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

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

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Introduction

In this page you can find the example usage for org.apache.commons.cli PosixParser 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:com.slothpetrochemical.bridgeprob.BridgeProblemApp.java

public static void main(final String[] args) throws ParseException {
    Options commandLineOptions = createOptions();
    PosixParser clParser = new PosixParser();
    CommandLine cl = clParser.parse(commandLineOptions, args);

    if (cl.getArgs().length == 0 || cl.hasOption("h")) {
        new HelpFormatter().printHelp("crossing_times...", commandLineOptions);
    } else {//from w w w  .  j  a v a 2s . c om
        String[] clArgs = cl.getArgs();
        Integer[] times = new Integer[clArgs.length];
        for (int i = 0; i < clArgs.length; ++i) {
            Integer intTime = Integer.parseInt(clArgs[i]);
            times[i] = intTime;
        }
        Arrays.sort(times);
        BridgeProblemApp app = new BridgeProblemApp(Arrays.asList(times));
        app.run();
    }
}

From source file:b2s.idea.mavenize.App.java

public static void main(String... args) throws ParseException {
    Options options = new Options();
    options.addOption("i", "idea-dir", true, "Path to root directory of an intellij instance");
    options.addOption("o", "output-dir", true, "Path to put the newly created jar");

    if (args.length == 0) {
        error("", options);
        return;//from   w w w . j  a v  a2 s.c o m
    }

    PosixParser parser = new PosixParser();
    CommandLine commandLine = parser.parse(options, args);

    if (commandLine.hasOption("i")) {
        String ideaDirValue = commandLine.getOptionValue("i");
        File ideaFolder = new File(ideaDirValue);
        if (!ideaFolder.exists()) {
            error("This path [" + ideaDirValue + "] can not be found", options);
            return;
        }

        File libFolder = new File(ideaFolder, "lib");
        if (!libFolder.exists()) {
            error("The [lib] folder was not found in the IDEA folder", options);
            return;
        }

        if (commandLine.hasOption("output-dir")) {
            File output = new File(commandLine.getOptionValue("output-dir"), determineFilename(ideaFolder));
            jarCombiner.combineAllJarsIn(libFolder, output);
            System.out.println("Combined Jar: " + output);
        } else {
            error("Please provide an output directory", options);
        }
    } else {
        error("Please provide the IDEA directory path", options);
    }
}

From source file:com.github.besherman.fingerprint.Main.java

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

    options.addOption(OptionBuilder.withDescription("creates a fingerprint file for the directory").hasArg()
            .withArgName("dir").create('c'));

    options.addOption(OptionBuilder.withDescription("shows a diff between two fingerprint files")
            .withArgName("left-file> <right-file").hasArgs(2).create('d'));

    options.addOption(OptionBuilder.withDescription("shows a diff between a fingerprint and a directory")
            .withArgName("fingerprint> <dir").hasArgs(2).create('t'));

    options.addOption(OptionBuilder.withDescription("shows duplicates in a directory").withArgName("dir")
            .hasArgs(1).create('u'));

    options.addOption(/* w  ww .  ja v a2 s .c o m*/
            OptionBuilder.withDescription("output to file").withArgName("output-file").hasArg().create('o'));

    PosixParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException ex) {
        System.out.println(ex.getMessage());
        System.out.println("");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("fingerprint-dir", options, true);
        System.exit(7);
    }

    if (cmd.hasOption('c')) {
        Path root = Paths.get(cmd.getOptionValue('c'));

        if (!Files.isDirectory(root)) {
            System.err.println("root is not a directory");
            System.exit(7);
        }

        OutputStream out = System.out;

        if (cmd.hasOption('o')) {
            Path p = Paths.get(cmd.getOptionValue('o'));
            out = Files.newOutputStream(p);
        }

        Fingerprint fp = new Fingerprint(root, "");
        fp.write(out);

    } else if (cmd.hasOption('d')) {
        String[] ar = cmd.getOptionValues('d');
        Path leftFingerprintFile = Paths.get(ar[0]), rightFingerprintFile = Paths.get(ar[1]);
        if (!Files.isRegularFile(leftFingerprintFile)) {
            System.out.printf("%s is not a file%n", leftFingerprintFile);
            System.exit(7);
        }
        if (!Files.isRegularFile(rightFingerprintFile)) {
            System.out.printf("%s is not a file%n", rightFingerprintFile);
            System.exit(7);
        }

