Example usage for org.apache.commons.cli OptionBuilder withDescription

List of usage examples for org.apache.commons.cli OptionBuilder withDescription

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Introduction

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

Prototype

public static OptionBuilder withDescription(String newDescription)

Source Link

Document

The next Option created will have the specified description

Usage

From source file:net.ladenthin.snowman.imager.run.CLI.java

@SuppressWarnings("static-access")
public static void main(String[] args) throws Exception {
    try {/* ww  w . j  a  v a  2  s.  c o m*/
        CommandLineParser parser = new PosixParser();
        Options options = new Options();

        options.addOption(cmdHelpS, cmdHelp, false, cmdHelpD);
        options.addOption(cmdVersionS, cmdVersion, false, cmdVersionD);

        options.addOption(OptionBuilder.withDescription(cmdConfigurationD).withLongOpt(cmdConfiguration)
                .hasArg().withArgName(cmdConfigurationA).create(cmdConfigurationS));

        // parse the command line arguments
        CommandLine line = parser.parse(options, args);

        final String cmdLineSyntax = "java -jar " + Imager.jarFilename;
        // automatically generate the help statement
        HelpFormatter formatter = new HelpFormatter();

        final String configurationPath;
        if (line.hasOption(cmdConfiguration)) {
            configurationPath = line.getOptionValue(cmdConfiguration);
        } else {
            System.out.println("Need configuration value.");
            formatter.printHelp(cmdLineSyntax, options);
            return;
        }

        // check parameter
        if (args.length == 0 || line.hasOption(cmdHelp)) {
            formatter.printHelp(cmdLineSyntax, options);
            return;
        }

        if (line.hasOption(cmdVersion)) {
            System.out.println(Imager.version);
            return;
        }

        Imager imager = new Imager(configurationPath);
        imager.waitForAllThreads();
        imager.restartAndExit();

    } catch (IllegalArgumentException | ParseException | IOException | InstantiationException
            | InterruptedException e) {
        LOGGER.error("Critical exception.", e);
        System.exit(-1);
    }
}

From source file:apps.quantification.QuantifySVMPerf.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = QuantifySVMPerf.class.getName()
            + " [OPTIONS] <path to svm_perf_classify> <testIndexDirectory> <quantificationModelDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("d");
    OptionBuilder.withDescription("Dump confidences file");
    OptionBuilder.withLongOpt("d");
    OptionBuilder.isRequired(false);//from   w ww.  j  a  v a 2 s .  co m
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("t");
    OptionBuilder.withDescription("Path for temporary files");
    OptionBuilder.withLongOpt("t");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("v");
    OptionBuilder.withDescription("Verbose output");
    OptionBuilder.withLongOpt("v");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("s");
    OptionBuilder.withDescription("Don't delete temporary files in svm_perf format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmPerfClassifierCustomizer customizer = null;

    GnuParser parser = new GnuParser();
    String[] remainingArgs = null;
    try {
        CommandLine line = parser.parse(options, args);

        remainingArgs = line.getArgs();

        customizer = new SvmPerfClassifierCustomizer(remainingArgs[0]);

        if (line.hasOption("v"))
            customizer.printSvmPerfOutput(true);

        if (line.hasOption("s")) {
            System.out.println("Keeping temporary files.");
            customizer.setDeleteTestFiles(false);
            customizer.setDeletePredictionsFiles(false);
        }

        if (line.hasOption("t"))
            customizer.setTempPath(line.getOptionValue("t"));

    } catch (Exception exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    if (remainingArgs.length != 3) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    String indexFile = remainingArgs[1];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String quantifierFilename = remainingArgs[2];

    FileSystemStorageManager indexFssm = new FileSystemStorageManager(indexPath, false);
    indexFssm.open();

    IIndex test = TroveReadWriteHelper.readIndex(indexFssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    indexFssm.close();

    FileSystemStorageManager quantifierFssm = new FileSystemStorageManager(quantifierFilename, false);
    quantifierFssm.open();

    SvmPerfDataManager classifierDataManager = new SvmPerfDataManager(customizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(quantifierFilename, false);
    fssm.open();

    IQuantifier[] quantifiers = QuantificationLearner.read(fssm, classifierDataManager,
            ClassificationMode.PER_CATEGORY);
    fssm.close();

    quantifierFssm.close();

    Quantification ccQuantification = quantifiers[0].quantify(test);
    Quantification paQuantification = quantifiers[1].quantify(test);
    Quantification accQuantification = quantifiers[2].quantify(test);
    Quantification maxQuantification = quantifiers[3].quantify(test);
    Quantification sccQuantification = quantifiers[4].quantify(test);
    Quantification spaQuantification = quantifiers[5].quantify(test);
    Quantification trueQuantification = new Quantification("True", test.getClassificationDB());

    File quantifierFile = new File(quantifierFilename);

    String quantificationName = quantifierFile.getParent() + Os.pathSeparator() + indexName + "_"
            + quantifierFile.getName() + ".txt";

    BufferedWriter writer = new BufferedWriter(new FileWriter(quantificationName));
    IShortIterator iterator = test.getCategoryDB().getCategories();
    while (iterator.hasNext()) {
        short category = iterator.next();
        String prefix = quantifierFile.getName() + "\t" + indexName + "\t"
                + test.getCategoryDB().getCategoryName(category) + "\t" + category + "\t"
                + trueQuantification.getQuantification(category) + "\t";

        writer.write(prefix + ccQuantification.getName() + "\t" + ccQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + paQuantification.getName() + "\t" + paQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + accQuantification.getName() + "\t" + accQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + maxQuantification.getName() + "\t" + maxQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + sccQuantification.getName() + "\t" + sccQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + spaQuantification.getName() + "\t" + spaQuantification.getQuantification(category)
                + "\n");
    }
    writer.close();

