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

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

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

Prototype

BasicParser

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From source file:com.tbodt.trp.TheRapidPermuter.java

/**
 * Main method for The Rapid Permuter.//from  www .ja  v a 2s  .  co  m
 *
 * @param args
 * @throws IOException
 */
public static void main(String[] args) throws IOException {
    CommandProcessor.processCommand("\"\": remove(\"\") in([words])").ifPresent(x -> x.forEach(y -> {
    })); // to load all the classes we need

    try {
        cmd = new BasicParser().parse(options, args);
    } catch (ParseException ex) {
        System.err.println(ex.getMessage());
        return;
    }

    if (Arrays.asList(cmd.getOptions()).contains(help)) { // another way commons cli is severely broken
        new HelpFormatter().printHelp("trp", options);
        return;
    }

    if (cmd.hasOption('c'))
        doCommand(cmd.getOptionValue('c'));
    else {
        BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
        System.out.print("trp> ");
        String input;
        while ((input = in.readLine()) != null) {
            if (input.equals("exit"))
                return; // exit
            doCommand(input);
            System.out.print("trp> ");
        }
    }
}

From source file:fr.tpt.atlanalyser.tests.TestPointsToLinesPost2Pre.java

@SuppressWarnings("static-access")
public static void main(String[] args) throws IOException {

    // URL resource = Thread.currentThread().getContextClassLoader()
    // .getResource("OldAGTExp");
    // System.out.println(resource.toString());
    // File f = new File(resource.getPath());
    // System.out.println(f.toString());
    // System.out.println(f.isDirectory());
    // System.exit(0);

    Options options = new Options();
    options.addOption(// ww w . j av  a  2 s  .  co  m
            OptionBuilder.hasArg().withArgName("N").withDescription("Number of parallel jobs").create("j"));
    options.addOption(OptionBuilder.withDescription("Display help").create("h"));

    CommandLineParser parser = new BasicParser();
    int jobs = 1;
    try {
        CommandLine cmd = parser.parse(options, args);
        if (cmd.hasOption("h")) {
            new HelpFormatter().printHelp(TestPointsToLinesPost2Pre.class.getSimpleName(), options);
            System.exit(0);
        }

        if (cmd.hasOption("j")) {
            jobs = Integer.parseInt(cmd.getOptionValue("j"));
        }
    } catch (Exception e) {
        System.out.println("Incorrect command line arguments");
        new HelpFormatter().printHelp(TestPointsToLinesPost2Pre.class.getSimpleName(), options);
        System.exit(1);
    }

    new TestPointsToLinesPost2Pre(models().get(1)[0], jobs).testPost2Pre();
}

From source file:fr.tpt.atlanalyser.tests.TestClass2RelationalPost2Pre.java

@SuppressWarnings("static-access")
public static void main(String[] args) throws IOException {

    // URL resource = Thread.currentThread().getContextClassLoader()
    // .getResource("OldAGTExp");
    // System.out.println(resource.toString());
    // File f = new File(resource.getPath());
    // System.out.println(f.toString());
    // System.out.println(f.isDirectory());
    // System.exit(0);

    Options options = new Options();
    options.addOption(//from   w w w .j  a  v a2s .  c o  m
            OptionBuilder.hasArg().withArgName("N").withDescription("Number of parallel jobs").create("j"));
    options.addOption(OptionBuilder.withDescription("Display help").create("h"));

    CommandLineParser parser = new BasicParser();
    int jobs = 2;
    try {
        CommandLine cmd = parser.parse(options, args);
        if (cmd.hasOption("h")) {
            new HelpFormatter().printHelp(TestClass2RelationalPost2Pre.class.getSimpleName(), options);
            System.exit(0);
        }

        if (cmd.hasOption("j")) {
            jobs = Integer.parseInt(cmd.getOptionValue("j"));
        }
    } catch (Exception e) {
        System.out.println("Incorrect command line arguments");
        new HelpFormatter().printHelp(TestClass2RelationalPost2Pre.class.getSimpleName(), options);
        System.exit(1);
    }

    new TestClass2RelationalPost2Pre(models().get(0)[0], jobs).testPost2Pre();
}

From source file:hyperloglog.tools.HyperLogLogCLI.java

public static void main(String[] args) {
    Options options = new Options();
    addOptions(options);//from w  w  w  .j  a v  a 2  s.  co  m

