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

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

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

Prototype

PosixParser

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Usage

From source file:com.opengamma.batch.BatchJobRunner.java

/**
 * Creates an runs a batch job based on a properties file and configuration.
 *///from ww w . j  a v a 2 s  . c o  m
public static void main(String[] args) throws Exception { // CSIGNORE
    if (args.length == 0) {
        usage();
        System.exit(-1);
    }

    CommandLine line = null;
    Properties configProperties = null;

    final String propertyFile = "batchJob.properties";

    String configPropertyFile = null;

    if (System.getProperty(propertyFile) != null) {
        configPropertyFile = System.getProperty(propertyFile);
        try {
            FileInputStream fis = new FileInputStream(configPropertyFile);
            configProperties = new Properties();
            configProperties.load(fis);
            fis.close();
        } catch (FileNotFoundException e) {
            s_logger.error("The system cannot find " + configPropertyFile);
            System.exit(-1);
        }
    } else {
        try {
            FileInputStream fis = new FileInputStream(propertyFile);
            configProperties = new Properties();
            configProperties.load(fis);
            fis.close();
            configPropertyFile = propertyFile;
        } catch (FileNotFoundException e) {
            // there is no config file so we expect command line arguments
            try {
                CommandLineParser parser = new PosixParser();
                line = parser.parse(getOptions(), args);
            } catch (ParseException e2) {
                usage();
                System.exit(-1);
            }
        }
    }

    RunCreationMode runCreationMode = getRunCreationMode(line, configProperties, configPropertyFile);
    if (runCreationMode == null) {
        // default
        runCreationMode = RunCreationMode.AUTO;
    }

    String engineURI = getProperty("engineURI", line, configProperties, configPropertyFile);

    String brokerURL = getProperty("brokerURL", line, configProperties, configPropertyFile);

    Instant valuationTime = getValuationTime(line, configProperties, configPropertyFile);
    LocalDate observationDate = getObservationDate(line, configProperties, configPropertyFile);

    UniqueId viewDefinitionUniqueId = getViewDefinitionUniqueId(line, configProperties);

    URI vpBase;
    try {
        vpBase = new URI(engineURI);
    } catch (URISyntaxException ex) {
        throw new OpenGammaRuntimeException("Invalid URI", ex);
    }

    ActiveMQConnectionFactory activeMQConnectionFactory = new ActiveMQConnectionFactory(brokerURL);
    activeMQConnectionFactory.setWatchTopicAdvisories(false);

    JmsConnectorFactoryBean jmsConnectorFactoryBean = new JmsConnectorFactoryBean();
    jmsConnectorFactoryBean.setConnectionFactory(activeMQConnectionFactory);
    jmsConnectorFactoryBean.setName("Masters");

    JmsConnector jmsConnector = jmsConnectorFactoryBean.getObjectCreating();
    ScheduledExecutorService heartbeatScheduler = Executors.newSingleThreadScheduledExecutor();
    try {
        ViewProcessor vp = new RemoteViewProcessor(vpBase, jmsConnector, heartbeatScheduler);
        ViewClient vc = vp.createViewClient(UserPrincipal.getLocalUser());

        HistoricalMarketDataSpecification marketDataSpecification = MarketData.historical(observationDate,
                null);

        ViewExecutionOptions executionOptions = ExecutionOptions.batch(valuationTime, marketDataSpecification,
                null);

        vc.attachToViewProcess(viewDefinitionUniqueId, executionOptions);
        vc.waitForCompletion();
    } finally {
        heartbeatScheduler.shutdown();
    }
}

From source file:com.genentech.chemistry.openEye.apps.SDFMDLSSSMatcher.java

public static void main(String... args) throws IOException, InterruptedException {
    oechem.OEUseJavaHeap(false);//www  .  j a va 2  s .c  o m

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("in", true, "input file [.sdf,...]");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("out", true, "output file oe-supported");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("ref", true, "refrence file with MDL query molecules");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("anyMatch", false, "if set all matches are reported not just the first.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("printAll", false, "if set even compounds that do not macht are outputted.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("nCpu", true, "number of CPU's used in parallel, dafault 1");
    opt.setRequired(false);
    options.addOption(opt);

