Example usage for java.lang Long parseLong

List of usage examples for java.lang Long parseLong

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Introduction

In this page you can find the example usage for java.lang Long parseLong.

Prototype

public static long parseLong(String s) throws NumberFormatException

Source Link

Document

Parses the string argument as a signed decimal long .

Usage

From source file:com.github.sdnwiselab.sdnwise.mote.standalone.Loader.java

/**
 * @param args the command line arguments
 *///w  ww  . j av  a  2 s. com
public static void main(final String[] args) {
    Options options = new Options();
    options.addOption(Option.builder("n").argName("net").hasArg().required().desc("Network ID of the node")
            .numberOfArgs(1).build());
    options.addOption(Option.builder("a").argName("address").hasArg().required()
            .desc("Address of the node <0-65535>").numberOfArgs(1).build());
    options.addOption(Option.builder("p").argName("port").hasArg().required().desc("Listening UDP port")
            .numberOfArgs(1).build());
    options.addOption(Option.builder("t").argName("filename").hasArg().required()
            .desc("Use given file for neighbors discovery").numberOfArgs(1).build());
    options.addOption(Option.builder("c").argName("ip:port").hasArg()
            .desc("IP address and TCP port of the controller. (SINK ONLY)").numberOfArgs(1).build());
    options.addOption(Option.builder("sp").argName("port").hasArg()
            .desc("Port number of the switch. (SINK ONLY)").numberOfArgs(1).build());
    options.addOption(Option.builder("sm").argName("mac").hasArg()
            .desc("MAC address of the switch. Example: <00:00:00:00:00:00>." + " (SINK ONLY)").numberOfArgs(1)
            .build());
    options.addOption(Option.builder("sd").argName("dpid").hasArg().desc("DPID of the switch (SINK ONLY)")
            .numberOfArgs(1).build());
    options.addOption(Option.builder("l").argName("level").hasArg()
            .desc("Use given log level. Values: SEVERE, WARNING, INFO, " + "CONFIG, FINE, FINER, FINEST.")
            .numberOfArgs(1).optionalArg(true).build());

    // create the parser
    CommandLineParser parser = new DefaultParser();
    try {
        CommandLine line = parser.parse(options, args);
        Thread th;

        byte cmdNet = (byte) Integer.parseInt(line.getOptionValue("n"));
        NodeAddress cmdAddress = new NodeAddress(Integer.parseInt(line.getOptionValue("a")));
        int cmdPort = Integer.parseInt(line.getOptionValue("p"));
        String cmdTopo = line.getOptionValue("t");

        String cmdLevel;

        if (!line.hasOption("l")) {
            cmdLevel = "SEVERE";
        } else {
            cmdLevel = line.getOptionValue("l");
        }

        if (line.hasOption("c")) {

            if (!line.hasOption("sd")) {
                throw new ParseException("-sd option missing");
            }
            if (!line.hasOption("sp")) {
                throw new ParseException("-sp option missing");
            }
            if (!line.hasOption("sm")) {
                throw new ParseException("-sm option missing");
            }

            String cmdSDpid = line.getOptionValue("sd");
            String cmdSMac = line.getOptionValue("sm");
            long cmdSPort = Long.parseLong(line.getOptionValue("sp"));
            String[] ipport = line.getOptionValue("c").split(":");
            th = new Thread(new Sink(cmdNet, cmdAddress, cmdPort,
                    new InetSocketAddress(ipport[0], Integer.parseInt(ipport[1])), cmdTopo, cmdLevel, cmdSDpid,
                    cmdSMac, cmdSPort));
        } else {
            th = new Thread(new Mote(cmdNet, cmdAddress, cmdPort, cmdTopo, cmdLevel));
        }
        th.start();
        th.join();
    } catch (InterruptedException | ParseException ex) {
        System.out.println("Parsing failed.  Reason: " + ex.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("sdn-wise-data -n id -a address -p port"
                + " -t filename [-l level] [-sd dpid -sm mac -sp port]", options);
    }
}

