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

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

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

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DefaultParser

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Usage

From source file:com.act.lcms.db.io.LoadTSVIntoDB.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    opts.addOption(Option.builder("t").argName("type")
            .desc("The type of TSV data to read, options are: " + StringUtils.join(TSV_TYPE.values(), ", "))
            .hasArg().required().longOpt("table-type").build());
    opts.addOption(Option.builder("i").argName("path").desc("The TSV file to read").hasArg().required()
            .longOpt("input-file").build());

    // DB connection options.
    opts.addOption(Option.builder().argName("database url")
            .desc("The url to use when connecting to the LCMS db").hasArg().longOpt("db-url").build());
    opts.addOption(Option.builder("u").argName("database user").desc("The LCMS DB user").hasArg()
            .longOpt("db-user").build());
    opts.addOption(Option.builder("p").argName("database password").desc("The LCMS DB password").hasArg()
            .longOpt("db-pass").build());
    opts.addOption(Option.builder("H").argName("database host")
            .desc(String.format("The LCMS DB host (default = %s)", DB.DEFAULT_HOST)).hasArg().longOpt("db-host")
            .build());/* w ww . j av a  2  s . c om*/
    opts.addOption(Option.builder("P").argName("database port")
            .desc(String.format("The LCMS DB port (default = %d)", DB.DEFAULT_PORT)).hasArg().longOpt("db-port")
            .build());
    opts.addOption(Option.builder("N").argName("database name")
            .desc(String.format("The LCMS DB name (default = %s)", DB.DEFAULT_DB_NAME)).hasArg()
            .longOpt("db-name").build());

    // Everybody needs a little help from their friends.
    opts.addOption(
            Option.builder("h").argName("help").desc("Prints this help message").longOpt("help").build());

    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());
        HelpFormatter fmt = new HelpFormatter();
        fmt.printHelp(LoadTSVIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        new HelpFormatter().printHelp(LoadTSVIntoDB.class.getCanonicalName(), opts, true);
        return;
    }

    File inputFile = new File(cl.getOptionValue("input-file"));
    if (!inputFile.exists()) {
        System.err.format("Unable to find input file at %s\n", cl.getOptionValue("input-file"));
        new HelpFormatter().printHelp(LoadTSVIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    TSV_TYPE contentType = null;
    try {
        contentType = TSV_TYPE.valueOf(cl.getOptionValue("table-type"));
    } catch (IllegalArgumentException e) {
        System.err.format("Unrecognized TSV type '%s'\n", cl.getOptionValue("table-type"));
        new HelpFormatter().printHelp(LoadTSVIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    DB db;

    if (cl.hasOption("db-url")) {
        db = new DB().connectToDB(cl.getOptionValue("db-url"));
    } else {
        Integer port = null;
        if (cl.getOptionValue("P") != null) {
            port = Integer.parseInt(cl.getOptionValue("P"));
        }
        db = new DB().connectToDB(cl.getOptionValue("H"), port, cl.getOptionValue("N"), cl.getOptionValue("u"),
                cl.getOptionValue("p"));
    }

    try {
        db.getConn().setAutoCommit(false);

        TSVParser parser = new TSVParser();
        parser.parse(inputFile);

        List<Pair<Integer, DB.OPERATION_PERFORMED>> results = null;
        switch (contentType) {
        case CURATED_CHEMICAL:
            results = CuratedChemical.insertOrUpdateCuratedChemicalsFromTSV(db, parser);
            break;
        case CONSTRUCT:
            results = ConstructEntry.insertOrUpdateCompositionMapEntriesFromTSV(db, parser);
            break;
        case CHEMICAL_OF_INTEREST:
            results = ChemicalOfInterest.insertOrUpdateChemicalOfInterestsFromTSV(db, parser);
            break;
        default:
            throw new RuntimeException(String.format("Unsupported TSV type: %s", contentType));
        }
        if (results != null) {
            for (Pair<Integer, DB.OPERATION_PERFORMED> r : results) {
                System.out.format("%d: %s\n", r.getLeft(), r.getRight());
            }
        }
        // If we didn't encounter an exception, commit the transaction.
        db.getConn().commit();
    } catch (Exception e) {
        System.err.format("Caught exception when trying to load plate composition, rolling back. %s\n",
                e.getMessage());
        db.getConn().rollback();
        throw (e);
    } finally {
        db.getConn().close();
    }
}

