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 java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; 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 fr.ens.biologie.genomique.eoulsan.Common; import fr.ens.biologie.genomique.eoulsan.EoulsanException; import fr.ens.biologie.genomique.eoulsan.Globals; import fr.ens.biologie.genomique.eoulsan.Main; import fr.ens.biologie.genomique.eoulsan.data.DataFile; import fr.ens.biologie.genomique.eoulsan.design.Design; import fr.ens.biologie.genomique.eoulsan.design.DesignBuilder; import fr.ens.biologie.genomique.eoulsan.design.DesignUtils; import fr.ens.biologie.genomique.eoulsan.design.io.DesignWriter; import fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter; import fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter; /** * This class define an action to create design file. * @since 1.0 * @author Laurent Jourdren */ public class CreateDesignAction extends AbstractAction { /** Name of this action. */ public static final String ACTION_NAME = "createdesign"; private static final int DEFAULT_DESIGN_FORMAT = 2; @Override public String getName() { return ACTION_NAME; } @Override public String getDescription() { return "create a design file from a list of files."; } @Override public boolean isCurrentArchCompatible() { return true; } @Override public void action(final List<String> arguments) { final Options options = makeOptions(); final CommandLineParser parser = new GnuParser(); String filename = "design.txt"; int argsOptions = 0; boolean pairedEndMode = false; final List<String> sampleSheetPaths = new ArrayList<>(); String samplesProjectName = null; boolean symlinks = false; int formatVersion = DEFAULT_DESIGN_FORMAT; try { // parse the command line arguments final CommandLine line = parser.parse(options, arguments.toArray(new String[arguments.size()]), true); // Pair-end option if (line.hasOption("paired-end")) { pairedEndMode = true; argsOptions += 1; } // Help option if (line.hasOption("help")) { help(options); } // Output option if (line.hasOption("o")) { filename = line.getOptionValue("o"); argsOptions += 2; } // Casava design option if (line.hasOption("s")) { String[] sampleSheets = line.getOptionValues("s"); sampleSheetPaths.addAll(Arrays.asList(sampleSheets)); argsOptions += sampleSheets.length * 2; } // Casava project option if (line.hasOption("n")) { samplesProjectName = line.getOptionValue("n"); argsOptions += 2; } // Symbolic links option if (line.hasOption("symlinks")) { symlinks = true; argsOptions++; } // Eoulsan design format version option if (line.hasOption("f")) { try { formatVersion = Integer.parseInt(line.getOptionValue("f").trim()); } catch (NumberFormatException e) { Common.errorExit(e, "Invalid Eoulsan design format version: " + e.getMessage()); } argsOptions += 2; } } catch (ParseException e) { Common.errorExit(e, "Error while parsing command line arguments: " + e.getMessage()); } // Write log entries Main.getInstance().flushLog(); Design design = null; final DataFile designFile = new DataFile(filename); try { final List<String> newArgs = arguments.subList(argsOptions, arguments.size()); final DesignBuilder db = new DesignBuilder(); // Add all the files of a Casava design if Casava design path is defined for (String sampleSheetPath : sampleSheetPaths) { db.addBcl2FastqSamplesheetProject(new File(sampleSheetPath), samplesProjectName); } // Add files in the command line db.addFiles(newArgs); design = db.getDesign(pairedEndMode); if (symlinks) { DesignUtils.replaceLocalPathBySymlinks(design, designFile.getParent()); } } catch (EoulsanException | IOException e) { Common.errorExit(e, "Error: " + e.getMessage()); } if (design.getSamples().isEmpty()) { Common.showErrorMessageAndExit( "Error: Nothing to create, no file found.\n" + " Use the -h option to get more information.\n" + "usage: " + Globals.APP_NAME_LOWER_CASE + " createdesign files"); } try { if (designFile.exists()) { throw new IOException("Output design file " + designFile + " already exists"); } final DesignWriter dw; switch (formatVersion) { case 1: dw = new Eoulsan1DesignWriter(designFile.create()); break; case 2: dw = new Eoulsan2DesignWriter(designFile.create()); break; default: Common.showErrorMessageAndExit("Unknown Eoulsan design format version: " + formatVersion); return; } dw.write(design); } catch (IOException e) { Common.errorExit(e, "File not found: " + e.getMessage()); } } // // 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(); // Pair end mode options.addOption("p", "paired-end", false, "Paired-end mode"); // Help option options.addOption("h", "help", false, "Display this help"); // Bcl2fastq samplesheet path option options.addOption(OptionBuilder.withArgName("file").hasArg().withDescription("Illumina samplesheet file") .withLongOpt("samplesheet").create('s')); // Bcl2fastq project option options.addOption(OptionBuilder.withArgName("name").hasArg().withDescription("Illumina project name") .withLongOpt("project-name").create('n')); // Create symbolic links options.addOption("l", "symlinks", false, "Create symbolic links in design file directory"); // Output option options.addOption(OptionBuilder.withArgName("file").hasArg().withDescription("Output file") .withLongOpt("output").create('o')); // Eoulsan design format version options.addOption(OptionBuilder.withArgName("version").hasArg() .withDescription("Eoulsan design format version").withLongOpt("format-version").create('f')); 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] file1 file2 ... fileN", options); Common.exit(0); } }