From source file:com.tamingtext.tagging.LuceneTagExtractor.java

public static void main(String[] args) throws IOException {
    DefaultOptionBuilder obuilder = new DefaultOptionBuilder();
    ArgumentBuilder abuilder = new ArgumentBuilder();
    GroupBuilder gbuilder = new GroupBuilder();

    Option inputOpt = obuilder.withLongName("dir").withRequired(true)
            .withArgument(abuilder.withName("dir").withMinimum(1).withMaximum(1).create())
            .withDescription("The Lucene directory").withShortName("d").create();

    Option outputOpt = obuilder.withLongName("output").withRequired(false)
            .withArgument(abuilder.withName("output").withMinimum(1).withMaximum(1).create())
            .withDescription("The output directory").withShortName("o").create();

    Option maxOpt = obuilder.withLongName("max").withRequired(false)
            .withArgument(abuilder.withName("max").withMinimum(1).withMaximum(1).create())
            .withDescription(/*from   www  .  j ava2  s .  com*/
                    "The maximum number of vectors to output.  If not specified, then it will loop over all docs")
            .withShortName("m").create();

    Option fieldOpt = obuilder.withLongName("field").withRequired(true)
            .withArgument(abuilder.withName("field").withMinimum(1).withMaximum(1).create())
            .withDescription("The field in the index").withShortName("f").create();

    Option helpOpt = obuilder.withLongName("help").withDescription("Print out help").withShortName("h")
            .create();

    Group group = gbuilder.withName("Options").withOption(inputOpt).withOption(outputOpt).withOption(maxOpt)
            .withOption(fieldOpt).create();

    try {
        Parser parser = new Parser();
        parser.setGroup(group);
        CommandLine cmdLine = parser.parse(args);

        if (cmdLine.hasOption(helpOpt)) {
            CommandLineUtil.printHelp(group);
            return;
        }

        File file = new File(cmdLine.getValue(inputOpt).toString());

        if (!file.isDirectory()) {
            throw new IllegalArgumentException(file + " does not exist or is not a directory");
        }

        long maxDocs = Long.MAX_VALUE;
        if (cmdLine.hasOption(maxOpt)) {
            maxDocs = Long.parseLong(cmdLine.getValue(maxOpt).toString());
        }

        if (maxDocs < 0) {
            throw new IllegalArgumentException("maxDocs must be >= 0");
        }

        String field = cmdLine.getValue(fieldOpt).toString();

        PrintWriter out = null;
        if (cmdLine.hasOption(outputOpt)) {
            out = new PrintWriter(new FileWriter(cmdLine.getValue(outputOpt).toString()));
        } else {
            out = new PrintWriter(new OutputStreamWriter(System.out, "UTF-8"));
        }

        File output = new File("/home/drew/taming-text/delicious/training");
        output.mkdirs();

        emitTextForTags(file, output);

        IOUtils.close(Collections.singleton(out));
    } catch (OptionException e) {
        log.error("Exception", e);
        CommandLineUtil.printHelp(group);
    }

}

From source file:com.tamingtext.tagging.LuceneCategoryExtractor.java

public static void main(String[] args) throws IOException {
    DefaultOptionBuilder obuilder = new DefaultOptionBuilder();
    ArgumentBuilder abuilder = new ArgumentBuilder();
    GroupBuilder gbuilder = new GroupBuilder();

    Option inputOpt = obuilder.withLongName("dir").withRequired(true)
            .withArgument(abuilder.withName("dir").withMinimum(1).withMaximum(1).create())
            .withDescription("The Lucene directory").withShortName("d").create();

    Option outputOpt = obuilder.withLongName("output").withRequired(false)
            .withArgument(abuilder.withName("output").withMinimum(1).withMaximum(1).create())
            .withDescription("The output directory").withShortName("o").create();

    Option maxOpt = obuilder.withLongName("max").withRequired(false)
            .withArgument(abuilder.withName("max").withMinimum(1).withMaximum(1).create())
            .withDescription(//from www  .  java 2s  . c o m
                    "The maximum number of documents to analyze.  If not specified, then it will loop over all docs")
            .withShortName("m").create();