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

    args = cmd.getArgs();
    if (args.length > 0) {
        exitWithHelp("Unknown param: " + args[0], options);
    }

    if (cmd.hasOption("d")) {
        System.err.println("Start debugger and press return:");
        new BufferedReader(new InputStreamReader(System.in)).readLine();
    }

    int nCpu = 1;
    boolean firstMatch = !cmd.hasOption("anyMatch");
    boolean printAll = cmd.hasOption("printAll");

    String d = cmd.getOptionValue("nCpu");
    if (d != null)
        nCpu = Integer.parseInt(d);

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    String refFile = cmd.getOptionValue("ref");

    SDFMDLSSSMatcher matcher = new SDFMDLSSSMatcher(refFile, outFile, firstMatch, printAll, nCpu);
    matcher.run(inFile);
    matcher.close();
}

From source file:edu.msu.cme.rdp.classifier.ClassifierCmd.java

/**
 * This is the main method to do classification.
 * <p>Usage: java ClassifierCmd queryFile outputFile [property file].
 * <br>/*  w  ww  .j a v  a  2s. c  o  m*/
 * queryFile can be one of the following formats: Fasta, Genbank and EMBL. 
 * <br>
 * outputFile will be used to save the classification output.
 * <br>
 * property file contains the mapping of the training files.
 * <br>
 * Note: the training files and the property file should be in the same directory.
 * The default property file is set to data/classifier/16srrna/rRNAClassifier.properties.
 */
public static void main(String[] args) throws Exception {

    String queryFile = null;
    String outputFile = null;
    String propFile = null;
    String gene = null;
    ClassificationResultFormatter.FORMAT format = CmdOptions.DEFAULT_FORMAT;
    int min_bootstrap_words = Classifier.MIN_BOOTSTRSP_WORDS;

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

        if (line.hasOption(CmdOptions.OUTFILE_SHORT_OPT)) {
            outputFile = line.getOptionValue(CmdOptions.OUTFILE_SHORT_OPT);
        } else {
            throw new Exception("outputFile must be specified");
        }

        if (line.hasOption(CmdOptions.TRAINPROPFILE_SHORT_OPT)) {
            if (gene != null) {
                throw new IllegalArgumentException(
                        "Already specified the gene from the default location. Can not specify train_propfile");
            } else {
                propFile = line.getOptionValue(CmdOptions.TRAINPROPFILE_SHORT_OPT);
            }
        }
        if (line.hasOption(CmdOptions.FORMAT_SHORT_OPT)) {
            String f = line.getOptionValue(CmdOptions.FORMAT_SHORT_OPT);
            if (f.equalsIgnoreCase("allrank")) {
                format = ClassificationResultFormatter.FORMAT.allRank;
            } else if (f.equalsIgnoreCase("fixrank")) {
                format = ClassificationResultFormatter.FORMAT.fixRank;
            } else if (f.equalsIgnoreCase("filterbyconf")) {
                format = ClassificationResultFormatter.FORMAT.filterbyconf;
            } else if (f.equalsIgnoreCase("db")) {
                format = ClassificationResultFormatter.FORMAT.dbformat;
            } else {
                throw new IllegalArgumentException(
                        "Not valid output format, only allrank, fixrank, filterbyconf and db allowed");
            }
        }
        if (line.hasOption(CmdOptions.GENE_SHORT_OPT)) {
            if (propFile != null) {
                throw new IllegalArgumentException(
                        "Already specified train_propfile. Can not specify gene any more");
            }
            gene = line.getOptionValue(CmdOptions.GENE_SHORT_OPT).toLowerCase();

            if (!gene.equals(ClassifierFactory.RRNA_16S_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALLSU_GENE)) {
                throw new IllegalArgumentException(gene + " is NOT valid, only allows "
                        + ClassifierFactory.RRNA_16S_GENE + " and " + ClassifierFactory.FUNGALLSU_GENE);
            }
        }
        if (line.hasOption(CmdOptions.MIN_BOOTSTRAP_WORDS_SHORT_OPT)) {
            min_bootstrap_words = Integer
                    .parseInt(line.getOptionValue(CmdOptions.MIN_BOOTSTRAP_WORDS_SHORT_OPT));
            if (min_bootstrap_words < Classifier.MIN_BOOTSTRSP_WORDS) {
                throw new IllegalArgumentException(CmdOptions.MIN_BOOTSTRAP_WORDS_LONG_OPT
                        + " must be at least " + Classifier.MIN_BOOTSTRSP_WORDS);
            }
        }

        args = line.getArgs();
        if (args.length != 1) {
            throw new Exception("Expect one query file");
        }
        queryFile = args[0];