    CommandLineParser parser = new BasicParser();
    CommandLine cli = null;
    long n = 0;
    long seed = 123;
    EncodingType enc = EncodingType.SPARSE;
    int p = 14;
    int hb = 64;
    boolean bitPack = true;
    boolean noBias = true;
    int unique = -1;
    String filePath = null;
    BufferedReader br = null;
    String outFile = null;
    String inFile = null;
    FileOutputStream fos = null;
    DataOutputStream out = null;
    FileInputStream fis = null;
    DataInputStream in = null;
    try {
        cli = parser.parse(options, args);

        if (!(cli.hasOption('n') || cli.hasOption('f') || cli.hasOption('d'))) {
            System.out.println("Example usage: hll -n 1000 " + "<OR> hll -f /tmp/input.txt "
                    + "<OR> hll -d -i /tmp/out.hll");
            usage(options);
            return;
        }

        if (cli.hasOption('n')) {
            n = Long.parseLong(cli.getOptionValue('n'));
        }

        if (cli.hasOption('e')) {
            String value = cli.getOptionValue('e');
            if (value.equals(EncodingType.DENSE.name())) {
                enc = EncodingType.DENSE;
            }
        }

        if (cli.hasOption('p')) {
            p = Integer.parseInt(cli.getOptionValue('p'));
            if (p < 4 && p > 16) {
                System.out.println("Warning! Out-of-range value specified for p. Using to p=14.");
                p = 14;
            }
        }

        if (cli.hasOption('h')) {
            hb = Integer.parseInt(cli.getOptionValue('h'));
        }

        if (cli.hasOption('c')) {
            noBias = Boolean.parseBoolean(cli.getOptionValue('c'));
        }

        if (cli.hasOption('b')) {
            bitPack = Boolean.parseBoolean(cli.getOptionValue('b'));
        }

        if (cli.hasOption('f')) {
            filePath = cli.getOptionValue('f');
            br = new BufferedReader(new FileReader(new File(filePath)));
        }

        if (filePath != null && cli.hasOption('n')) {
            System.out.println("'-f' (input file) specified. Ignoring -n.");
        }

        if (cli.hasOption('s')) {
            if (cli.hasOption('o')) {
                outFile = cli.getOptionValue('o');
                fos = new FileOutputStream(new File(outFile));
                out = new DataOutputStream(fos);
            } else {
                System.err.println("Specify output file. Example usage: hll -s -o /tmp/out.hll");
                usage(options);
                return;
            }
        }

        if (cli.hasOption('d')) {
            if (cli.hasOption('i')) {
                inFile = cli.getOptionValue('i');
                fis = new FileInputStream(new File(inFile));
                in = new DataInputStream(fis);
            } else {
                System.err.println("Specify input file. Example usage: hll -d -i /tmp/in.hll");
                usage(options);
                return;
            }
        }

        // return after deserialization
        if (fis != null && in != null) {
            long start = System.currentTimeMillis();
            HyperLogLog deserializedHLL = HyperLogLogUtils.deserializeHLL(in);
            long end = System.currentTimeMillis();
            System.out.println(deserializedHLL.toString());
            System.out.println("Count after deserialization: " + deserializedHLL.count());
            System.out.println("Deserialization time: " + (end - start) + " ms");
            return;
        }