    Option fieldOpt = obuilder.withLongName("field").withRequired(true)
            .withArgument(abuilder.withName("field").withMinimum(1).withMaximum(1).create())
            .withDescription("The field in the index").withShortName("f").create();

    Option helpOpt = obuilder.withLongName("help").withDescription("Print out help").withShortName("h")
            .create();

    Group group = gbuilder.withName("Options").withOption(inputOpt).withOption(outputOpt).withOption(maxOpt)
            .withOption(fieldOpt).create();

    try {
        Parser parser = new Parser();
        parser.setGroup(group);
        CommandLine cmdLine = parser.parse(args);

        if (cmdLine.hasOption(helpOpt)) {
            CommandLineUtil.printHelp(group);
            return;
        }

        File inputDir = new File(cmdLine.getValue(inputOpt).toString());

        if (!inputDir.isDirectory()) {
            throw new IllegalArgumentException(inputDir + " does not exist or is not a directory");
        }

        long maxDocs = Long.MAX_VALUE;
        if (cmdLine.hasOption(maxOpt)) {
            maxDocs = Long.parseLong(cmdLine.getValue(maxOpt).toString());
        }

        if (maxDocs < 0) {
            throw new IllegalArgumentException("maxDocs must be >= 0");
        }

        String field = cmdLine.getValue(fieldOpt).toString();

        PrintWriter out = null;
        if (cmdLine.hasOption(outputOpt)) {
            out = new PrintWriter(new FileWriter(cmdLine.getValue(outputOpt).toString()));
        } else {
            out = new PrintWriter(new OutputStreamWriter(System.out, "UTF-8"));
        }

        dumpDocumentFields(inputDir, field, maxDocs, out);

        IOUtils.close(Collections.singleton(out));
    } catch (OptionException e) {
        log.error("Exception", e);
        CommandLineUtil.printHelp(group);
    }

}

From source file:com.bt.aloha.batchtest.WeekendBatchTest.java

public static void main(String[] args) throws Exception {
    ClassPathXmlApplicationContext ctx = new ClassPathXmlApplicationContext("batchTestApplicationContext.xml");
    BatchTest batchTest = (BatchTest) ctx.getBean("batchTestBean");
    batchTest.setApplicationContext(ctx);
    batchTest.init();// w  w w.ja v a2s.  c o  m
    batchTest.assignNewCollectionsToBeans();

    while (true) {
        configure(batchTest);
        if (stop)
            break;
        batchTest.run();
        logStatistics(log, batchTest);
        batchTest.reset();
        if (sleepTime > 0) {
            log.info(String.format("sleeping for %d minutes", sleepTime / 60 / 1000));
            Thread.sleep(sleepTime);
        }
    }
    // wait until all things in collection should be ready for housekeeping
    Properties batchProps = new Properties();
    InputStream is = batchTest.getClass().getResourceAsStream("/batchrun.sip.properties");
    batchProps.load(is);
    is.close();
    Thread.sleep(Long.parseLong(batchProps.getProperty("dialog.max.time.to.live", "900000"))
            + Long.parseLong(batchProps.getProperty("housekeeping.interval", "300000")));
    // housekeeping should have happend
    // log out all things still left
    logCollections(batchTest);

    batchTest.destroy();
}

From source file:cc.twittertools.search.api.SearchStatusesThrift.java

@SuppressWarnings("static-access")
public static void main(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(new Option(HELP_OPTION, "show help"));
    options.addOption(OptionBuilder.withArgName("string").hasArg().withDescription("host").create(HOST_OPTION));
    options.addOption(OptionBuilder.withArgName("port").hasArg().withDescription("port").create(PORT_OPTION));
    options.addOption(/* ww w  .  ja v  a 2 s .com*/
            OptionBuilder.withArgName("string").hasArg().withDescription("query id").create(QID_OPTION));
    options.addOption(
            OptionBuilder.withArgName("string").hasArg().withDescription("query text").create(QUERY_OPTION));
    options.addOption(
            OptionBuilder.withArgName("string").hasArg().withDescription("runtag").create(RUNTAG_OPTION));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("maxid").create(MAX_ID_OPTION));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("number of results to return")
            .create(NUM_RESULTS_OPTION));
    options.addOption(
            OptionBuilder.withArgName("string").hasArg().withDescription("group id").create(GROUP_OPTION));
    options.addOption(
            OptionBuilder.withArgName("string").hasArg().withDescription("access token").create(TOKEN_OPTION));
    options.addOption(new Option(VERBOSE_OPTION, "print out complete document"));

