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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Usage

From source file:edu.cornell.med.icb.geo.tools.CalculateRanks.java

private void proccess(final String[] args) throws IOException {
    // create the Options
    final Options options = new Options();

    // help//from w w w.j a  v a  2  s  . co  m
    options.addOption("h", "help", false,
            "print this message. This program compares the performance measures obtained "
                    + "with each gene list and determines the rank of each gene list.");

    // input file name
    final Option inputOption = new Option("i", "input", true,
            "specify the path to the statistics file created by MicroarrayTrainEvaluate.");
    inputOption.setArgName("file");
    inputOption.setRequired(true);
    options.addOption(inputOption);

    // output file name
    final Option outputOption = new Option("o", "output", true,
            "specify the destination file where post-processed statistics will be written");
    outputOption.setArgName("file");
    outputOption.setRequired(true);
    options.addOption(outputOption);

    // tallies file name
    final Option talliesOption = new Option("t", "tallies", true,
            "specify the file where tallies of rank per gene list will be written");
    talliesOption.setArgName("file");
    talliesOption.setRequired(false);
    options.addOption(talliesOption);

    // filter by shuffle test P-value
    final Option filterShuffleTestOption = new Option("f", "filter-shuffle-test", false,
            "indicate that only those results that pass the shuffle significance test should be used to calculate ranks and tallies.");
    filterShuffleTestOption.setRequired(false);

    options.addOption(filterShuffleTestOption);

    // parse the command line arguments
    CommandLine line = null;
    try {
        // create the command line parser
        final CommandLineParser parser = new BasicParser();
        line = parser.parse(options, args, true);

    } catch (ParseException e) {
        System.err.println(e.getMessage());
        usage(options);
        System.exit(1);
    }
    // print help and exit
    if (line.hasOption("h")) {
        usage(options);
        System.exit(0);
    }
    this.filterWithShuffleTest = line.hasOption("f");
    if (this.filterWithShuffleTest) {
        System.out.println("Filtering classification results by shuffle test.");
    }
    postProcess(line.getOptionValue("i"), line.getOptionValue("o"), line.getOptionValue("t"));
}

From source file:com.amazonaws.mturk.cmd.AbstractCmd.java

public void run(String[] args) {
    try {//from   ww w. j  a v  a  2s . c  o  m
        BasicParser parser = new BasicParser();
        CommandLine cmdLine = parser.parse(opt, args);

        if (cmdLine.hasOption(ARG_HELP) || cmdLine.hasOption(ARG_HELP_SHORT)) {
            printHelp();
            System.exit(-1);
        }

        if (cmdLine.hasOption(ARG_SANDBOX)
                && !ClientConfig.SANDBOX_SERVICE_URL.equalsIgnoreCase(config.getServiceURL())) {
            log.info("Sandbox override");

            setSandBoxMode();
        } else {
            initService();
        }

        log.debug(String.format("Running command against %s", config.getServiceURL()));

        runCommand(cmdLine);
    } catch (Exception e) {
        log.error("An error occurred: " + e.getLocalizedMessage(), e);
        System.exit(-1);
    }
}

From source file:com.asakusafw.yaess.tools.Explain.java

static Configuration parseConfiguration(String[] args) throws ParseException {
    assert args != null;
    LOG.debug("Analyzing YAESS Explain arguments: {}", Arrays.toString(args));

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(OPTIONS, args);

    String script = cmd.getOptionValue(OPT_SCRIPT.getOpt());
    LOG.debug("Script: {}", script);

    Configuration result = new Configuration();
    LOG.debug("Loading script: {}", script);
    try {/*from  www . j  a  v  a 2  s.c om*/
        Properties properties = CommandLineUtil.loadProperties(new File(script));
        result.script = BatchScript.load(properties);
    } catch (Exception e) {
        throw new IllegalArgumentException(MessageFormat.format("Invalid script \"{0}\".", script), e);
    }

    LOG.debug("Analyzed YAESS Explain arguments");
    return result;
}

From source file:edu.cornell.med.icb.geo.tools.GDS2InsightfulMiner.java

private void proccess(final String[] args) {
    // create the Options
    final Options options = new Options();