    } catch (Exception e) {
        System.out.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(120,
                "ClassifierCmd [options] <samplefile>\nNote this is the legacy command for one sample classification ",
                "", options, "");

        return;
    }

    if (propFile == null && gene == null) {
        gene = CmdOptions.DEFAULT_GENE;
    }
    ClassifierCmd classifierCmd = new ClassifierCmd();

    printLicense();
    classifierCmd.doClassify(queryFile, outputFile, propFile, format, gene, min_bootstrap_words);

}

From source file:edu.msu.cme.rdp.unifrac.Unifrac.java

public static void main(String[] args) throws Exception {
    CommandLineParser parser = new PosixParser();
    CommandLine line = null;/*from w w w . j  av  a 2 s  .  co  m*/
    try {
        line = parser.parse(options, args);
    } catch (UnrecognizedOptionException e) {
        System.err.println(e.getMessage());
        printUsage();
        return;
    }
    UnifracTree unifracTree = null;
    PrintStream out = System.out;

    if (line.hasOption("tree") && line.hasOption("sequence-files")) {
        printUsage();
    } else if (!(line.hasOption("weighted") || line.hasOption("unweighted")
            || line.hasOption("significance"))) {
        System.err.println("Must specify at least one calculation option");
        printUsage();
    } else if (line.hasOption("sample-mapping")) {
        Map<String, UnifracSample> sampleMap = readSampleMap(line.getOptionValue("sample-mapping"));

        if (line.hasOption("tree")) {
            unifracTree = parseNewickTree(line.getOptionValue("tree"), sampleMap);
        }
    } else {
        if (!line.hasOption("sample-mapping")) {
            System.err.println("A sample mapping file must be provided");
        }
        printUsage();
    }

    if (line.hasOption("outfile")) {
        out = new PrintStream(line.getOptionValue("outfile"));
    }

    if (unifracTree != null) {
        if (line.hasOption("unweighted")) {
            printResults(out, unifracTree.computeUnifrac(), "Unweighted Unifrac");
            if (line.hasOption("significance")) {
                printResults(out, unifracTree.computeUnifracSig(1000, false),
                        "Unweighted Unifrac Significance");
            }
        }

        if (line.hasOption("weighted")) {
            printResults(out, unifracTree.computeWeightedUnifrac(), "Weighted Unifrac");
            if (line.hasOption("significance")) {
                printResults(out, unifracTree.computeUnifracSig(1000, true), "Weighted Unifrac Significance");
            }
        }
    }
}

From source file:edu.msu.cme.rdp.multicompare.Main.java

public static void main(String[] args) throws Exception {
    PrintStream hier_out = null;//from   ww w.  j av  a  2  s.  c  om
    PrintWriter assign_out = new PrintWriter(new NullWriter());
    PrintStream bootstrap_out = null;
    File hier_out_filename = null;
    String propFile = null;
    File biomFile = null;
    File metadataFile = null;
    PrintWriter shortseq_out = null;
    List<MCSample> samples = new ArrayList();
    ClassificationResultFormatter.FORMAT format = ClassificationResultFormatter.FORMAT.allRank;
    float conf = CmdOptions.DEFAULT_CONF;
    String gene = null;
    int min_bootstrap_words = Classifier.MIN_BOOTSTRSP_WORDS;

