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

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

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From source file:edu.msu.cme.rdp.readseq.utils.QualityTrimmer.java

public static void main(String[] args) throws Exception {
    Options options = new Options();
    options.addOption("f", "fastq-out", false, "Write fastq instead of fasta file");
    options.addOption("l", "less-than", false, "Trim at <= instead of strictly =");
    options.addOption("i", "illumina", false, "Illumina trimming mode");

    FastqWriter fastqOut = null;/*  ww  w .  j av a 2 s .co m*/
    FastaWriter fastaOut = null;

    byte qualTrim = -1;

    boolean writeFasta = true;
    boolean trimle = false;
    boolean illumina = false;

    List<SeqReader> readers = new ArrayList();
    List<File> seqFiles = new ArrayList();

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

        if (line.hasOption("fastq-out")) {
            writeFasta = false;
        }

        if (line.hasOption("less-than")) {
            trimle = true;
        }
        if (line.hasOption("illumina")) {
            illumina = true;
        }

        args = line.getArgs();

        if (args.length < 2) {
            throw new Exception("Unexpected number of arguments");
        }

        if (args[0].length() != 1) {
            throw new Exception("Expected single character quality score");
        }

        qualTrim = FastqCore.Phred33QualFunction.translate(args[0].charAt(0));

        for (int index = 1; index < args.length; index++) {
            File seqFile = new File(args[index]);
            SeqReader reader;
            if (SeqUtils.guessFileFormat(seqFile) == SequenceFormat.FASTA) {
                if (index + 1 == args.length) {
                    throw new Exception("Fasta files must be immediately followed by their quality file");
                }

                File qualFile = new File(args[index + 1]);
                if (SeqUtils.guessFileFormat(qualFile) != SequenceFormat.FASTA) {
                    throw new Exception(seqFile + " was not followed by a fasta quality file");
                }

                reader = new QSeqReader(seqFile, qualFile);
                index++;
            } else {
                if (seqFile.getName().endsWith(".gz")) {
                    reader = new SequenceReader(new GZIPInputStream(new FileInputStream(seqFile)));
                } else {
                    reader = new SequenceReader(seqFile);
                }
            }

            readers.add(reader);
            seqFiles.add(seqFile);
        }
    } catch (Exception e) {
        new HelpFormatter().printHelp("USAGE: QualityTrimmer [options] <ascii_score> <seq_file> [qual_file]",
                options, true);
        System.err.println("Error: " + e.getMessage());
        System.exit(1);
    }

    for (int readerIndex = 0; readerIndex < readers.size(); readerIndex++) {
        File seqFile = seqFiles.get(readerIndex);
        String outStem = "trimmed_" + seqFile.getName().substring(0, seqFile.getName().lastIndexOf("."));
        if (writeFasta) {
            fastaOut = new FastaWriter(outStem + ".fasta");
        } else {
            fastqOut = new FastqWriter(outStem + ".fastq", FastqCore.Phred33QualFunction);
        }

        int[] lengthHisto = new int[200];

        SeqReader reader = readers.get(readerIndex);

        QSequence qseq;

        long totalLength = 0;
        int totalSeqs = 0;
        long trimmedLength = 0;
        int trimmedSeqs = 0;

        int zeroLengthAfterTrimming = 0;

        long startTime = System.currentTimeMillis();

        while ((qseq = (QSequence) reader.readNextSequence()) != null) {
            char[] bases = qseq.getSeqString().toCharArray();
            byte[] qual = qseq.getQuality();

            if (bases.length != qual.length) {
                System.err.println(qseq.getSeqName() + ": Quality length doesn't match seq length for seq");
                continue;
            }

            totalSeqs++;
            totalLength += bases.length;

            int trimIndex = -1;
            if (illumina && qual[bases.length - 1] == qualTrim) {
                trimIndex = bases.length - 1;
                while (trimIndex >= 0 && qual[trimIndex] == qualTrim) {
                    trimIndex--;
                }

                trimIndex++; //Technically we're positioned over the first good base, move back to the last bad base
            } else if (!illumina) {
                for (int index = 0; index < bases.length; index++) {
                    if (qual[index] == qualTrim || (trimle && qual[index] < qualTrim)) {
                        trimIndex = index;
                        break;
                    }
                }
            }