    // help/*from  w  w w. j  av  a 2  s  .  c o m*/
    options.addOption("h", "help", false, "print this message");

    // input file name
    final Option inputOption = new Option("i", "input", true, "specify a GEO data set file (GDS file)");
    inputOption.setArgName("file");
    inputOption.setRequired(true);
    options.addOption(inputOption);

    // output file name
    final Option outputOption = new Option("o", "output", true, "specify the destination file");
    outputOption.setArgName("file");
    outputOption.setRequired(true);
    options.addOption(outputOption);
    // label values
    final Option labelOptions = new Option("l", "label", true, "specify a label to tag a set of columns");
    labelOptions.setArgName("double-value");
    labelOptions.setRequired(false);
    options.addOption(labelOptions);

    // group file names
    final Option groupOptions = new Option("g", "group", true,
            "specify a file that named columns associated to a label. Each -group option must match a -label option. Matching is done according to the order on the command line. Each line of the group file identifies a column in the GEO data set that is to be labeled according to the corresponding label");
    groupOptions.setArgName("file");
    groupOptions.setRequired(false);
    options.addOption(groupOptions);

    // default label value
    final Option defaultLabelOption = new Option("dl", "default-label", true,
            "Specify the label to use for columns that are not identified by -l -g pairs. Default value is zero.");
    groupOptions.setArgName("double-value");
    groupOptions.setRequired(false);
    options.addOption(defaultLabelOption);
    // parse the command line arguments
    CommandLine line = null;
    double defaultLabelValue = 0;
    try {
        // create the command line parser
        final CommandLineParser parser = new BasicParser();
        line = parser.parse(options, args, true);
        if ((line.hasOption("l") && !line.hasOption("g")) || (line.hasOption("g") && !line.hasOption("l"))) {
            System.err.println("Options -label and -group must be used together.");
            System.exit(10);
        }
        if (line.hasOption("l") && line.getOptionValues("l").length != line.getOptionValues("g").length) {
            System.err.println("The number of -label and -group options must match exactly.");
            System.exit(10);
        }
        if (line.hasOption("dl")) {
            defaultLabelValue = Double.parseDouble(line.getOptionValue("dl"));
        }

    } catch (ParseException e) {
        System.err.println(e.getMessage());
        usage(options);
        System.exit(1);
    }
    // print help and exit
    if (line.hasOption("h")) {
        usage(options);
        System.exit(0);
    }
    try {
        final Map<Double, Set<String>> labels = readLabelGroups(line.getOptionValues("l"),
                line.getOptionValues("g")); //labels
        convert(line.getOptionValue("i"), line.getOptionValue("o"), labels, defaultLabelValue);
        System.exit(0);
    } catch (FileNotFoundException e) {

        System.err.println("Error opening file: \n");
        printGroups(line);
    } catch (IOException e) {
        System.err.println("An error occurred reading one of the group files:\n");
        printGroups(line);
    }

}

From source file:com.asakusafw.yaess.tools.log.cli.Main.java

static Configuration parseConfiguration(String[] args) throws ParseException {
    assert args != null;
    LOG.debug("Analyzing arguments: {}", Arrays.toString(args));

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(OPTIONS, args);

    ClassLoader classLoader = Main.class.getClassLoader();

    YaessLogInput source = create(cmd, OPT_INPUT, YaessLogInput.class, classLoader);
    YaessLogOutput sink = create(cmd, OPT_OUTPUT, YaessLogOutput.class, classLoader);
    Map<String, String> sourceArgs = parseArgs(cmd, OPT_INPUT_ARGUMENT);
    Map<String, String> sinkArgs = parseArgs(cmd, OPT_OUTPUT_ARGUMENT);

    return new Configuration(source, sourceArgs, sink, sinkArgs);
}

From source file:com.asakusafw.testdriver.tools.runner.BatchTestTruncator.java

static Conf parseArguments(String[] args) throws ParseException {
    assert args != null;
    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(OPTIONS, args);