    BufferedWriter bfs = new BufferedWriter(new FileWriter(quantifierFile.getParent() + Os.pathSeparator()
            + indexName + "_" + quantifierFile.getName() + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = ((CCQuantifier) quantifiers[0]).getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = ((CCQuantifier) quantifiers[0]).getSimpleFPRs();
    TShortDoubleHashMap maxTPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier())
            .getSimpleTPRs();
    TShortDoubleHashMap maxFPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier())
            .getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = ((PAQuantifier) quantifiers[1]).getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = ((PAQuantifier) quantifiers[1]).getScaledFPRs();

    ContingencyTableSet simpleContingencyTableSet = ((CCQuantifier) quantifiers[0]).getContingencyTableSet();
    ContingencyTableSet maxContingencyTableSet = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3])
            .getInternalQuantifier()).getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = test.getCategoryDB().getCategoryName(cat);
        ContingencyTable simpleContingencyTable = simpleContingencyTableSet.getCategoryContingencyTable(cat);
        ContingencyTable maxContingencyTable = maxContingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double maxTPR = maxTPRs.get(cat);
        double maxFPR = maxFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = indexName + "_" + quantifierFile.getName() + "\ttest\tsimple\t" + catName + "\t" + cat
                + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t"
                + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + simpleTPR + "\t"
                + simpleFPR + "\n";
        bfs.write(line);
        line = indexName + "_" + quantifierFile.getName() + "\ttest\tmax\t" + catName + "\t" + cat + "\t"
                + maxContingencyTable.tp() + "\t" + maxContingencyTable.fp() + "\t" + maxContingencyTable.fn()
                + "\t" + maxContingencyTable.tn() + "\t" + maxTPR + "\t" + maxFPR + "\n";
        bfs.write(line);
        line = indexName + "_" + quantifierFile.getName() + "\ttest\tscaled\t" + catName + "\t" + cat + "\t"
                + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t"
                + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + scaledTPR + "\t"
                + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}

From source file:apps.quantification.QuantifySVMLight.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = QuantifySVMLight.class.getName()
            + " [OPTIONS] <path to svm_light_classify> <testIndexDirectory> <quantificationModelDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("d");
    OptionBuilder.withDescription("Dump confidences file");
    OptionBuilder.withLongOpt("d");
    OptionBuilder.isRequired(false);/*from w  ww.j  av a 2 s. c om*/
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("t");
    OptionBuilder.withDescription("Path for temporary files");
    OptionBuilder.withLongOpt("t");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("v");
    OptionBuilder.withDescription("Verbose output");
    OptionBuilder.withLongOpt("v");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("s");
    OptionBuilder.withDescription("Don't delete temporary files in svm_light format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmLightClassifierCustomizer customizer = null;

    GnuParser parser = new GnuParser();
    String[] remainingArgs = null;
    try {
        CommandLine line = parser.parse(options, args);

        remainingArgs = line.getArgs();

        customizer = new SvmLightClassifierCustomizer(remainingArgs[0]);

        if (line.hasOption("v"))
            customizer.printSvmLightOutput(true);

        if (line.hasOption("s")) {
            System.out.println("Keeping temporary files.");
            customizer.setDeleteTestFiles(false);
            customizer.setDeletePredictionsFiles(false);
        }

        if (line.hasOption("t"))
            customizer.setTempPath(line.getOptionValue("t"));

    } catch (Exception exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    if (remainingArgs.length != 3) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    String indexFile = remainingArgs[1];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String quantifierFilename = remainingArgs[2];

    FileSystemStorageManager indexFssm = new FileSystemStorageManager(indexPath, false);
    indexFssm.open();

    IIndex test = TroveReadWriteHelper.readIndex(indexFssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    indexFssm.close();

    FileSystemStorageManager quantifierFssm = new FileSystemStorageManager(quantifierFilename, false);
    quantifierFssm.open();

    SvmLightDataManager classifierDataManager = new SvmLightDataManager(customizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(quantifierFilename, false);
    fssm.open();

    IQuantifier[] quantifiers = QuantificationLearner.read(fssm, classifierDataManager,
            ClassificationMode.PER_CATEGORY);
    fssm.close();

    quantifierFssm.close();

    Quantification ccQuantification = quantifiers[0].quantify(test);
    Quantification paQuantification = quantifiers[1].quantify(test);
    Quantification accQuantification = quantifiers[2].quantify(test);
    Quantification maxQuantification = quantifiers[3].quantify(test);
    Quantification sccQuantification = quantifiers[4].quantify(test);
    Quantification spaQuantification = quantifiers[5].quantify(test);
    Quantification trueQuantification = new Quantification("True", test.getClassificationDB());

    File quantifierFile = new File(quantifierFilename);

    String quantificationName = quantifierFile.getParent() + Os.pathSeparator() + indexName + "_"
            + quantifierFile.getName() + ".txt";

    BufferedWriter writer = new BufferedWriter(new FileWriter(quantificationName));
    IShortIterator iterator = test.getCategoryDB().getCategories();
    while (iterator.hasNext()) {
        short category = iterator.next();
        String prefix = quantifierFile.getName() + "\t" + indexName + "\t"
                + test.getCategoryDB().getCategoryName(category) + "\t" + category + "\t"
                + trueQuantification.getQuantification(category) + "\t";

        writer.write(prefix + ccQuantification.getName() + "\t" + ccQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + paQuantification.getName() + "\t" + paQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + accQuantification.getName() + "\t" + accQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + maxQuantification.getName() + "\t" + maxQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + sccQuantification.getName() + "\t" + sccQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + spaQuantification.getName() + "\t" + spaQuantification.getQuantification(category)
                + "\n");
    }
    writer.close();