    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();
    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        System.exit(-1);
    }

    if (cmdline.hasOption(HELP_OPTION) || !cmdline.hasOption(HOST_OPTION) || !cmdline.hasOption(PORT_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(SearchStatusesThrift.class.getName(), options);
        System.exit(-1);
    }

    String qid = cmdline.hasOption(QID_OPTION) ? cmdline.getOptionValue(QID_OPTION) : DEFAULT_QID;
    String query = cmdline.hasOption(QUERY_OPTION) ? cmdline.getOptionValue(QUERY_OPTION) : DEFAULT_Q;
    String runtag = cmdline.hasOption(RUNTAG_OPTION) ? cmdline.getOptionValue(RUNTAG_OPTION) : DEFAULT_RUNTAG;
    long maxId = cmdline.hasOption(MAX_ID_OPTION) ? Long.parseLong(cmdline.getOptionValue(MAX_ID_OPTION))
            : DEFAULT_MAX_ID;
    int numResults = cmdline.hasOption(NUM_RESULTS_OPTION)
            ? Integer.parseInt(cmdline.getOptionValue(NUM_RESULTS_OPTION))
            : DEFAULT_NUM_RESULTS;
    boolean verbose = cmdline.hasOption(VERBOSE_OPTION);

    String group = cmdline.hasOption(GROUP_OPTION) ? cmdline.getOptionValue(GROUP_OPTION) : null;
    String token = cmdline.hasOption(TOKEN_OPTION) ? cmdline.getOptionValue(TOKEN_OPTION) : null;
    TrecSearchThriftClient client = new TrecSearchThriftClient(cmdline.getOptionValue(HOST_OPTION),
            Integer.parseInt(cmdline.getOptionValue(PORT_OPTION)), group, token);

    System.err.println("qid: " + qid);
    System.err.println("q: " + query);
    System.err.println("max_id: " + maxId);
    System.err.println("num_results: " + numResults);

    PrintStream out = new PrintStream(System.out, true, "UTF-8");

    List<TResult> results = client.search(query, maxId, numResults);
    int i = 1;
    for (TResult result : results) {
        out.println(String.format("%s Q0 %d %d %f %s", qid, result.id, i, result.rsv, runtag));
        if (verbose) {
            System.out.println("# " + result.toString().replaceAll("[\\n\\r]+", " "));
        }
        i++;
    }
    out.close();
}

From source file:com.act.biointerpretation.mechanisminspection.ReactionValidator.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*  ww  w. ja  va  2  s. c om*/
    }

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

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(ReactionDesalter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    NoSQLAPI api = new NoSQLAPI(cl.getOptionValue(OPTION_READ_DB), cl.getOptionValue(OPTION_READ_DB));
    MechanisticValidator validator = new MechanisticValidator(api);
    validator.init();

    Map<Integer, List<Ero>> results = validator
            .validateOneReaction(Long.parseLong(cl.getOptionValue(OPTION_RXN_ID)));

    if (results == null) {
        System.out.format("ERROR: validation results are null.\n");
    } else if (results.size() == 0) {
        System.out.format("No matching EROs were found for the specified reaction.\n");
    } else {
        for (Map.Entry<Integer, List<Ero>> entry : results.entrySet()) {
            List<String> eroIds = entry.getValue().stream().map(x -> x.getId().toString())
                    .collect(Collectors.toList());
            System.out.format("%d: %s\n", entry.getKey(), StringUtils.join(eroIds, ", "));
        }
    }
}