    Conf conf = new Conf();
    String descriptionClass = cmd.getOptionValue(OPT_DESCRIPTION.getLongOpt());
    Class<?> description;//from  www.j  av a  2  s.  c o m
    try {
        description = Class.forName(descriptionClass);
    } catch (Exception e) {
        throw new IllegalArgumentException(
                MessageFormat.format(Messages.getString("BatchTestTruncator.errorFailedToAnalyze"), //$NON-NLS-1$
                        descriptionClass),
                e);
    }
    conf.context = new TestDriverContext(description);
    resolveDescription(conf, description);

    Properties arguments = cmd.getOptionProperties(OPT_ARGUMENT.getOpt());
    conf.context.getBatchArgs().putAll(toMap(arguments));

    Properties properties = cmd.getOptionProperties(OPT_PROPERTY.getOpt());
    conf.context.getExtraConfigurations().putAll(toMap(properties));

    return conf;
}

From source file:com.github.cereda.sucuri.utils.CommandLineAnalyzer.java

/**
 * Parses the command line arguments./* w  w w.ja  v a 2  s. c o m*/
 * 
 * @return A boolean indicating if the parsing was successful.
 */
public boolean parse() {

    // create the options
    Option optVersion = new Option("v", "version", false, "print the application version");
    Option optHelp = new Option("h", "help", false, "print the help message");
    Option optReport = new Option("r", "report", false, "generate report");
    Option optTemplate = new Option("t", "template", true, "set the master template");
    Option optInput = new Option("i", "input", true, "set the input file");
    Option optOutput = new Option("o", "output", true, "set the output file");
    Option optEncoding = new Option("e", "encoding", true, "set the input encoding");

    // add them
    commandLineOptions.addOption(optVersion);
    commandLineOptions.addOption(optHelp);
    commandLineOptions.addOption(optReport);
    commandLineOptions.addOption(optTemplate);
    commandLineOptions.addOption(optInput);
    commandLineOptions.addOption(optOutput);
    commandLineOptions.addOption(optEncoding);

    // create a new parser
    CommandLineParser parser = new BasicParser();

    try {

        // parse the line
        CommandLine line = parser.parse(commandLineOptions, args);

        // check for help
        if (line.hasOption("help")) {

            printVersion();
            printUsage();
            return false;

        } else {

            // check for version
            if (line.hasOption("version")) {

                printVersion();
                return false;

            }

            // check if there are anything else
            if (line.getArgs().length != 0) {

                printVersion();
                printUsage();
                return false;

            } else {

                // check for template
                if (line.hasOption("template")) {

                    // check for input
                    if (line.hasOption("input")) {

                        // check for output
                        if (line.hasOption("output")) {

                            // get the report flag
                            report = line.hasOption("report");

                            // check for encoding
                            if (line.hasOption("encoding")) {
                                encoding = line.getOptionValue("encoding");
                            }

                            // set everything
                            input = new File(line.getOptionValue("input"));
                            output = new File(line.getOptionValue("output"));
                            template = new File(line.getOptionValue("template"));
                            return true;

                        } else {

                            printVersion();
                            System.out.println("The output file is required.".concat("\n"));
                            printUsage();
                            return false;

                        }
                    } else {

                        printVersion();
                        System.out.println("The input file is required.".concat("\n"));
                        printUsage();
                        return false;

                    }
                } else {

                    printVersion();
                    System.out.println("The template file is required.".concat("\n"));
                    printUsage();
                    return false;

                }
            }
        }

    } catch (ParseException parseException) {

        printVersion();
        printUsage();
        return false;

    }
}

From source file:com.asakusafw.testdriver.tools.runner.BatchTestVerifier.java

static Conf parseArguments(String[] args) throws ParseException {
    assert args != null;
    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(OPTIONS, args);

    Conf conf = new Conf();
    String exporterClass = cmd.getOptionValue(OPT_EXPORTER.getLongOpt());
    try {//from  ww  w  .  j  a  v  a2s. c o  m
        conf.exporter = Class.forName(exporterClass).asSubclass(ExporterDescription.class).newInstance();
    } catch (Exception e) {
        throw new IllegalArgumentException(
                MessageFormat.format(Messages.getString("BatchTestVerifier.errorInvalidExporterDescription"), //$NON-NLS-1$
                        exporterClass),
                e);
    }
    conf.data = cmd.getOptionValue(OPT_DATA.getLongOpt());
    conf.rule = cmd.getOptionValue(OPT_RULE.getLongOpt());
    conf.context = new TestDriverContext(conf.exporter.getClass());