From source file:com.uber.stream.kafka.mirrormaker.manager.ManagerStarter.java

public static void main(String[] args) throws Exception {
    CommandLineParser parser = new DefaultParser();
    CommandLine cmd = parser.parse(ManagerConf.constructManagerOptions(), args);
    if (cmd.getOptions().length == 0 || cmd.hasOption("help")) {
        HelpFormatter f = new HelpFormatter();
        f.printHelp("OptionsTip", ManagerConf.constructManagerOptions());
        System.exit(0);/*from  www .  j  av a  2  s  .  c  o  m*/
    }
    final ManagerStarter managerStarter = ManagerStarter.init(cmd);

    Runtime.getRuntime().addShutdownHook(new Thread() {
        public void run() {
            try {
                managerStarter.stop();
            } catch (Exception e) {
                LOGGER.error("Caught error during shutdown! ", e);
            }
        }
    });

    try {
        managerStarter.start();
    } catch (Exception e) {
        LOGGER.error("Cannot start uReplicator-Manager: ", e);
    }
}

From source file:it.uniud.ailab.dcore.launchers.Launcher.java

/**
 * Starts the Distiller using the specified configuration, analyzing the
 * specified file, writing the output in the specified folder.
 *
 * @param args the command-line parameters.
 *///from w w  w.j a v a 2 s . co m
public static void main(String[] args) {

    CommandLineParser parser = new DefaultParser();

    createOptions();

    CommandLine cmd;

    try {
        // parse the command line arguments
        cmd = parser.parse(options, args);
    } catch (ParseException exp) {
        // oops, something went wrong
        printError("Error while parsing command line options: " + exp.getLocalizedMessage());
        return;
    }

    // if no options has been selected, just return.
    if (cmd.getOptions().length == 0) {
        printHelp();
        return;
    }

    // read the options.
    if (readOptions(cmd)) {
        // everything's good! proceed
        doWork();
    } else {
        printError("Unexpected error while parsing command line options\n"
                + "Please contact the developers of the framwork to get " + "additional help.");
        return;
    }
}

From source file:com.act.biointerpretation.analytics.ReactionDeletion.java

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

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

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

    if (!cl.hasOption(OPTION_OUTPUT_PATH)) {
        LOGGER.error("Input -o prefix");
        return;
    }

    NoSQLAPI srcApi = new NoSQLAPI(cl.getOptionValue(OPTION_SOURCE_DB), cl.getOptionValue(OPTION_SOURCE_DB));
    NoSQLAPI sinkApi = new NoSQLAPI(cl.getOptionValue(OPTION_SINK_DB), cl.getOptionValue(OPTION_SINK_DB));

    searchForDroppedReactions(srcApi, sinkApi, new File(cl.getOptionValue(OPTION_OUTPUT_PATH)));
}

From source file:com.dattack.dbtools.ping.Ping.java

/**
 * The <code>main</code> method.
 *
 * @param args/*from   w ww  . java  2s .  c o  m*/
 *            the program arguments
 */
public static void main(final String[] args) {

    final Options options = createOptions();

    try {
        final CommandLineParser parser = new DefaultParser();
        final CommandLine cmd = parser.parse(options, args);
        final String[] filenames = cmd.getOptionValues(FILE_OPTION);
        final String[] taskNames = cmd.getOptionValues(TASK_NAME_OPTION);

        HashSet<String> hs = null;
        if (taskNames != null) {
            hs = new HashSet<>(Arrays.asList(taskNames));
        }

        final Ping ping = new Ping();
        ping.execute(filenames, hs);

    } catch (@SuppressWarnings("unused") final ParseException e) {
        showUsage(options);
    } catch (final ConfigurationException | DbpingParserException e) {
        System.err.println(e.getMessage());
    }
}

From source file:com.act.biointerpretation.analytics.ReactionCountProvenance.java

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

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

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

    if (!cl.hasOption(OPTION_OUTPUT_PREFIX)) {
        LOGGER.error("Input -o prefix");
        return;
    }

    List<String> dbs = new ArrayList<>(Arrays.asList(cl.getOptionValues(OPTION_ORDERED_LIST_OF_DBS)));
    ReactionCountProvenance reactionCountProvenance = new ReactionCountProvenance(dbs,
            cl.getOptionValue(OPTION_OUTPUT_PREFIX));
    reactionCountProvenance.run();
    reactionCountProvenance.writeToDisk();
}

From source file:com.act.analysis.surfactant.AnalysisDriver.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*from   ww  w .  j  ava2 s  .  c o  m*/
    }

    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(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        return;
    }