        Fingerprint left, right;
        try (InputStream input = Files.newInputStream(leftFingerprintFile)) {
            left = new Fingerprint(input);
        }

        try (InputStream input = Files.newInputStream(rightFingerprintFile)) {
            right = new Fingerprint(input);
        }

        Diff diff = new Diff(left, right);

        // TODO: if we have redirected output
        diff.print(System.out);
    } else if (cmd.hasOption('t')) {
        throw new RuntimeException("Not yet implemented");
    } else if (cmd.hasOption('u')) {
        Path root = Paths.get(cmd.getOptionValue('u'));
        Fingerprint fp = new Fingerprint(root, "");
        Map<String, FilePrint> map = new HashMap<>();
        fp.stream().forEach(f -> {
            if (map.containsKey(f.getHash())) {
                System.out.println("  " + map.get(f.getHash()).getPath());
                System.out.println("= " + f.getPath());
                System.out.println("");
            } else {
                map.put(f.getHash(), f);
            }
        });
    } else {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("fingd", options, true);
    }
}

From source file:com.genentech.chemistry.tool.sdf2DAlign.java

public static void main(String[] args) throws IOException {

    final String OPT_INFILE = "in";
    final String OPT_OUTFILE = "out";
    final String OPT_TEMPLATEFILE = "templates";
    final String OPT_RESETCOORDS = "reset";
    final String OPT_DEBUG = "debug";

    Options options = new Options();

    Option opt = new Option(OPT_INFILE, true, "Input file (oe-supported). Use .sdf to specify the file type.");
    opt.setRequired(true);//from   www  .j  a  v a 2s .co  m
    options.addOption(opt);

    opt = new Option(OPT_OUTFILE, true, "Output file (oe-supported). Use .sdf to specify the file type.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_TEMPLATEFILE, true,
            "Template file (oe-supported). Use .sdf to specify the file type.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_RESETCOORDS, false,
            "Reset coordinates in input file when aligning. This will delete original 2D coords and create new ones.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_DEBUG, false, "Print debug statements.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("h", false, "print usage statement");
    opt.setRequired(false);
    options.addOption(opt);

    PosixParser parser = new PosixParser();
    CommandLine cl = null;

    try {
        cl = parser.parse(options, args);
    } catch (Exception exp) {
        System.err.println(exp.getMessage());
        exitWithHelp(options);
    }

    //get command line parameters
    String inFile = cl.getOptionValue(OPT_INFILE);
    String outFile = cl.getOptionValue(OPT_OUTFILE);
    String templateFile = cl.getOptionValue(OPT_TEMPLATEFILE);
    boolean resetCoords = cl.hasOption(OPT_RESETCOORDS);
    boolean debug = cl.hasOption(OPT_DEBUG);

    sdf2DAlign myAlign = new sdf2DAlign(inFile, outFile, templateFile, resetCoords);
    myAlign.setDebug(debug);

    //get templates as subsearches
    List<OESubSearch> templates = myAlign.getTemplates();

    //apply template to input molecules
    myAlign.applyTemplates(templates);

    for (OESubSearch ss : templates)
        ss.delete();
}

From source file:com.denimgroup.threadfix.cli.CommandLineParser.java

public static void main(String[] args) {

    Options options = getOptions();/*from  w w  w. j a  v  a  2s.  c  o m*/

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

        if (cmd.hasOption("help")) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("java -jar tfcli.jar", options);

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

            String[] setArgs = cmd.getOptionValues("s");
            if (setArgs == null || setArgs.length != 2) {
                throw new ParseException("Bad arguments for set.");
            }

            if ("url".equals(setArgs[0])) {
                System.out.println("Setting URL to " + setArgs[1]);
                client.setUrl(setArgs[1]);
            } else if ("key".equals(setArgs[0])) {
                System.out.println("Setting API Key to " + setArgs[1]);
                client.setKey(setArgs[1]);
            } else {
                throw new ParseException("First argument to set must be url or key");
            }

        } else if (cmd.hasOption("ct")) {
            String[] createArgs = cmd.getOptionValues("ct");
            if (createArgs.length != 1) {
                throw new ParseException("Wrong number of arguments.");
            }
            System.out.println("Creating a Team with the name " + createArgs[0] + ".");
            System.out.println(client.createTeam(createArgs[0]));