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

        if (line.hasOption(CmdOptions.OUTFILE_SHORT_OPT)) {
            assign_out = new PrintWriter(line.getOptionValue(CmdOptions.OUTFILE_SHORT_OPT));
        } else {
            throw new IllegalArgumentException("Require the output file for classification assignment");
        }
        if (line.hasOption(CmdOptions.HIER_OUTFILE_SHORT_OPT)) {
            hier_out_filename = new File(line.getOptionValue(CmdOptions.HIER_OUTFILE_SHORT_OPT));
            hier_out = new PrintStream(hier_out_filename);
        }
        if (line.hasOption(CmdOptions.BIOMFILE_SHORT_OPT)) {
            biomFile = new File(line.getOptionValue(CmdOptions.BIOMFILE_SHORT_OPT));
        }
        if (line.hasOption(CmdOptions.METADATA_SHORT_OPT)) {
            metadataFile = new File(line.getOptionValue(CmdOptions.METADATA_SHORT_OPT));
        }

        if (line.hasOption(CmdOptions.TRAINPROPFILE_SHORT_OPT)) {
            if (gene != null) {
                throw new IllegalArgumentException(
                        "Already specified the gene from the default location. Can not specify train_propfile");
            } else {
                propFile = line.getOptionValue(CmdOptions.TRAINPROPFILE_SHORT_OPT);
            }
        }
        if (line.hasOption(CmdOptions.FORMAT_SHORT_OPT)) {
            String f = line.getOptionValue(CmdOptions.FORMAT_SHORT_OPT);
            if (f.equalsIgnoreCase("allrank")) {
                format = ClassificationResultFormatter.FORMAT.allRank;
            } else if (f.equalsIgnoreCase("fixrank")) {
                format = ClassificationResultFormatter.FORMAT.fixRank;
            } else if (f.equalsIgnoreCase("filterbyconf")) {
                format = ClassificationResultFormatter.FORMAT.filterbyconf;
            } else if (f.equalsIgnoreCase("db")) {
                format = ClassificationResultFormatter.FORMAT.dbformat;
            } else if (f.equalsIgnoreCase("biom")) {
                format = ClassificationResultFormatter.FORMAT.biom;
            } else {
                throw new IllegalArgumentException(
                        "Not an valid output format, only allrank, fixrank, biom, filterbyconf and db allowed");
            }
        }
        if (line.hasOption(CmdOptions.GENE_SHORT_OPT)) {
            if (propFile != null) {
                throw new IllegalArgumentException(
                        "Already specified train_propfile. Can not specify gene any more");
            }
            gene = line.getOptionValue(CmdOptions.GENE_SHORT_OPT).toLowerCase();

            if (!gene.equals(ClassifierFactory.RRNA_16S_GENE) && !gene.equals(ClassifierFactory.FUNGALLSU_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALITS_warcup_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALITS_unite_GENE)) {
                throw new IllegalArgumentException(gene + " not found, choose from"
                        + ClassifierFactory.RRNA_16S_GENE + ", " + ClassifierFactory.FUNGALLSU_GENE + ", "
                        + ClassifierFactory.FUNGALITS_warcup_GENE + ", "
                        + ClassifierFactory.FUNGALITS_unite_GENE);
            }
        }
        if (line.hasOption(CmdOptions.MIN_BOOTSTRAP_WORDS_SHORT_OPT)) {
            min_bootstrap_words = Integer
                    .parseInt(line.getOptionValue(CmdOptions.MIN_BOOTSTRAP_WORDS_SHORT_OPT));
            if (min_bootstrap_words < Classifier.MIN_BOOTSTRSP_WORDS) {
                throw new IllegalArgumentException(CmdOptions.MIN_BOOTSTRAP_WORDS_LONG_OPT
                        + " must be at least " + Classifier.MIN_BOOTSTRSP_WORDS);
            }
        }
        if (line.hasOption(CmdOptions.BOOTSTRAP_SHORT_OPT)) {
            String confString = line.getOptionValue(CmdOptions.BOOTSTRAP_SHORT_OPT);
            try {
                conf = Float.valueOf(confString);
            } catch (NumberFormatException e) {
                throw new IllegalArgumentException("Confidence must be a decimal number");
            }

