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

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

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Introduction

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

Prototype

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

Source Link

Document

Parses the specified arguments based on the specifed Options .

Usage

From source file:jfractus.app.Main.java

public static void main(String[] args) {
    createCommandLineOptions();/* w ww. ja  va 2 s  .  c om*/
    GnuParser parser = new GnuParser();
    HelpFormatter helpFormatter = new HelpFormatter();
    helpFormatter.setOptionComparator(null);

    CommandLine cmdLine = null;

    try {
        cmdLine = parser.parse(cliOptions, args);
    } catch (ParseException e) {
        System.err.println(Resources.getString("CLIParseError"));
        return;
    }

    String functionsLibPaths = cmdLine.getOptionValue("libraries");
    int threadsNum = FractusPreferencesFactory.prefs.getThreadsNumber();
    Dimension outSize = new Dimension(FractusPreferencesFactory.prefs.getDefaultImageWidth(),
            FractusPreferencesFactory.prefs.getDefaultImageHeight());
    AntialiasConfig aaConfig = FractusPreferencesFactory.prefs.getDefaultAntialiasConfig();
    boolean printProgress = cmdLine.hasOption("progress");

    try {
        String threadsNumString = cmdLine.getOptionValue("threads");
        String imageSizeString = cmdLine.getOptionValue("image-size");
        String aaMethodString = cmdLine.getOptionValue("antialias");
        String samplingSizeString = cmdLine.getOptionValue("sampling-size");

        if (functionsLibPaths != null)
            FunctionsLoaderFactory.loader.setClassPathsFromString(functionsLibPaths);

        if (aaMethodString != null) {
            if (aaMethodString.equals("none"))
                aaConfig.setMethod(AntialiasConfig.Method.NONE);
            else if (aaMethodString.equals("normal"))
                aaConfig.setMethod(AntialiasConfig.Method.NORMAL);
            else
                throw new BadValueOfArgumentException("Bad value of argument");
        }
        if (threadsNumString != null)
            threadsNum = Integer.valueOf(threadsNumString).intValue();
        if (imageSizeString != null)
            parseSize(imageSizeString, outSize);
        if (samplingSizeString != null) {
            Dimension samplingSize = new Dimension();
            parseSize(samplingSizeString, samplingSize);
            aaConfig.setSamplingSize(samplingSize.width, samplingSize.height);
        }

        if (cmdLine.hasOption("save-prefs")) {
            FunctionsLoaderFactory.loader.putClassPathsToPrefs();
            FractusPreferencesFactory.prefs.setThreadsNumber(threadsNum);
            FractusPreferencesFactory.prefs.setDefaultImageSize(outSize.width, outSize.height);
            FractusPreferencesFactory.prefs.setDefaultAntialiasConfig(aaConfig);
        }
    } catch (ArgumentParseException e) {
        System.err.println(Resources.getString("CLIParseError"));
        return;
    } catch (NumberFormatException e) {
        System.err.println(Resources.getString("CLIParseError"));
        return;
    } catch (BadValueOfArgumentException e) {
        System.err.println(Resources.getString("CLIBadValueError"));
        return;
    }

    if (cmdLine.hasOption('h') || (cmdLine.hasOption('n') && cmdLine.getArgs().length < 2)) {
        helpFormatter.printHelp(Resources.getString("CLISyntax"), cliOptions);
        return;
    }

    if (!cmdLine.hasOption('n')) {
        SwingUtilities.invokeLater(new Runnable() {
            public void run() {
                createAndShowGUI();
            }
        });
    } else {
        String[] cmdArgs = cmdLine.getArgs();
        try {
            FractalDocument fractal = new FractalDocument();
            fractal.readFromFile(new File(cmdArgs[0]));
            FractalRenderer renderer = new FractalRenderer(outSize.width, outSize.height, aaConfig, fractal);
            FractalImageWriter imageWriter = new FractalImageWriter(renderer, cmdArgs[1]);

            renderer.setThreadNumber(threadsNum);
            renderer.prepareFractal();
            if (printProgress) {
                renderer.addRenderProgressListener(new CMDLineProgressEventListener());
                imageWriter.addImageWriterProgressListener(new CMDLineImageWriteProgressListener());
            }

            imageWriter.write();
        } catch (Exception e) {
            System.err.println(e.getMessage());
        }
    }
}

