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

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

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Introduction

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

Prototype

GnuParser

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Usage

From source file:fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction.java

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

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

    int argsOptions = 0;

    try {/*from  w  w w  . j  av a 2  s .com*/

        // 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);
}

From source file:com.digitalpebble.behemoth.util.CorpusFilter.java

public int run(String[] args) throws Exception {

    Options options = new Options();
    // automatically generate the help statement
    HelpFormatter formatter = new HelpFormatter();
    // create the parser
    CommandLineParser parser = new GnuParser();

    options.addOption("h", "help", false, "print this message");
    options.addOption("i", "input", true, "input Behemoth corpus");
    options.addOption("o", "output", true, "output Behemoth corpus");

    // parse the command line arguments
    CommandLine line = null;/*from   w  ww. j av a 2s  . c  o m*/
    try {
        line = parser.parse(options, args);
        String input = line.getOptionValue("i");
        String output = line.getOptionValue("o");
        if (line.hasOption("help")) {
            formatter.printHelp("CorpusFilter", options);
            return 0;
        }
        if (input == null | output == null) {
            formatter.printHelp("CorpusFilter", options);
            return -1;
        }
    } catch (ParseException e) {
        formatter.printHelp("CorpusFilter", options);
    }

    final FileSystem fs = FileSystem.get(getConf());

    Path inputPath = new Path(line.getOptionValue("i"));
    Path outputPath = new Path(line.getOptionValue("o"));

    JobConf job = new JobConf(getConf());
    job.setJarByClass(this.getClass());

    job.setJobName("CorpusFilter : " + inputPath.toString());

    job.setInputFormat(SequenceFileInputFormat.class);
    job.setOutputFormat(SequenceFileOutputFormat.class);

    job.setMapOutputKeyClass(Text.class);
    job.setMapOutputValueClass(BehemothDocument.class);
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(BehemothDocument.class);

    boolean isFilterRequired = BehemothMapper.isRequired(job);
    // should be the case here
    if (!isFilterRequired) {
        System.err.println("No filters configured. Check your behemoth-site.xml");
        return -1;
    }
    job.setMapperClass(BehemothMapper.class);
    job.setNumReduceTasks(0);

    FileInputFormat.addInputPath(job, inputPath);
    FileOutputFormat.setOutputPath(job, outputPath);

    try {
        JobClient.runJob(job);
    } catch (Exception e) {
        e.printStackTrace();
        fs.delete(outputPath, true);
    } finally {
    }

    return 0;
}

From source file:TikaServiceWinRun4J.java

public int serviceMain(String[] args) {
    Properties properties = new Properties();
    try {/*from  w w  w  .ja v a  2 s .  c  om*/
        properties.load(ClassLoader.getSystemResourceAsStream("tikaserver-version.properties"));
    } catch (IOException e) {
        throw new RuntimeException(e);
    }

    logger.info("Starting Tika server " + properties.getProperty("tikaserver.version"));

    try {
        Options options = getOptions();

        CommandLineParser cliParser = new GnuParser();
        CommandLine line = cliParser.parse(options, args);

        int port = DEFAULT_PORT;

        if (line.hasOption("port")) {
            port = Integer.valueOf(line.getOptionValue("port"));
        }
        if (line.hasOption("help")) {
            HelpFormatter helpFormatter = new HelpFormatter();
            helpFormatter.printHelp("tikaserver", options);
            System.exit(-1);
        }

        server = new Server(port);
        ServletContextHandler context = new ServletContextHandler(ServletContextHandler.NO_SESSIONS);
        context.setContextPath("/");
        server.setHandler(context);

        context.addServlet(
                new ServletHolder(new ServletContainer(new PackagesResourceConfig("org.apache.tika.server"))),
                "/*");

        server.start();
        logger.info("Started");
        server.join();

        return 0;
    } catch (Exception ex) {
        logger.fatal("Can't start", ex);
        return 1;
    }
}

From source file:edu.umd.shrawanraina.HBaseWordCountFetch.java

/**
 * Runs this tool.//  ww w .  ja v  a 2  s.  co m
 */
@SuppressWarnings({ "static-access" })
public int run(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(
            OptionBuilder.withArgName("table").hasArg().withDescription("HBase table name").create(TABLE));
    options.addOption(
            OptionBuilder.withArgName("word").hasArg().withDescription("word to look up").create(WORD));