            String outSeq;
            byte[] outQual;
            if (trimIndex == -1) {
                outSeq = qseq.getSeqString();
                outQual = qseq.getQuality();
            } else {
                outSeq = new String(bases, 0, trimIndex);
                outQual = Arrays.copyOfRange(qual, 0, trimIndex);
                trimmedSeqs++;
            }
            int len = outSeq.length();
            trimmedLength += len;

            if (len >= lengthHisto.length) {
                lengthHisto = Arrays.copyOf(lengthHisto, len + 1);
            }
            lengthHisto[len]++;

            if (outSeq.length() == 0) {
                //System.err.println(qseq.getSeqName() + ": length 0 after trimming");
                zeroLengthAfterTrimming++;
                continue;
            }

            if (writeFasta) {
                fastaOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq);
            } else {
                fastqOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq, outQual);
            }
        }

        reader.close();

        if (writeFasta) {
            fastaOut.close();
        } else {
            fastqOut.close();
        }

        System.out.println(
                "Processed " + seqFile + " in " + (System.currentTimeMillis() - startTime) / 1000.0 + "s");
        System.out.println("Before trimming:");
        System.out.println("Total Sequences:           " + totalSeqs);
        System.out.println("Total Sequence Data:       " + totalLength);
        System.out.println("Average sequence length:   " + ((float) totalLength / totalSeqs));
        System.out.println();
        System.out.println("After trimming:");
        System.out.println("Total Sequences:           " + (totalSeqs - zeroLengthAfterTrimming));
        System.out.println("Sequences Trimmed:         " + trimmedSeqs);
        System.out.println("Total Sequence Data:       " + trimmedLength);
        System.out.println("Average sequence length:   "
                + ((float) trimmedLength / (totalSeqs - zeroLengthAfterTrimming)));
        System.out.println();

        System.out.println("Length\tCount");
        for (int index = 0; index < lengthHisto.length; index++) {
            if (lengthHisto[index] == 0) {
                continue;
            }

            System.out.println(index + "\t" + lengthHisto[index]);
        }

        System.out.println();
        System.out.println();
        System.out.println();
    }
}

From source file:com.alibaba.rocketmq.example.benchmark.Consumer.java

public static void main(String[] args) throws MQClientException {
    Options options = ServerUtil.buildCommandlineOptions(new Options());
    CommandLine commandLine = ServerUtil.parseCmdLine("benchmarkConsumer", args,
            buildCommandlineOptions(options), new PosixParser());
    if (null == commandLine) {
        System.exit(-1);/*from   w  w  w.j a  va 2 s  .c om*/
    }

    final String topic = commandLine.hasOption('t') ? commandLine.getOptionValue('t').trim() : "BenchmarkTest";
    final String groupPrefix = commandLine.hasOption('g') ? commandLine.getOptionValue('g').trim()
            : "benchmark_consumer";
    final String isPrefixEnable = commandLine.hasOption('p') ? commandLine.getOptionValue('p').trim() : "true";
    String group = groupPrefix;
    if (Boolean.parseBoolean(isPrefixEnable)) {
        group = groupPrefix + "_" + Long.toString(System.currentTimeMillis() % 100);
    }