From source file:contract_net.main.java

/**
 * Starts the {@link main}.//from  w ww .j a v  a  2 s  .  co m
 * @param args The first option may optionally indicate the end time of the
 *          simulation.
 */
public static void main(@Nullable String[] args) {
    final long endTime = args != null && args.length >= 1 ? Long.parseLong(args[0]) : Long.MAX_VALUE;

    final String graphFile = args != null && args.length >= 2 ? args[1] : MAP_FILE;
    run(true, endTime, graphFile, null /* new Display() */, null, null);
}

From source file:org.apache.s4.MainApp.java

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

    options.addOption(OptionBuilder.withArgName("corehome").hasArg().withDescription("core home").create("c"));

    options.addOption(/*from  ww w  . j  ava 2 s . com*/
            OptionBuilder.withArgName("appshome").hasArg().withDescription("applications home").create("a"));

    options.addOption(OptionBuilder.withArgName("s4clock").hasArg().withDescription("s4 clock").create("d"));

    options.addOption(OptionBuilder.withArgName("seedtime").hasArg()
            .withDescription("event clock initialization time").create("s"));

    options.addOption(
            OptionBuilder.withArgName("extshome").hasArg().withDescription("extensions home").create("e"));

    options.addOption(
            OptionBuilder.withArgName("instanceid").hasArg().withDescription("instance id").create("i"));

    options.addOption(
            OptionBuilder.withArgName("configtype").hasArg().withDescription("configuration type").create("t"));

    CommandLineParser parser = new GnuParser();
    CommandLine commandLine = null;
    String clockType = "wall";

    try {
        commandLine = parser.parse(options, args);
    } catch (ParseException pe) {
        System.err.println(pe.getLocalizedMessage());
        System.exit(1);
    }

    int instanceId = -1;
    if (commandLine.hasOption("i")) {
        String instanceIdStr = commandLine.getOptionValue("i");
        try {
            instanceId = Integer.parseInt(instanceIdStr);
        } catch (NumberFormatException nfe) {
            System.err.println("Bad instance id: %s" + instanceIdStr);
            System.exit(1);
        }
    }

    if (commandLine.hasOption("c")) {
        coreHome = commandLine.getOptionValue("c");
    }

    if (commandLine.hasOption("a")) {
        appsHome = commandLine.getOptionValue("a");
    }

    if (commandLine.hasOption("d")) {
        clockType = commandLine.getOptionValue("d");
    }

    if (commandLine.hasOption("e")) {
        extsHome = commandLine.getOptionValue("e");
    }

    String configType = "typical";
    if (commandLine.hasOption("t")) {
        configType = commandLine.getOptionValue("t");
    }

    long seedTime = 0;
    if (commandLine.hasOption("s")) {
        seedTime = Long.parseLong(commandLine.getOptionValue("s"));
    }

    File coreHomeFile = new File(coreHome);
    if (!coreHomeFile.isDirectory()) {
        System.err.println("Bad core home: " + coreHome);
        System.exit(1);
    }

    File appsHomeFile = new File(appsHome);
    if (!appsHomeFile.isDirectory()) {
        System.err.println("Bad applications home: " + appsHome);
        System.exit(1);
    }

    if (instanceId > -1) {
        System.setProperty("instanceId", "" + instanceId);
    } else {
        System.setProperty("instanceId", "" + S4Util.getPID());
    }

    List loArgs = commandLine.getArgList();

    if (loArgs.size() < 1) {
        // System.err.println("No bean configuration file specified");
        // System.exit(1);
    }

    // String s4ConfigXml = (String) loArgs.get(0);
    // System.out.println("s4ConfigXml is " + s4ConfigXml);

    ClassPathResource propResource = new ClassPathResource("s4-core.properties");
    Properties prop = new Properties();
    if (propResource.exists()) {
        prop.load(propResource.getInputStream());
    } else {
        System.err.println("Unable to find s4-core.properties. It must be available in classpath");
        System.exit(1);
    }

    ApplicationContext coreContext = null;
    String configBase = coreHome + File.separatorChar + "conf" + File.separatorChar + configType;
    String configPath = "";
    List<String> coreConfigUrls = new ArrayList<String>();
    File configFile = null;

    // load clock configuration
    configPath = configBase + File.separatorChar + clockType + "-clock.xml";
    coreConfigUrls.add(configPath);