    CommandLine cmdline;
    CommandLineParser parser = new GnuParser();

    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        return -1;
    }

    if (!cmdline.hasOption(TABLE) || !cmdline.hasOption(WORD)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(this.getClass().getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        return -1;
    }

    String tableName = cmdline.getOptionValue(TABLE);
    String word = cmdline.getOptionValue(WORD);

    Configuration conf = getConf();
    conf.addResource(new Path("/etc/hbase/conf/hbase-site.xml"));

    Configuration hbaseConfig = HBaseConfiguration.create(conf);
    HConnection hbaseConnection = HConnectionManager.createConnection(hbaseConfig);
    HTableInterface table = hbaseConnection.getTable(tableName);

    Get get = new Get(Bytes.toBytes(word));
    Result result = table.get(get);

    int count = Bytes.toInt(result.getValue(HBaseWordCount.CF, HBaseWordCount.COUNT));

    LOG.info("word: " + word + ", count: " + count);
    LOG.info("word: " + word + ", result: " + result.getValue(HBaseWordCount.CF, HBaseWordCount.COUNT));
    return 0;
}

From source file:edu.umd.cloud9.example.hbase.HBaseWordCountFetch.java

/**
 * Runs this tool.//  w w w  .j  a v a 2s  .  c  om
 */
@SuppressWarnings({ "static-access" })
public int run(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(
            OptionBuilder.withArgName("table").hasArg().withDescription("HBase table name").create(TABLE));
    options.addOption(
            OptionBuilder.withArgName("word").hasArg().withDescription("word to look up").create(WORD));

    CommandLine cmdline;
    CommandLineParser parser = new GnuParser();

    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        return -1;
    }

    if (!cmdline.hasOption(TABLE) || !cmdline.hasOption(WORD)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(this.getClass().getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        return -1;
    }

    String tableName = cmdline.getOptionValue(TABLE);
    String word = cmdline.getOptionValue(WORD);

    Configuration conf = getConf();
    conf.addResource(new Path("/etc/hbase/conf/hbase-site.xml"));

    Configuration hbaseConfig = HBaseConfiguration.create(conf);
    HConnection hbaseConnection = HConnectionManager.createConnection(hbaseConfig);
    HTableInterface table = hbaseConnection.getTable(tableName);

    Get get = new Get(Bytes.toBytes(word));
    Result result = table.get(get);

    int count = Bytes.toInt(result.getValue(HBaseWordCount.CF, HBaseWordCount.COUNT));

    LOG.info("word: " + word + ", count: " + count);

    return 0;
}

From source file:com.zimbra.cs.mailclient.smtp.SmtpClient.java

@Override
protected void parseArguments(String[] args, MailConfig config) {
    CommandLineParser parser = new GnuParser();
    CommandLine cl = null;/*from w  w  w  .  ja  v a2s.  co m*/
    try {
        cl = parser.parse(options, args);
    } catch (ParseException e) {
        System.err.println(e.getMessage());
        System.exit(1);
    }

    if (cl.hasOption('p')) {
        config.setPort(Integer.parseInt(cl.getOptionValue('p')));
    } else {
        config.setPort(SmtpConfig.DEFAULT_PORT);
    }
    if (cl.hasOption('m')) {
        config.setMechanism(cl.getOptionValue('m').toUpperCase());
    }
    if (cl.hasOption('u')) {
        config.setAuthenticationId(cl.getOptionValue('u'));
    }
    if (cl.hasOption('w')) {
        setPassword(cl.getOptionValue('w'));
    }
    if (cl.hasOption('r')) {
        config.setRealm(cl.getOptionValue('r'));
    }
    if (cl.hasOption('s')) {
        config.setSecurity(MailConfig.Security.SSL);
    }
    if (cl.hasOption('d')) {
        config.getLogger().setLevel(Log.Level.trace);
    }
    if (cl.hasOption('h')) {
        usage();
        System.exit(0);
    }

    String[] remaining = cl.getArgs();
    config.setHost(remaining.length > 0 ? remaining[0] : "localhost");
}

From source file:LookupPostings.java

/**
 * Runs this tool./*w w  w.j av a2s .c o  m*/
 */
@SuppressWarnings({ "static-access" })
public int run(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INDEX));
    options.addOption(
            OptionBuilder.withArgName("path").hasArg().withDescription("output path").create(COLLECTION));

    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();