    Set<String> seenOutputIds = new HashSet<>();

    TSVWriter<String, String> tsvWriter = null;
    if (cl.hasOption(OPTION_OUTPUT_FILE)) {
        File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_FILE));
        List<Map<String, String>> oldResults = null;
        if (outputFile.exists()) {
            System.err.format(
                    "Output file already exists, reading old results and skipping processed molecules.\n");
            TSVParser outputParser = new TSVParser();
            outputParser.parse(outputFile);
            oldResults = outputParser.getResults();
            for (Map<String, String> row : oldResults) {
                // TODO: verify that the last row was written cleanly/completely.
                seenOutputIds.add(row.get("id"));
            }
        }

        List<String> header = new ArrayList<>();
        header.add("name");
        header.add("id");
        header.add("inchi");
        header.add("label");
        for (SurfactantAnalysis.FEATURES f : SurfactantAnalysis.FEATURES.values()) {
            header.add(f.toString());
        }
        // TODO: make this API more auto-closable friendly.
        tsvWriter = new TSVWriter<>(header);
        tsvWriter.open(outputFile);
        if (oldResults != null) {
            System.out.format("Re-writing %d existing result rows\n", oldResults.size());
            tsvWriter.append(oldResults);
        }
    }

    try {
        Map<SurfactantAnalysis.FEATURES, Double> analysisFeatures;

        LicenseManager.setLicenseFile(cl.getOptionValue(OPTION_LICENSE_FILE));
        if (cl.hasOption(OPTION_INCHI)) {
            analysisFeatures = SurfactantAnalysis.performAnalysis(cl.getOptionValue(OPTION_INCHI),
                    cl.hasOption(OPTION_DISPLAY));
            Map<String, String> tsvFeatures = new HashMap<>();
            // Convert features to strings to avoid some weird formatting issues.  It's ugly, but it works.
            for (Map.Entry<SurfactantAnalysis.FEATURES, Double> entry : analysisFeatures.entrySet()) {
                tsvFeatures.put(entry.getKey().toString(), String.format("%.6f", entry.getValue()));
            }
            tsvFeatures.put("name", "direct-inchi-input");
            if (tsvWriter != null) {
                tsvWriter.append(tsvFeatures);
            }
        } else if (cl.hasOption(OPTION_INPUT_FILE)) {
            TSVParser parser = new TSVParser();
            parser.parse(new File(cl.getOptionValue(OPTION_INPUT_FILE)));
            int i = 0;
            List<Map<String, String>> inputRows = parser.getResults();

            for (Map<String, String> row : inputRows) {
                i++; // Just for warning messages.
                if (!row.containsKey("name") || !row.containsKey("id") || !row.containsKey("inchi")) {
                    System.err.format(
                            "WARNING: TSV rows must contain at least name, id, and inchi, skipping row %d\n",
                            i);
                    continue;
                }
                if (seenOutputIds.contains(row.get("id"))) {
                    System.out.format("Skipping input row with id already in output: %s\n", row.get("id"));
                    continue;
                }

                System.out.format("Analysis for chemical %s\n", row.get("name"));
                try {
                    analysisFeatures = SurfactantAnalysis.performAnalysis(row.get("inchi"), false);
                } catch (Exception e) {
                    // Ignore exceptions for now.  Sometimes the regression analysis or Chemaxon processing chokes unexpectedly.
                    System.err.format("ERROR caught exception while processing '%s':\n", row.get("name"));
                    System.err.format("%s\n", e.getMessage());
                    e.printStackTrace(System.err);
                    System.err.println("Skipping...");
                    continue;
                }
                System.out.format("--- Done analysis for chemical %s\n", row.get("name"));

                // This is a duplicate of the OPTION_INCHI block code, but it's inside of a tight loop, so...
                Map<String, String> tsvFeatures = new HashMap<>();
                for (Map.Entry<SurfactantAnalysis.FEATURES, Double> entry : analysisFeatures.entrySet()) {
                    tsvFeatures.put(entry.getKey().toString(), String.format("%.6f", entry.getValue()));
                }
                tsvFeatures.put("name", row.get("name"));
                tsvFeatures.put("id", row.get("id"));
                tsvFeatures.put("inchi", row.get("inchi"));
                tsvFeatures.put("label", row.containsKey("label") ? row.get("label") : "?");
                if (tsvWriter != null) {
                    tsvWriter.append(tsvFeatures);
                    // Flush every time in case we crash or get interrupted.  The features must flow!
                    tsvWriter.flush();
                }
            }
        } else {
            throw new RuntimeException("Must specify inchi or input file");
        }
    } finally {
        if (tsvWriter != null) {
            tsvWriter.close();
        }
    }
}