        } else if (cmd.hasOption("cw")) {
            String[] createArgs = cmd.getOptionValues("cw");
            if (createArgs.length != 2) {
                throw new ParseException("Wrong number of arguments.");
            }
            System.out.println("Creating a Waf with the name " + createArgs[0] + ".");
            System.out.println(client.createWaf(createArgs[0], createArgs[1]));

        } else if (cmd.hasOption("ca")) {
            String[] createArgs = cmd.getOptionValues("ca");
            if (createArgs.length != 3) {
                throw new ParseException("Wrong number of arguments.");
            }
            System.out.println("Creating an Application with the name " + createArgs[1] + ".");
            System.out.println(client.createApplication(createArgs[0], createArgs[1], createArgs[2]));

        } else if (cmd.hasOption("teams")) {
            System.out.println("Getting all teams.");
            System.out.println(client.getAllTeams());

        } else if (cmd.hasOption("u")) {
            String[] uploadArgs = cmd.getOptionValues("u");
            // Upload a scan
            if (uploadArgs.length != 2) {
                throw new ParseException("Wrong number of arguments.");
            }
            System.out.println("Uploading " + uploadArgs[1] + " to Application " + uploadArgs[0] + ".");
            System.out.println(client.uploadScan(uploadArgs[0], uploadArgs[1]));

        } else if (cmd.hasOption("st")) {
            String[] searchArgs = cmd.getOptionValues("st");
            if (searchArgs.length != 2) {
                throw new ParseException("Wrong number of arguments.");
            }
            if ("id".equals(searchArgs[0])) {
                System.out.println("Searching for team with the id " + searchArgs[1] + ".");
                System.out.println(client.searchForTeamById(searchArgs[1]));
            } else if ("name".equals(searchArgs[0])) {
                System.out.println("Searching for team with the name " + searchArgs[1] + ".");
                System.out.println(client.searchForTeamByName(searchArgs[1]));
            } else {
                System.out.println("Unknown property argument. Try either id or name.");
                return;
            }

        } else if (cmd.hasOption("sw")) {
            String[] searchArgs = cmd.getOptionValues("sw");
            if (searchArgs.length != 4) {
                throw new ParseException("Wrong number of arguments.");
            }
            if ("id".equals(searchArgs[0])) {
                System.out.println("Searching for WAF with the id " + searchArgs[1] + ".");
                System.out.println(client.searchForWafById(searchArgs[1]));
            } else if ("name".equals(searchArgs[0])) {
                System.out.println("Searching for WAF with the name " + searchArgs[1] + ".");
                System.out.println(client.searchForWafByName(searchArgs[1]));
            } else {
                throw new ParseException("Unknown property argument. Try either id or name.");
            }

        } else if (cmd.hasOption("sa")) {
            String[] searchArgs = cmd.getOptionValues("sa");
            if ("id".equals(searchArgs[0])) {
                if (searchArgs.length != 2) {
                    System.out.println("Wrong number of arguments.");
                    return;
                }
                System.out.println("Searching for application with the id " + searchArgs[1] + ".");
                System.out.println(client.searchForApplicationById(searchArgs[1]));
            } else if ("name".equals(searchArgs[0])) {
                if (searchArgs.length != 3) {
                    System.out.println(
                            "Wrong number of arguments. You need to input application name and team name as well.");
                    return;
                }
                System.out.println("Searching for application with the name " + searchArgs[1] + " of team "
                        + searchArgs[2]);
                System.out.println(client.searchForApplicationByName(searchArgs[1], searchArgs[2]));
            } else {
                System.out.println("Unknown property argument. Try either id or name.");
                return;
            }

        } else if (cmd.hasOption("r")) {
            String[] ruleArgs = cmd.getOptionValues("r");
            if (ruleArgs.length != 1) {
                System.out.println("Wrong number of arguments.'");
            }
            System.out.println("Downloading rules from WAF with ID " + ruleArgs[0] + ".");
            System.out.println(client.getRules(ruleArgs[0]));

        } else {
            throw new ParseException("No arguments found.");
        }

    } catch (ParseException e) {
        if (e.getMessage() != null) {
            System.out.println(e.getMessage());
        }
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar tfcli.jar", options);
    }
}

