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

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

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Introduction

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

Prototype

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

Source Link

Document

Parse the arguments according to the specified options.

Usage

From source file:eu.scape_project.tb.lsdr.hocrparser.HocrParser.java

/**
 * The main entry point.//from ww  w .j ava2  s . c  om
 */
public static void main(String[] args) throws ParseException {
    Configuration conf = new Configuration();

    //conf.setBoolean("mapreduce.client.genericoptionsparser.used", true);
    GenericOptionsParser gop = new GenericOptionsParser(conf, args);
    HocrParserCliConfig pc = new HocrParserCliConfig();
    CommandLineParser cmdParser = new PosixParser();
    CommandLine cmd = cmdParser.parse(HocrParserOptions.OPTIONS, gop.getRemainingArgs());
    if ((args.length == 0) || (cmd.hasOption(HocrParserOptions.HELP_OPT))) {
        HocrParserOptions.exit("Usage", 0);
    } else {
        HocrParserOptions.initOptions(cmd, pc);
    }
    String dir = pc.getDirStr();

    String name = pc.getHadoopJobName();
    if (name == null || name.equals("")) {
        name = "hocr_parser";
    }

    try {
        Job job = new Job(conf, name);
        job.setJarByClass(HocrParser.class);

        job.setMapperClass(HocrParserMapper.class);
        //job.setCombinerClass(HocrParserReducer.class);
        job.setReducerClass(HocrParserReducer.class);

        job.setInputFormatClass(SequenceFileInputFormat.class);

        job.setOutputFormatClass(TextOutputFormat.class);
        //SequenceFileOutputFormat.setOutputCompressionType(job, SequenceFile.CompressionType.NONE);

        //conf.setMapOutputKeyClass(Text.class);
        job.setMapOutputKeyClass(Text.class);
        job.setMapOutputValueClass(Text.class);

        job.setOutputKeyClass(Text.class);
        job.setOutputValueClass(LongWritable.class);

        SequenceFileInputFormat.addInputPath(job, new Path(dir));
        String outpath = "output/" + System.currentTimeMillis() + "hop";
        FileOutputFormat.setOutputPath(job, new Path(outpath));
        job.waitForCompletion(true);
        System.out.print(outpath);
        System.exit(0);
    } catch (Exception e) {
        logger.error("IOException occurred", e);
    }
}

From source file:is.merkor.core.cli.Main.java

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

    List<String> results = new ArrayList<String>();
    PrintStream out = new PrintStream(System.out, true, "UTF-8");

    CommandLineParser parser = new GnuParser();
    try {/*from w  ww. j  a  v a  2  s . c om*/

        MerkorCoreCommandLineOptions.createOptions();
        results = processCommandLine(parser.parse(MerkorCoreCommandLineOptions.options, args));
        out.print("\n");
        for (String str : results) {
            if (!str.equals("no message"))
                out.println(str);
        }
        out.print("\n");
        if (results.isEmpty()) {
            out.println("nothing found for parameters: ");
            for (int i = 0; i < args.length; i++)
                out.println("\t" + args[i]);
            out.println("for help type: -help or see README.markdown");
            out.print("\n");
        }
    } catch (ParseException e) {
        System.err.println("Parsing failed.  Reason: " + e.getMessage());
    }
}

From source file:cz.muni.fi.mir.mathmlcanonicalization.MathMLCanonicalizerCommandLineTool.java

/**
 * @param args the command line arguments
 *//*from ww w  .ja  va  2  s  .  c o  m*/
public static void main(String[] args) throws FileNotFoundException, XMLStreamException {
    final Options options = new Options();
    options.addOption("c", true, "load configuration file");
    options.addOption("dtd", false,
            "enforce injection of XHTML + MathML 1.1 DTD reference into input documents");
    options.addOption("w", false, "overwrite input files by canonical outputs");
    options.addOption("h", false, "print help");

    final CommandLineParser parser = new PosixParser();
    CommandLine line = null;
    try {
        line = parser.parse(options, args);
    } catch (ParseException ex) {
        printHelp(options);
        System.exit(1);
    }