    System.out.printf("topic %s group %s prefix %s%n", topic, group, isPrefixEnable);

    final StatsBenchmarkConsumer statsBenchmarkConsumer = new StatsBenchmarkConsumer();

    final Timer timer = new Timer("BenchmarkTimerThread", true);

    final LinkedList<Long[]> snapshotList = new LinkedList<Long[]>();

    timer.scheduleAtFixedRate(new TimerTask() {
        @Override
        public void run() {
            snapshotList.addLast(statsBenchmarkConsumer.createSnapshot());
            if (snapshotList.size() > 10) {
                snapshotList.removeFirst();
            }
        }
    }, 1000, 1000);

    timer.scheduleAtFixedRate(new TimerTask() {
        private void printStats() {
            if (snapshotList.size() >= 10) {
                Long[] begin = snapshotList.getFirst();
                Long[] end = snapshotList.getLast();

                final long consumeTps = (long) (((end[1] - begin[1]) / (double) (end[0] - begin[0])) * 1000L);
                final double averageB2CRT = (end[2] - begin[2]) / (double) (end[1] - begin[1]);
                final double averageS2CRT = (end[3] - begin[3]) / (double) (end[1] - begin[1]);

                System.out.printf(
                        "Consume TPS: %d Average(B2C) RT: %7.3f Average(S2C) RT: %7.3f MAX(B2C) RT: %d MAX(S2C) RT: %d%n",
                        consumeTps, averageB2CRT, averageS2CRT, end[4], end[5]);
            }
        }

        @Override
        public void run() {
            try {
                this.printStats();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }, 10000, 10000);

    DefaultMQPushConsumer consumer = new DefaultMQPushConsumer(group);
    consumer.setInstanceName(Long.toString(System.currentTimeMillis()));

    consumer.subscribe(topic, "*");

    consumer.registerMessageListener(new MessageListenerConcurrently() {
        @Override
        public ConsumeConcurrentlyStatus consumeMessage(List<MessageExt> msgs,
                ConsumeConcurrentlyContext context) {
            MessageExt msg = msgs.get(0);
            long now = System.currentTimeMillis();

            statsBenchmarkConsumer.getReceiveMessageTotalCount().incrementAndGet();

            long born2ConsumerRT = now - msg.getBornTimestamp();
            statsBenchmarkConsumer.getBorn2ConsumerTotalRT().addAndGet(born2ConsumerRT);

            long store2ConsumerRT = now - msg.getStoreTimestamp();
            statsBenchmarkConsumer.getStore2ConsumerTotalRT().addAndGet(store2ConsumerRT);

            compareAndSetMax(statsBenchmarkConsumer.getBorn2ConsumerMaxRT(), born2ConsumerRT);

            compareAndSetMax(statsBenchmarkConsumer.getStore2ConsumerMaxRT(), store2ConsumerRT);

            return ConsumeConcurrentlyStatus.CONSUME_SUCCESS;
        }
    });

    consumer.start();

    System.out.printf("Consumer Started.%n");
}

From source file:edu.cmu.lti.oaqa.annographix.apps.SolrSimpleIndexApp.java

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

    options.addOption("i", null, true, "Input File");
    options.addOption("u", null, true, "Solr URI");
    options.addOption("n", null, true, "Batch size");

    CommandLineParser parser = new org.apache.commons.cli.GnuParser();

    try {//w  w  w  .  ja v a 2s  . com
        CommandLine cmd = parser.parse(options, args);

        if (cmd.hasOption("i")) {
            inputFile = cmd.getOptionValue("i");
        } else {
            Usage("Specify Input File");
        }

        if (cmd.hasOption("u")) {
            solrURI = cmd.getOptionValue("u");
        } else {
            Usage("Specify Solr URI");
        }

        if (cmd.hasOption("n")) {
            batchQty = Integer.parseInt(cmd.getOptionValue("n"));
        }

        SolrServerWrapper solrServer = new SolrServerWrapper(solrURI);

        BufferedReader inpText = new BufferedReader(
                new InputStreamReader(CompressUtils.createInputStream(inputFile)));

        XmlHelper xmlHlp = new XmlHelper();

        String docText = XmlHelper.readNextXMLIndexEntry(inpText);

        for (int docNum = 1; docText != null; ++docNum, docText = XmlHelper.readNextXMLIndexEntry(inpText)) {

