Example usage for org.apache.commons.cli Options Options

List of usage examples for org.apache.commons.cli Options Options

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In this page you can find the example usage for org.apache.commons.cli Options Options.

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From source file:com.rabbitmq.examples.FileConsumer.java

public static void main(String[] args) {
    Options options = new Options();
    options.addOption(new Option("h", "uri", true, "AMQP URI"));
    options.addOption(new Option("q", "queue", true, "queue name"));
    options.addOption(new Option("t", "type", true, "exchange type"));
    options.addOption(new Option("e", "exchange", true, "exchange name"));
    options.addOption(new Option("k", "routing-key", true, "routing key"));
    options.addOption(new Option("d", "directory", true, "output directory"));

    CommandLineParser parser = new GnuParser();

    try {//  w  ww. j  a v  a 2  s  .  co  m
        CommandLine cmd = parser.parse(options, args);

        String uri = strArg(cmd, 'h', "amqp://localhost");
        String requestedQueueName = strArg(cmd, 'q', "");
        String exchangeType = strArg(cmd, 't', "direct");
        String exchange = strArg(cmd, 'e', null);
        String routingKey = strArg(cmd, 'k', null);
        String outputDirName = strArg(cmd, 'd', ".");

        File outputDir = new File(outputDirName);
        if (!outputDir.exists() || !outputDir.isDirectory()) {
            System.err.println("Output directory must exist, and must be a directory.");
            System.exit(2);
        }

        ConnectionFactory connFactory = new ConnectionFactory();
        connFactory.setUri(uri);
        Connection conn = connFactory.newConnection();

        final Channel ch = conn.createChannel();

        String queueName = (requestedQueueName.equals("") ? ch.queueDeclare()
                : ch.queueDeclare(requestedQueueName, false, false, false, null)).getQueue();

        if (exchange != null || routingKey != null) {
            if (exchange == null) {
                System.err.println("Please supply exchange name to bind to (-e)");
                System.exit(2);
            }
            if (routingKey == null) {
                System.err.println("Please supply routing key pattern to bind to (-k)");
                System.exit(2);
            }
            ch.exchangeDeclare(exchange, exchangeType);
            ch.queueBind(queueName, exchange, routingKey);
        }

        QueueingConsumer consumer = new QueueingConsumer(ch);
        ch.basicConsume(queueName, consumer);
        while (true) {
            QueueingConsumer.Delivery delivery = consumer.nextDelivery();
            Map<String, Object> headers = delivery.getProperties().getHeaders();
            byte[] body = delivery.getBody();
            Object headerFilenameO = headers.get("filename");
            String headerFilename = (headerFilenameO == null) ? UUID.randomUUID().toString()
                    : headerFilenameO.toString();
            File givenName = new File(headerFilename);
            if (givenName.getName().equals("")) {
                System.out.println("Skipping file with empty name: " + givenName);
            } else {
                File f = new File(outputDir, givenName.getName());
                System.out.print("Writing " + f + " ...");
                FileOutputStream o = new FileOutputStream(f);
                o.write(body);
                o.close();
                System.out.println(" done.");
            }
            ch.basicAck(delivery.getEnvelope().getDeliveryTag(), false);
        }
    } catch (Exception ex) {
        System.err.println("Main thread caught exception: " + ex);
        ex.printStackTrace();
        System.exit(1);
    }
}

From source file:eu.scape_project.sanselan_wrapper.SanselanCli.java

public static void main(String[] args) {
    try {/*from  w  w w .jav  a  2  s . c  o m*/
        Options options = new Options();
        options.addOption("i", "input-file", true, "input file");
        options.addOption("o", "output-file", true, "output file");

        CommandLineParser parser = new PosixParser();
        CommandLine cmd = parser.parse(options, args);
        if (cmd.hasOption("i") && cmd.hasOption("o")) {
            BufferedImage inImage = SanselanWrapper.load(cmd.getOptionValue("i"), null);
            SanselanWrapper.convert(inImage, cmd.getOptionValue("o"), null);
        } else {
            System.out.println("usage: (-i|--input-file=) INPUT_FILE (-o|--output-file=) OUTPUT_FILE");
            System.exit(1);
        }
    } catch (Exception e) {
        System.err.println(e);
        System.exit(1);
    }
    System.exit(0);
}

From source file:eu.scape_project.imageio_wrapper.ImageIOCli.java

public static void main(String[] args) {
    try {/*from  w  w w  .  j  a v a 2 s.c  om*/
        Options options = new Options();
        options.addOption("i", "input-file", true, "input file");
        options.addOption("o", "output-file", true, "output file");