    Properties arguments = cmd.getOptionProperties(OPT_ARGUMENT.getOpt());
    conf.context.getBatchArgs().putAll(toMap(arguments));

    Properties properties = cmd.getOptionProperties(OPT_PROPERTY.getOpt());
    conf.context.getExtraConfigurations().putAll(toMap(properties));

    return conf;
}

From source file:com.comcast.oscar.cli.CommandRun.java

/**
 * Checks all the commands from the user. Order is IMPORTANT. Do not rearrange without full understanding.
 * @param args/*  w  w w  . ja va2 s.c om*/
 */
public void run(String[] args) {
    BasicParser parser = new BasicParser();
    Options options = new Options();
    BuildOptions.run(options);

    try {
        CommandLine line = parser.parse(options, args);
        HelpFormatter hf = new HelpFormatter();
        hf.setWidth(180);
        hf.setLeftPadding(5);
        hf.setDescPadding(5);

        if (line.hasOption("h")) {
            hf.printHelp(Constants.OSCAR_CLI_USAGE, options);
        }

        if (line.hasOption("version")) {
            System.out.println(Constants.APACHE_20_LICENCE_DISCLAIMER);
            System.out.println(Constants.OSCAR_VERSION);
        }

        if (line.hasOption("s")) {
            comSpecification.setValues(line.getOptionValues("s"));

            if (comSpecification.getConfigurationFileType() == -1) {
                System.err.println(Specification.ERROR);
                System.exit(1);
            }

            if (comSpecification.getTlvDisassemble() == null) {
                System.err.println(Specification.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("i")) {
            comInput = new Input(line.getOptionValues("i"));

            if (!comInput.hasInput()) {
                System.err.println(Input.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("o")) {
            comOutput = new Output(line.getOptionValues("o"));
        }

        if (line.hasOption("k")) {
            comKey.setKey(line.getOptionValues("k"));
        }

        if (line.hasOption("mbb")) {
            comMergeBulk = new MergeBulk(line.getOptionValues("mbb"));

            if (comMergeBulk.hasInputDir()) {
                comMergeBulk.mergeFiles(comSpecification.getConfigurationFileType(), comKey.getKey());
            } else {
                System.err.println(MergeBulk.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("f")) {
            comFirmware = new Firmware(line.getOptionValues("f"));
        }

        if (line.hasOption("T")) {
            comTFTPServer = new TFTPServer(line.getOptionValues("T"));

            if (!comTFTPServer.hasAddress()) {
                System.err.println(TFTPServer.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("m")) {
            comMaxCPE = new MaxCPE(line.getOptionValues("m"));
        }

        if (line.hasOption("df")) {
            comDownstreamFrequency = new DownstreamFrequency(line.getOptionValues("df"));
        }

        if (line.hasOption("cvc")) {
            comCVC = new CVC(line.getOptionValues("cvc"));

            if (!comCVC.hasCVC()) {
                System.err.println(CVC.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("t")) {
            comTLV = new TLV(line.getOptionValues("t"));
        }

        if (line.hasOption("dm")) {
            comDigitmapInsert = new DigitmapInsert(line.getOptionValues("dm"));

            if (!comDigitmapInsert.hasDigitmap()) {
                System.err.println(DigitmapInsert.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("O")) {
            comOID = new OID(line.getOptionValues("O"));

            if (!comOID.hasOID()) {
                System.err.println(OID.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("d")) {
            comDecompile = new Decompile(line.getOptionValues("d"));
            decompile();
        }

        if (line.hasOption("c")) {
            compile();
        }

        if (line.hasOption("b")) {
            String[] optionValues = line.getOptionValues("b");

            if (optionValues.length >= 3) {
                bulkBuild(optionValues[0]);
                bulkBuildCommand(new File(optionValues[1]), new File(optionValues[2]));
            } else if (optionValues.length >= 2) {
                bulkBuild(optionValues[0]);
                bulkBuildCommand(new File(optionValues[1]));
            } else {
                System.err.println(Constants.ERR_MIS_PAR);
                hf.printHelp(Constants.OSCAR_CLI_USAGE, options);
            }
        }

