Example usage for org.apache.commons.cli CommandLineParser parse

List of usage examples for org.apache.commons.cli CommandLineParser parse

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Introduction

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

Prototype

CommandLine parse(Options options, String[] arguments) throws ParseException;

Source Link

Document

Parse the arguments according to the specified options.

Usage

From source file:gr.demokritos.iit.demos.Demo.java

public static void main(String[] args) {
    try {/* www  .  j  a v  a2  s . com*/
        Options options = new Options();
        options.addOption("h", HELP, false, "show help.");
        options.addOption("i", INPUT, true,
                "The file containing JSON " + " representations of tweets or SAG posts - 1 per line"
                        + " default file looked for is " + DEFAULT_INFILE);
        options.addOption("o", OUTPUT, true,
                "Where to write the output " + " default file looked for is " + DEFAULT_OUTFILE);
        options.addOption("p", PROCESS, true, "Type of processing to do "
                + " ner for Named Entity Recognition re for Relation Extraction" + " default is NER");
        options.addOption("s", SAG, false,
                "Whether to process as SAG posts" + " default is off - if passed means process as SAG posts");

        CommandLineParser parser = new BasicParser();
        CommandLine cmd = parser.parse(options, args);
        // DEFAULTS
        String filename = DEFAULT_INFILE;
        String outfilename = DEFAULT_OUTFILE;
        String process = NER;
        boolean isSAG = false;

        if (cmd.hasOption(HELP)) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("NER + RE extraction module", options);
            System.exit(0);
        }
        if (cmd.hasOption(INPUT)) {
            filename = cmd.getOptionValue(INPUT);
        }
        if (cmd.hasOption(OUTPUT)) {
            outfilename = cmd.getOptionValue(OUTPUT);
        }
        if (cmd.hasOption(SAG)) {
            isSAG = true;
        }
        if (cmd.hasOption(PROCESS)) {
            process = cmd.getOptionValue(PROCESS);
        }
        System.out.println();
        System.out.println("Reading from file: " + filename);
        System.out.println("Process type: " + process);
        System.out.println("Processing SAG: " + isSAG);
        System.out.println("Writing to file: " + outfilename);
        System.out.println();

        List<String> jsoni = new ArrayList();
        Scanner in = new Scanner(new FileReader(filename));
        while (in.hasNextLine()) {
            String json = in.nextLine();
            jsoni.add(json);
        }
        PrintWriter writer = new PrintWriter(outfilename, "UTF-8");
        System.out.println("Read " + jsoni.size() + " lines from " + filename);
        if (process.equalsIgnoreCase(RE)) {
            System.out.println("Running Relation Extraction");
            System.out.println();
            String json = API.RE(jsoni, isSAG);
            System.out.println(json);
            writer.print(json);
        } else {
            System.out.println("Running Named Entity Recognition");
            System.out.println();
            jsoni = API.NER(jsoni, isSAG);
            /*
            for(String json: jsoni){
               NamedEntityList nel = NamedEntityList.fromJSON(json);
               nel.prettyPrint();
            }
            */
            for (String json : jsoni) {
                System.out.println(json);
                writer.print(json);
            }
        }
        writer.close();
    } catch (ParseException | UnsupportedEncodingException | FileNotFoundException ex) {
        Logger.getLogger(Demo.class.getName()).log(Level.SEVERE, null, ex);
    }
}

From source file:com.picdrop.security.SecureStoreMain.java

static public void main(String[] args)
        throws ParseException, IOException, FileNotFoundException, NoSuchAlgorithmException,
        CertificateException, KeyStoreException, KeyStoreException, InterruptedException {

    CommandLineParser cliP = new DefaultParser();

    Options ops = generateBasicOptions();
    CommandLine cli = cliP.parse(ops, args);
    HelpFormatter hlp = new HelpFormatter();