    File config = null;
    boolean overwrite = false;
    boolean dtdInjectionMode = false;
    if (line != null) {
        if (line.hasOption('c')) {
            config = new File(args[1]);
        }

        if (line.hasOption("dtd")) {
            dtdInjectionMode = true;
        }

        if (line.hasOption('w')) {
            overwrite = true;
        }

        if (line.hasOption('h')) {
            printHelp(options);
            System.exit(0);
        }

        final List<String> arguments = Arrays.asList(line.getArgs());
        if (arguments.size() > 0) {
            for (String arg : arguments) {
                try {
                    List<File> files = getFiles(new File(arg));
                    for (File file : files) {
                        canonicalize(file, config, dtdInjectionMode, overwrite);
                    }
                } catch (IOException ex) {
                    Logger.getLogger(MathMLCanonicalizerCommandLineTool.class.getName()).log(Level.SEVERE,
                            ex.getMessage(), ex);
                } catch (ConfigException ex) {
                    Logger.getLogger(MathMLCanonicalizerCommandLineTool.class.getName()).log(Level.SEVERE,
                            ex.getMessage(), ex);
                } catch (JDOMException ex) {
                    Logger.getLogger(MathMLCanonicalizerCommandLineTool.class.getName()).log(Level.SEVERE,
                            ex.getMessage(), ex);
                } catch (ModuleException ex) {
                    Logger.getLogger(MathMLCanonicalizerCommandLineTool.class.getName()).log(Level.SEVERE,
                            ex.getMessage(), ex);
                }
            }
        } else {
            printHelp(options);
            System.exit(0);
        }
    }
}

From source file:com.act.biointerpretation.sars.SarGenerationDriver.java

public static void main(String[] args) throws Exception {
    // Build command line parser.
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());//w  ww  .  j  ava  2  s .c  o m
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        LOGGER.error("Argument parsing failed: %s", e.getMessage());
        HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    // Print help.
    if (cl.hasOption(OPTION_HELP)) {
        HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    // Create DB and DbAPI
    MongoDB mongoDB = new MongoDB(LOCAL_HOST, MONGO_PORT, cl.getOptionValue(OPTION_DB));
    DbAPI dbApi = new DbAPI(mongoDB);

    // Handle output file
    File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_PATH));
    if (outputFile.isDirectory() || outputFile.exists()) {
        LOGGER.error("Supplied output file is a directory or already exists.");
        HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }
    outputFile.createNewFile();

    // Check that there is exactly one reaction group input option
    if (cl.hasOption(OPTION_REACTION_LIST) && cl.hasOption(OPTION_REACTIONS_FILE)) {
        LOGGER.error("Cannot process both a reaction list and a reactions file as input.");
        HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }
    if (!cl.hasOption(OPTION_REACTION_LIST) && !cl.hasOption(OPTION_REACTIONS_FILE)) {
        LOGGER.error("Must supply either a reaction list or a reactions file as input.");
        HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    // Build input reaction group corpus.
    Iterable<ReactionGroup> groups = null;
    if (cl.hasOption(OPTION_REACTION_LIST)) {
        LOGGER.info("Using specific input reactions.");
        ReactionGroup group = new ReactionGroup("ONLY_GROUP", "NO_DB");
        for (String idString : cl.getOptionValues(OPTION_REACTION_LIST)) {
            group.addReactionId(Long.parseLong(idString));
        }
        groups = Arrays.asList(group);
    }
    if (cl.hasOption(OPTION_REACTIONS_FILE)) {
        LOGGER.info("Using reactions file.");
        File inputFile = new File(cl.getOptionValue(OPTION_REACTIONS_FILE));
        try {
            groups = ReactionGroupCorpus.loadFromJsonFile(inputFile);
            LOGGER.info("Successfully parsed input as json file.");
        } catch (IOException e) {
            LOGGER.info("Input file not json file. Trying txt format.");
            try {
                groups = ReactionGroupCorpus.loadFromTextFile(inputFile);
                LOGGER.info("Successfully parsed input as text file.");
            } catch (IOException f) {
                LOGGER.error("Reactions input file not parseable. %s", f.getMessage());
                throw f;
            }
        }
    }

    // Build all pieces of SAR generator
    ReactionProjector projector = new ReactionProjector();
    ExpandedReactionSearcher generalizer = new ExpandedReactionSearcher(projector);

    McsCalculator reactionMcsCalculator = new McsCalculator(McsCalculator.REACTION_BUILDING_OPTIONS);
    McsCalculator sarMcsCalculator = new McsCalculator(McsCalculator.SAR_OPTIONS);

    FullReactionBuilder reactionBuilder = new FullReactionBuilder(reactionMcsCalculator, generalizer,
            projector);

    SarFactory substructureSarFactory = new OneSubstrateSubstructureSar.Factory(sarMcsCalculator);
    SarFactory carbonCountSarFactory = new OneSubstrateCarbonCountSar.Factory();
    List<SarFactory> sarFactories = Arrays.asList(carbonCountSarFactory, substructureSarFactory);