    BufferedWriter bfs = new BufferedWriter(new FileWriter(quantifierFile.getParent() + Os.pathSeparator()
            + indexName + "_" + quantifierFile.getName() + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = ((CCQuantifier) quantifiers[0]).getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = ((CCQuantifier) quantifiers[0]).getSimpleFPRs();
    TShortDoubleHashMap maxTPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier())
            .getSimpleTPRs();
    TShortDoubleHashMap maxFPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier())
            .getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = ((PAQuantifier) quantifiers[1]).getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = ((PAQuantifier) quantifiers[1]).getScaledFPRs();

    ContingencyTableSet simpleContingencyTableSet = ((CCQuantifier) quantifiers[0]).getContingencyTableSet();
    ContingencyTableSet maxContingencyTableSet = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3])
            .getInternalQuantifier()).getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = test.getCategoryDB().getCategoryName(cat);
        ContingencyTable simpleContingencyTable = simpleContingencyTableSet.getCategoryContingencyTable(cat);
        ContingencyTable maxContingencyTable = maxContingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double maxTPR = maxTPRs.get(cat);
        double maxFPR = maxFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = indexName + "_" + quantifierFile.getName() + "\ttest\tsimple\t" + catName + "\t" + cat
                + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t"
                + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + simpleTPR + "\t"
                + simpleFPR + "\n";
        bfs.write(line);
        line = indexName + "_" + quantifierFile.getName() + "\ttest\tmax\t" + catName + "\t" + cat + "\t"
                + maxContingencyTable.tp() + "\t" + maxContingencyTable.fp() + "\t" + maxContingencyTable.fn()
                + "\t" + maxContingencyTable.tn() + "\t" + maxTPR + "\t" + maxFPR + "\n";
        bfs.write(line);
        line = indexName + "_" + quantifierFile.getName() + "\ttest\tscaled\t" + catName + "\t" + cat + "\t"
                + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t"
                + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + scaledTPR + "\t"
                + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}

From source file:com.enioka.jqm.tools.Main.java

/**
 * Startup method for the packaged JAR/*  ww  w  . j a  va 2s .com*/
 * 
 * @param args
 *            0 is node name
 */
@SuppressWarnings("static-access")
public static void main(String[] args) {
    Helpers.setLogFileName("cli");
    Option o00 = OptionBuilder.withArgName("nodeName").hasArg().withDescription("name of the JQM node to start")
            .isRequired().create("startnode");
    Option o01 = OptionBuilder.withDescription("display help").withLongOpt("help").create("h");
    Option o11 = OptionBuilder.withArgName("applicationname").hasArg()
            .withDescription("name of the application to launch").isRequired().create("enqueue");
    Option o21 = OptionBuilder.withArgName("xmlpath").hasArg()
            .withDescription("path of the XML configuration file to import").isRequired()
            .create("importjobdef");
    Option o31 = OptionBuilder.withArgName("xmlpath").hasArg()
            .withDescription("export all queue definitions into an XML file").isRequired()
            .create("exportallqueues");
    OptionBuilder.withArgName("xmlpath").hasArg()
            .withDescription("export some queue definitions into an XML file").isRequired()
            .create("exportqueuefile");
    OptionBuilder.withArgName("queues").hasArg().withDescription("queues to export").withValueSeparator(',')
            .isRequired().create("queue");
    Option o51 = OptionBuilder.withArgName("xmlpath").hasArg()
            .withDescription("import all queue definitions from an XML file").isRequired()
            .create("importqueuefile");
    Option o61 = OptionBuilder.withArgName("nodeName").hasArg()
            .withDescription("creates a JQM node of this name, or updates it if it exists. Implies -u.")
            .isRequired().create("createnode");
    Option o71 = OptionBuilder.withDescription("display JQM engine version").withLongOpt("version").create("v");
    Option o81 = OptionBuilder.withDescription("upgrade JQM database").withLongOpt("upgrade").create("u");
    Option o91 = OptionBuilder.withArgName("jobInstanceId").hasArg()
            .withDescription("get job instance status by ID").isRequired().withLongOpt("getstatus").create("g");
    Option o101 = OptionBuilder.withArgName("password").hasArg()
            .withDescription("creates or resets root admin account password").isRequired().withLongOpt("root")
            .create("r");
    Option o111 = OptionBuilder.withArgName("option").hasArg()
            .withDescription(
                    "ws handling. Possible values are: enable, disable, ssl, nossl, internalpki, externalapi")
            .isRequired().withLongOpt("gui").create("w");
    Option o121 = OptionBuilder.withArgName("id[,logfilepath]").hasArg().withDescription("single launch mode")
            .isRequired().withLongOpt("gui").create("s");
    Option o131 = OptionBuilder.withArgName("resourcefile").hasArg()
            .withDescription("resource parameter file to use. Default is resources.xml")
            .withLongOpt("resources").create("p");
    Option o141 = OptionBuilder.withArgName("login,password,role1,role2,...").hasArgs(Option.UNLIMITED_VALUES)
            .withValueSeparator(',')
            .withDescription("Create or update a JQM account. Roles must exist beforehand.").create("U");

    Options options = new Options();
    OptionGroup og1 = new OptionGroup();
    og1.setRequired(true);
    og1.addOption(o00);
    og1.addOption(o01);
    og1.addOption(o11);
    og1.addOption(o21);
    og1.addOption(o31);
    og1.addOption(o51);
    og1.addOption(o61);
    og1.addOption(o71);
    og1.addOption(o81);
    og1.addOption(o91);
    og1.addOption(o101);
    og1.addOption(o111);
    og1.addOption(o121);
    og1.addOption(o141);
    options.addOptionGroup(og1);
    OptionGroup og2 = new OptionGroup();
    og2.addOption(o131);
    options.addOptionGroup(og2);