From source file:edu.ksu.cis.indus.staticanalyses.flow.instances.ofa.OFAXMLizerCLI.java

/**
 * The entry point to the program via command line.
 * //from w  w  w .ja v a  2  s  . c o  m
 * @param args is the command line arguments.
 * @throws RuntimeException when object flow analysis fails.
 */
public static void main(final String[] args) {
    final Options _options = new Options();
    Option _option = new Option("c", "cumulative", false, "Consider all root methods in the same execution.");
    _options.addOption(_option);
    _option = new Option("o", "output", true, "Directory into which xml files will be written into.");
    _option.setArgs(1);
    _options.addOption(_option);
    _option = new Option("j", "jimple", false, "Dump xmlized jimple.");
    _options.addOption(_option);
    _option = new Option("h", "help", false, "Display message.");
    _options.addOption(_option);
    _option = new Option("p", "soot-classpath", false, "Prepend this to soot class path.");
    _option.setArgs(1);
    _option.setArgName("classpath");
    _option.setOptionalArg(false);
    _options.addOption(_option);
    _option = new Option("t", "ofa-type", false, "Type of analysis : fioi, fsoi, fios, fsos, fioirt, fsoirt.");
    _option.setArgs(1);
    _option.setArgName("type");
    _option.setOptionalArg(false);
    _option.setRequired(true);
    _options.addOption(_option);
    _option = new Option("S", "scope", true, "The scope that should be analyzed.");
    _option.setArgs(1);
    _option.setArgName("scope");
    _option.setRequired(false);
    _options.addOption(_option);

    final PosixParser _parser = new PosixParser();

    try {
        final CommandLine _cl = _parser.parse(_options, args);

        if (_cl.hasOption("h")) {
            printUsage(_options);
            System.exit(1);
        }

        String _outputDir = _cl.getOptionValue('o');

        if (_outputDir == null) {
            if (LOGGER.isWarnEnabled()) {
                LOGGER.warn("Defaulting to current directory for output.");
            }
            _outputDir = ".";
        }

        if (_cl.getArgList().isEmpty()) {
            throw new MissingArgumentException("Please specify atleast one class.");
        }

        final OFAXMLizerCLI _cli = new OFAXMLizerCLI();
        _cli.xmlizer.setXmlOutputDir(_outputDir);
        _cli.xmlizer.setGenerator(new UniqueJimpleIDGenerator());
        _cli.setCumulative(_cl.hasOption('c'));
        _cli.setClassNames(_cl.getArgList());
        _cli.type = _cl.getOptionValue('t');

        if (_cl.hasOption('p')) {
            _cli.addToSootClassPath(_cl.getOptionValue('p'));
        }

        if (_cl.hasOption('S')) {
            _cli.setScopeSpecFile(_cl.getOptionValue('S'));
        }

        _cli.initialize();

        _cli.<ITokens>execute(_cl.hasOption('j'));
    } catch (final ParseException _e) {
        LOGGER.error("Error while parsing command line.", _e);
        System.out.println("Error while parsing command line. \n" + _e);
        printUsage(_options);
    } catch (final Throwable _e) {
        LOGGER.error("Beyond our control. May day! May day!", _e);
        throw new RuntimeException(_e);
    }
}

From source file:edu.ksu.cis.indus.staticanalyses.callgraphs.CallGraphXMLizerCLI.java

/**
 * The entry point to the program via command line.
 * /*w  w w  . j av  a2s. com*/
 * @param args is the command line arguments.
 * @throws RuntimeException when the analyses fail.
 */
public static void main(final String[] args) {
    final Options _options = new Options();
    Option _option = new Option("c", "cumulative", false,
            "Builds one call graph that includes all root methods.");
    _options.addOption(_option);
    _option = new Option("o", "output", true,
            "Directory into which xml files will be written into.  Defaults to current directory if omitted");
    _option.setArgs(1);
    _option.setArgName("output-dir");
    _options.addOption(_option);
    _option = new Option("j", "jimple", false, "Dump xmlized jimple.");
    _option.setArgName("dump-jimple");
    _options.addOption(_option);
    _option = new Option("p", "soot-classpath", true, "Prepend this to soot class path.");
    _option.setArgs(1);
    _option.setArgName("classpath");
    _option.setOptionalArg(false);
    _options.addOption(_option);
    _option = new Option("h", "help", false, "Display message.");
    _option.setOptionalArg(false);
    _options.addOption(_option);
    _option = new Option("t", "call-graph-type", true,
            "Call graph type.  This has to be one of {cha, rta, ofa-oi, " + "ofa-oirt, ofa-os}.");
    _option.setArgs(1);
    _option.setArgName("type");
    _option.setRequired(true);
    _options.addOption(_option);
    _option = new Option("S", "scope", true, "The scope that should be analyzed.");
    _option.setArgs(1);
    _option.setArgName("scope");
    _option.setRequired(false);
    _options.addOption(_option);