    SecureStore ss;/*from  w w  w .ja va  2  s  .  c  o  m*/
    String path = ".";

    try {
        if (cli.hasOption("help")) {
            hlp.printHelp("SecureStore", ops);
            System.exit(0);
        }

        if (cli.hasOption("keystore")) {
            path = cli.getOptionValue("keystore", ".");
        }

        if (cli.hasOption("create")) {
            ss = new SecureStore(path, false);
            ss.createKeyStore();
            System.exit(0);
        } else {
            ss = new SecureStore(path, true);
        }

        if (cli.hasOption("list")) {
            Enumeration<String> en = ss.listAlias();
            while (en.hasMoreElements()) {
                System.out.println(en.nextElement());
            }
            System.exit(0);
        }

        if (cli.hasOption("store")) {
            ss.storeValue(cli.getOptionValues("store")[0], cli.getOptionValues("store")[1]);
            ss.writeStore();
            System.exit(0);
        }

        if (cli.hasOption("clear")) {
            ss.deleteValue(cli.getOptionValue("clear"));
            ss.writeStore();
            System.exit(0);
        }
    } finally {
        hlp.printHelp("SecureStore", ops);
        System.exit(0);
    }
}

From source file:com.act.lcms.db.io.ExportPlateCompositionFromDB.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    opts.addOption(Option.builder("b").argName("barcode").desc("The barcode of the plate to print").hasArg()
            .longOpt("barcode").build());
    opts.addOption(Option.builder("n").argName("name").desc("The name of the plate to print").hasArg()
            .longOpt("name").build());

    opts.addOption(Option.builder("o").argName("output file").desc(
            "An output file to which to write this plate's composition table (writes to stdout if omitted")
            .hasArg().longOpt("output-file").build());

    // DB connection options.
    opts.addOption(Option.builder().argName("database url")
            .desc("The url to use when connecting to the LCMS db").hasArg().longOpt("db-url").build());
    opts.addOption(Option.builder("u").argName("database user").desc("The LCMS DB user").hasArg()
            .longOpt("db-user").build());
    opts.addOption(Option.builder("p").argName("database password").desc("The LCMS DB password").hasArg()
            .longOpt("db-pass").build());
    opts.addOption(Option.builder("H").argName("database host")
            .desc(String.format("The LCMS DB host (default = %s)", DB.DEFAULT_HOST)).hasArg().longOpt("db-host")
            .build());//from   w w  w . java2s . co  m
    opts.addOption(Option.builder("P").argName("database port")
            .desc(String.format("The LCMS DB port (default = %d)", DB.DEFAULT_PORT)).hasArg().longOpt("db-port")
            .build());
    opts.addOption(Option.builder("N").argName("database name")
            .desc(String.format("The LCMS DB name (default = %s)", DB.DEFAULT_DB_NAME)).hasArg()
            .longOpt("db-name").build());

    // Everybody needs a little help from their friends.
    opts.addOption(
            Option.builder("h").argName("help").desc("Prints this help message").longOpt("help").build());

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        return;
    }

    if (!cl.hasOption("b") && !cl.hasOption("n")) {
        System.err.format("Must specify either plate barcode or plate name.");
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    DB db = null;
    try {
        if (cl.hasOption("db-url")) {
            db = new DB().connectToDB(cl.getOptionValue("db-url"));
        } else {
            Integer port = null;
            if (cl.getOptionValue("P") != null) {
                port = Integer.parseInt(cl.getOptionValue("P"));
            }
            db = new DB().connectToDB(cl.getOptionValue("H"), port, cl.getOptionValue("N"),
                    cl.getOptionValue("u"), cl.getOptionValue("p"));
        }

        Writer writer = null;
        if (cl.hasOption("o")) {
            writer = new FileWriter(cl.getOptionValue("o"));
        } else {
            writer = new OutputStreamWriter(System.out);
        }