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);//w  ww  .  j  av a2s  . c  om
    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.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 w  w  .  j a  v  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: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  w w. jav  a  2 s  .c  o 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:com.eucalyptus.simpleworkflow.common.client.WorkflowClientStandalone.java

public static void main(String[] args) {
    final WorkflowClientStandalone instance = WorkflowClientStandalone.getInstance();
    final Options opts = buildOptions();
    final GnuParser cliParser = new GnuParser();
    CommandLine cmd = null;//from  w w  w.  j a  v  a2 s .c  om
    try {
        cmd = cliParser.parse(opts, args);
    } catch (final ParseException ex) {
        printHelp(opts, null);
        System.exit(1);
    }

    try {
        instance.readOptions(cmd);
    } catch (final NumberFormatException ex) {
        printHelp(opts, "Some number format arguents are not recognizable");
        System.exit(1);
    }

    initLogs();

    LOG.debug("Starting Workflow Standalone Host");
    try {
        instance.discoverWorkflows();
    } catch (final Exception ex) {
        LOG.debug("Failed to discover workflow and activities implementation");
        printHelp(opts, "Failed to discover implementation classes");
        System.exit(1);
    }

    try {
        final AmazonSimpleWorkflow swfClient = instance.getAWSClient();
        addShutdownHook(swfClient);

        final WorkflowClient workflowClient = new WorkflowClient(
                instance.workflowClasses.toArray(new Class<?>[instance.workflowClasses.size()]),
                instance.activityClasses.toArray(new Class<?>[instance.activityClasses.size()]), false,
                swfClient, instance.domain, instance.taskList, instance.buildWorkflowWorkerConfig(),
                instance.buildActivityWorkerConfig());
        workflowClient.start();
        instance.clients.add(workflowClient);
    } catch (final Exception ex) {
        LOG.debug("Failed to create workflow clients", ex);
        System.exit(1);
    }

    do {
        try {
            Thread.sleep(1000);
        } catch (final Exception ex) {
        }
    } while (true);
}

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);/*w  ww.  jav a 2  s .  c o  m*/
    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:com.gsma.iariauth.validator.util.IARIValidatorMain.java

public static void main(String[] args) {
    String formatstr = "IARIValidator [-d <authorization document>] [-n <package name>] [-ps <package signer fingerprint>] [-pk <package signer keystore>] [-pa <package signer certificate alias>] [-pp <package signer keystore password>] -k <keystore> -p <password> [-v]";

    HelpFormatter formatter = new HelpFormatter();
    GnuParser parser = new GnuParser();
    Options opts = new Options();

    opts.addOption(new ArgOption("d", "document", "IARI Authorization document"));
    opts.addOption(new ArgOption("pkgname", "package-name", "package name"));
    opts.addOption(new ArgOption("pkgsigner", "package-signer", "package signer fingerprint"));
    opts.addOption(new ArgOption("pkgkeystore", "package-keystore", "package signing keystore"));
    opts.addOption(new ArgOption("pkgalias", "package-key-alias", "package signing certificate alias"));
    opts.addOption(new ArgOption("pkgstorepass", "package-keystore-pass", "package signing keystore password"));
    opts.addOption(new Option("v", "verbose", false, "verbose output"));

    CommandLine cli = null;//from  w w  w  . j a v  a 2s  .co  m
    try {
        cli = parser.parse(opts, args);
    } catch (ParseException e) {
        formatter.printHelp(formatstr, opts);
        return;
    }

    boolean verbose = cli.hasOption("v");