        if (line.hasOption("ftd")) {
            comFullTLVDisplay.printFullTLVDisplay(comSpecification.getConfigurationFileType());
        }

        if (line.hasOption("x")) {
            comHexDisplay = new HexDisplay(line.getOptionValues("x"));

            if (comInput.hasInput()) {
                if (comInput.isBinary()) {
                    comHexDisplay.printHexDisplayFromBinary(comInput.getInput());
                } else {
                    comHexDisplay.printHexDisplayFromText(comInput.getInput(),
                            comSpecification.getConfigurationFileType());
                }
            } else {
                System.err.println(Input.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("j")) {
            if (comInput.hasInput()) {
                if (comInput.isBinary()) {
                    comJSONDisplay.printJSONDisplayFromBinary(comInput.getInput(),
                            comSpecification.getTlvDisassemble(), comSpecification.getConfigurationFileType());
                } else {
                    comJSONDisplay.printJSONDisplayFromText(comInput.getInput(),
                            comSpecification.getTlvDisassemble());
                }
            } else {
                System.err.println(Input.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("ddm")) {
            if (comInput.hasInput()) {
                if (comInput.isBinary()) {
                    comDigitmapDisplay.printDigitmapDisplayFromBinary(comInput.getInput());
                } else {
                    comDigitmapDisplay.printDigitmapDisplayFromText(comInput.getInput());
                }
            }
        }

        if (line.hasOption("j2t")) {
            comJSONtoTLV = new JSONtoTLV(line.getOptionValues("j2t"));

            if (comJSONtoTLV.fileExists()) {
                comJSONtoTLV.printTLV();
            } else {
                System.err.println(JSONtoTLV.ERROR);
            }
        }

        if (line.hasOption("t2j")) {
            comTLVtoJSON = new TLVtoJSON(line.getOptionValues("t2j"));
            comTLVtoJSON.printJSON(comSpecification.getTlvDisassemble());
        }

        if (line.hasOption("td")) {
            comTLVDescription = new TLVDescription(line.getOptionValues("td"));
            comTLVDescription.printTLVDescription(comSpecification.getConfigurationFileType());
        }

        if (line.hasOption("tr")) {
            comTranslate = new Translate(line.getOptionValues("tr"));
            comTranslate.translate();
        }
    } catch (ParseException exp) {
        System.err.println("Parsing failed. Reason: " + exp.getMessage());
    }
}

From source file:cn.edu.pku.cbi.mosaichunter.MosaicHunter.java

private static boolean loadConfiguration(String[] args, String configFile) throws Exception {
    OptionBuilder.withArgName("file");
    OptionBuilder.hasArg();/*from  w w  w . j  a  v  a2  s. co m*/
    OptionBuilder.withDescription("config file");
    OptionBuilder.withLongOpt("config");
    Option configFileOption = OptionBuilder.create("C");

    OptionBuilder.withArgName("property=value");
    OptionBuilder.hasArgs(2);
    OptionBuilder.withValueSeparator();
    OptionBuilder.withDescription("properties that overrides the ones in config file");
    OptionBuilder.withLongOpt("properties");
    Option propertiesOption = OptionBuilder.create("P");

    Options options = new Options();
    options.addOption(configFileOption);
    options.addOption(propertiesOption);

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException pe) {
        System.out.println(pe.getMessage());
        return false;
    }

    InputStream in = null;

    if (configFile == null || configFile.trim().isEmpty()) {
        configFile = cmd.getOptionValue("C");
        if (configFile != null && new File(configFile).isFile()) {
            in = new FileInputStream(configFile);
        }
    } else {
        in = MosaicHunter.class.getClassLoader().getResourceAsStream(configFile);
    }
    if (in != null) {
        try {
            ConfigManager.getInstance().loadProperties(in);
        } catch (IOException ioe) {
            System.out.println("invalid config file: " + configFile);
            return false;
        } finally {
            in.close();
        }
    }

    Properties properties = cmd.getOptionProperties("P");
    if (properties != null) {
        ConfigManager.getInstance().putAll(properties);
    }

    return !ConfigManager.getInstance().getProperties().isEmpty();
}