    // load core config xml
    configPath = configBase + File.separatorChar + "s4-core-conf.xml";
    configFile = new File(configPath);
    if (!configFile.exists()) {
        System.err.printf("S4 core config file %s does not exist\n", configPath);
        System.exit(1);
    }

    coreConfigUrls.add(configPath);
    String[] coreConfigFiles = new String[coreConfigUrls.size()];
    coreConfigUrls.toArray(coreConfigFiles);

    String[] coreConfigFileUrls = new String[coreConfigFiles.length];
    for (int i = 0; i < coreConfigFiles.length; i++) {
        coreConfigFileUrls[i] = "file:" + coreConfigFiles[i];
    }

    coreContext = new FileSystemXmlApplicationContext(coreConfigFileUrls, coreContext);
    ApplicationContext context = coreContext;

    Clock clock = (Clock) context.getBean("clock");
    if (clock instanceof EventClock && seedTime > 0) {
        EventClock s4EventClock = (EventClock) clock;
        s4EventClock.updateTime(seedTime);
        System.out.println("Intializing event clock time with seed time " + s4EventClock.getCurrentTime());
    }

    PEContainer peContainer = (PEContainer) context.getBean("peContainer");

    Watcher w = (Watcher) context.getBean("watcher");
    w.setConfigFilename(configPath);

    // load extension modules
    String[] configFileNames = getModuleConfigFiles(extsHome, prop);
    if (configFileNames.length > 0) {
        String[] configFileUrls = new String[configFileNames.length];
        for (int i = 0; i < configFileNames.length; i++) {
            configFileUrls[i] = "file:" + configFileNames[i];
        }
        context = new FileSystemXmlApplicationContext(configFileUrls, context);
    }

    // load application modules
    configFileNames = getModuleConfigFiles(appsHome, prop);
    if (configFileNames.length > 0) {
        String[] configFileUrls = new String[configFileNames.length];
        for (int i = 0; i < configFileNames.length; i++) {
            configFileUrls[i] = "file:" + configFileNames[i];
        }
        context = new FileSystemXmlApplicationContext(configFileUrls, context);
        // attach any beans that implement ProcessingElement to the PE
        // Container
        String[] processingElementBeanNames = context.getBeanNamesForType(AbstractPE.class);
        for (String processingElementBeanName : processingElementBeanNames) {
            AbstractPE bean = (AbstractPE) context.getBean(processingElementBeanName);
            bean.setClock(clock);
            try {
                bean.setSafeKeeper((SafeKeeper) context.getBean("safeKeeper"));
            } catch (NoSuchBeanDefinitionException ignored) {
                // no safe keeper = no checkpointing / recovery
            }
            // if the application did not specify an id, use the Spring bean name
            if (bean.getId() == null) {
                bean.setId(processingElementBeanName);
            }
            System.out.println("Adding processing element with bean name " + processingElementBeanName + ", id "
                    + ((AbstractPE) bean).getId());
            peContainer.addProcessor((AbstractPE) bean);
        }
    }
}

From source file:com.act.biointerpretation.cofactorremoval.ReactionCofactorRemover.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());//w w  w .  java 2 s  .com
    }

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

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(ReactionDesalter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    NoSQLAPI api = new NoSQLAPI(cl.getOptionValue(OPTION_READ_DB), cl.getOptionValue(OPTION_READ_DB));

    CofactorRemover cofactorRemover = new CofactorRemover(api);
    cofactorRemover.init();

    Pair<Reaction, Reaction> results = cofactorRemover
            .removeCofactorsFromOneReaction(Long.parseLong(cl.getOptionValue(OPTION_RXN_ID)));

    System.out.format("Reaction before processing:\n");
    printReport(results.getLeft());
    System.out.println();
    System.out.format("Reaction after processing:\n");
    printReport(results.getRight());
    System.out.println();
}