            if (conf < 0 || conf > 1) {
                throw new IllegalArgumentException("Confidence must be in the range [0,1]");
            }
        }
        if (line.hasOption(CmdOptions.SHORTSEQ_OUTFILE_SHORT_OPT)) {
            shortseq_out = new PrintWriter(line.getOptionValue(CmdOptions.SHORTSEQ_OUTFILE_SHORT_OPT));
        }
        if (line.hasOption(CmdOptions.BOOTSTRAP_OUTFILE_SHORT_OPT)) {
            bootstrap_out = new PrintStream(line.getOptionValue(CmdOptions.BOOTSTRAP_OUTFILE_SHORT_OPT));
        }

        if (format.equals(ClassificationResultFormatter.FORMAT.biom) && biomFile == null) {
            throw new IllegalArgumentException("biom format requires an input biom file");
        }
        if (biomFile != null) { // if input biom file provided, use biom format
            format = ClassificationResultFormatter.FORMAT.biom;
        }

        args = line.getArgs();
        for (String arg : args) {
            String[] inFileNames = arg.split(",");
            File inputFile = new File(inFileNames[0]);
            File idmappingFile = null;
            if (!inputFile.exists()) {
                throw new IllegalArgumentException("Failed to find input file \"" + inFileNames[0] + "\"");
            }
            if (inFileNames.length == 2) {
                idmappingFile = new File(inFileNames[1]);
                if (!idmappingFile.exists()) {
                    throw new IllegalArgumentException("Failed to find input file \"" + inFileNames[1] + "\"");
                }
            }

            MCSample nextSample = new MCSample(inputFile, idmappingFile);
            samples.add(nextSample);
        }
        if (propFile == null && gene == null) {
            gene = CmdOptions.DEFAULT_GENE;
        }
        if (samples.size() < 1) {
            throw new IllegalArgumentException("Require at least one sample files");
        }
    } catch (Exception e) {
        System.out.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(80, " [options] <samplefile>[,idmappingfile] ...", "", options, "");
        return;
    }

    MultiClassifier multiClassifier = new MultiClassifier(propFile, gene, biomFile, metadataFile);
    MultiClassifierResult result = multiClassifier.multiCompare(samples, conf, assign_out, format,
            min_bootstrap_words);
    assign_out.close();
    if (hier_out != null) {
        DefaultPrintVisitor printVisitor = new DefaultPrintVisitor(hier_out, samples);
        result.getRoot().topDownVisit(printVisitor);
        hier_out.close();
        if (multiClassifier.hasCopyNumber()) {
            // print copy number corrected counts
            File cn_corrected_s = new File(hier_out_filename.getParentFile(),
                    "cnadjusted_" + hier_out_filename.getName());
            PrintStream cn_corrected_hier_out = new PrintStream(cn_corrected_s);
            printVisitor = new DefaultPrintVisitor(cn_corrected_hier_out, samples, true);
            result.getRoot().topDownVisit(printVisitor);
            cn_corrected_hier_out.close();
        }
    }

    if (bootstrap_out != null) {
        for (MCSample sample : samples) {
            MCSamplePrintUtil.printBootstrapCountTable(bootstrap_out, sample);
        }
        bootstrap_out.close();
    }

    if (shortseq_out != null) {
        for (String id : result.getBadSequences()) {
            shortseq_out.write(id + "\n");
        }
        shortseq_out.close();
    }

}

From source file:eu.scape_project.tika_identify.TikaIdentification.java

public static void main(String[] args)
        throws ParseException, IOException, InterruptedException, ClassNotFoundException {
    CommandLineParser cmdParser = new PosixParser();

    TikaCliOptions tikaCliOpts = new TikaCliOptions();
    appConfig = new TikaCliConfig();

    CommandLine cmd = cmdParser.parse(tikaCliOpts.options, args);
    if ((args.length == 0) || (cmd.hasOption(tikaCliOpts.HELP_OPT))) {
        tikaCliOpts.exit("Help", 0);
    } else {/*from  w  ww .ja v a  2  s.  c  om*/
        tikaCliOpts.initOptions(cmd, appConfig);
        TikaIdentification tc = new TikaIdentification();
        if (appConfig.isLocal()) {
            tc.startApplication();
        } else {
            tc.startHadoopJob();
        }
    }
}