        // construct hll and serialize it if required
        HyperLogLog hll = HyperLogLog.builder().enableBitPacking(bitPack).enableNoBias(noBias).setEncoding(enc)
                .setNumHashBits(hb).setNumRegisterIndexBits(p).build();

        if (br != null) {
            Set<String> hashset = new HashSet<String>();
            String line;
            while ((line = br.readLine()) != null) {
                hll.addString(line);
                hashset.add(line);
            }
            n = hashset.size();
        } else {
            Random rand = new Random(seed);
            for (int i = 0; i < n; i++) {
                if (unique < 0) {
                    hll.addLong(rand.nextLong());
                } else {
                    int val = rand.nextInt(unique);
                    hll.addLong(val);
                }
            }
        }

        long estCount = hll.count();
        System.out.println("Actual count: " + n);
        System.out.println(hll.toString());
        System.out.println("Relative error: " + HyperLogLogUtils.getRelativeError(n, estCount) + "%");
        if (fos != null && out != null) {
            long start = System.currentTimeMillis();
            HyperLogLogUtils.serializeHLL(out, hll);
            long end = System.currentTimeMillis();
            System.out.println("Serialized hyperloglog to " + outFile);
            System.out.println("Serialized size: " + out.size() + " bytes");
            System.out.println("Serialization time: " + (end - start) + " ms");
            out.close();
        }
    } catch (ParseException e) {
        System.err.println("Invalid parameter.");
        usage(options);
    } catch (NumberFormatException e) {
        System.err.println("Invalid type for parameter.");
        usage(options);
    } catch (FileNotFoundException e) {
        System.err.println("Specified file not found.");
        usage(options);
    } catch (IOException e) {
        System.err.println("Exception occured while reading file.");
        usage(options);
    }
}

From source file:it.tizianofagni.sparkboost.BoostClassifierExe.java

public static void main(String[] args) {

    Options options = new Options();
    options.addOption("b", "binaryProblem", false,
            "Indicate if the input dataset contains a binary problem and not a multilabel one");
    options.addOption("z", "labels0based", false,
            "Indicate if the labels IDs in the dataset to classifyLibSvmWithResults are already assigned in the range [0, numLabels-1] included");
    options.addOption("l", "enableSparkLogging", false, "Enable logging messages of Spark");
    options.addOption("w", "windowsLocalModeFix", true,
            "Set the directory containing the winutils.exe command");
    options.addOption("p", "parallelismDegree", true,
            "Set the parallelism degree (default: number of available cores in the Spark runtime");

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = null;/*from w w  w  . j  av a2  s . c om*/
    String[] remainingArgs = null;
    try {
        cmd = parser.parse(options, args);
        remainingArgs = cmd.getArgs();
        if (remainingArgs.length != 3)
            throw new ParseException("You need to specify all mandatory parameters");
    } catch (ParseException e) {
        System.out.println("Parsing failed.  Reason: " + e.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(
                BoostClassifierExe.class.getSimpleName() + " [OPTIONS] <inputFile> <inputModel> <outputFile>",
                options);
        System.exit(-1);
    }

    boolean binaryProblem = false;
    if (cmd.hasOption("b"))
        binaryProblem = true;
    boolean labels0Based = false;
    if (cmd.hasOption("z"))
        labels0Based = true;
    boolean enablingSparkLogging = false;
    if (cmd.hasOption("l"))
        enablingSparkLogging = true;

    if (cmd.hasOption("w")) {
        System.setProperty("hadoop.home.dir", cmd.getOptionValue("w"));
    }

    String inputFile = remainingArgs[0];
    String inputModel = remainingArgs[1];
    String outputFile = remainingArgs[2];

    long startTime = System.currentTimeMillis();

    // Disable Spark logging.
    if (!enablingSparkLogging) {
        Logger.getLogger("org").setLevel(Level.OFF);
        Logger.getLogger("akka").setLevel(Level.OFF);
    }

    // Create and configure Spark context.
    SparkConf conf = new SparkConf().setAppName("Spark MPBoost classifier");
    JavaSparkContext sc = new JavaSparkContext(conf);

    // Load boosting classifier from disk.
    BoostClassifier classifier = DataUtils.loadModel(sc, inputModel);