From source file:com.mvdb.etl.actions.ModifyCustomerData.java

public static void main(String[] args) {

    ActionUtils.assertEnvironmentSetupOk();
    ActionUtils.assertFileExists("~/.mvdb", "~/.mvdb missing. Existing.");
    ActionUtils.assertFileExists("~/.mvdb/status.InitCustomerData.complete",
            "300init-customer-data.sh not executed yet. Exiting");
    //This check is not required as data can be modified any number of times
    //ActionUtils.assertFileDoesNotExist("~/.mvdb/status.ModifyCustomerData.complete", "ModifyCustomerData already done. Start with 100init.sh if required. Exiting");
    ActionUtils.setUpInitFileProperty();
    ActionUtils.createMarkerFile("~/.mvdb/status.ModifyCustomerData.start", true);

    String customerName = null;// ww  w. j a v  a  2  s  .  c o m
    //Date startDate  = null;
    //Date endDate  = null;
    final CommandLineParser cmdLinePosixParser = new PosixParser();
    final Options posixOptions = constructPosixOptions();
    CommandLine commandLine;
    try {
        commandLine = cmdLinePosixParser.parse(posixOptions, args);
        //            if (commandLine.hasOption("startDate"))
        //            {
        //                String startDateStr = commandLine.getOptionValue("startDate");
        //                startDate = ActionUtils.getDate(startDateStr);
        //            }
        //            if (commandLine.hasOption("endDate"))
        //            {
        //                String endDateStr = commandLine.getOptionValue("endDate");
        //                endDate = ActionUtils.getDate(endDateStr);
        //            }
        if (commandLine.hasOption("customerName")) {
            customerName = commandLine.getOptionValue("customerName");
        }
    } catch (ParseException parseException) // checked exception
    {
        System.err.println(
                "Encountered exception while parsing using PosixParser:\n" + parseException.getMessage());
    }

    if (customerName == null) {
        System.err.println("customerName has not been specified.  Aborting...");
        System.exit(1);
    }

    //        if (startDate == null)
    //        {
    //            System.err.println("startDate has not been specified with the correct format YYYYMMddHHmmss.  Aborting...");
    //            System.exit(1);
    //        }
    //        
    //        if (endDate == null)
    //        {
    //            System.err.println("endDate has not been specified with the correct format YYYYMMddHHmmss.  Aborting...");
    //            System.exit(1);
    //        }
    //        
    //        if (endDate.after(startDate) == false)
    //        {
    //            System.err.println("endDate must be after startDate.  Aborting...");
    //            System.exit(1);
    //        }

    ApplicationContext context = Top.getContext();

    final OrderDAO orderDAO = (OrderDAO) context.getBean("orderDAO");

    long maxId = orderDAO.findMaxId();
    long totalOrders = orderDAO.findTotalOrders();

    long modifyCount = (long) (totalOrders * 0.1);

    String lastUsedEndTimeStr = ActionUtils.getConfigurationValue(customerName,
            ConfigurationKeys.LAST_USED_END_TIME);
    long lastUsedEndTime = Long.parseLong(lastUsedEndTimeStr);
    Date startDate1 = new Date();
    startDate1.setTime(lastUsedEndTime + 1000 * 60 * 60 * 24 * 1);
    Date endDate1 = new Date(startDate1.getTime() + 1000 * 60 * 60 * 24 * 1);

    for (int i = 0; i < modifyCount; i++) {
        Date updateDate = RandomUtil.getRandomDateInRange(startDate1, endDate1);
        long orderId = (long) Math.floor((Math.random() * maxId)) + 1L;
        logger.info("Modify Id " + orderId + " in orders");
        Order theOrder = orderDAO.findByOrderId(orderId);
        //             System.out.println("theOrder : " + theOrder);
        theOrder.setNote(RandomUtil.getRandomString(4));
        theOrder.setUpdateTime(updateDate);
        theOrder.setSaleCode(RandomUtil.getRandomInt());
        orderDAO.update(theOrder);
        //             System.out.println("theOrder Modified: " + theOrder);

    }
    ActionUtils.setConfigurationValue(customerName, ConfigurationKeys.LAST_USED_END_TIME,
            String.valueOf(endDate1.getTime()));
    logger.info("Modified " + modifyCount + " orders");
    ActionUtils.createMarkerFile("~/.mvdb/status.ModifyCustomerData.complete", true);
}