    String packageName = cli.getOptionValue("pkgname");
    String packageSigner = cli.getOptionValue("pkgsigner");
    if (packageSigner == null) {
        String packageSignerKeystore = cli.getOptionValue("pkgkeystore");
        String packageSignerKeystoreAlias = cli.getOptionValue("pkgalias");
        String packageSignerKeystorePasswd = cli.getOptionValue("pkgstorepass");
        if (packageSignerKeystore != null) {
            if (packageSignerKeystoreAlias == null) {
                System.err.println("No alias given for package signing certificate");
                System.exit(1);
            }
            if (packageSignerKeystorePasswd == null) {
                System.err.println("No password given for package signing keystore");
                System.exit(1);
            }
            KeyStore packageKeystore = loadKeyStore(packageSignerKeystore, packageSignerKeystorePasswd);
            if (packageKeystore == null) {
                System.err.println("Unable to read package keystore");
                System.exit(1);
            }
            try {
                X509Certificate c = (X509Certificate) packageKeystore
                        .getCertificate(packageSignerKeystoreAlias);
                if (c == null) {
                    System.err.println("Unable to access package signing certificate");
                    System.exit(1);
                }
                packageSigner = getFingerprint(c);
            } catch (KeyStoreException e) {
                System.err.println("Unable to access package signing certificate");
                System.exit(1);
            } catch (CertificateEncodingException e) {
                e.printStackTrace();
                System.err.println("Unable to read package signing certificate");
                System.exit(1);
            }
        }
    }

    String authDocumentPath = cli.getOptionValue("d");
    if (authDocumentPath == null) {
        System.err.println("No auth document specified");
        System.exit(1);
    }
    File authDocument = new File(authDocumentPath);
    if (!authDocument.exists() || !authDocument.isFile()) {
        System.err.println("Unable to read specified auth document");
        System.exit(1);
    }

    PackageProcessor processor = new PackageProcessor(packageName, packageSigner);
    ProcessingResult result = processor.processIARIauthorization(authDocument);
    if (result.getStatus() != ProcessingResult.STATUS_OK) {
        System.err.println("Error validating authDocument:");
        System.err.println(result.getError().toString());
        System.exit(1);
    }

    if (verbose) {
        System.out.println(result.getAuthDocument().toString());
    }
    System.exit(0);
}

From source file:de.huberlin.cuneiform.main.Main.java

public static void main(String[] args)
        throws ParseException, IOException, NotDerivableException, InterruptedException, JSONException {

    GnuParser gnuParser;
    CommandLine cmdline;/*from  w w  w  .j  a v  a 2  s  .c  om*/
    Options opt;
    String value;
    int platform;
    File outputDir;
    String[] fileList;
    StringBuffer buf;
    String line;
    String dagid;
    File logFile;

    opt = new Options();

    opt.addOption("p", "platform", true, "The platform to perform the Cuneiform script's interpretation. "
            + "Possible platforms are: 'dot', 'local', and 'debug'. Default is 'local'.");

    opt.addOption("d", "directory", true,
            "The output directory, to put the interpretation intermediate and output result as well as the default location to store the log.");

    opt.addOption("c", "clean", false,
            "If set, the execution engine ignores all cached results and starts a clean workflow run.");

    opt.addOption("r", "runid", true,
            "If set, a custom id is set for this workflow run. By default a UUID string is used.");

    opt.addOption("f", "file", true,
            "Override the default location of the log file and use the specified filename instead. If the platform is 'dot', this option sets the name of the output dot-file.");

    opt.addOption("h", "help", false, "Print help text.");

    gnuParser = new GnuParser();
    cmdline = gnuParser.parse(opt, args);

    if (cmdline.hasOption("help")) {

        System.out.println("CUNEIFORM - A Functional Workflow Language\n" + LABEL_VERSION);
        new HelpFormatter().printHelp("java -jar cuneiform.jar [OPTION]*", opt);

        return;
    }

    if (cmdline.hasOption("platform")) {

        value = cmdline.getOptionValue("platform");

        if (value.equals("dot"))
            platform = PLATFORM_DOT;
        else if (value.equals("local"))
            platform = PLATFORM_LOCAL;
        else if (value.equals("debug"))
            platform = PLATFORM_DEBUG;
        else
            throw new RuntimeException("Specified platform '" + value + "' not recognized.");