    final PosixParser _parser = new PosixParser();

    try {
        final CommandLine _cl = _parser.parse(_options, args);

        if (_cl.hasOption('h')) {
            printUsage(_options);
            System.exit(1);
        }

        String _outputDir = _cl.getOptionValue('o');

        if (_outputDir == null) {
            if (LOGGER.isWarnEnabled()) {
                LOGGER.warn("Defaulting to current directory for output.");
            }
            _outputDir = ".";
        }

        if (_cl.getArgList().isEmpty()) {
            throw new MissingArgumentException("Please specify atleast one class.");
        }

        final CallGraphXMLizerCLI _cli = new CallGraphXMLizerCLI();

        _cli.xmlizer.setXmlOutputDir(_outputDir);
        _cli.xmlizer.setGenerator(new UniqueJimpleIDGenerator());
        _cli.setCumulative(_cl.hasOption('c'));
        _cli.setClassNames(_cl.getArgList());
        _cli.addToSootClassPath(_cl.getOptionValue('p'));

        if (_cl.hasOption('S')) {
            _cli.setScopeSpecFile(_cl.getOptionValue('S'));
        }

        _cli.initialize();

        _cli.execute(_cl.hasOption('j'), _cl.getOptionValue('t'));
    } catch (final ParseException _e) {
        LOGGER.error("Error while parsing command line.", _e);
        System.out.println("Error while parsing command line." + _e);
        printUsage(_options);
    } catch (final Throwable _e) {
        LOGGER.error("Beyond our control. May day! May day!", _e);
        throw new RuntimeException(_e);
    }
}

From source file:com.intuit.s3encrypt.S3Encrypt.java

public static void main(String[] args) throws IOException, NoSuchAlgorithmException, InvalidKeySpecException {

    // create Options object
    Options options = new Options();
    options.addOption(create_bucket);/*from   w w w .  ja v a  2  s  .  c  om*/
    options.addOption(create_key);
    options.addOption(delete_bucket);
    options.addOption(get);
    options.addOption(help);
    options.addOption(inspect);
    options.addOption(keyfile);
    options.addOption(list_buckets);
    options.addOption(list_objects);
    options.addOption(put);
    options.addOption(remove);
    options.addOption(rotate);
    options.addOption(rotateall);
    options.addOption(rotateKey);

    //      CommandLineParser parser = new GnuParser();
    //       Changed from above GnuParser to below PosixParser because I found code which allows for multiple arguments 
    PosixParser parser = new PosixParser();
    CommandLine cmd;
    try {
        cmd = parser.parse(options, args);
        Logger.getRootLogger().setLevel(Level.OFF);

        if (cmd.hasOption("help")) {
            HelpFormatter help = new HelpFormatter();
            System.out.println();
            help.printHelp("S3Encrypt", options);
            System.out.println();
            System.exit(1);
        } else if (cmd.hasOption("create_key")) {
            keyname = cmd.getOptionValue("keyfile");
            createKeyFile(keyname);
            key = new File(keyname);
        } else {
            if (cmd.hasOption("keyfile")) {
                keyname = cmd.getOptionValue("keyfile");
            }
            key = new File(keyname);
        }

        if (!(key.exists())) {
            System.out.println("Key does not exist or not provided");
            System.exit(1);
        }