    ErosCorpus roCorpus = new ErosCorpus();
    roCorpus.loadValidationCorpus();

    ReactionGroupCharacterizer reactionGroupCharacterizer = new OneSubstrateOneRoCharacterizer(dbApi,
            sarFactories, reactionBuilder, roCorpus);
    SarCorpusBuilder corpusBuilder = new SarCorpusBuilder(groups, reactionGroupCharacterizer);
    LOGGER.info("Parsed arguments and constructed SAR corpus builder. Building corpus.");

    SarCorpus sarCorpus = corpusBuilder.build();
    LOGGER.info("Built sar corpus. Printing to file in json format.");

    sarCorpus.printToJsonFile(outputFile);
    LOGGER.info("Complete!");
}

From source file:com.hurence.logisland.utils.avro.eventgenerator.DataGenerator.java

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

    // load and verify the options
    CommandLineParser parser = new PosixParser();
    Options opts = loadOptions();/*from  ww  w  .java  2 s.  c  o m*/

    CommandLine cmd = null;
    try {
        cmd = parser.parse(opts, args);
    } catch (org.apache.commons.cli.ParseException parseEx) {
        LOG.error("Invalid option");
        printHelp(opts);
        return;
    }

    // check for necessary options
    String fileLoc = cmd.getOptionValue("schemaLocation");
    if (fileLoc == null) {
        LOG.error("schemaLocation not specified");
        printHelp(opts);
    }

    //get string length and check if min is greater than 0

    // Generate the record
    File schemaFile = new File(fileLoc);
    DataGenerator dataGenerator = new DataGenerator(schemaFile);
    GenericRecord record = dataGenerator.generateRandomRecord();
    if (cmd.hasOption(PRINT_AVRO_JSON_OPTNAME)) {
        String outname = cmd.getOptionValue(PRINT_AVRO_JSON_OPTNAME);
        OutputStream outs = System.out;
        if (!outname.equals("-")) {
            outs = new FileOutputStream(outname);
        }
        printAvroJson(record, outs);
        if (!outname.equals("-")) {
            outs.close();
        }
    } else {
        DataGenerator.prettyPrint(record);
    }

}

From source file:com.genentech.chemistry.tool.SDF2HtmlTab.java

public static void main(String[] args) throws ParseException, JDOMException, IOException {
    long start = System.currentTimeMillis();

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("in", true, "input sd file");
    opt.setRequired(true);//ww  w .ja v a2s.co  m
    options.addOption(opt);

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

    String inFile = cmd.getOptionValue("in");

    args = cmd.getArgs();
    if (args.length > 0) {
        exitWithHelp(options);
    }

    oemolistream ifs;
    Set<String> tagSet = getTagSet(inFile);

    System.out.println(
            "<html xmlns:v='urn:schemas-microsoft-com:vml' xmlns:o='urn:schemas-microsoft-com:office:office'>");
    System.out.println("<head>");
    System.out.println("<BASE href='" + BASEUrl + "'/>");
    System.out.println(
            "<link href='/" + Settings.SERVLET_CONTEXT + "/css/Aestel.css' rel='stylesheet' type='text/css'/>");

    System.out.println("<style type='text/css'>");
    System.out.println("td.stru { width: " + (IMGWidth + 2) + "px; height: " + (IMGHeigth + 4)
            + "px; vertical-align: top; }");
    System.out.println("table.grid tr.first { border-top: 3px solid black; }");
    // for tables in tables
    System.out.println("table.grid table td { border: 0px; text-align: right;}");
    System.out.println("table.grid table td:first-child { text-align: left;}");
    System.out.println("th.head { border-left: 1px solid black; border-bottom: 2px solid black;\n"
            + "          empty-cells: show; background-color: #6297ff; color: #000000;\n"
            + "          padding: 0em .3em 0em .3em; vertical-align: middle; }");
    System.out.println("</style>");

    System.out.println("</head>");
    System.out.println("<body>");

    System.out.println("<table class='grid'><tr>");
    System.out.println("<th class='head'>Structure</th>");

    for (String tag : tagSet)
        System.out.println("<th class='head'>" + tag + "</th>");
    System.out.println("</tr>");