From source file:com.hpe.nv.samples.basic.BasicAnalyzeNVTest.java

public static void main(String[] args) {
    try {//from   w w  w.ja va 2  s  .  c  o m
        // program arguments
        Options options = new Options();
        options.addOption("i", "server-ip", true, "[mandatory] NV Test Manager IP");
        options.addOption("o", "server-port", true, "[mandatory] NV Test Manager port");
        options.addOption("u", "username", true, "[mandatory] NV username");
        options.addOption("w", "password", true, "[mandatory] NV password");
        options.addOption("e", "ssl", true, "[optional] Pass true to use SSL. Default: false");
        options.addOption("y", "proxy", true, "[optional] Proxy server host:port");
        options.addOption("z", "zip-result-file-path", true,
                "[optional] File path to store the analysis results as a .zip file");
        options.addOption("k", "analysis-ports", true,
                "[optional] A comma-separated list of ports for test analysis");
        options.addOption("b", "browser", true,
                "[optional] The browser for which the Selenium WebDriver is built. Possible values: Chrome and Firefox. Default: Firefox");
        options.addOption("d", "debug", true,
                "[optional] Pass true to view console debug messages during execution. Default: false");
        options.addOption("h", "help", false, "[optional] Generates and prints help information");

        // parse and validate the command line arguments
        CommandLineParser parser = new DefaultParser();
        CommandLine line = parser.parse(options, args);

        if (line.hasOption("help")) {
            // print help if help argument is passed
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("BasicAnalyzeNVTest.java", options);
            return;
        }

        if (line.hasOption("server-ip")) {
            serverIp = line.getOptionValue("server-ip");
            if (serverIp.equals("0.0.0.0")) {
                throw new Exception(
                        "Please replace the server IP argument value (0.0.0.0) with your NV Test Manager IP");
            }
        } else {
            throw new Exception("Missing argument -i/--server-ip <serverIp>");
        }

        if (line.hasOption("server-port")) {
            serverPort = Integer.parseInt(line.getOptionValue("server-port"));
        } else {
            throw new Exception("Missing argument -o/--server-port <serverPort>");
        }

        if (line.hasOption("username")) {
            username = line.getOptionValue("username");
        } else {
            throw new Exception("Missing argument -u/--username <username>");
        }

        if (line.hasOption("password")) {
            password = line.getOptionValue("password");
        } else {
            throw new Exception("Missing argument -w/--password <password>");
        }

        if (line.hasOption("ssl")) {
            ssl = Boolean.parseBoolean(line.getOptionValue("ssl"));
        }

        if (line.hasOption("zip-result-file-path")) {
            zipResultFilePath = line.getOptionValue("zip-result-file-path");
        }

        if (line.hasOption("proxy")) {
            proxySetting = line.getOptionValue("proxy");
        }

        if (line.hasOption("analysis-ports")) {
            String analysisPortsStr = line.getOptionValue("analysis-ports");
            analysisPorts = analysisPortsStr.split(",");
        } else {
            analysisPorts = new String[] { "80", "8080" };
        }

        if (line.hasOption("browser")) {
            browser = line.getOptionValue("browser");
        } else {
            browser = "Firefox";
        }

        if (line.hasOption("debug")) {
            debug = Boolean.parseBoolean(line.getOptionValue("debug"));
        }

        String newLine = System.getProperty("line.separator");
        String testDescription = "***   This sample demonstrates the use of the most basic NV methods.                                                      ***"
                + newLine
                + "***                                                                                                                       ***"
                + newLine
                + "***   First, the sample creates a TestManager object and initializes it.                                                  ***"
                + newLine
                + "***   The sample starts an NV test over an emulated \"3G Busy\" network.                                                    ***"
                + newLine
                + "***                                                                                                                       ***"
                + newLine
                + "***   Next, the sample navigates to the home page in the HPE Network Virtualization website                               ***"
                + newLine
                + "***   using the Selenium WebDriver.                                                                                       ***"
                + newLine
                + "***                                                                                                                       ***"
                + newLine
                + "***   Finally, the sample stops the NV test, analyzes it, and prints the path of the analysis .zip file to the console.   ***"
                + newLine
                + "***                                                                                                                       ***"
                + newLine
                + "***   You can view the actual steps of this sample in the BasicAnalyzeNVTest.java file.                                   ***"
                + newLine;