    } else
        platform = PLATFORM_LOCAL;

    if (cmdline.hasOption('d')) {

        value = cmdline.getOptionValue('d');
    } else
        value = "build";

    outputDir = new File(value);

    if (outputDir.exists()) {

        if (!outputDir.isDirectory())
            throw new IOException(
                    "Output directory '" + outputDir.getAbsolutePath() + "' exists but is not a directory.");

        else if (cmdline.hasOption('c')) {

            FileUtils.deleteDirectory(outputDir);

            if (!outputDir.mkdirs())
                throw new IOException(
                        "Could not create output directory '" + outputDir.getAbsolutePath() + "'");
        }
    } else if (!outputDir.mkdirs())
        throw new IOException("Could not create output directory '" + outputDir.getAbsolutePath() + "'");

    if (cmdline.hasOption('r'))
        dagid = cmdline.getOptionValue('r');
    else
        dagid = UUID.randomUUID().toString();

    if (cmdline.hasOption('f'))
        logFile = new File(cmdline.getOptionValue('f'));
    else
        logFile = null;

    fileList = cmdline.getArgs();
    buf = new StringBuffer();
    if (fileList.length == 0) {

        try (BufferedReader reader = new BufferedReader(new InputStreamReader(System.in))) {

            while ((line = reader.readLine()) != null)
                buf.append(line).append('\n');
        }

        switch (platform) {

        case PLATFORM_DOT:
            createDot(buf.toString(), outputDir, logFile);
            break;
        case PLATFORM_LOCAL:
            runLocal(buf.toString(), outputDir, logFile, dagid);
            break;
        case PLATFORM_DEBUG:
            runDebug(buf.toString(), outputDir, logFile, dagid);
            break;
        default:
            throw new RuntimeException("Platform not recognized.");
        }
    } else

        switch (platform) {

        case PLATFORM_DOT:
            createDot(fileList, outputDir, logFile);
            break;
        case PLATFORM_LOCAL:
            runLocal(fileList, outputDir, logFile, dagid);
            break;
        case PLATFORM_DEBUG:
            runDebug(fileList, outputDir, logFile, dagid);
            break;
        default:
            throw new RuntimeException("Platform not recognized.");
        }

}

From source file:AndroidUninstallStock.java

@SuppressWarnings("static-access")
public static void main(String[] args) {
    try {/*from w  w w.j  a v  a 2  s . co  m*/
        String lang = Locale.getDefault().getLanguage();
        GnuParser cmdparser = new GnuParser();
        Options cmdopts = new Options();
        for (String fld : Arrays.asList("shortOpts", "longOpts", "optionGroups")) {
            // hack for printOptions
            java.lang.reflect.Field fieldopt = cmdopts.getClass().getDeclaredField(fld);
            fieldopt.setAccessible(true);
            fieldopt.set(cmdopts, new LinkedHashMap<>());
        }
        cmdopts.addOption("h", "help", false, "Help");
        cmdopts.addOption("t", "test", false, "Show only report");
        cmdopts.addOption(OptionBuilder.withLongOpt("adb").withArgName("file").hasArg()
                .withDescription("Path to ADB from Android SDK").create("a"));
        cmdopts.addOption(OptionBuilder.withLongOpt("dev").withArgName("device").hasArg()
                .withDescription("Select device (\"adb devices\")").create("d"));
        cmdopts.addOption(null, "restore", false,
                "If packages have not yet removed and are disabled, " + "you can activate them again");
        cmdopts.addOption(null, "google", false, "Delete packages are in the Google section");
        cmdopts.addOption(null, "unapk", false, "Delete /system/app/ *.apk *.odex *.dex"
                + System.lineSeparator() + "(It is required to repeat command execution)");
        cmdopts.addOption(null, "unlib", false, "Delete /system/lib/[libs in apk]");
        //cmdopts.addOption(null, "unfrw", false, "Delete /system/framework/ (special list)");
        cmdopts.addOption(null, "scanlibs", false,
                "(Dangerous!) Include all the libraries of selected packages." + " Use with --unlib");