        //         AmazonS3 s3 = new AmazonS3Client(new ClasspathPropertiesFileCredentialsProvider());
        ClasspathPropertiesFileCredentialsProvider credentials = new ClasspathPropertiesFileCredentialsProvider(
                ".s3encrypt");
        EncryptionMaterials encryptionMaterials = new EncryptionMaterials(getKeyFile(keyname));
        AmazonS3EncryptionClient s3 = new AmazonS3EncryptionClient(credentials.getCredentials(),
                encryptionMaterials);
        //          Region usWest2 = Region.getRegion(Regions.US_WEST_2);
        //          s3.setRegion(usWest2);

        if (cmd.hasOption("create_bucket")) {
            String bucket = cmd.getOptionValue("create_bucket");
            System.out.println("Creating bucket " + bucket + "\n");
            s3.createBucket(bucket);
        } else if (cmd.hasOption("delete_bucket")) {
            String bucket = cmd.getOptionValue("delete_bucket");
            System.out.println("Deleting bucket " + bucket + "\n");
            s3.deleteBucket(bucket);
        } else if (cmd.hasOption("get")) {
            String[] searchArgs = cmd.getOptionValues("get");
            String bucket = searchArgs[0];
            String filename = searchArgs[1];
            getS3Object(cmd, s3, bucket, filename);
        } else if (cmd.hasOption("inspect")) {
            String[] searchArgs = cmd.getOptionValues("inspect");
            String bucket = searchArgs[0];
            String filename = searchArgs[1];
            String keyname = "encryption_key";
            String metadata = inspectS3Object(cmd, s3, bucket, filename, keyname);
            System.out.println(metadata);
        } else if (cmd.hasOption("list_buckets")) {
            System.out.println("Listing buckets");
            for (Bucket bucket : s3.listBuckets()) {
                System.out.println(bucket.getName());
            }
            System.out.println();
        } else if (cmd.hasOption("list_objects")) {
            String bucket = cmd.getOptionValue("list_objects");
            System.out.println("Listing objects");
            ObjectListing objectListing = s3.listObjects(new ListObjectsRequest().withBucketName(bucket));
            for (S3ObjectSummary objectSummary : objectListing.getObjectSummaries()) {
                System.out.println(objectSummary.getKey() + "  " + "(size = " + objectSummary.getSize() + ")");
            }
            System.out.println();
        } else if (cmd.hasOption("put")) {
            String[] searchArgs = cmd.getOptionValues("put");
            String bucket = searchArgs[0];
            String filename = searchArgs[1];
            String metadataKeyname = "encryption_key";
            String key = keyname;
            putS3Object(cmd, s3, bucket, filename, metadataKeyname, key);
        } else if (cmd.hasOption("remove")) {
            String[] searchArgs = cmd.getOptionValues("remove");
            String bucket = searchArgs[0];
            String filename = searchArgs[1];
            System.out.println("Removing object in S3 from BUCKET = " + bucket + " FILENAME = " + filename);
            s3.deleteObject(new DeleteObjectRequest(bucket, filename));
            System.out.println();
        } else if (cmd.hasOption("rotate")) {
            String[] searchArgs = cmd.getOptionValues("rotate");
            String bucket = searchArgs[0];
            String filename = searchArgs[1];
            String key1 = cmd.getOptionValue("keyfile");
            String key2 = cmd.getOptionValue("rotateKey");
            String metadataKeyname = "encryption_key";
            System.out.println("Supposed to get object from here OPTION VALUE = " + bucket + " FILENAME = "
                    + filename + " KEY1 = " + key1 + " KEY2 = " + key2);

            EncryptionMaterials rotateEncryptionMaterials = new EncryptionMaterials(getKeyFile(key2));
            AmazonS3EncryptionClient rotateS3 = new AmazonS3EncryptionClient(credentials.getCredentials(),
                    rotateEncryptionMaterials);

            getS3Object(cmd, s3, bucket, filename);
            putS3Object(cmd, rotateS3, bucket, filename, metadataKeyname, key2);
        } else if (cmd.hasOption("rotateall")) {
            String[] searchArgs = cmd.getOptionValues("rotateall");
            String bucket = searchArgs[0];
            String key1 = searchArgs[1];
            String key2 = searchArgs[2];
            System.out.println("Supposed to rotateall here for BUCKET NAME = " + bucket + " KEY1 = " + key1
                    + " KEY2 = " + key2);
        } else {
            System.out.println("Something went wrong... ");
            System.exit(1);
        }