        CommandLineParser parser = new PosixParser();
        CommandLine cmd = parser.parse(options, args);
        if (cmd.hasOption("i") && cmd.hasOption("o")) {
            BufferedImage inImage = ImageIOWrapper.load(cmd.getOptionValue("i"), null);
            if (inImage != null) {
                ImageIOWrapper.convert(inImage, cmd.getOptionValue("o"), null);
            } else {
                System.out.println("Unsuported input image file format!");
                System.exit(1);
            }
        } else {
            System.out.println("usage: (-i|--input-file=) INPUT_FILE (-o|--output-file=) OUTPUT_FILE");
            System.exit(1);
        }
    } catch (Exception e) {
        System.err.println(e);
        System.exit(1);
    }
    System.exit(0);
}

From source file:com.artistech.tuio.dispatch.TuioPublish.java

public static void main(String[] args) throws InterruptedException {
    //read off the TUIO port from the command line
    int tuio_port = 3333;
    int zeromq_port = 5565;
    TuioSink.SerializeType serialize_method = TuioSink.SerializeType.PROTOBUF;

    Options options = new Options();
    options.addOption("t", "tuio-port", true, "TUIO Port to listen on. (Default = 3333)");
    options.addOption("z", "zeromq-port", true, "ZeroMQ Port to publish on. (Default = 5565)");
    options.addOption("s", "serialize-method", true,
            "Serialization Method (JSON, OBJECT, Default = PROTOBUF).");
    options.addOption("h", "help", false, "Show this message.");
    HelpFormatter formatter = new HelpFormatter();

    try {//ww w . j av  a2s. c om
        CommandLineParser parser = new org.apache.commons.cli.BasicParser();
        CommandLine cmd = parser.parse(options, args);

        if (cmd.hasOption("help")) {
            formatter.printHelp("tuio-zeromq-publish", options);
            return;
        } else {
            if (cmd.hasOption("t") || cmd.hasOption("tuio-port")) {
                tuio_port = Integer.parseInt(cmd.getOptionValue("t"));
            }
            if (cmd.hasOption("z") || cmd.hasOption("zeromq-port")) {
                zeromq_port = Integer.parseInt(cmd.getOptionValue("z"));
            }
            if (cmd.hasOption("s") || cmd.hasOption("serialize-method")) {
                serialize_method = (TuioSink.SerializeType) Enum.valueOf(TuioSink.SerializeType.class,
                        cmd.getOptionValue("s"));
            }
        }
    } catch (ParseException | IllegalArgumentException ex) {
        System.err.println("Error Processing Command Options:");
        formatter.printHelp("tuio-zeromq-publish", options);
        return;
    }

    //start up the zmq publisher
    ZMQ.Context context = ZMQ.context(1);
    // We send updates via this socket
    try (ZMQ.Socket publisher = context.socket(ZMQ.PUB)) {
        // We send updates via this socket
        publisher.bind("tcp://*:" + Integer.toString(zeromq_port));

        //create a new TUIO sink connected at the specified port
        TuioSink sink = new TuioSink();
        sink.setSerializationType(serialize_method);
        TuioClient client = new TuioClient(tuio_port);

        System.out.println(
                MessageFormat.format("Listening to TUIO message at port: {0}", Integer.toString(tuio_port)));
        System.out.println(
                MessageFormat.format("Publishing to ZeroMQ at port: {0}", Integer.toString(zeromq_port)));
        System.out.println(MessageFormat.format("Serializing as: {0}", serialize_method));
        client.addTuioListener(sink);
        client.connect();

        //while not halted (infinite loop...)
        //read any available messages and publish
        while (!sink.mailbox.isHalted()) {
            ImmutablePair<String, byte[]> msg = sink.mailbox.getMessage();
            publisher.sendMore(msg.left + "." + serialize_method.toString());
            publisher.send(msg.right, 0);
        }