        PlateCompositionWriter cw = new PlateCompositionWriter();
        if (cl.hasOption("b")) {
            cw.writePlateCompositionByBarcode(db, cl.getOptionValue("b"), writer);
        } else if (cl.hasOption("n")) {
            cw.writePlateCompositionByName(db, cl.getOptionValue("n"), writer);
        }

        writer.close();
    } finally {
        if (db != null) {
            db.close();
        }
    }
}

From source file:com.etsy.arbiter.Arbiter.java

public static void main(String[] args) throws ParseException, ConfigurationException, IOException,
        ParserConfigurationException, TransformerException {
    Options options = getOptions();//from www .ja  va2  s  .  c  o  m

    CommandLineParser cmd = new GnuParser();
    CommandLine parsed = cmd.parse(options, args);

    if (parsed.hasOption("h")) {
        printUsage(options);
    }

    if (!parsed.hasOption("i")) {
        throw new ParseException("Missing required argument: i");
    }

    if (!parsed.hasOption("o")) {
        throw new ParseException("Missing required argument: o");
    }

    String[] configFiles = parsed.getOptionValues("c");
    String[] lowPrecedenceConfigFiles = parsed.getOptionValues("l");

    String[] inputFiles = parsed.getOptionValues("i");
    String outputDir = parsed.getOptionValue("o");

    List<Config> parsedConfigFiles = readConfigFiles(configFiles, false);
    parsedConfigFiles.addAll(readConfigFiles(lowPrecedenceConfigFiles, true));
    Config merged = ConfigurationMerger.mergeConfiguration(parsedConfigFiles);

    List<Workflow> workflows = readWorkflowFiles(inputFiles);

    boolean generateGraphviz = parsed.hasOption("g");
    String graphvizFormat = parsed.getOptionValue("g", "svg");

    OozieWorkflowGenerator generator = new OozieWorkflowGenerator(merged);
    generator.generateOozieWorkflows(outputDir, workflows, generateGraphviz, graphvizFormat);
}

From source file:com.act.lcms.db.io.LoadConstructAnalysisTableIntoDB.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    opts.addOption(Option.builder("i").argName("path").desc("The TSV file to read").hasArg().required()
            .longOpt("input-file").build());

    // DB connection options.
    opts.addOption(Option.builder().argName("database url")
            .desc("The url to use when connecting to the LCMS db").hasArg().longOpt("db-url").build());
    opts.addOption(Option.builder("u").argName("database user").desc("The LCMS DB user").hasArg()
            .longOpt("db-user").build());
    opts.addOption(Option.builder("p").argName("database password").desc("The LCMS DB password").hasArg()
            .longOpt("db-pass").build());
    opts.addOption(Option.builder("H").argName("database host")
            .desc(String.format("The LCMS DB host (default = %s)", DB.DEFAULT_HOST)).hasArg().longOpt("db-host")
            .build());/*from www .j av a  2 s .c om*/
    opts.addOption(Option.builder("P").argName("database port")
            .desc(String.format("The LCMS DB port (default = %d)", DB.DEFAULT_PORT)).hasArg().longOpt("db-port")
            .build());
    opts.addOption(Option.builder("N").argName("database name")
            .desc(String.format("The LCMS DB name (default = %s)", DB.DEFAULT_DB_NAME)).hasArg()
            .longOpt("db-name").build());

    // Everybody needs a little help from their friends.
    opts.addOption(
            Option.builder("h").argName("help").desc("Prints this help message").longOpt("help").build());

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HelpFormatter fmt = new HelpFormatter();
        fmt.printHelp(LoadConstructAnalysisTableIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        new HelpFormatter().printHelp(LoadConstructAnalysisTableIntoDB.class.getCanonicalName(), opts, true);
        return;
    }

