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.FileNotFoundException; 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 com.google.common.collect.Lists; 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.core.Module; import fr.ens.biologie.genomique.eoulsan.core.workflow.Executor; import fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments; import fr.ens.biologie.genomique.eoulsan.data.DataFile; import fr.ens.biologie.genomique.eoulsan.modules.TerminalModule; import fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule; import fr.ens.biologie.genomique.eoulsan.util.StringUtils; /** * This class define the Local Upload S3 Action. * @since 1.0 * @author Laurent Jourdren */ public class UploadS3Action extends AbstractAction { /** Name of this action. */ public static final String ACTION_NAME = "s3upload"; @Override public String getName() { return ACTION_NAME; } @Override public String getDescription() { return "upload data on Amazon S3."; } @Override public boolean isCurrentArchCompatible() { return true; } @Override public void action(final List<String> arguments) { System.err.println( "WARNING: the action \"" + getName() + "\" is currently under development for the next version of " + Globals.APP_NAME + " and may actually not work."); 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 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 DataFile s3Path = new DataFile( StringUtils.replacePrefix(arguments.get(argsOptions + 2), "s3:/", "s3n:/")); final String jobDescription = "Upload data to " + s3Path; // Upload data run(paramFile, designFile, s3Path, jobDescription); } // // Command line parsing // /** * Create options for command line * @return an Options object */ private static 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 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 s3://mybucket/test", options); Common.exit(0); } // // Execution // /** * Run Eoulsan in hadoop mode. * @param workflowFile workflow file * @param designFile design file * @param s3Path path of data on S3 file system * @param jobDescription job description */ private static void run(final File workflowFile, final File designFile, final DataFile s3Path, final String jobDescription) { checkNotNull(workflowFile, "paramFile is null"); checkNotNull(designFile, "designFile is null"); checkNotNull(s3Path, "s3Path is null"); getLogger().info("Parameter file: " + workflowFile); getLogger().info("Design file: " + designFile); try { // Test if worklflow file exists if (!workflowFile.exists()) { throw new FileNotFoundException(workflowFile.toString()); } // Test if design file exists if (!designFile.exists()) { throw new FileNotFoundException(designFile.toString()); } // Create ExecutionArgument object final ExecutorArguments arguments = new ExecutorArguments(workflowFile, designFile); arguments.setJobDescription(jobDescription); // Create the log Files Main.getInstance().createLogFiles(arguments.logPath(Globals.LOG_FILENAME), arguments.logPath(Globals.OTHER_LOG_FILENAME)); // Create the executor final Executor e = new Executor(arguments); // Launch executor e.execute(Lists.newArrayList((Module) new LocalUploadModule(s3Path), new TerminalModule()), null); } catch (FileNotFoundException e) { Common.errorExit(e, "File not found: " + e.getMessage()); } catch (Throwable e) { Common.errorExit(e, "Error while executing " + Globals.APP_NAME_LOWER_CASE + ": " + e.getMessage()); } } }