        //cleanup
    }
    context.term();
}

From source file:msuresh.raftdistdb.AtomixDB.java

/**
 * Main Method which runs a Apache CLI which takes 3 different options for the 3 operations <br>
 * @param args <br>//ww  w  .j a va 2  s  .  c  om
 * Options : <br>
 * -setup numberOfReplicas numberOfPartitions -- which sets the system given thenumber of partitions number of replicas per partition<br>
 * -set key Value -- adds a key value pair to the DB<br>
 * -get key -- returns a value for the key if it exists<br>
 * @throws InterruptedException 
 */
public static void main(String[] args) throws InterruptedException, ExecutionException, FileNotFoundException {
    Options options = new Options();
    Option opt = new Option("setup", true, "Sets up the replica that run the Raft Consensus Algorithm.");
    opt.setArgs(3);
    options.addOption(opt);
    opt = new Option("set", true, " Add a key-value pair into the Distributed Database.");
    opt.setArgs(3);
    options.addOption(opt);
    opt = new Option("get", true, "Given a key gets the value from the DB");
    opt.setArgs(2);
    options.addOption(opt);
    opt = new Option("clean", false, "Cleans the state information.");
    options.addOption(opt);
    opt = new Option("test", true, "Cleans the state information.");
    opt.setArgs(2);
    options.addOption(opt);
    try {
        CommandLineParser parser = new BasicParser();
        CommandLine line = null;
        line = parser.parse(options, args);
        if (line.hasOption("setup")) {
            String[] vals = line.getOptionValues("setup");
            System.out.println(vals[0]);
            RaftCluster.createCluster(vals[0], Integer.parseInt(vals[1]), Integer.parseInt(vals[2]));
        } else if (line.hasOption("set")) {
            String[] vals = line.getOptionValues("set");
            addKey(vals[0], vals[1], vals[2]);
        } else if (line.hasOption("get")) {
            String[] vals = line.getOptionValues("get");
            getKey(vals[0], vals[1]);
        } else if (line.hasOption("clean")) {
            cleanState();
        } else if (line.hasOption("test")) {
            String[] vals = line.getOptionValues("test");
            TestAtomix.createCluster(vals[0], Integer.parseInt(vals[1]));
        }
    } catch (ParseException exp) {
        System.out.println("Unexpected exception:" + exp.getMessage());
    }
}

From source file:com.genentech.chemistry.tool.align.SDFAlign.java

public static void main(String... args) {
    Options options = new Options();
    Option opt = new Option("in", true, "input sd file");
    opt.setRequired(true);//  ww  w . java 2  s  .c o m
    options.addOption(opt);

    opt = new Option("out", true, "output file");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("method", true, "fss|sss|MCS|clique (default mcs).");
    options.addOption(opt);

    opt = new Option("ref", true,
            "reference molecule if not given first in file is used. If multiple ref molecules are read the min RMSD is reported");
    options.addOption(opt);

    opt = new Option("mirror", false, "If given and the molecule is not chiral, return best mirror image.");
    options.addOption(opt);

    opt = new Option("rmsdTag", true, "Tagname for output of rmsd, default: no output.");
    options.addOption(opt);

    opt = new Option("atomMatch", true,
            "Sequence of none|default|hcount|noAromatic specifing how atoms are matched cf. oe document.\n"
                    + "noAromatic can be used to make terminal atoms match aliphatic and aromatic atoms.\n"
                    + "Queryfeatures are considered only if default is used.");
    options.addOption(opt);

    opt = new Option("bondMatch", true,
            "Sequence of none|default specifing how bonds are matched cf. oe document.");
    options.addOption(opt);

    opt = new Option("keepCoreHydrogens", false,
            "If not specified the hydrigen atoms are removed from the core.");
    options.addOption(opt);

    opt = new Option("outputMol", true, "aligned|original (def: aligned) use original to just compute rmsd.");
    options.addOption(opt);

    opt = new Option("doNotOptimize", false,
            "If specified the RMSD is computed without moving optimizing the overlay.");
    options.addOption(opt);

    opt = new Option("quiet", false, "Reduced warining messages");
    options.addOption(opt);

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        exitWithHelp(e.getMessage(), options);
    }

    if (cmd.getArgs().length > 0)
        exitWithHelp("To many arguments", options);

    // do not check aromaticity on atoms so that a terminal atom matches aromatic and non aromatic atoms
    int atomExpr = OEExprOpts.DefaultAtoms;
    int bondExpr = OEExprOpts.DefaultBonds;

    String atomMatch = cmd.getOptionValue("atomMatch");
    if (atomMatch == null)
        atomMatch = "";
    atomMatch = '|' + atomMatch.toLowerCase() + '|';

    String bondMatch = cmd.getOptionValue("bondMatch");
    if (bondMatch == null)
        bondMatch = "";
    bondMatch = '|' + bondMatch.toLowerCase() + '|';

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    String refFile = cmd.getOptionValue("ref");
    String method = cmd.getOptionValue("method");
    String rmsdTag = cmd.getOptionValue("rmsdTag");
    String oMol = cmd.getOptionValue("outputMol");
    boolean doMirror = cmd.hasOption("mirror");
    boolean doOptimize = !cmd.hasOption("doNotOptimize");
    boolean quiet = cmd.hasOption("quiet");