    // Get the parallelism degree.
    int parallelismDegree = sc.defaultParallelism();
    if (cmd.hasOption("p")) {
        parallelismDegree = Integer.parseInt(cmd.getOptionValue("p"));
    }

    // Classify documents available on specified input file.
    classifier.classifyLibSvm(sc, inputFile, parallelismDegree, labels0Based, binaryProblem, outputFile);
    long endTime = System.currentTimeMillis();
    System.out.println("Execution time: " + (endTime - startTime) + " milliseconds.");
}

From source file:com.adobe.aem.demo.Analytics.java

public static void main(String[] args) {

    String hostname = null;/*from  w w w .  j av a  2 s .  c om*/
    String url = null;
    String eventfile = null;

    // Command line options for this tool
    Options options = new Options();
    options.addOption("h", true, "Hostname");
    options.addOption("u", true, "Url");
    options.addOption("f", true, "Event data file");
    CommandLineParser parser = new BasicParser();
    try {
        CommandLine cmd = parser.parse(options, args);

        if (cmd.hasOption("u")) {
            url = cmd.getOptionValue("u");
        }

        if (cmd.hasOption("f")) {
            eventfile = cmd.getOptionValue("f");
        }

        if (cmd.hasOption("h")) {
            hostname = cmd.getOptionValue("h");
        }

        if (eventfile == null || hostname == null || url == null) {
            System.out.println("Command line parameters: -h hostname -u url -f path_to_XML_file");
            System.exit(-1);
        }

    } catch (ParseException ex) {

        logger.error(ex.getMessage());

    }

    URLConnection urlConn = null;
    DataOutputStream printout = null;
    BufferedReader input = null;
    String u = "http://" + hostname + "/" + url;
    String tmp = null;
    try {

        URL myurl = new URL(u);
        urlConn = myurl.openConnection();
        urlConn.setDoInput(true);
        urlConn.setDoOutput(true);
        urlConn.setUseCaches(false);
        urlConn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded");

        printout = new DataOutputStream(urlConn.getOutputStream());

        String xml = readFile(eventfile, StandardCharsets.UTF_8);
        printout.writeBytes(xml);
        printout.flush();
        printout.close();

        input = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));

        logger.debug(xml);
        while (null != ((tmp = input.readLine()))) {
            logger.debug(tmp);
        }
        printout.close();
        input.close();

    } catch (Exception ex) {

        logger.error(ex.getMessage());

    }

}

From source file:com.redhat.poc.jdg.bankofchina.function.TestCase411RemoteMultiThreads.java

public static void main(String[] args) throws Exception {
    CommandLine commandLine;//from  www .j av a 2s.  c  om
    Options options = new Options();
    options.addOption("s", true, "The start csv file number option");
    options.addOption("e", true, "The end csv file number option");
    BasicParser parser = new BasicParser();
    parser.parse(options, args);
    commandLine = parser.parse(options, args);
    if (commandLine.getOptions().length > 0) {
        if (commandLine.hasOption("s")) {
            String start = commandLine.getOptionValue("s");
            if (start != null && start.length() > 0) {
                csvFileStart = Integer.parseInt(start);
            }
        }
        if (commandLine.hasOption("e")) {
            String end = commandLine.getOptionValue("e");
            if (end != null && end.length() > 0) {
                csvFileEnd = Integer.parseInt(end);
            }
        }
    }

    System.out.println(
            "%%%%%%%%%  csv ?, ?, ?(ms),"
                    + new Date().getTime());

    for (int i = csvFileStart; i <= csvFileEnd; i++) {
        new TestCase411RemoteMultiThreads(i).start();
    }
}

From source file:com.genentech.chemistry.tool.SDF2HtmlTab.java

public static void main(String[] args) throws ParseException, JDOMException, IOException {
    long start = System.currentTimeMillis();

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("in", true, "input sd file");
    opt.setRequired(true);/*from w  w w  .ja  v  a2 s.  c o  m*/
    options.addOption(opt);