    HelpFormatter formatter = new HelpFormatter();
    formatter.setWidth(160);

    try {
        // Parse arguments
        CommandLineParser parser = new BasicParser();
        CommandLine line = parser.parse(options, args);

        // Other db connection?
        if (line.getOptionValue(o131.getOpt()) != null) {
            jqmlogger.info("Using resource XML file " + line.getOptionValue(o131.getOpt()));
            Helpers.resourceFile = line.getOptionValue(o131.getOpt());
        }

        // Set db connection
        Helpers.registerJndiIfNeeded();

        // Enqueue
        if (line.getOptionValue(o11.getOpt()) != null) {
            enqueue(line.getOptionValue(o11.getOpt()));
        }
        // Get status
        if (line.getOptionValue(o91.getOpt()) != null) {
            getStatus(Integer.parseInt(line.getOptionValue(o91.getOpt())));
        }
        // Import XML
        else if (line.getOptionValue(o21.getOpt()) != null) {
            importJobDef(line.getOptionValue(o21.getOpt()));
        }
        // Start engine
        else if (line.getOptionValue(o00.getOpt()) != null) {
            startEngine(line.getOptionValue(o00.getOpt()));
        }
        // Export all Queues
        else if (line.getOptionValue(o31.getOpt()) != null) {
            exportAllQueues(line.getOptionValue(o31.getOpt()));
        }
        // Import queues
        else if (line.getOptionValue(o51.getOpt()) != null) {
            importQueues(line.getOptionValue(o51.getOpt()));
        }
        // Create node
        else if (line.getOptionValue(o61.getOpt()) != null) {
            createEngine(line.getOptionValue(o61.getOpt()));
        }
        // Upgrade
        else if (line.hasOption(o81.getOpt())) {
            upgrade();
        }
        // Help
        else if (line.hasOption(o01.getOpt())) {
            formatter.printHelp("java -jar jqm-engine.jar", options, true);
        }
        // Version
        else if (line.hasOption(o71.getOpt())) {
            jqmlogger.info("Engine version: " + Helpers.getMavenVersion());
        }
        // Root password
        else if (line.hasOption(o101.getOpt())) {
            root(line.getOptionValue(o101.getOpt()));
        }
        // Web options
        else if (line.hasOption(o111.getOpt())) {
            ws(line.getOptionValue(o111.getOpt()));
        }
        // Web options
        else if (line.hasOption(o121.getOpt())) {
            single(line.getOptionValue(o121.getOpt()));
        }
        // User handling
        else if (line.hasOption(o141.getOpt())) {
            user(line.getOptionValues(o141.getOpt()));
        }
    } catch (ParseException exp) {
        jqmlogger.fatal("Could not read command line: " + exp.getMessage());
        formatter.printHelp("java -jar jqm-engine.jar", options, true);
        return;
    }
}

From source file:jp.primecloud.auto.tool.management.main.Main.java

public static void main(String args[]) {
    Options options = new Options();
    options.addOption("Z", false, "Zabbix mode");
    options.addOption("U", false, "UPDATE mode");
    options.addOption("S", false, "SELECT mode");
    options.addOption("C", false, "Create Mode");
    options.addOption("P", false, "Show Platform");
    options.addOption("L", false, "Show Users");
    options.addOption("E", false, "Ecrypt UserPassword");
    options.addOption("I", false, "IaasGateway Mode");
    options.addOption("A", false, "PCC-API Genarate ID or Key Mode");
    options.addOption("W", false, "Decrypt UserPassword");

    options.addOption("username", true, "Create the username");
    options.addOption("password", true, "Create the password");
    options.addOption("firstname", true, "Create the firstname");
    options.addOption("familyname", true, "Create the familyname");
    options.addOption("userno", true, "Create the userno");

    options.addOption("dburl", "connectionurl", true, "PrimeCloud Controller database url");
    options.addOption("dbuser", "username", true, "PrimeCloud Controller database username");
    options.addOption("dbpass", "password", true, "PrimeCloud Controller database password");

    options.addOption("sql", true, "SQL");
    options.addOption("columnname", true, "columnName");
    options.addOption("columntype", true, "columnType");
    options.addOption("salt", true, "Salt");

    OptionBuilder.withLongOpt("prepared");
    OptionBuilder.hasArgs();//ww w. j a  v  a 2 s.c  o  m
    OptionBuilder.withDescription("execute as PreparedStatement");
    OptionBuilder.withArgName("params");
    Option optionPrepared = OptionBuilder.create();
    options.addOption(optionPrepared);

    // for Zabbix
    options.addOption("enable", false, "enable");
    options.addOption("disable", false, "disable");
    options.addOption("get", false, "getUser from zabbix");
    options.addOption("check", false, "API setting check for zabbix");

    options.addOption("config", true, "Property can obtain from management-config.properties");
    options.addOption("platformkind", true, "Platform kind. e.g. ec2 and ec2_vpc or vmware");
    options.addOption("platformname", true, "Platform can obtain from auto-config.xml");
    options.addOption("platformno", true, "Platform can obtain from auto-config.xml");

    // for IaasGateway(AWS, Cloudstack)
    options.addOption("keyname", true, "import your key pair as keyName");
    options.addOption("publickey", true, "import your public key");

    // for PCC
    options.addOption("accessid", true, "accessid for PCC-API");
    options.addOption("secretkey", true, "secretkey for PCC-API");
    options.addOption("generatetype", true, "genarateType for PCC-API");

    options.addOption("h", "help", false, "help");

    CommandLineParser parser = new BasicParser();

    CommandLine commandLine;
    try {
        commandLine = parser.parse(options, args);
    } catch (ParseException e) {
        System.out.println(
                "???????? -h?????????");
        return;
    }

    if (commandLine.hasOption("h")) {
        HelpFormatter f = new HelpFormatter();
        f.printHelp("PCC script ", options);
    }

    ManagementConfigLoader.init();
    //?