    OUTType outputMol = oMol == null ? OUTType.ALIGNED : OUTType.valueOf(oMol.toUpperCase());

    if (atomMatch.startsWith("|none"))
        atomExpr = 0;
    if (atomMatch.contains("|hcount|"))
        atomExpr |= OEExprOpts.HCount;
    if (atomMatch.contains("|noAromatic|"))
        atomExpr &= (~OEExprOpts.Aromaticity);

    if (bondMatch.startsWith("|none"))
        bondExpr = 0;

    ArrayList<OEMol> refmols = new ArrayList<OEMol>();
    if (refFile != null) {
        oemolistream reffs = new oemolistream(refFile);
        if (!is3DFormat(reffs.GetFormat()))
            oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates");
        reffs.SetFormat(OEFormat.MDL);

        int aromodel = OEIFlavor.Generic.OEAroModelOpenEye;
        int qflavor = reffs.GetFlavor(reffs.GetFormat());
        reffs.SetFlavor(reffs.GetFormat(), (qflavor | aromodel));

        OEMol rmol = new OEMol();
        while (oechem.OEReadMDLQueryFile(reffs, rmol)) {
            if (!cmd.hasOption("keepCoreHydrogens"))
                oechem.OESuppressHydrogens(rmol);
            refmols.add(rmol);
            rmol = new OEMol();
        }
        rmol.delete();

        if (refmols.size() == 0)
            throw new Error("reference file had no entries");

        reffs.close();
    }

    oemolistream fitfs = new oemolistream(inFile);
    if (!is3DFormat(fitfs.GetFormat()))
        oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates");

    oemolostream ofs = new oemolostream(outFile);
    if (!is3DFormat(ofs.GetFormat()))
        oechem.OEThrow.Fatal("Invalid output format: need 3D coordinates");

    AlignInterface aligner = null;
    OEGraphMol fitmol = new OEGraphMol();

    if (oechem.OEReadMolecule(fitfs, fitmol)) {
        if (refmols.size() == 0) {
            OEMol rmol = new OEMol(fitmol);
            if (!cmd.hasOption("keepCoreHydrogens"))
                oechem.OESuppressHydrogens(rmol);

            refmols.add(rmol);
        }

        if ("sss".equalsIgnoreCase(method)) {
            aligner = new SSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);

        } else if ("clique".equalsIgnoreCase(method)) {
            aligner = new CliqueAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);

        } else if ("fss".equalsIgnoreCase(method)) {
            if (cmd.hasOption("atomMatch") || cmd.hasOption("bondMatch"))
                exitWithHelp("method fss does not support '-atomMatch' or '-bondMatch'", options);
            aligner = new FSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror);

        } else {
            aligner = new McsAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);
        }

        do {
            aligner.align(fitmol);
            oechem.OEWriteMolecule(ofs, fitmol);
        } while (oechem.OEReadMolecule(fitfs, fitmol));

    }

    fitmol.delete();
    if (aligner != null)
        aligner.close();
    for (OEMolBase mol : refmols)
        mol.delete();
    fitfs.close();
    ofs.close();
}

From source file:hisqisnoten.HisqisNoten.java

public static void main(String[] args) {
    options = new Options();
    options.addOption("h", "help", false, "this help");
    options.addOption("u", "user", true, "username for hisqis");
    options.addOption("p", "pass", true, "password for hisqis");
    options.addOption("c", "console", false, "console mode instead of gui mode");

    CommandLineParser parser = new PosixParser();

    try {// ww  w .j  av  a2  s . c om
        CommandLine cmdline = parser.parse(options, args);

        if (cmdline.hasOption("help")) {
            printHelp();
            System.exit(0);
        }

        if (cmdline.getArgList().size() != 0) {
            System.err.println("Please use the new commandline options.");
            System.out.println();

            printHelp();
            System.exit(1);
        }

        HisqisSettings settings = null;
        HisqisSettings.genConfigPath();

        for (File configpath : HisqisSettings.configpath) {
            if (configpath.exists() && configpath.canRead()) {
                settings = HisqisSettingsReader.loadDocument(configpath);

                if (settings != null) {
                    break;
                }
            }
        }

        if (settings == null) {
            settings = new HisqisSettings();
        }

        String user = cmdline.getOptionValue("user", null);
        String pass = cmdline.getOptionValue("pass", null);

        if (user != null) {
            settings.username = user;
        }
        if (pass != null) {
            settings.password = pass;
        }

        if (cmdline.hasOption("console")) {
            new HisqisConsole(settings);
        } else {
            new HisqisGUI(settings);
        }
    } catch (ParseException e) {
        printHelp();
    }
}