            // 1. Read document text
            Map<String, String> docFields = null;
            HashMap<String, Object> objDocFields = new HashMap<String, Object>();

            try {
                docFields = xmlHlp.parseXMLIndexEntry(docText);
            } catch (SAXException e) {
                System.err.println("Parsing error, offending DOC:" + NL + docText);
                throw new Exception("Parsing error.");
            }

            for (Map.Entry<String, String> e : docFields.entrySet()) {
                //System.out.println(e.getKey() + " " + e.getValue());
                objDocFields.put(e.getKey(), e.getValue());
            }

            solrServer.indexDocument(objDocFields);
            if ((docNum - 1) % batchQty == 0)
                solrServer.indexCommit();
        }
        solrServer.indexCommit();

    } catch (ParseException e) {
        Usage("Cannot parse arguments");
    } catch (Exception e) {
        System.err.println("Terminating due to an exception: " + e);
        System.exit(1);
    }

}

From source file:com.aerospike.client.rest.AerospikeRESTfulService.java

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

    Options options = new Options();
    options.addOption("h", "host", true, "Server hostname (default: localhost)");
    options.addOption("p", "port", true, "Server port (default: 3000)");

    // parse the command line args
    CommandLineParser parser = new PosixParser();
    CommandLine cl = parser.parse(options, args, false);

    // set properties
    Properties as = System.getProperties();
    String host = cl.getOptionValue("h", "localhost");
    as.put("seedHost", host);
    String portString = cl.getOptionValue("p", "3000");
    as.put("port", portString);

    // start app/*from w  ww  .j a  va 2s.c  o  m*/
    SpringApplication.run(AerospikeRESTfulService.class, args);

}

From source file:com.akana.demo.freemarker.templatetester.App.java

public static void main(String[] args) {

    final Options options = new Options();

    @SuppressWarnings("static-access")
    Option optionContentType = OptionBuilder.withArgName("content-type").hasArg()
            .withDescription("content type of model").create("content");
    @SuppressWarnings("static-access")
    Option optionUrlPath = OptionBuilder.withArgName("httpRequestLine").hasArg()
            .withDescription("url path and parameters in HTTP Request Line format").create("url");
    @SuppressWarnings("static-access")
    Option optionRootMessageName = OptionBuilder.withArgName("messageName").hasArg()
            .withDescription("root data object name, defaults to 'message'").create("root");
    @SuppressWarnings("static-access")
    Option optionAdditionalMessages = OptionBuilder.withArgName("dataModelPaths")
            .hasArgs(Option.UNLIMITED_VALUES).withDescription("additional message object data sources")
            .create("messages");
    @SuppressWarnings("static-access")
    Option optionDebugMessages = OptionBuilder.hasArg(false)
            .withDescription("Shows debug information about template processing").create("debug");

    Option optionHelp = new Option("help", "print this message");

    options.addOption(optionHelp);/*from   www. j av  a  2 s .c o m*/
    options.addOption(optionContentType);
    options.addOption(optionUrlPath);
    options.addOption(optionRootMessageName);
    options.addOption(optionAdditionalMessages);
    options.addOption(optionDebugMessages);

    CommandLineParser parser = new DefaultParser();

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

        // Check for help flag
        if (cmd.hasOption("help")) {
            showHelp(options);
            return;
        }

        String[] remainingArguments = cmd.getArgs();
        if (remainingArguments.length < 2) {
            showHelp(options);
            return;
        }
        String ftlPath, dataPath = "none";

        ftlPath = remainingArguments[0];
        dataPath = remainingArguments[1];