    //Zabbix?
    if (commandLine.hasOption("Z")) {
        if (commandLine.hasOption("C")) {
            //Zabbix?
            ZabbixMain.createExecute(commandLine);
        } else if (commandLine.hasOption("U")) {
            //Zabbix
            ZabbixMain.updateExecute(commandLine);
        } else if (commandLine.hasOption("disable")) {
            //Zabbix
            ZabbixMain.disableExecute(commandLine);
        } else if (commandLine.hasOption("enable")) {
            //Zabbix
            ZabbixMain.enableExecute(commandLine);
        } else if (commandLine.hasOption("get")) {
            //Zabbix?
            ZabbixMain.getUser(commandLine);
        } else if (commandLine.hasOption("check")) {
            //Zabbix??
            ZabbixMain.checkApiVersion();
        }
        //PCC?
    } else if (commandLine.hasOption("U")) {
        if (commandLine.hasOption("prepared")) {
            SQLMain.updateExecutePrepared(commandLine);
        } else {
            //Update?
            SQLMain.updateExecute(commandLine);
        }
    } else if (commandLine.hasOption("S")) {
        //Select?
        SQLMain.selectExecute(commandLine);
    } else if (commandLine.hasOption("P")) {
        //?
        ConfigMain.showPlatforms();
    } else if (commandLine.hasOption("L")) {
        //PCC?
        UserService.showUserPlatform();
    } else if (commandLine.hasOption("config")) {
        //???
        ConfigMain.getProperty(commandLine.getOptionValue("config"));
    } else if (commandLine.hasOption("platformname") && commandLine.hasOption("platformkind")) {
        //??????
        ConfigMain.getPlatformNo(commandLine.getOptionValue("platformname"),
                commandLine.getOptionValue("platformkind"));
    } else if (commandLine.hasOption("E")) {
        //PCC??
        UserService.encryptUserPassword(commandLine.getOptionValue("password"));
    } else if (commandLine.hasOption("I")) {
        //IaasGatewayCall??AWS or Cloudstack???
        IaasGatewayMain.importExecute(commandLine);
    } else if (commandLine.hasOption("A")) {
        PccApiGenerateService.genarate(commandLine);
    } else if (commandLine.hasOption("W")) {
        //PCC??
        UserService.decryptUserPassword(commandLine.getOptionValue("password"),
                commandLine.getOptionValue("salt"));
    }
}

From source file:apps.quantification.LearnQuantificationSVMLight.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = LearnQuantificationSVMLight.class.getName()
            + " [OPTIONS] <path to svm_light_learn> <path to svm_light_classify> <trainingIndexDirectory> <outputDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("f");
    OptionBuilder.withDescription("Number of folds");
    OptionBuilder.withLongOpt("f");
    OptionBuilder.isRequired(true);//  ww w.j  a  v  a  2  s  . c o  m
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("c");
    OptionBuilder.withDescription("The c value for svm_light (default 1)");
    OptionBuilder.withLongOpt("c");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("k");
    OptionBuilder.withDescription("Kernel type (default 0: linear, 1: polynomial, 2: RBF, 3: sigmoid)");
    OptionBuilder.withLongOpt("k");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("t");
    OptionBuilder.withDescription("Path for temporary files");
    OptionBuilder.withLongOpt("t");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("v");
    OptionBuilder.withDescription("Verbose output");
    OptionBuilder.withLongOpt("v");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("s");
    OptionBuilder.withDescription("Don't delete temporary training file in svm_light format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmLightLearnerCustomizer classificationLearnerCustomizer = null;
    SvmLightClassifierCustomizer classificationCustomizer = null;

    int folds = -1;

    GnuParser parser = new GnuParser();
    String[] remainingArgs = null;
    try {
        CommandLine line = parser.parse(options, args);

        remainingArgs = line.getArgs();

        classificationLearnerCustomizer = new SvmLightLearnerCustomizer(remainingArgs[0]);
        classificationCustomizer = new SvmLightClassifierCustomizer(remainingArgs[1]);

        folds = Integer.parseInt(line.getOptionValue("f"));

        if (line.hasOption("c"))
            classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c")));

        if (line.hasOption("k")) {
            System.out.println("Kernel type: " + line.getOptionValue("k"));
            classificationLearnerCustomizer.setKernelType(Integer.parseInt(line.getOptionValue("k")));
        }

        if (line.hasOption("v"))
            classificationLearnerCustomizer.printSvmLightOutput(true);

        if (line.hasOption("s"))
            classificationLearnerCustomizer.setDeleteTrainingFiles(false);

        if (line.hasOption("t")) {
            classificationLearnerCustomizer.setTempPath(line.getOptionValue("t"));
            classificationCustomizer.setTempPath(line.getOptionValue("t"));
        }

    } catch (Exception exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    assert (classificationLearnerCustomizer != null);

    if (remainingArgs.length != 4) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    String indexFile = remainingArgs[2];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String outputPath = remainingArgs[3];

    SvmLightLearner classificationLearner = new SvmLightLearner();

    classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(indexPath, false);
    fssm.open();

    IIndex training = TroveReadWriteHelper.readIndex(fssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    final TextualProgressBar progressBar = new TextualProgressBar("Learning the quantifiers");

    IOperationStatusListener status = new IOperationStatusListener() {

        @Override
        public void operationStatus(double percentage) {
            progressBar.signal((int) percentage);
        }
    };

    QuantificationLearner quantificationLearner = new QuantificationLearner(folds, classificationLearner,
            classificationLearnerCustomizer, classificationCustomizer, ClassificationMode.PER_CATEGORY,
            new LogisticFunction(), status);