        cmdopts.addOptionGroup(new OptionGroup() {
            {
                addOption(OptionBuilder.withLongOpt("genfile").withArgName("file").hasArg().isRequired()
                        .withDescription("Create file with list packages").create());
                addOption(OptionBuilder.withLongOpt("lang").withArgName("ISO 639").hasArg().create());
            }
        });
        cmdopts.getOption("lang").setDescription(
                "See hl= in Google URL (default: " + lang + ") " + "for description from Google Play Market");
        CommandLine cmd = cmdparser.parse(cmdopts, args);

        if (args.length == 0 || cmd.hasOption("help")) {
            PrintWriter console = new PrintWriter(System.out);
            HelpFormatter cmdhelp = new HelpFormatter();
            cmdhelp.setOptionComparator(new Comparator<Option>() {
                @Override
                public int compare(Option o1, Option o2) {
                    return 0;
                }
            });
            console.println("WARNING: Before use make a backup with ClockworkMod Recovery!");
            console.println();
            console.println("AndroidUninstallStock [options] [AndroidListSoft.xml]");
            cmdhelp.printOptions(console, 80, cmdopts, 3, 2);
            console.flush();
            return;
        }

        String adb = cmd.getOptionValue("adb", "adb");
        try {
            run(adb, "start-server");
        } catch (IOException e) {
            System.out.println("Error: Not found ADB! Use -a or --adb");
            return;
        }

        final boolean NotTest = !cmd.hasOption("test");

        String deverror = getDeviceStatus(adb, cmd.getOptionValue("dev"));
        if (!deverror.isEmpty()) {
            System.out.println(deverror);
            return;
        }

        System.out.println("Getting list packages:");
        LinkedHashMap<String, String> apklist = new LinkedHashMap<String, String>();
        for (String ln : run(adb, "-s", lastdevice, "shell", "pm list packages -s -f")) {
            // "pm list packages" give list sorted by packages ;)
            String pckg = ln.substring("package:".length());
            String pckgname = ln.substring(ln.lastIndexOf('=') + 1);
            pckg = pckg.substring(0, pckg.length() - pckgname.length() - 1);
            if (!pckgname.equals("android") && !pckgname.equals("com.android.vending")/*Google Play Market*/) {
                apklist.put(pckg, pckgname);
            }
        }
        for (String ln : run(adb, "-s", lastdevice, "shell", "ls /system/app/")) {
            String path = "/system/app/" + ln.replace(".odex", ".apk").replace(".dex", ".apk");
            if (!apklist.containsKey(path)) {
                apklist.put(path, "");
            }
        }
        apklist.remove("/system/app/mcRegistry");
        for (Map.Entry<String, String> info : sortByValues(apklist).entrySet()) {
            System.out.println(info.getValue() + " = " + info.getKey());
        }

        String genfile = cmd.getOptionValue("genfile");
        if (genfile != null) {
            Path genpath = Paths.get(genfile);
            try (BufferedWriter gen = Files.newBufferedWriter(genpath, StandardCharsets.UTF_8,
                    new StandardOpenOption[] { StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING,
                            StandardOpenOption.WRITE })) {
                if (cmd.getOptionValue("lang") != null) {
                    lang = cmd.getOptionValue("lang");
                }

                LinkedHashSet<String> listsystem = new LinkedHashSet<String>() {
                    {
                        add("com.android");
                        add("com.google.android");
                        //add("com.sec.android.app");
                        add("com.monotype.android");
                        add("eu.chainfire.supersu");
                    }
                };