        String contentType = "text/xml";
        // Discover content type from file extension
        String ext = FilenameUtils.getExtension(dataPath);
        if (ext.equals("json")) {
            contentType = "json";
        } else if (ext.equals("txt")) {
            contentType = "txt";
        }
        // Override discovered content type
        if (cmd.hasOption("content")) {
            contentType = cmd.getOptionValue("content");
        }
        // Root data model name
        String rootMessageName = "message";
        if (cmd.hasOption("root")) {
            rootMessageName = cmd.getOptionValue("root");
        }
        // Additional data models
        String[] additionalModels = new String[0];
        if (cmd.hasOption("messages")) {
            additionalModels = cmd.getOptionValues("messages");
        }
        // Debug Info
        if (cmd.hasOption("debug")) {
            System.out.println(" Processing ftl   : " + ftlPath);
            System.out.println("   with data model: " + dataPath);
            System.out.println(" with content-type: " + contentType);
            System.out.println(" data model object: " + rootMessageName);
            if (cmd.hasOption("messages")) {
                System.out.println("additional models: " + additionalModels.length);
            }
        }

        Configuration cfg = new Configuration(Configuration.VERSION_2_3_23);
        cfg.setDirectoryForTemplateLoading(new File("."));
        cfg.setDefaultEncoding("UTF-8");
        cfg.setTemplateExceptionHandler(TemplateExceptionHandler.RETHROW_HANDLER);

        /* Create the primary data-model */
        Map<String, Object> message = new HashMap<String, Object>();
        if (contentType.contains("json") || contentType.contains("txt")) {
            message.put("contentAsString",
                    FileUtils.readFileToString(new File(dataPath), StandardCharsets.UTF_8));
        } else {
            message.put("contentAsXml", freemarker.ext.dom.NodeModel.parse(new File(dataPath)));
        }

        if (cmd.hasOption("url")) {
            message.put("getProperty", new AkanaGetProperty(cmd.getOptionValue("url")));
        }

        Map<String, Object> root = new HashMap<String, Object>();
        root.put(rootMessageName, message);
        if (additionalModels.length > 0) {
            for (int i = 0; i < additionalModels.length; i++) {
                Map<String, Object> m = createMessageFromFile(additionalModels[i], contentType);
                root.put("message" + i, m);
            }
        }

        /* Get the template (uses cache internally) */
        Template temp = cfg.getTemplate(ftlPath);

        /* Merge data-model with template */
        Writer out = new OutputStreamWriter(System.out);
        temp.process(root, out);

    } catch (ParseException e) {
        showHelp(options);
        System.exit(1);
    } catch (IOException e) {
        System.out.println("Unable to parse ftl.");
        e.printStackTrace();
    } catch (SAXException e) {
        System.out.println("XML parsing issue.");
        e.printStackTrace();
    } catch (ParserConfigurationException e) {
        System.out.println("Unable to configure parser.");
        e.printStackTrace();
    } catch (TemplateException e) {
        System.out.println("Unable to parse template.");
        e.printStackTrace();
    }

}

From source file:com.guye.baffle.obfuscate.Main.java

public static void main(String[] args) throws IOException, BaffleException {
    Options opt = new Options();

    opt.addOption("c", "config", true, "config file path,keep or mapping");

    opt.addOption("o", "output", true, "output mapping writer file");

    opt.addOption("v", "verbose", false, "explain what is being done.");

    opt.addOption("h", "help", false, "print help for the command.");

    opt.getOption("c").setArgName("file list");

    opt.getOption("o").setArgName("file path");

    String formatstr = "baffle [-c/--config filepaths list ][-o/--output filepath][-h/--help] ApkFile TargetApkFile";

    HelpFormatter formatter = new HelpFormatter();
    CommandLineParser parser = new PosixParser();
    CommandLine cl = null;/*from w  w w  .  j av a2s .com*/
    try {
        // ?Options?
        cl = parser.parse(opt, args);

    } catch (ParseException e) {
        formatter.printHelp(formatstr, opt); // ???
        return;
    }

    if (cl == null || cl.getArgs() == null || cl.getArgs().length == 0) {
        formatter.printHelp(formatstr, opt);
        return;
    }

    // ?-h--help??
    if (cl.hasOption("h")) {
        HelpFormatter hf = new HelpFormatter();
        hf.printHelp(formatstr, "", opt, "");
        return;
    }