    IQuantifier[] quantifiers = quantificationLearner.learn(training);

    File executableFile = new File(classificationLearnerCustomizer.getSvmLightLearnPath());
    IDataManager classifierDataManager = new SvmLightDataManager(new SvmLightClassifierCustomizer(
            executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_light_classify"));
    String description = "_SVMLight_C-" + classificationLearnerCustomizer.getC() + "_K-"
            + classificationLearnerCustomizer.getKernelType();
    if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0)
        description += "_" + classificationLearnerCustomizer.getAdditionalParameters();
    String quantifierPrefix = indexName + "_Quantifier-" + folds + description;

    FileSystemStorageManager fssmo = new FileSystemStorageManager(
            outputPath + File.separatorChar + quantifierPrefix, true);
    fssmo.open();
    QuantificationLearner.write(quantifiers, fssmo, classifierDataManager);
    fssmo.close();

    BufferedWriter bfs = new BufferedWriter(
            new FileWriter(outputPath + File.separatorChar + quantifierPrefix + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = quantificationLearner.getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = quantificationLearner.getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = quantificationLearner.getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = quantificationLearner.getScaledFPRs();

    ContingencyTableSet contingencyTableSet = quantificationLearner.getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = training.getCategoryDB().getCategoryName(cat);
        ContingencyTable contingencyTable = contingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = quantifierPrefix + "\ttrain\tsimple\t" + catName + "\t" + cat + "\t"
                + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t"
                + contingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n";
        bfs.write(line);
        line = quantifierPrefix + "\ttrain\tscaled\t" + catName + "\t" + cat + "\t" + contingencyTable.tp()
                + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn()
                + "\t" + scaledTPR + "\t" + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}

From source file:apps.quantification.LearnQuantificationSVMPerf.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = LearnQuantificationSVMPerf.class.getName()
            + " [OPTIONS] <path to svm_perf_learn> <path to svm_perf_classify> <trainingIndexDirectory> <outputDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("f");
    OptionBuilder.withDescription("Number of folds");
    OptionBuilder.withLongOpt("f");
    OptionBuilder.isRequired(true);//from www . ja va2 s . com
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("c");
    OptionBuilder.withDescription("The c value for svm_perf (default 0.01)");
    OptionBuilder.withLongOpt("c");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("t");
    OptionBuilder.withDescription("Path for temporary files");
    OptionBuilder.withLongOpt("t");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("l");
    OptionBuilder.withDescription("The loss function to optimize (default 2):\n"
            + "               0  Zero/one loss: 1 if vector of predictions contains error, 0 otherwise.\n"
            + "               1  F1: 100 minus the F1-score in percent.\n"
            + "               2  Errorrate: Percentage of errors in prediction vector.\n"
            + "               3  Prec/Rec Breakeven: 100 minus PRBEP in percent.\n"
            + "               4  Prec@p: 100 minus precision at p in percent.\n"
            + "               5  Rec@p: 100 minus recall at p in percent.\n"
            + "               10  ROCArea: Percentage of swapped pos/neg pairs (i.e. 100 - ROCArea).");
    OptionBuilder.withLongOpt("l");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("w");
    OptionBuilder.withDescription("Choice of structural learning algorithm (default 9):\n"
            + "               0: n-slack algorithm described in [2]\n"
            + "               1: n-slack algorithm with shrinking heuristic\n"
            + "               2: 1-slack algorithm (primal) described in [5]\n"
            + "               3: 1-slack algorithm (dual) described in [5]\n"
            + "               4: 1-slack algorithm (dual) with constraint cache [5]\n"
            + "               9: custom algorithm in svm_struct_learn_custom.c");
    OptionBuilder.withLongOpt("w");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("p");
    OptionBuilder.withDescription("The value of p used by the prec@p and rec@p loss functions (default 0)");
    OptionBuilder.withLongOpt("p");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("v");
    OptionBuilder.withDescription("Verbose output");
    OptionBuilder.withLongOpt("v");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("s");
    OptionBuilder.withDescription("Don't delete temporary training file in svm_perf format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmPerfLearnerCustomizer classificationLearnerCustomizer = null;
    SvmPerfClassifierCustomizer classificationCustomizer = null;

    int folds = -1;

    GnuParser parser = new GnuParser();
    String[] remainingArgs = null;
    try {
        CommandLine line = parser.parse(options, args);

        remainingArgs = line.getArgs();

        classificationLearnerCustomizer = new SvmPerfLearnerCustomizer(remainingArgs[0]);
        classificationCustomizer = new SvmPerfClassifierCustomizer(remainingArgs[1]);

        folds = Integer.parseInt(line.getOptionValue("f"));

        if (line.hasOption("c"))
            classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c")));

        if (line.hasOption("w"))
            classificationLearnerCustomizer.setW(Integer.parseInt(line.getOptionValue("w")));

        if (line.hasOption("p"))
            classificationLearnerCustomizer.setP(Integer.parseInt(line.getOptionValue("p")));

        if (line.hasOption("l"))
            classificationLearnerCustomizer.setL(Integer.parseInt(line.getOptionValue("l")));

        if (line.hasOption("v"))
            classificationLearnerCustomizer.printSvmPerfOutput(true);

        if (line.hasOption("s"))
            classificationLearnerCustomizer.setDeleteTrainingFiles(false);

        if (line.hasOption("t")) {
            classificationLearnerCustomizer.setTempPath(line.getOptionValue("t"));
            classificationCustomizer.setTempPath(line.getOptionValue("t"));
        }

    } catch (Exception exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    assert (classificationLearnerCustomizer != null);

    if (remainingArgs.length != 4) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    String indexFile = remainingArgs[2];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String outputPath = remainingArgs[3];

    SvmPerfLearner classificationLearner = new SvmPerfLearner();

    classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(indexPath, false);
    fssm.open();