                // \r\n for Windows Notepad
                gen.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n");
                gen.write("<!-- & raplace with &amp; or use <![CDATA[ ]]> -->\r\n");
                gen.write("<AndroidUninstallStock>\r\n\r\n");
                gen.write("<Normal>\r\n");
                System.out.println();
                System.out.println("\tNormal:");
                writeInfo(gen, apklist, lang, listsystem, true);
                gen.write("\t<apk name=\"Exclude Google and etc\">\r\n");
                for (String exc : listsystem) {
                    gen.write("\t\t<exclude global=\"true\" in=\"package\" pattern=\"" + exc + "\" />\r\n");
                }
                gen.write("\t</apk>\r\n");
                gen.write("</Normal>\r\n\r\n");
                gen.write("<Google>\r\n");
                System.out.println();
                System.out.println("\tGoogle:");
                writeInfo(gen, apklist, lang, listsystem, false);
                gen.write("</Google>\r\n\r\n");
                gen.write("</AndroidUninstallStock>\r\n");
                System.out.println("File " + genpath.toAbsolutePath() + " created.");
            }
            return;
        }

        String[] FileName = cmd.getArgs();
        if (!(FileName.length > 0 && Files.isReadable(Paths.get(FileName[0])))) {
            System.out.println("Error: File " + FileName[0] + " not found!");
            return;
        }

        DocumentBuilderFactory xmlfactory = getXmlDocFactory();

        // DocumentBuilder.setErrorHandler() for print errors
        Document xml = xmlfactory.newDocumentBuilder().parse(new File(FileName[0]));

        LinkedList<AusInfo> Normal = new LinkedList<AusInfo>();
        LinkedList<AusInfo> Google = new LinkedList<AusInfo>();

        NodeList ndaus = xml.getElementsByTagName("AndroidUninstallStock").item(0).getChildNodes();
        for (int ndausx = 0, ndausc = ndaus.getLength(); ndausx < ndausc; ndausx++) {
            Node ndnow = ndaus.item(ndausx);
            NodeList nd = ndnow.getChildNodes();
            String ndname = ndnow.getNodeName();
            for (int ndx = 0, ndc = nd.getLength(); ndx < ndc; ndx++) {
                if (!nd.item(ndx).getNodeName().equalsIgnoreCase("apk")) {
                    continue;
                }
                if (ndname.equalsIgnoreCase("Normal")) {
                    Normal.add(getApkInfo(nd.item(ndx)));
                } else if (ndname.equalsIgnoreCase("Google")) {
                    Google.add(getApkInfo(nd.item(ndx)));
                }
            }
        }

        // FIXME This part must be repeated until the "pm uninstall" will not issue "Failure" on all packages.
        //       Now requires a restart.
        System.out.println();
        System.out.println("Include and Exclude packages (Normal):");
        LinkedHashMap<String, String> apkNormal = getApkFromPattern(apklist, Normal, false);
        System.out.println();
        System.out.println("Global Exclude packages (Normal):");
        apkNormal = getApkFromPattern(apkNormal, Normal, true);
        System.out.println();
        System.out.println("Final list packages (Normal):");
        for (Map.Entry<String, String> info : sortByValues(apkNormal).entrySet()) {
            System.out.println(info.getValue() + " = " + info.getKey());
        }

        LinkedHashMap<String, String> apkGoogle = new LinkedHashMap<String, String>();
        if (cmd.hasOption("google")) {
            System.out.println();
            System.out.println("Include and Exclude packages (Google):");
            apkGoogle = getApkFromPattern(apklist, Google, false);
            System.out.println();
            System.out.println("Global Exclude packages (Google):");
            apkGoogle = getApkFromPattern(apkGoogle, Google, true);
            System.out.println();
            System.out.println("Final list packages (Google):");
            for (Map.Entry<String, String> info : sortByValues(apkGoogle).entrySet()) {
                System.out.println(info.getValue() + " = " + info.getKey());
            }
        }

        if (NotTest) {
            if (!hasRoot(adb)) {
                System.out.println("No Root");
                System.out.println();
                System.out.println("FINISH :)");
                return;
            }
        }