    // ???DirectoryName
    String[] str = cl.getArgs();
    if (str == null || str.length != 2) {
        HelpFormatter hf = new HelpFormatter();
        hf.printHelp("not specify apk file or taget apk file", opt);
        return;
    }

    if (str[1].equals(str[0])) {
        HelpFormatter hf = new HelpFormatter();
        hf.printHelp("apk file can not rewrite , please specify new target file", opt);
        return;
    }
    File apkFile = new File(str[0]);
    if (!apkFile.exists()) {
        HelpFormatter hf = new HelpFormatter();
        hf.printHelp("apk file not exists", opt);
        return;
    }

    File[] configs = null;
    if (cl.hasOption("c")) {
        String cfg = cl.getOptionValue("c");
        String[] fs = cfg.split(",");
        int len = fs.length;
        configs = new File[fs.length];
        for (int i = 0; i < len; i++) {
            configs[i] = new File(fs[i]);
            if (!configs[i].exists()) {
                HelpFormatter hf = new HelpFormatter();
                hf.printHelp("config file " + fs[i] + " not exists", opt);
                return;
            }
        }
    }

    File mappingfile = null;
    if (cl.hasOption("o")) {
        String mfile = cl.getOptionValue("o");
        mappingfile = new File(mfile);

        if (mappingfile.getParentFile() != null) {
            mappingfile.getParentFile().mkdirs();
        }

    }

    if (cl.hasOption('v')) {
        Logger.getLogger(Obfuscater.LOG_NAME).setLevel(Level.CONFIG);
    } else {
        Logger.getLogger(Obfuscater.LOG_NAME).setLevel(Level.OFF);
    }

    Logger.getLogger(Obfuscater.LOG_NAME).addHandler(new ConsoleHandler());

    Obfuscater obfuscater = new Obfuscater(configs, mappingfile, apkFile, str[1]);

    obfuscater.obfuscate();
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.CdoQueryRenameAllMethods.java

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

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input CDO resource directory");
    inputOpt.setArgs(1);//  www.  j  a  va 2 s .  c o m
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option repoOpt = OptionBuilder.create(REPO_NAME);
    repoOpt.setArgName("REPO_NAME");
    repoOpt.setDescription("CDO Repository name");
    repoOpt.setArgs(1);
    repoOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);
    options.addOption(repoOpt);

    CommandLineParser parser = new PosixParser();

    try {
        CommandLine commandLine = parser.parse(options, args);

        String repositoryDir = commandLine.getOptionValue(IN);
        String repositoryName = commandLine.getOptionValue(REPO_NAME);

        Class<?> inClazz = CdoQueryRenameAllMethods.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        EmbeddedCDOServer server = new EmbeddedCDOServer(repositoryDir, repositoryName);
        try {
            server.run();
            CDOSession session = server.openSession();
            ((CDONet4jSession) session).options().setCommitTimeout(50 * 1000);
            CDOTransaction transaction = session.openTransaction();
            Resource resource = transaction.getRootResource();

            String name = UUID.randomUUID().toString();
            {
                LOG.log(Level.INFO, "Start query");
                long begin = System.currentTimeMillis();
                JavaQueries.renameAllMethods(resource, name);
                long end = System.currentTimeMillis();
                transaction.commit();
                LOG.log(Level.INFO, "End query");
                LOG.log(Level.INFO,
                        MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
            }

            //            {
            //               transaction.close();
            //               session.close();
            //               
            //               session = server.openSession();
            //               transaction = session.openTransaction();
            //               resource = transaction.getRootResource();
            //               
            //               EList<? extends EObject> methodList = JavaQueries.getAllInstances(resource, JavaPackage.eINSTANCE.getMethodDeclaration());
            //               int i = 0;
            //               for (EObject eObject: methodList) {
            //                  MethodDeclaration method = (MethodDeclaration) eObject;
            //                  if (name.equals(method.getName())) {
            //                     i++;
            //                  }
            //               }
            //               LOG.log(Level.INFO, MessageFormat.format("Renamed {0} methods", i));
            //            }