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

    String inFile = cmd.getOptionValue("in");

    args = cmd.getArgs();
    if (args.length > 0) {
        exitWithHelp(options);
    }

    oemolistream ifs;
    Set<String> tagSet = getTagSet(inFile);

    System.out.println(
            "<html xmlns:v='urn:schemas-microsoft-com:vml' xmlns:o='urn:schemas-microsoft-com:office:office'>");
    System.out.println("<head>");
    System.out.println("<BASE href='" + BASEUrl + "'/>");
    System.out.println(
            "<link href='/" + Settings.SERVLET_CONTEXT + "/css/Aestel.css' rel='stylesheet' type='text/css'/>");

    System.out.println("<style type='text/css'>");
    System.out.println("td.stru { width: " + (IMGWidth + 2) + "px; height: " + (IMGHeigth + 4)
            + "px; vertical-align: top; }");
    System.out.println("table.grid tr.first { border-top: 3px solid black; }");
    // for tables in tables
    System.out.println("table.grid table td { border: 0px; text-align: right;}");
    System.out.println("table.grid table td:first-child { text-align: left;}");
    System.out.println("th.head { border-left: 1px solid black; border-bottom: 2px solid black;\n"
            + "          empty-cells: show; background-color: #6297ff; color: #000000;\n"
            + "          padding: 0em .3em 0em .3em; vertical-align: middle; }");
    System.out.println("</style>");

    System.out.println("</head>");
    System.out.println("<body>");

    System.out.println("<table class='grid'><tr>");
    System.out.println("<th class='head'>Structure</th>");

    for (String tag : tagSet)
        System.out.println("<th class='head'>" + tag + "</th>");
    System.out.println("</tr>");

    OEGraphMol mol = new OEGraphMol();
    ifs = new oemolistream(inFile);
    int iCounter = 0;
    while (oechem.OEReadMolecule(ifs, mol)) {
        iCounter++;
        System.out.println("<tr>");
        String smi = OETools.molToCanSmi(mol, true);
        String img = DepictHelper.DEFAULT.getExcelSmilesImageElement(BASEUrl, 120, 120, ImageType.PNG, smi,
                null);

        System.out.print(" <td class='stru'>");
        System.out.print(img);
        System.out.println("</td>");

        for (String tag : tagSet) {
            String val = oechem.OEGetSDData(mol, tag);

            System.out.print(" <td>");
            System.out.print(val);
            System.out.println("</td>");
        }

        System.out.println("</tr>");
    }

    System.out.println("</table></body></html>");

    System.err.printf("SDF2HtmlTab: Exported %d structures in %dsec\n", iCounter,
            (System.currentTimeMillis() - start) / 1000);
}

From source file:net.forkwait.imageautomator.ImageAutomator.java

public static void main(String[] args) throws IOException {
    String inputImage = "";

    Options options = new Options();
    options.addOption("o", true, "output file name (e.g. thumb.jpg), default thumbnail.filename.ext");
    options.addOption("q", true, "jpeg quality (e.g. 0.9, max 1.0), default 0.97");
    options.addOption("s", true, "output max side length in px (e.g. 800), default 1200");
    options.addOption("w", true, "watermark image file");
    options.addOption("wt", true, "watermark transparency (e.g. 0.5, max 1.0), default 1.0");
    options.addOption("wp", true, "watermark position (e.g. 0.9, max 1.0), default BOTTOM_RIGHT");

    /*//w w w . java 2  s  .c o  m
    TOP_LEFT
    TOP_CENTER
    TOP_RIGHT
    CENTER_LEFT
    CENTER
    CENTER_RIGHT
    BOTTOM_LEFT
    BOTTOM_CENTER
    BOTTOM_RIGHT
     */

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
        if (cmd.getArgs().length < 1) {
            throw new ParseException("Too few arguments");
        } else if (cmd.getArgs().length > 1) {
            throw new ParseException("Too many arguments");
        }
        inputImage = cmd.getArgs()[0];
    } catch (ParseException e) {
        showHelp(options, e.getLocalizedMessage());
        System.exit(-1);
    }

