV = "HADOOP_CLIENT_OPTS"; @Override public String getName() { return ACTION_NAME; } @Override public String getDescription() { return "execute " + Globals.APP_NAME + " on local hadoop cluster."; } @Override public void action(final List<String> arguments) { final Options options = makeOptions(); final CommandLineParser parser = new GnuParser(); String jobDescription = null; 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); } if (line.hasOption("d")) { jobDescription = line.getOptionValue("d"); argsOptions += 2; } } catch (ParseException e) { Common.errorExit(e, "Error while parsing command line arguments: " + e.getMessage()); } if (arguments.size() != argsOptions + 3) { help(options); } final File paramFile = new File(arguments.get(argsOptions)); final File designFile = new File(arguments.get(argsOptions + 1)); final String hdfsPath = arguments.get(argsOptions + 2); // Execute program in hadoop mode run(paramFile, designFile, hdfsPath, jobDescription); } // // Command line parsing // /** * Create options for command line * @return an Options object */ @SuppressWarnings("static-access") private static Options makeOptions() { // create Options object final Options options = new Options(); // Help option options.addOption("h", "help", false, "display this help"); // Description option options.addOption(OptionBuilder.withArgName("description").hasArg().withDescription("job description") .withLongOpt("desc").create('d')); return options; } /** * Show command line help. * @param options Options of the software */ private static void help(final Options options) { // Show help message final HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(Globals.APP_NAME_LOWER_CASE + ".sh " + ACTION_NAME + " [options] workflow.xml design.txt hdfs://server/path", options); Common.exit(0); } // // Execution // /** * Get the JVM arguments as a string. * @return a String with the JVM arguments */ private static String getJVMArgs() { final List<String> result = new ArrayList<>(); for (String a : Main.getInstance().getJVMArgs()) { if (a.startsWith("-Xm")) { result.add(a); } } final Main main = Main.getInstance(); if (main.getEoulsanScriptPath() != null) { result.add("-D" + Main.EOULSAN_SCRIPT + "=" + main.getEoulsanScriptPath()); } if (main.getClassPath() != null) { result.add("-D" + Main.EOULSAN_CLASSPATH_JVM_ARG + "=" + main.getClassPath()); } return Joiner.on(' ').join(result); } /** * Run Eoulsan in hadoop mode. * @param workflowFile workflow file * @param designFile design file * @param hdfsPath path of data on hadoop file system * @param jobDescription job description */ private static void run(final File workflowFile, final File designFile, final String hdfsPath, final String jobDescription) { checkNotNull(workflowFile, "paramFile is null"); checkNotNull(designFile, "designFile is null"); checkNotNull(hdfsPath, "hdfsPath is null"); // Write log entries Main.getInstance().flushLog(); // Repackage application for Hadoop System.out.println("Package " + Globals.APP_NAME + " for hadoop mode..."); final File repackagedJarFile; try { repackagedJarFile = HadoopJarRepackager.repack(); } catch (IOException e) { Common.errorExit(e, "Error while repackaging " + Globals.APP_NAME_LOWER_CASE + ": " + e.getMessage()); // Never called return; } getLogger().info("Launch Eoulsan in Hadoop mode."); // Create command line final List<String> argsList = new ArrayList<>(); argsList.add("hadoop"); argsList.add("jar"); argsList.add(repackagedJarFile.getAbsolutePath()); final Main main = Main.getInstance(); if (main.getLogLevelArgument() != null) { argsList.add("-loglevel"); argsList.add(main.getLogLevelArgument()); } if (main.getConfigurationFileArgument() != null) { argsList.add("-conf"); argsList.add(main.getConfigurationFileArgument()); } for (String setting : main.getCommandLineSettings()) { argsList.add("-s"); argsList.add(setting); } argsList.add(ExecJarHadoopAction.ACTION_NAME); if (jobDescription != null) { argsList.add("-d"); argsList.add(jobDescription.trim()); } argsList.add("-e"); argsList.add("local hadoop cluster"); argsList.add(workflowFile.toString()); argsList.add(designFile.toString()); argsList.add(hdfsPath); // execute Hadoop System.out.println("Launch " + Globals.APP_NAME + " in hadoop mode..."); try { // Create the process builder the the command line final ProcessBuilder builder = new ProcessBuilder(argsList).inheritIO(); // Set the JVM arguments for Hadoop in the process builder builder.environment().put(HADOOP_CLIENT_OPTS_ENV, getJVMArgs()); // Execute the hadoop jar command final int exitCode = builder.start().waitFor(); // Exit with the same exit of the child process System.exit(exitCode); } catch (IOException | InterruptedException e) { Common.errorExit(e, "Error while executing " + Globals.APP_NAME_LOWER_CASE + ": " + e.getMessage()); } } }