            transaction.close();
            session.close();
        } finally {
            server.stop();
        }
    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:com.redhat.poc.jdg.bankofchina.function.TestCase413RemoteMultiThreads.java

public static void main(String[] args) throws Exception {
    CommandLine commandLine;//from   www . j  a  v  a  2  s.co m
    Options options = new Options();
    options.addOption("s", true, "The start csv file number option");
    options.addOption("e", true, "The end csv file number option");
    BasicParser parser = new BasicParser();
    parser.parse(options, args);
    commandLine = parser.parse(options, args);
    if (commandLine.getOptions().length > 0) {
        if (commandLine.hasOption("s")) {
            String start = commandLine.getOptionValue("s");
            if (start != null && start.length() > 0) {
                csvFileStart = Integer.parseInt(start);
            }
        }
        if (commandLine.hasOption("e")) {
            String end = commandLine.getOptionValue("e");
            if (end != null && end.length() > 0) {
                csvFileEnd = Integer.parseInt(end);
            }
        }
    }

    System.out.println(
            "%%%%%%%%%  csv ?, ?, ?(ms),"
                    + new Date().getTime());
    for (int i = csvFileStart; i <= csvFileEnd; i++) {
        new TestCase413RemoteMultiThreads(i).start();
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.CdoQueryInvisibleMethodDeclarations.java

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

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input CDO resource directory");
    inputOpt.setArgs(1);/*from  w ww  .  ja  va  2s.c o  m*/
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option repoOpt = OptionBuilder.create(REPO_NAME);
    repoOpt.setArgName("REPO_NAME");
    repoOpt.setDescription("CDO Repository name");
    repoOpt.setArgs(1);
    repoOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);
    options.addOption(repoOpt);

    CommandLineParser parser = new PosixParser();

    try {
        CommandLine commandLine = parser.parse(options, args);

        String repositoryDir = commandLine.getOptionValue(IN);
        String repositoryName = commandLine.getOptionValue(REPO_NAME);

        Class<?> inClazz = CdoQueryInvisibleMethodDeclarations.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        EmbeddedCDOServer server = new EmbeddedCDOServer(repositoryDir, repositoryName);
        try {
            server.run();
            CDOSession session = server.openSession();
            CDOTransaction transaction = session.openTransaction();
            Resource resource = transaction.getRootResource();

            {
                LOG.log(Level.INFO, "Start query");
                long begin = System.currentTimeMillis();
                EList<MethodDeclaration> list = JavaQueries.getInvisibleMethodDeclarations(resource);
                long end = System.currentTimeMillis();
                LOG.log(Level.INFO, "End query");
                LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size()));
                LOG.log(Level.INFO,
                        MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
            }

            transaction.close();
            session.close();
        } finally {
            server.stop();
        }
    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:com.redhat.poc.jdg.bankofchina.function.TestCase412RemoteMultiThreads.java

public static void main(String[] args) throws Exception {
    CommandLine commandLine;/*from  w ww.  j  a  va  2 s  . co  m*/
    Options options = new Options();
    options.addOption("s", true, "The start csv file number option");
    options.addOption("e", true, "The end csv file number option");
    BasicParser parser = new BasicParser();
    parser.parse(options, args);
    commandLine = parser.parse(options, args);
    if (commandLine.getOptions().length > 0) {
        if (commandLine.hasOption("s")) {
            String start = commandLine.getOptionValue("s");
            if (start != null && start.length() > 0) {
                csvFileStart = Integer.parseInt(start);
            }
        }
        if (commandLine.hasOption("e")) {
            String end = commandLine.getOptionValue("e");
            if (end != null && end.length() > 0) {
                csvFileEnd = Integer.parseInt(end);
            }
        }
    }

    System.out.println(
            "%%%%%%%%%  csv ?, ?, ?(ms),"
                    + new Date().getTime());
    for (int i = csvFileStart; i <= csvFileEnd; i++) {
        new TestCase412RemoteMultiThreads(i).start();
    }
}