        if (cmd.hasOption("restore")) {
            System.out.println();
            System.out.println("Enable (Restore) packages (Normal):");
            damage(adb, "pm enable ", NotTest, apkNormal, 2);
            if (cmd.hasOption("google")) {
                System.out.println();
                System.out.println("Enable (Restore) packages (Google):");
                damage(adb, "pm enable ", NotTest, apkGoogle, 2);
            }
            System.out.println();
            System.out.println("FINISH :)");
            return;
        } else {
            System.out.println();
            System.out.println("Disable packages (Normal):");
            damage(adb, "pm disable ", NotTest, apkNormal, 2);
            if (cmd.hasOption("google")) {
                System.out.println();
                System.out.println("Disable packages (Google):");
                damage(adb, "pm disable ", NotTest, apkGoogle, 2);
            }
        }

        if (!cmd.hasOption("unapk") && !cmd.hasOption("unlib")) {
            System.out.println();
            System.out.println("FINISH :)");
            return;
        }

        // Reboot now not needed
        /*if (NotTest) {
        reboot(adb, "-s", lastdevice, "reboot");
        if (!hasRoot(adb)) {
            System.out.println("No Root");
            System.out.println();
            System.out.println("FINISH :)");
            return;
        }
        }*/

        if (cmd.hasOption("unlib")) {
            // "find" not found
            System.out.println();
            System.out.println("Getting list libraries:");
            LinkedList<String> liblist = new LinkedList<String>();
            liblist.addAll(run(adb, "-s", lastdevice, "shell", "ls -l /system/lib/"));
            String dircur = "/system/lib/";
            for (int x = 0; x < liblist.size(); x++) {
                if (liblist.get(x).startsWith("scan:")) {
                    dircur = liblist.get(x).substring("scan:".length());
                    liblist.remove(x);
                    x--;
                } else if (liblist.get(x).startsWith("d")) {
                    String dir = liblist.get(x).substring(liblist.get(x).lastIndexOf(':') + 4) + "/";
                    liblist.remove(x);
                    x--;
                    liblist.add("scan:/system/lib/" + dir);
                    liblist.addAll(run(adb, "-s", lastdevice, "shell", "ls -l /system/lib/" + dir));
                    continue;
                }
                liblist.set(x, dircur + liblist.get(x).substring(liblist.get(x).lastIndexOf(':') + 4));
                System.out.println(liblist.get(x));
            }

            final boolean scanlibs = cmd.hasOption("scanlibs");
            LinkedHashMap<String, String> libNormal = getLibFromPatternInclude(adb, liblist, apkNormal, Normal,
                    "Normal", scanlibs);
            libNormal = getLibFromPatternGlobalExclude(libNormal, Normal, "Normal");
            System.out.println();
            System.out.println("Final list libraries (Normal):");
            for (Map.Entry<String, String> info : sortByValues(libNormal).entrySet()) {
                System.out.println(info.getKey() + " = " + info.getValue());
            }

            LinkedHashMap<String, String> libGoogle = new LinkedHashMap<String, String>();
            if (cmd.hasOption("google")) {
                libGoogle = getLibFromPatternInclude(adb, liblist, apkGoogle, Google, "Google", scanlibs);
                libGoogle = getLibFromPatternGlobalExclude(libGoogle, Google, "Google");
                System.out.println();
                System.out.println("Final list libraries (Google):");
                for (Map.Entry<String, String> info : sortByValues(libGoogle).entrySet()) {
                    System.out.println(info.getKey() + " = " + info.getValue());
                }
            }

            LinkedHashMap<String, String> apkExclude = new LinkedHashMap<String, String>(apklist);
            for (String key : apkNormal.keySet()) {
                apkExclude.remove(key);
            }
            for (String key : apkGoogle.keySet()) {
                apkExclude.remove(key);
            }