    IIndex training = TroveReadWriteHelper.readIndex(fssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    final TextualProgressBar progressBar = new TextualProgressBar("Learning the quantifiers");

    IOperationStatusListener status = new IOperationStatusListener() {

        @Override
        public void operationStatus(double percentage) {
            progressBar.signal((int) percentage);
        }
    };

    QuantificationLearner quantificationLearner = new QuantificationLearner(folds, classificationLearner,
            classificationLearnerCustomizer, classificationCustomizer, ClassificationMode.PER_CATEGORY,
            new LogisticFunction(), status);

    IQuantifier[] quantifiers = quantificationLearner.learn(training);

    File executableFile = new File(classificationLearnerCustomizer.getSvmPerfLearnPath());
    IDataManager classifierDataManager = new SvmPerfDataManager(new SvmPerfClassifierCustomizer(
            executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_perf_classify"));
    String description = "_SVMPerf_C-" + classificationLearnerCustomizer.getC() + "_W-"
            + classificationLearnerCustomizer.getW() + "_L-" + classificationLearnerCustomizer.getL();
    if (classificationLearnerCustomizer.getL() == 4 || classificationLearnerCustomizer.getL() == 5)
        description += "_P-" + classificationLearnerCustomizer.getP();
    if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0)
        description += "_" + classificationLearnerCustomizer.getAdditionalParameters();
    String quantifierPrefix = indexName + "_Quantifier-" + folds + description;

    FileSystemStorageManager fssmo = new FileSystemStorageManager(
            outputPath + File.separatorChar + quantifierPrefix, true);
    fssmo.open();
    QuantificationLearner.write(quantifiers, fssmo, classifierDataManager);
    fssmo.close();

    BufferedWriter bfs = new BufferedWriter(
            new FileWriter(outputPath + File.separatorChar + quantifierPrefix + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = quantificationLearner.getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = quantificationLearner.getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = quantificationLearner.getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = quantificationLearner.getScaledFPRs();

    ContingencyTableSet contingencyTableSet = quantificationLearner.getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = training.getCategoryDB().getCategoryName(cat);
        ContingencyTable contingencyTable = contingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = quantifierPrefix + "\ttrain\tsimple\t" + catName + "\t" + cat + "\t"
                + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t"
                + contingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n";
        bfs.write(line);
        line = quantifierPrefix + "\ttrain\tscaled\t" + catName + "\t" + cat + "\t" + contingencyTable.tp()
                + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn()
                + "\t" + scaledTPR + "\t" + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}

From source file:net.extemporal.test.Main.java

public static void main(String[] args) throws IOException {
    Options opts = new Options();
    opts.addOption(OptionBuilder.withDescription("email id for 1st account").hasArg(true).create("e1"));
    opts.addOption(//from ww  w .ja v  a  2s  .  c  om
            OptionBuilder.withDescription("either gmail password or full URNs for Store and Transport servers")
                    .hasOptionalArgs(3).create("c1"));

    opts.addOption(OptionBuilder.withDescription("email id for 2nd account").hasArg(true).create("e2"));
    opts.addOption(
            OptionBuilder.withDescription("either gmail password or full URNs for Store and Transport servers")
                    .hasOptionalArgs(3).create("c2"));

    // this parses the command line but doesn't throw an exception on unknown options
    try {
        CommandLine cmd = new GnuParser().parse(opts, args, true);
        if (cmd.hasOption("e1") && cmd.hasOption("c1")) {
            String e = cmd.getOptionValue("e1");
            String[] accounts = cmd.getOptionValues("c1");
            if (accounts.length == 1)
                email1 = EmailTestPlatform.getGMailCredentials(e, accounts[0]);
            else if (email1.length == 2) {
                email1 = new String[] { e, accounts[0], accounts[1] };
            }
        }
        if (cmd.hasOption("e2") && cmd.hasOption("c2")) {
            String e = cmd.getOptionValue("e2");
            String[] accounts = cmd.getOptionValues("c2");
            if (accounts.length == 1)
                email2 = EmailTestPlatform.getGMailCredentials(e, accounts[0]);
            else if (email2.length == 2) {
                email2 = new String[] { e, accounts[0], accounts[1] };
            }
        }
    } catch (ParseException pex) {
        System.err.println("error parsing commandline: " + pex);
    }

    ShellFactory.createConsoleShell("test-harness", "Type '?list' to see valid commands", new Main())
            .commandLoop();
}

From source file:de.dominicscheurer.passwords.Main.java

/**
 * @param args//from w  w w.j a v a2 s.  co m
 *            Command line arguments (see code or output of program when
 *            started with no arguments).
 */
@SuppressWarnings("static-access")
public static void main(String[] args) {
    Options options = new Options();

    Option seedPwdOpt = OptionBuilder.withArgName("Seed Password").isRequired().hasArg()
            .withDescription("Password used as a seed").withLongOpt("seed-password").create("s");

    Option serviceIdOpt = OptionBuilder.withArgName("Service Identifier").isRequired().hasArg()
            .withDescription("The service that the password is created for, e.g. facebook.com")
            .withLongOpt("service-identifier").create("i");

    Option pwdLengthOpt = OptionBuilder.withArgName("Password Length").withType(Integer.class).hasArg()
            .withDescription("Length of the password in characters").withLongOpt("pwd-length").create("l");

    Option specialChars = OptionBuilder.withArgName("With special chars (TRUE|false)").withType(Boolean.class)
            .hasArg().withDescription("Set to true if special chars !-_?=@/+* are desired, else false")
            .withLongOpt("special-chars").create("c");

    Option suppressPwdOutpOpt = OptionBuilder
            .withDescription("Suppress password output (copy to clipboard only)").withLongOpt("hide-password")
            .hasArg(false).create("x");