    } catch (ParseException e) {
        e.printStackTrace();
    } catch (AmazonServiceException ase) {
        System.out.println("Caught an AmazonServiceException, which " + "means your request made it "
                + "to Amazon S3, but was rejected with an error response" + " for some reason.");
        System.out.println("Error Message:    " + ase.getMessage());
        System.out.println("HTTP Status Code: " + ase.getStatusCode());
        System.out.println("AWS Error Code:   " + ase.getErrorCode());
        System.out.println("Error Type:       " + ase.getErrorType());
        System.out.println("Request ID:       " + ase.getRequestId());
    } catch (AmazonClientException ace) {
        System.out.println("Caught an AmazonClientException, which " + "means the client encountered "
                + "an internal error while trying to " + "communicate with S3, "
                + "such as not being able to access the network.");
        System.out.println("Error Message: " + ace.getMessage());
    }

}

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

private static void processOptions(String[] args) {
    Options options = new Options();

    Option opt = new Option("in", true, "Input file oe-supported Use .sdf to specify the file type.");
    opt.setRequired(true);//  w  w  w. ja v  a  2 s  .co  m
    options.addOption(opt);

    opt = new Option("out", true, "Output file oe-supported Use .sdf to specify the file type.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("bin", true,
            "bin definition. Use format \"bin_1_upperbound=bin_1_name|bin_2_upperbound=bin_2_name|bin_3_upperbound_=bin_3_name\"");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("dataTag", true, "SD tag containing data for binning");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("binTag", true, "SD tag used for storing bin names");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("ignoreModifier", false, "ignore leading '><= ~'");
    options.addOption(opt);

    opt = new Option("h", false, "print usage statement");
    opt.setRequired(false);
    options.addOption(opt);

    PosixParser parser = new PosixParser();
    CommandLine cl = null;

    try {
        cl = parser.parse(options, args);
    } catch (Exception exp) {
        // catch (ParseException exp) {
        System.err.println(exp.getMessage());
        exitWithHelp(options);
    }
    inFile = cl.getOptionValue("in");
    outFile = cl.getOptionValue("out");
    ignoreModifier = cl.hasOption("ignoreModifier");
    String binDefinition = cl.getOptionValue("bin");
    parseBins(binDefinition);

    binTag = cl.getOptionValue("binTag");
    dataTag = cl.getOptionValue("dataTag");
}

From source file:com.cloudera.beeswax.Server.java

/**
 * Parse command line options./* ww w  . j a v  a2s  .  c  o  m*/
 *
 * -b <port> specifies the port for beeswax to use.
 * -m <port>, if given, starts the metastore at this port.
 */
private static void parseArgs(String[] args) throws ParseException {
    Options options = new Options();

    Option metastoreOpt = new Option("m", "metastore", true, "port to use for metastore");
    metastoreOpt.setRequired(false);
    options.addOption(metastoreOpt);

    Option beeswaxOpt = new Option("b", "beeswax", true, "port to use for beeswax");
    beeswaxOpt.setRequired(true);
    options.addOption(beeswaxOpt);

    Option dtHostOpt = new Option("h", "desktop-host", true, "host running desktop");
    dtHostOpt.setRequired(true);
    options.addOption(dtHostOpt);

    Option dtHttpsOpt = new Option("s", "desktop-https", true, "desktop is running https");
    options.addOption(dtHttpsOpt);

    Option dtPortOpt = new Option("p", "desktop-port", true, "port used by desktop");
    dtPortOpt.setRequired(true);
    options.addOption(dtPortOpt);

    Option superUserOpt = new Option("u", "superuser", true, "Username of Hadoop superuser (default: hadoop)");
    superUserOpt.setRequired(false);
    options.addOption(superUserOpt);

    PosixParser parser = new PosixParser();
    CommandLine cmd = parser.parse(options, args);
    if (!cmd.getArgList().isEmpty()) {
        throw new ParseException("Unexpected extra arguments: " + cmd.getArgList());
    }

    for (Option opt : cmd.getOptions()) {
        if (opt.getOpt() == "m") {
            mport = parsePort(opt);
        } else if (opt.getOpt() == "b") {
            bport = parsePort(opt);
        } else if (opt.getOpt() == "u") {
            superUser = opt.getValue();
        } else if (opt.getOpt() == "h") {
            dtHost = opt.getValue();
        } else if (opt.getOpt() == "p") {
            dtPort = parsePort(opt);
        } else if (opt.getOpt() == "s") {
            dtHttps = true;
        }
    }
}