            System.out.println();
            System.out.println("Include libraries from Exclude packages:");
            LinkedHashMap<String, String> libExclude = getLibFromPackage(adb, liblist, apkExclude);
            System.out.println();
            System.out.println("Enclude libraries from Exclude packages (Normal):");
            for (Map.Entry<String, String> info : sortByValues(libNormal).entrySet()) {
                if (libExclude.containsKey(info.getKey())) {
                    System.out.println("exclude: " + info.getKey() + " = " + libExclude.get(info.getKey()));
                    libNormal.remove(info.getKey());
                }
            }
            System.out.println();
            System.out.println("Enclude libraries from Exclude packages (Google):");
            for (Map.Entry<String, String> info : sortByValues(libGoogle).entrySet()) {
                if (libExclude.containsKey(info.getKey())) {
                    System.out.println("exclude: " + info.getKey() + " = " + libExclude.get(info.getKey()));
                    libGoogle.remove(info.getKey());
                }
            }

            System.out.println();
            System.out.println("Delete libraries (Normal):");
            damage(adb, "rm ", NotTest, libNormal, 1);
            if (cmd.hasOption("google")) {
                System.out.println();
                System.out.println("Delete libraries (Google):");
                damage(adb, "rm ", NotTest, libGoogle, 1);
            }
        }

        if (cmd.hasOption("unapk")) {
            System.out.println();
            System.out.println("Cleaning data packages (Normal):");
            damage(adb, "pm clear ", NotTest, apkNormal, 2);
            if (cmd.hasOption("google")) {
                System.out.println();
                System.out.println("Cleaning data packages (Google):");
                damage(adb, "pm clear ", NotTest, apkGoogle, 2);
            }

            System.out.println();
            System.out.println("Uninstall packages (Normal):");
            damage(adb, "pm uninstall ", NotTest, apkNormal, 2);
            if (cmd.hasOption("google")) {
                System.out.println();
                System.out.println("Uninstall packages (Google):");
                damage(adb, "pm uninstall ", NotTest, apkGoogle, 2);
            }
        }

        if (cmd.hasOption("unapk")) {
            System.out.println();
            System.out.println("Delete packages (Normal):");
            LinkedHashMap<String, String> dexNormal = new LinkedHashMap<String, String>();
            for (Map.Entry<String, String> apk : apkNormal.entrySet()) {
                dexNormal.put(apk.getKey(), apk.getValue());
                dexNormal.put(apk.getKey().replace(".apk", ".dex"), apk.getValue());
                dexNormal.put(apk.getKey().replace(".apk", ".odex"), apk.getValue());
            }
            damage(adb, "rm ", NotTest, dexNormal, 1);
            if (cmd.hasOption("google")) {
                System.out.println();
                System.out.println("Delete packages (Google):");
                LinkedHashMap<String, String> dexGoogle = new LinkedHashMap<String, String>();
                for (Map.Entry<String, String> apk : apkGoogle.entrySet()) {
                    dexGoogle.put(apk.getKey(), apk.getValue());
                    dexGoogle.put(apk.getKey().replace(".apk", ".dex"), apk.getValue());
                    dexGoogle.put(apk.getKey().replace(".apk", ".odex"), apk.getValue());
                }
                damage(adb, "rm ", NotTest, dexGoogle, 1);
            }
        }

        if (NotTest) {
            run(adb, "-s", lastdevice, "reboot");
        }
        System.out.println();
        System.out.println("FINISH :)");
    } catch (SAXException e) {
        System.out.println("Error parsing list: " + e);
    } catch (Throwable e) {
        e.printStackTrace();
    }
}

From source file:com.aliyun.openservices.odps.console.commands.DescribeInstanceCommand.java

private static CommandLine getCommandLine(String[] args) throws ODPSConsoleException {
    try {/*  w  w w . j av a 2  s . c  om*/
        GnuParser parser = new GnuParser();
        return parser.parse(getOptions(), args);
    } catch (ParseException e) {
        throw new ODPSConsoleException(ODPSConsoleConstants.BAD_COMMAND + " " + e.getMessage(), e);
    }
}