    File inputFile = new File(cl.getOptionValue("input-file"));
    if (!inputFile.exists()) {
        System.err.format("Unable to find input file at %s\n", cl.getOptionValue("input-file"));
        new HelpFormatter().printHelp(LoadConstructAnalysisTableIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    DB db;

    if (cl.hasOption("db-url")) {
        db = new DB().connectToDB(cl.getOptionValue("db-url"));
    } else {
        Integer port = null;
        if (cl.getOptionValue("P") != null) {
            port = Integer.parseInt(cl.getOptionValue("P"));
        }
        db = new DB().connectToDB(cl.getOptionValue("H"), port, cl.getOptionValue("N"), cl.getOptionValue("u"),
                cl.getOptionValue("p"));
    }

    try {
        db.getConn().setAutoCommit(false);

        ConstructAnalysisFileParser parser = new ConstructAnalysisFileParser();
        parser.parse(inputFile);

        List<Pair<Integer, DB.OPERATION_PERFORMED>> results = ChemicalAssociatedWithPathway
                .insertOrUpdateChemicalsAssociatedWithPathwayFromParser(db, parser);
        if (results != null) {
            for (Pair<Integer, DB.OPERATION_PERFORMED> r : results) {
                System.out.format("%d: %s\n", r.getLeft(), r.getRight());
            }
        }
        // If we didn't encounter an exception, commit the transaction.
        db.getConn().commit();
    } catch (Exception e) {
        System.err.format("Caught exception when trying to load plate composition, rolling back. %s\n",
                e.getMessage());
        db.getConn().rollback();
        throw (e);
    } finally {
        db.getConn().close();
    }

}

From source file:com.example.geomesa.kafka08.KafkaListener.java

public static void main(String[] args) throws Exception {
    // read command line args for a connection to Kafka
    CommandLineParser parser = new BasicParser();
    Options options = getCommonRequiredOptions();
    CommandLine cmd = parser.parse(options, args);

    // create the consumer KafkaDataStore object
    Map<String, String> dsConf = getKafkaDataStoreConf(cmd);
    dsConf.put("isProducer", "false");
    DataStore consumerDS = DataStoreFinder.getDataStore(dsConf);

    // verify that we got back our KafkaDataStore object properly
    if (consumerDS == null) {
        throw new Exception("Null consumer KafkaDataStore");
    }/*from  ww w .ja v  a 2  s  .  co  m*/

    // create the schema which creates a topic in Kafka
    // (only needs to be done once)
    // TODO: This should be rolled into the Command line options to make this more general.
    registerListeners(consumerDS);

    while (true) {
        // Wait for user to terminate with ctrl-C.
    }
}

From source file:eu.scape_project.pc.hadoop.DroidIdentifyHadoopJob.java

/**
 * The main entry point.//  w  ww.ja  va 2  s  .co  m
 */
public static void main(String[] args) throws ParseException {
    Configuration conf = new Configuration();
    GenericOptionsParser gop = new GenericOptionsParser(conf, args);
    HadoopJobCliConfig pc = new HadoopJobCliConfig();
    CommandLineParser cmdParser = new PosixParser();
    CommandLine cmd = cmdParser.parse(HadoopJobOptions.OPTIONS, gop.getRemainingArgs());
    if ((args.length == 0) || (cmd.hasOption(HadoopJobOptions.HELP_OPT))) {
        HadoopJobOptions.exit("Usage", 0);
    } else {
        HadoopJobOptions.initOptions(cmd, pc);
    }
    String dir = pc.getDirStr();

    String name = pc.getHadoopJobName();
    if (name == null || name.equals("")) {
        name = "droid_identification";
    }

    try {
        Job job = new Job(conf, name);

        // local debugging
        //            job.getConfiguration().set("mapred.job.tracker", "local");
        //            job.getConfiguration().set("fs.default.name", "file:///");

        job.setJarByClass(DroidIdentifyHadoopJob.class);

        job.setMapperClass(DroidIdentifyMapper.class);
        //job.setCombinerClass(DroidIdentifyReducer.class);
        job.setReducerClass(DroidIdentifyReducer.class);

        job.setInputFormatClass(TextInputFormat.class);

        job.setOutputFormatClass(TextOutputFormat.class);
        //SequenceFileOutputFormat.setOutputCompressionType(job, SequenceFile.CompressionType.NONE);