    Option helpOpt = OptionBuilder.withDescription("Prints this help message").withLongOpt("help").create("h");

    options.addOption(seedPwdOpt);
    options.addOption(serviceIdOpt);
    options.addOption(pwdLengthOpt);
    options.addOption(specialChars);
    options.addOption(suppressPwdOutpOpt);
    options.addOption(helpOpt);

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

        if (cmd.hasOption("h")) {
            SafePwdGen.printHelp(options);
            System.exit(0);
        }

        int pwdLength = STD_PWD_LENGTH;
        if (cmd.hasOption("l")) {
            pwdLength = new Integer(cmd.getOptionValue("l"));
        }

        boolean useSpecialChars = true;
        if (cmd.hasOption("c")) {
            useSpecialChars = new Boolean(cmd.getOptionValue("c"));
        }

        if (pwdLength > MAX_PWD_LENGTH_64 && !useSpecialChars) {
            System.out.println(PASSWORD_SIZE_TOO_BIG + MAX_PWD_LENGTH_64);
        }

        if (pwdLength > MAX_PWD_LENGTH_71 && useSpecialChars) {
            System.out.println(PASSWORD_SIZE_TOO_BIG + MAX_PWD_LENGTH_71);
        }

        boolean suppressPwdOutput = cmd.hasOption('x');

        String pwd = SafePwdGen.createPwd(cmd.getOptionValue("s"), cmd.getOptionValue("i"), pwdLength,
                useSpecialChars);

        if (!suppressPwdOutput) {
            System.out.print(GENERATED_PASSWORD);
            System.out.println(pwd);
        }
        System.out.println(CLIPBOARD_COPIED_MSG);
        SystemClipboardInterface.copy(pwd);

        System.in.read();
    } catch (ParseException e) {
        System.out.println(e.getLocalizedMessage());
        SafePwdGen.printHelp(options);
    } catch (UnsupportedEncodingException e) {
        System.out.println(e.getLocalizedMessage());
    } catch (NoSuchAlgorithmException e) {
        System.out.println(e.getLocalizedMessage());
    } catch (IOException e) {
        System.out.println(e.getLocalizedMessage());
    }
}

From source file:edu.harvard.med.screensaver.io.screenresults.ScreenResultImporter.java

@SuppressWarnings("static-access")
public static void main(String[] args) {
    ScreenResultImporter app = new ScreenResultImporter(args);
    app.addCommandLineOption(OptionBuilder.hasArg().withArgName("screen facility ID").isRequired()
            .withDescription(//from  w w w  .jav  a  2s.  c o  m
                    "the facility-assigned ID of the screen for which the screen result is being parsed")
            .withLongOpt(SCREEN_OPTION[LONG_OPTION]).create(SCREEN_OPTION[SHORT_OPTION]));
    app.addCommandLineOption(OptionBuilder.hasArg().withArgName("file").isRequired()
            .withDescription("the file location of the Excel workbook file holding the Screen Result metadata")
            .withLongOpt(INPUT_FILE_OPTION[LONG_OPTION]).create(INPUT_FILE_OPTION[SHORT_OPTION]));
    app.addCommandLineOption(OptionBuilder.hasArg().withArgName("comments").isRequired(false)
            .withDescription("comments to associate with the data loading activity")
            .withLongOpt(COMMENTS[LONG_OPTION]).create(COMMENTS[SHORT_OPTION]));
    app.addCommandLineOption(OptionBuilder.withDescription("The first plate number to parse/import").hasArg()
            .withArgName("#").withLongOpt(PLATE_NUMBER_START_OPTION[LONG_OPTION])
            .create(PLATE_NUMBER_START_OPTION[SHORT_OPTION]));
    app.addCommandLineOption(OptionBuilder.withDescription("The last plate number to parse/import").hasArg()
            .withArgName("#").withLongOpt(PLATE_NUMBER_END_OPTION[LONG_OPTION])
            .create(PLATE_NUMBER_END_OPTION[SHORT_OPTION]));
    app.addCommandLineOption(OptionBuilder
            .withDescription("Import screen result into database if parsing is successful.  "
                    + "(By default, the parser only validates the input and then exits.)")
            .withLongOpt(IMPORT_OPTION[LONG_OPTION]).create(IMPORT_OPTION[SHORT_OPTION]));
    app.addCommandLineOption(OptionBuilder.withDescription("Ignore any subsequent duplicates of a well")
            .isRequired(false).withLongOpt(IGNORE_DUPLICATE_ERRORS_OPTION[LONG_OPTION])
            .create(IGNORE_DUPLICATE_ERRORS_OPTION[SHORT_OPTION]));

    app.addCommandLineOption(OptionBuilder.withDescription(
            "Set the incremental flushing option; this is necessary for conserving memory in large imports (default=\"true\")")
            .isRequired(false).withArgName("value").withLongOpt(INCREMENTAL_FLUSH_OPTION[LONG_OPTION])
            .create(INCREMENTAL_FLUSH_OPTION[SHORT_OPTION]));
    app.addCommandLineOption(OptionBuilder.withDescription(DELETE_EXISTING[2]).hasArg(false)
            .withLongOpt(DELETE_EXISTING[LONG_OPTION]).create(DELETE_EXISTING[SHORT_OPTION]));

    app.processOptions(/* acceptDatabaseOptions= */true, /* acceptAdminUserOptions= */true);
    try {
        execute(app);
    } catch (ParseErrorsException e) {
        if (!e.getErrors().isEmpty()) {
            for (ParseError pe : e.getErrors()) {
                log.error("" + pe);
            }
            log.error("" + e.getErrors().size() + " errors found.");
        }
        System.exit(1);
    } catch (Exception e) {
        log.error("Failed to create the screen result", e);
        System.exit(1);
    }

}