From source file:lee.util.jtap.JTapCli.java

/**
 * @param args//from w  ww  .  ja  va 2 s  .com
 */
public static void main(String[] args) {
    Options options = constructOptions();

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        System.out.println("Cmd Parsing Error:   " + e.getMessage());
        JTapCli.printHelp(options);
    }
    String resultMessage = "Done.";
    if (cmd.hasOption("dumpkeys")) {
        resultMessage = JTapCli.dumpKeys();
    } else if (cmd.hasOption("dumpall")) {
        resultMessage = JTapCli.dumpAll();
    } else if (cmd.hasOption("s") || cmd.hasOption("session")) {
        HashMap<String, String> argsMap = getMappedArgs(cmd, "host", "bucket", "password", "port");
        resultMessage = ">> " + JTapCli.setSession(argsMap);
    } else if (cmd.hasOption("dk") || cmd.hasOption("deletekey")) {
        resultMessage = JTapCli.deleteKey(cmd.getOptionValues("dk"));
    } else if (cmd.hasOption("gk") || cmd.hasOption("getkey")) {
        resultMessage = JTapCli.dumpKey(cmd.getOptionValues("gk"));
    } else if (cmd.hasOption("cs") || cmd.hasOption("clearsession")) {
        boolean removed = JTapCli.session.delete();
        if (removed) {
            System.out
                    .println("Saved session data has been cleared. To set the values again call with -session");
        }
    } else {
        JTapCli.printHelp(options);
        resultMessage = "";
    }
    System.out.println(resultMessage);
    return;
}

From source file:com.ottogroup.bi.spqr.websocket.server.SPQRWebSocketServer.java

/**
 * Checks the command-line settings and ramps up the server
 * @param args arguments passed from command-line
 * @throws ParseException indicates that parsing the command-line failed for any reason
 * @throws InterruptedException //from  www.ja  va 2  s.co m
 * @throws IOException 
 */
public static void main(String[] args) throws ParseException, IOException, InterruptedException {

    ////////////////////////////////////////////////////////////////////////
    // evaluate command-line and ensure that it provides valid input
    CommandLineParser parser = new PosixParser();
    CommandLine commandLine = parser.parse(getOptions(), args);

    if (commandLine.hasOption(CFG_HELP)) {
        new HelpFormatter().printHelp("spqr-websocket-server", getOptions());
        return;
    }

    if (!commandLine.hasOption(CFG_CONFIGURATION_FILE)) {
        new HelpFormatter().printHelp("spqr-websocket-server", "", getOptions(),
                "Missing required configuration file");
        return;
    }
    //
    ////////////////////////////////////////////////////////////////////////

    new SPQRWebSocketServer().run(commandLine.getOptionValue(CFG_CONFIGURATION_FILE));
}

From source file:LNISmokeTest.java

/**
 * Execute command line. See Usage string for options and arguments.
 * //  w w  w . jav  a  2 s .  com
 * @param argv the argv
 * 
 * @throws Exception the exception
 */
public static void main(String[] argv) throws Exception {
    Options options = new Options();

    OptionGroup func = new OptionGroup();
    func.addOption(new Option("c", "copy", true, "copy <Item> to -C <Collection>"));
    func.addOption(new Option("s", "submit", true, "submit <collection> -P <packager> -i <file>"));
    func.addOption(new Option("d", "disseminate", true, "disseminate <item> -P <packager> -o <file>"));
    func.addOption(new Option("f", "propfind", true, "propfind of all properties or -N <propname>"));
    func.addOption(new Option("r", "rpropfind", true, "recursive propfind, only collections"));
    func.addOption(new Option("n", "names", true, "list all property names on resource"));
    func.addOption(new Option("p", "proppatch", true, "set property: <handle> -N <property> -V <newvalue>"));
    func.setRequired(true);
    options.addOptionGroup(func);

    options.addOption("h", "help", false, "show help message");
    options.addOption("e", "endpoint", true, "SOAP endpoint URL (REQUIRED)");
    options.addOption("P", "packager", true, "Packager to use to import/export a package.");
    options.addOption("C", "collection", true, "Target collection of -c copy");
    options.addOption("o", "output", true, "file to create for new package");
    options.addOption("i", "input", true, "file containing package to submit");
    options.addOption("N", "name", true, "name of property to query/set");
    options.addOption("V", "value", true, "new value for property being set");

    try {
        CommandLine line = (new PosixParser()).parse(options, argv);
        if (line.hasOption("h")) {
            usage(options, 0, null);
        }