    Thumbnails.Builder<File> st = Thumbnails.of(inputImage);

    if (cmd.hasOption("q")) {
        st.outputQuality(Double.parseDouble(cmd.getOptionValue("q")));
    } else {
        st.outputQuality(0.97f);
    }

    if (cmd.hasOption("s")) {
        st.size(Integer.parseInt(cmd.getOptionValue("s")), Integer.parseInt(cmd.getOptionValue("s")));
    } else {
        st.size(1200, 1200);
    }
    if (cmd.hasOption("w")) {
        Positions position = Positions.BOTTOM_RIGHT;
        float trans = 0.5f;
        if (cmd.hasOption("wp")) {
            position = Positions.valueOf(cmd.getOptionValue("wp"));
        }
        if (cmd.hasOption("wt")) {
            trans = Float.parseFloat(cmd.getOptionValue("wt"));
        }

        st.watermark(position, ImageIO.read(new File(cmd.getOptionValue("w"))), trans);
    }
    if (cmd.hasOption("o")) {
        st.toFile(new File(cmd.getOptionValue("o")));
    } else {
        st.toFiles(Rename.PREFIX_DOT_THUMBNAIL);
    }

    //.outputFormat("jpg")
    System.exit(0);
}

From source file:com.novadart.silencedetect.SilenceDetect.java

public static void main(String[] args) {

    // create the parser
    CommandLineParser parser = new BasicParser();
    try {//from   w ww  .j  a  v a  2 s.  com
        // parse the command line arguments
        CommandLine line = parser.parse(OPTIONS, args);

        if (line.hasOption("h")) {

            printHelp();

        } else {

            String decibels = "-10";
            if (line.hasOption("b")) {
                decibels = "-" + line.getOptionValue("b");
            } else {
                throw new RuntimeException();
            }

            String videoFile = null;

            if (line.hasOption("i")) {

                videoFile = line.getOptionValue("i");

                Boolean debug = line.hasOption("d");

                if (line.hasOption("t")) {

                    System.out.println(printAudioTracksList(videoFile, debug));

                } else if (line.hasOption("s")) {

                    int trackNumber = Integer.parseInt(line.getOptionValue("s"));
                    System.out.println(printAudioTrackSilenceDuration(videoFile, trackNumber, decibels, debug));

                } else {

                    printHelp();

                }

            } else if (line.hasOption("-j")) {

                // choose file
                final JFileChooser fc = new JFileChooser();
                fc.setVisible(true);
                int returnVal = fc.showOpenDialog(null);
                if (returnVal == JFileChooser.APPROVE_OPTION) {

                    videoFile = fc.getSelectedFile().getAbsolutePath();

                } else {
                    return;
                }

                JTextArea tracks = new JTextArea();
                tracks.setText(printAudioTracksList(videoFile, true));
                JSpinner trackNumber = new JSpinner();
                trackNumber.setValue(1);
                final JComponent[] inputs = new JComponent[] { new JLabel("Audio Tracks"), tracks,
                        new JLabel("Track to analyze"), trackNumber };
                JOptionPane.showMessageDialog(null, inputs, "Select Audio Track", JOptionPane.PLAIN_MESSAGE);

                JTextArea results = new JTextArea();
                results.setText(printAudioTrackSilenceDuration(videoFile, (int) trackNumber.getValue(),
                        decibels, false));
                final JComponent[] resultsInputs = new JComponent[] { new JLabel("Results"), results };
                JOptionPane.showMessageDialog(null, resultsInputs, "RESULTS!", JOptionPane.PLAIN_MESSAGE);

            } else {
                printHelp();
                return;
            }

        }

    } catch (ParseException | IOException | InterruptedException exp) {
        // oops, something went wrong
        System.out.println("There was a problem :(\nReason: " + exp.getMessage());
    }
}