        //conf.setMapOutputKeyClass(Text.class);
        job.setMapOutputKeyClass(Text.class);
        job.setMapOutputValueClass(LongWritable.class);

        job.setOutputKeyClass(Text.class);
        job.setOutputValueClass(LongWritable.class);

        SequenceFileInputFormat.addInputPath(job, new Path(dir));
        String outpath = "output/" + System.currentTimeMillis() + "dri";
        FileOutputFormat.setOutputPath(job, new Path(outpath));
        job.waitForCompletion(true);
        System.out.print(outpath);
        System.exit(0);
    } catch (Exception e) {
        logger.error("I/O error", e);
    }
}

From source file:is.iclt.icenlp.runner.RunLemmald.java

public static void main(String[] args) {

    CommandLineParser parser = new GnuParser();
    try {/* ww  w.j a  v  a  2 s .c  o  m*/
        // parse the command line arguments
        CommandLine cmdLine = parser.parse(options, args);
        if (cmdLine.hasOption("h")) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("lemmatize.sh", options);
        } else {
            runConsole(cmdLine);
        }
    } catch (ParseException exp) {
        // oops, something went wrong
        System.err.println("Could not parse command line arguments.  Reason: " + exp.getMessage());
    }

}

From source file:net.sf.brunneng.iqdb.db.DBWorker.java

public static void main(String[] args) {
    Options options = new Options();

    Option actionOpt = new Option("a", "action", true, "The action on db, which should be executed." + BR_LINE
            + " Possible actions: " + BR_LINE + createActionsDescription());
    actionOpt.setRequired(true);/*from   w  ww . ja  v a2 s  .  c om*/
    options.addOption(actionOpt);

    CommandLineParser parser = new GnuParser();
    try {
        CommandLine commandLine = parser.parse(options, args);

        String actionStr = commandLine.getOptionValue("action");
        DBAction action = null;
        try {
            action = DBAction.valueOf(actionStr);
        } catch (IllegalStateException exc) {
            System.out.println("Unknown action: " + actionStr);
            System.out.println("Possible actions: " + createActionsDescription());
            System.exit(-1);
        }

        DBWorker worker = new DBWorker(action, null, null, null);
        worker.execute();
    } catch (ParseException exc) {
        System.out.println("Unable to parse command line arguments. Error: " + exc.getMessage());
        printUsageAndExit(options);
    }
}

From source file:com.github.r351574nc3.amex.assignment1.App.java

public static void main(final String... args) {
    if (args.length < 1) {
        printUsage();//from w ww . j a v a 2  s  .  c  o m
        System.exit(0);
    }

    final Options options = new Options();
    options.addOption(OptionBuilder.withArgName("output").hasArg(true).withDescription("Path for CSV output")
            .create("o"));
    options.addOption(
            OptionBuilder.withArgName("input").hasArg(true).withDescription("Path for CSV input").create("i"));

    final CommandLineParser parser = new BasicParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.out.println(e.getMessage());
        printUsage();
        System.exit(0);
    }

    if ((cmd.hasOption('o') && cmd.hasOption('i')) || !(cmd.hasOption('o') || cmd.hasOption('i'))
            || (cmd.hasOption('o') && cmd.getArgs().length < 1)) {
        printUsage();
        System.exit(0);
    }

    if (cmd.hasOption('o') && cmd.getArgs().length > 0) {
        final String outputName = cmd.getOptionValue("o");
        final int iterations = Integer.parseInt(cmd.getArgs()[cmd.getArgs().length - 1]);
        new App().run(new File(outputName), iterations);
    } else if (cmd.hasOption('i')) {
        final String inputName = cmd.getOptionValue("i");
        new App().run(new File(inputName));
    }

    System.exit(0);
}