        // get SOAP client connection, using the endpoint URL
        String endpoint = line.getOptionValue("e");
        if (endpoint == null) {
            usage(options, 2, "Missing the required -e endpoint argument");
        }
        LNISoapServletServiceLocator loc = new LNISoapServletServiceLocator();
        LNISoapServlet lni = loc.getDSpaceLNI(new URL(endpoint));

        // propfind - with optional single-property Name
        if (line.hasOption("f")) {
            String pfXml = (line.hasOption("N"))
                    ? specificPropPrefix + line.getOptionValue("N") + specificPropSuffix
                    : allProp;
            doPropfind(lni, line.getOptionValue("f"), pfXml, 0, null);
        }

        // recursive propfind limited to collection, community objects
        else if (line.hasOption("r")) {
            doPropfind(lni, line.getOptionValue("r"), someProp, -1, "collection,community");
        } else if (line.hasOption("n")) {
            doPropfind(lni, line.getOptionValue("n"), nameProp, 0, null);
        } else if (line.hasOption("p")) {
            if (line.hasOption("N") && line.hasOption("V")) {
                doProppatch(lni, line.getOptionValue("p"), line.getOptionValue("N"), line.getOptionValue("V"));
            } else {
                usage(options, 13, "Missing required args: -N <name> -V <value>n");
            }
        }

        // submit a package
        else if (line.hasOption("s")) {
            if (line.hasOption("P") && line.hasOption("i")) {
                doPut(lni, line.getOptionValue("s"), line.getOptionValue("P"), line.getOptionValue("i"),
                        endpoint);
            } else {
                usage(options, 13, "Missing required args after -s: -P <packager> -i <file>");
            }
        }

        // Disseminate (GET) item as package
        else if (line.hasOption("d")) {
            if (line.hasOption("P") && line.hasOption("o")) {
                doGet(lni, line.getOptionValue("d"), line.getOptionValue("P"), line.getOptionValue("o"),
                        endpoint);
            } else {
                usage(options, 13, "Missing required args after -d: -P <packager> -o <file>");
            }
        }

        // copy from src to dst
        else if (line.hasOption("c")) {
            if (line.hasOption("C")) {
                doCopy(lni, line.getOptionValue("c"), line.getOptionValue("C"));
            } else {
                usage(options, 13, "Missing required args after -c: -C <collection>\n");
            }
        } else {
            usage(options, 14, "Missing command option.\n");
        }

    } catch (ParseException pe) {
        usage(options, 1, "Error in arguments: " + pe.toString());

    } catch (java.rmi.RemoteException de) {
        System.out.println("ERROR, got RemoteException, message=" + de.getMessage());

        de.printStackTrace();

        die(1, "  Exception class=" + de.getClass().getName());
    }
}

From source file:javadepchecker.Main.java

/**
 * @param args the command line arguments
 *///w w w. j  a  va  2  s.co  m
public static void main(String[] args) throws IOException {
    int exit = 0;
    try {
        CommandLineParser parser = new PosixParser();
        Options options = new Options();
        options.addOption("h", "help", false, "print help");
        options.addOption("i", "image", true, "image directory");
        options.addOption("v", "verbose", false, "print verbose output");
        CommandLine line = parser.parse(options, args);
        String[] files = line.getArgs();
        if (line.hasOption("h") || files.length == 0) {
            HelpFormatter h = new HelpFormatter();
            h.printHelp("java-dep-check [-i <image] <package.env>+", options);
        } else {
            image = line.getOptionValue("i", "");

            for (String arg : files) {
                if (line.hasOption('v'))
                    System.out.println("Checking " + arg);
                if (!checkPkg(new File(arg))) {
                    exit = 1;
                }
            }
        }
    } catch (ParseException ex) {
        Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
    }
    System.exit(exit);
}