    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        System.exit(-1);
    }

    if (!cmdline.hasOption(INDEX) || !cmdline.hasOption(COLLECTION)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(LookupPostings.class.getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        System.exit(-1);
    }

    String indexPath = cmdline.getOptionValue(INDEX);
    String collectionPath = cmdline.getOptionValue(COLLECTION);

    if (collectionPath.endsWith(".gz")) {
        System.out.println("gzipped collection is not seekable: use compressed version!");
        System.exit(-1);
    }

    Configuration config = new Configuration();
    FileSystem fs = FileSystem.get(config);
    MapFile.Reader reader = new MapFile.Reader(new Path(indexPath + "/part-r-00000"), config);

    FSDataInputStream collection = fs.open(new Path(collectionPath));
    BufferedReader d = new BufferedReader(new InputStreamReader(collection));

    Text key = new Text();
    PairOfWritables<IntWritable, ArrayListWritable<PairOfInts>> value = new PairOfWritables<IntWritable, ArrayListWritable<PairOfInts>>();

    System.out.println("Looking up postings for the term \"starcross'd\"");
    key.set("starcross'd");

    reader.get(key, value);

    ArrayListWritable<PairOfInts> postings = value.getRightElement();
    for (PairOfInts pair : postings) {
        System.out.println(pair);
        collection.seek(pair.getLeftElement());
        System.out.println(d.readLine());
    }

    key.set("gold");
    reader.get(key, value);
    System.out.println("Complete postings list for 'gold': " + value);

    Int2IntFrequencyDistribution goldHist = new Int2IntFrequencyDistributionEntry();
    postings = value.getRightElement();
    for (PairOfInts pair : postings) {
        goldHist.increment(pair.getRightElement());
    }

    System.out.println("histogram of tf values for gold");
    for (PairOfInts pair : goldHist) {
        System.out.println(pair.getLeftElement() + "\t" + pair.getRightElement());
    }

    key.set("silver");
    reader.get(key, value);
    System.out.println("Complete postings list for 'silver': " + value);

    Int2IntFrequencyDistribution silverHist = new Int2IntFrequencyDistributionEntry();
    postings = value.getRightElement();
    for (PairOfInts pair : postings) {
        silverHist.increment(pair.getRightElement());
    }

    System.out.println("histogram of tf values for silver");
    for (PairOfInts pair : silverHist) {
        System.out.println(pair.getLeftElement() + "\t" + pair.getRightElement());
    }

    key.set("bronze");
    Writable w = reader.get(key, value);

    if (w == null) {
        System.out.println("the term bronze does not appear in the collection");
    }

    collection.close();
    reader.close();

    return 0;
}

From source file:com.github.hdl.tensorflow.yarn.app.TFServerLauncher.java

public boolean init(String[] args) throws ParseException, IOException {

    CommandLine cliParser = new GnuParser().parse(opts, args);

    if (args.length == 0) {
        throw new IllegalArgumentException("No args specified for tf server to initialize");
    }/* w w w  . ja  v a 2 s.c o  m*/

    if (!cliParser.hasOption(OPT_CS) || !cliParser.hasOption(OPT_JN) || !cliParser.hasOption(OPT_TI)) {
        LOG.error("invalid args for tf server!");
        return false;
    }

    clusterSpecString = ClusterSpec.decodeJsonString(cliParser.getOptionValue(OPT_CS));
    jobName = cliParser.getOptionValue(OPT_JN);
    taskIndex = Integer.parseInt(cliParser.getOptionValue(OPT_TI));
    LOG.info("cs: " + clusterSpecString + "; + jn: " + jobName + "; ti: " + taskIndex);
    cluster = ClusterSpec.toClusterMapFromJsonString(clusterSpecString);
    return true;
}

From source file:com.strider.appinv.agent.Scanner.java

/**
 * Parses command line arguments/* www.j  a  v  a2s  . com*/
 *
 * @param options
 * @param args
 * @return CommandLine
 * @throws ParseException
 */
private static CommandLine getCommandLine(final Options options, final String[] args) throws ParseException {
    final CommandLineParser parser = new GnuParser();
    CommandLine line = null;

    try {
        line = parser.parse(options, args);
    } catch (ParseException e) {
        help(options);
    }

    return line;
}

From source file:fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction.java

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

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

    String jobDescription = null;

    int argsOptions = 0;

    try {//from   w w  w.  j  av a  2  s .c o  m

        // 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);
}