From source file:edu.msu.cme.rdp.readseq.ToFasta.java

public static void main(String[] args) throws Exception {
    Options options = new Options();
    options.addOption("m", "mask", true, "Mask sequence name indicating columns to drop");
    String maskSeqid = null;//ww  w .ja  va  2 s .  com

    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption("mask")) {
            maskSeqid = line.getOptionValue("mask");
        }

        args = line.getArgs();
        if (args.length == 0) {
            throw new Exception("");
        }

    } catch (Exception e) {
        new HelpFormatter().printHelp("USAGE: to-fasta <input-file>", options);
        System.err.println("ERROR: " + e.getMessage());
        System.exit(1);
        return;
    }

    SeqReader reader = null;

    FastaWriter out = new FastaWriter(System.out);
    Sequence seq;
    int totalSeqs = 0;
    long totalTime = System.currentTimeMillis();

    for (String fname : args) {
        if (fname.equals("-")) {
            reader = new SequenceReader(System.in);
        } else {
            File seqFile = new File(fname);

            if (maskSeqid == null) {
                reader = new SequenceReader(seqFile);
            } else {
                reader = new IndexedSeqReader(seqFile, maskSeqid);
            }
        }

        long startTime = System.currentTimeMillis();
        int thisFileTotalSeqs = 0;
        while ((seq = reader.readNextSequence()) != null) {
            out.writeSeq(seq.getSeqName().replace(" ", "_"), seq.getDesc(), seq.getSeqString());
            thisFileTotalSeqs++;
        }
        totalSeqs += thisFileTotalSeqs;
        System.err.println("Converted " + thisFileTotalSeqs + " (total sequences: " + totalSeqs
                + ") sequences from " + fname + " (" + reader.getFormat() + ") to fasta in "
                + (System.currentTimeMillis() - startTime) / 1000 + " s");
    }
    System.err.println("Converted " + totalSeqs + " to fasta in "
            + (System.currentTimeMillis() - totalTime) / 1000 + " s");

    out.close();
}

From source file:au.id.hazelwood.xmltvguidebuilder.runner.Main.java

public static void main(String[] args) throws Exception {
    SLF4JBridgeHandler.install();//w  w  w  . j  ava 2s  .  c om

    Options options = new Options();
    options.addOption(createOptionWithArg("config", true, "file", File.class, "Config file location"));
    options.addOption(createOptionWithArg("out", true, "file", File.class, "Output file name"));

    try {
        CommandLineParser parser = new GnuParser();
        CommandLine line = parser.parse(options, args);
        App app = new App();
        app.run((File) line.getParsedOptionValue("config"), (File) line.getParsedOptionValue("out"));
    } catch (ParseException exp) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("Main", options, true);
    }
}

From source file:edu.upc.eetac.dsa.exercices.java.lang.exceptions.App.java

public static void main(String[] args) throws FileNotFoundException {
    String filename = null;//  ww w  . j ava 2s . c  o  m
    String maxInteger = null;

    Options options = new Options();
    Option optionFile = OptionBuilder.withArgName("file").hasArg().withDescription("file with integers")
            .withLongOpt("file").create("f");
    options.addOption(optionFile);
    Option optionMax = OptionBuilder.withArgName("max").hasArg()
            .withDescription("maximum integer allowed in the file").withLongOpt("max").create("M");
    options.addOption(optionFile);
    options.addOption(optionMax);

    options.addOption("h", "help", false, "prints this message");

    CommandLineParser parser = new GnuParser();
    CommandLine line = null;
    try {
        // parse the command line arguments
        line = parser.parse(options, args);
        if (line.hasOption("h")) { // No hace falta preguntar por el parmetro "help". Ambos son sinnimos
            new HelpFormatter().printHelp(App.class.getCanonicalName(), options);
            return;
        }
        filename = line.getOptionValue("f");
        if (filename == null) {
            throw new org.apache.commons.cli.ParseException(
                    "You must provide the path to the file with numbers.");
        }
        maxInteger = line.getOptionValue("M");
    } catch (ParseException exp) {
        System.err.println(exp.getMessage());
        new HelpFormatter().printHelp(App.class.getCanonicalName(), options);
        return;
    }

    try {
        int[] numbers = (maxInteger != null) ? FileNumberReader.readFile(filename, Integer.parseInt(maxInteger))
                : FileNumberReader.readFile(filename);
        for (int i = 0; i < numbers.length; i++) {
            System.out.println("Integer read: " + numbers[i]);
        }
    } catch (IOException e) {
        e.printStackTrace();
    } catch (BigNumberException e) {
        e.printStackTrace();
    }
}