    OEGraphMol mol = new OEGraphMol();
    ifs = new oemolistream(inFile);
    int iCounter = 0;
    while (oechem.OEReadMolecule(ifs, mol)) {
        iCounter++;
        System.out.println("<tr>");
        String smi = OETools.molToCanSmi(mol, true);
        String img = DepictHelper.DEFAULT.getExcelSmilesImageElement(BASEUrl, 120, 120, ImageType.PNG, smi,
                null);

        System.out.print(" <td class='stru'>");
        System.out.print(img);
        System.out.println("</td>");

        for (String tag : tagSet) {
            String val = oechem.OEGetSDData(mol, tag);

            System.out.print(" <td>");
            System.out.print(val);
            System.out.println("</td>");
        }

        System.out.println("</tr>");
    }

    System.out.println("</table></body></html>");

    System.err.printf("SDF2HtmlTab: Exported %d structures in %dsec\n", iCounter,
            (System.currentTimeMillis() - start) / 1000);
}

From source file:edu.isi.mtandao.twitter.StreamCrawler.java

public static void main(String[] args)
        throws ParseException, InstantiationException, IllegalAccessException, ClassNotFoundException {
    // extract command line arguments
    CommandLineParser parser = new PosixParser();
    CommandLine cmd = parser.parse(CLI_OPTIONS, args);

    // get crawler class
    String crawlerClass = cmd.getOptionValue("crawlerClass");
    if (crawlerClass == null) {
        printUsage(CLI_OPTIONS);// ww  w  . j  av  a  2s.  com
    }

    // instantiate and initialize the crawler
    StreamCrawler crawler = (StreamCrawler) Class.forName(crawlerClass).newInstance();

    try {
        crawler.initialize(cmd);
    } catch (Exception e) {
        printUsage(CLI_OPTIONS);
    }

    // start crawling
    crawler.crawl();
}

From source file:glacierpipe.GlacierPipeMain.java

public static void main(String[] args) throws IOException, ParseException {
    CommandLineParser parser = new GnuParser();

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

    if (cmd.hasOption("help")) {
        try (PrintWriter writer = new PrintWriter(System.err)) {
            printHelp(writer);//from   w  w w . j a va  2 s.  c  o  m
        }

        System.exit(0);
    } else if (cmd.hasOption("upload")) {

        // Turn the CommandLine into Properties
        Properties cliProperties = new Properties();
        for (Iterator<?> i = cmd.iterator(); i.hasNext();) {
            Option o = (Option) i.next();

            String opt = o.getLongOpt();
            opt = opt != null ? opt : o.getOpt();

            String value = o.getValue();
            value = value != null ? value : "";

            cliProperties.setProperty(opt, value);
        }

        // Build up a configuration
        ConfigBuilder configBuilder = new ConfigBuilder();

        // Archive name
        List<?> archiveList = cmd.getArgList();
        if (archiveList.size() > 1) {
            throw new ParseException("Too many arguments");
        } else if (archiveList.isEmpty()) {
            throw new ParseException("No archive name provided");
        }

        configBuilder.setArchive(archiveList.get(0).toString());

        // All other arguments on the command line
        configBuilder.setFromProperties(cliProperties);

        // Load any config from the properties file
        Properties fileProperties = new Properties();
        try (InputStream in = new FileInputStream(configBuilder.propertiesFile)) {
            fileProperties.load(in);
        } catch (IOException e) {
            System.err.printf("Warning: unable to read properties file %s; %s%n", configBuilder.propertiesFile,
                    e);
        }

        configBuilder.setFromProperties(fileProperties);

        // ...
        Config config = new Config(configBuilder);

        IOBuffer buffer = new MemoryIOBuffer(config.partSize);

        AmazonGlacierClient client = new AmazonGlacierClient(
                new BasicAWSCredentials(config.accessKey, config.secretKey));
        client.setEndpoint(config.endpoint);

        // Actual upload
        try (InputStream in = new BufferedInputStream(System.in, 4096);
                PrintWriter writer = new PrintWriter(System.err);
                ObservableProperties configMonitor = config.reloadProperties
                        ? new ObservableProperties(config.propertiesFile)
                        : null;
                ProxyingThrottlingStrategy throttlingStrategy = new ProxyingThrottlingStrategy(config);) {
            TerminalGlacierPipeObserver observer = new TerminalGlacierPipeObserver(writer);

            if (configMonitor != null) {
                configMonitor.registerObserver(throttlingStrategy);
            }

            GlacierPipe pipe = new GlacierPipe(buffer, observer, config.maxRetries, throttlingStrategy);
            pipe.pipe(client, config.vault, config.archive, in);
        } catch (Exception e) {
            e.printStackTrace(System.err);
        }

        System.exit(0);
    } else {
        try (PrintWriter writer = new PrintWriter(System.err)) {
            writer.println("No action specified.");
            printHelp(writer);
        }

        System.exit(-1);
    }
}

From source file:net.sourceforge.dita4publishers.tools.ditadxpunpacker.DitaDxpUnpacker.java

/**
 * @param args/*from w ww. j  av  a2s . co  m*/
 */
public static void main(String[] args) {

    Options cmdlineOptions = configureOptions();

    CommandLineParser parser = new PosixParser();

    CommandLine cmdline = null;
    try {
        // parse the command line arguments
        cmdline = parser.parse(cmdlineOptions, args);
    } catch (ParseException exp) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(DitaDxpUnpacker.class.getSimpleName(), cmdlineOptions);
        System.exit(-1);
    }

    if (!cmdline.hasOption(INPUT_OPTION_ONE_CHAR)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(DitaDxpUnpacker.class.getSimpleName(), cmdlineOptions);
        System.exit(-1);
    }

    DitaDxpUnpacker app = new DitaDxpUnpacker(cmdline);
    try {
        app.run();
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(1);
    }

}

From source file:gobblin.runtime.util.JobStateToJsonConverter.java

@SuppressWarnings("all")
public static void main(String[] args) throws Exception {
    Option sysConfigOption = Option.builder("sc").argName("system configuration file")
            .desc("Gobblin system configuration file").longOpt("sysconfig").hasArgs().build();
    Option storeUrlOption = Option.builder("u").argName("gobblin state store URL")
            .desc("Gobblin state store root path URL").longOpt("storeurl").hasArgs().required().build();
    Option jobNameOption = Option.builder("n").argName("gobblin job name").desc("Gobblin job name")
            .longOpt("name").hasArgs().required().build();
    Option jobIdOption = Option.builder("i").argName("gobblin job id").desc("Gobblin job id").longOpt("id")
            .hasArgs().build();/* ww w .  j av a 2s  . c  om*/
    Option convertAllOption = Option.builder("a")
            .desc("Whether to convert all past job states of the given job").longOpt("all").build();
    Option keepConfigOption = Option.builder("kc").desc("Whether to keep all configuration properties")
            .longOpt("keepConfig").build();
    Option outputToFile = Option.builder("t").argName("output file name").desc("Output file name")
            .longOpt("toFile").hasArgs().build();

    Options options = new Options();
    options.addOption(sysConfigOption);
    options.addOption(storeUrlOption);
    options.addOption(jobNameOption);
    options.addOption(jobIdOption);
    options.addOption(convertAllOption);
    options.addOption(keepConfigOption);
    options.addOption(outputToFile);

    CommandLine cmd = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cmd = parser.parse(options, args);
    } catch (ParseException pe) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("JobStateToJsonConverter", options);
        System.exit(1);
    }

    Properties sysConfig = new Properties();
    if (cmd.hasOption(sysConfigOption.getLongOpt())) {
        sysConfig = JobConfigurationUtils.fileToProperties(cmd.getOptionValue(sysConfigOption.getLongOpt()));
    }

    JobStateToJsonConverter converter = new JobStateToJsonConverter(sysConfig, cmd.getOptionValue('u'),
            cmd.hasOption("kc"));
    StringWriter stringWriter = new StringWriter();
    if (cmd.hasOption('i')) {
        converter.convert(cmd.getOptionValue('n'), cmd.getOptionValue('i'), stringWriter);
    } else {
        if (cmd.hasOption('a')) {
            converter.convertAll(cmd.getOptionValue('n'), stringWriter);
        } else {
            converter.convert(cmd.getOptionValue('n'), stringWriter);
        }
    }

    if (cmd.hasOption('t')) {
        Closer closer = Closer.create();
        try {
            FileOutputStream fileOutputStream = closer.register(new FileOutputStream(cmd.getOptionValue('t')));
            OutputStreamWriter outputStreamWriter = closer.register(
                    new OutputStreamWriter(fileOutputStream, ConfigurationKeys.DEFAULT_CHARSET_ENCODING));
            BufferedWriter bufferedWriter = closer.register(new BufferedWriter(outputStreamWriter));
            bufferedWriter.write(stringWriter.toString());
        } catch (Throwable t) {
            throw closer.rethrow(t);
        } finally {
            closer.close();
        }
    } else {
        System.out.println(stringWriter.toString());
    }
}