        // print the sample's description
        System.out.println(testDescription);

        // start console spinner
        if (!debug) {
            spinner = new Thread(new Spinner());
            spinner.start();
        }

        // sample execution steps
        /*****    Part 1 - Create a TestManager object and initialize it                                            *****/
        printPartDescription("\b------    Part 1 - Create a TestManager object and initialize it");
        initTestManager();
        printPartSeparator();
        /*****    Part 2 - Start the NV test with the "3G Busy" network scenario                                    *****/
        printPartDescription("------    Part 2 - Start the NV test with the \"3G Busy\" network scenario");
        startTest();
        testRunning = true;
        printPartSeparator();
        /*****    Part 3 - Navigate to the HPE Network Virtualization website                                       *****/
        printPartDescription("------    Part 3 - Navigate to the HPE Network Virtualization website");
        buildSeleniumWebDriver();
        seleniumNavigateToPage();
        driverCloseAndQuit();
        printPartSeparator();
        /*****    Part 4 - Stop the NV test, analyze it and print the results to the console                        *****/
        printPartDescription(
                "------    Part 4 - Stop the NV test, analyze it and print the results to the console");
        stopTestAndAnalyze();
        testRunning = false;
        printPartSeparator();
        doneCallback();
    } catch (Exception e) {
        try {
            handleError(e.getMessage());
        } catch (Exception e2) {
            System.out.println("Error occurred: " + e2.getMessage());
        }
    }
}

From source file:com.act.biointerpretation.sarinference.ProductScorer.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());/*from w w w  .  j a  v  a2 s .c  om*/
    }
    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(L2FilteringDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    File inputCorpusFile = new File(cl.getOptionValue(OPTION_PREDICTION_CORPUS));
    File lcmsFile = new File(cl.getOptionValue(OPTION_LCMS_RESULTS));
    File scoredSarsFile = new File(cl.getOptionValue(OPTION_SCORED_SARS));
    File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_PATH));

    JavaRunnable productScoreRunner = getProductScorer(inputCorpusFile, scoredSarsFile, lcmsFile, outputFile);

    LOGGER.info("Scoring products.");
    productScoreRunner.run();
    LOGGER.info("Complete!.");
}

From source file:com.act.lcms.db.io.LoadPlateCompositionIntoDB.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    opts.addOption(Option.builder("t").argName("type")
            .desc("The type of plate composition in this file, valid options are: "
                    + StringUtils.join(Arrays.asList(Plate.CONTENT_TYPE.values()), ", "))
            .hasArg().longOpt("plate-type").required().build());
    opts.addOption(Option.builder("i").argName("path").desc("The plate composition file to read").hasArg()
            .longOpt("input-file").required().build());

    // DB connection options.
    opts.addOption(Option.builder().argName("database url")
            .desc("The url to use when connecting to the LCMS db").hasArg().longOpt("db-url").build());
    opts.addOption(Option.builder("u").argName("database user").desc("The LCMS DB user").hasArg()
            .longOpt("db-user").build());
    opts.addOption(Option.builder("p").argName("database password").desc("The LCMS DB password").hasArg()
            .longOpt("db-pass").build());
    opts.addOption(Option.builder("H").argName("database host")
            .desc(String.format("The LCMS DB host (default = %s)", DB.DEFAULT_HOST)).hasArg().longOpt("db-host")
            .build());/*  w  ww. j  a  va 2  s .c  o  m*/
    opts.addOption(Option.builder("P").argName("database port")
            .desc(String.format("The LCMS DB port (default = %d)", DB.DEFAULT_PORT)).hasArg().longOpt("db-port")
            .build());
    opts.addOption(Option.builder("N").argName("database name")
            .desc(String.format("The LCMS DB name (default = %s)", DB.DEFAULT_DB_NAME)).hasArg()
            .longOpt("db-name").build());

    // Everybody needs a little help from their friends.
    opts.addOption(
            Option.builder("h").argName("help").desc("Prints this help message").longOpt("help").build());

    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());
        HelpFormatter fmt = new HelpFormatter();
        fmt.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        return;
    }

    File inputFile = new File(cl.getOptionValue("input-file"));
    if (!inputFile.exists()) {
        System.err.format("Unable to find input file at %s\n", cl.getOptionValue("input-file"));
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    PlateCompositionParser parser = new PlateCompositionParser();
    parser.processFile(inputFile);

    Plate.CONTENT_TYPE contentType = null;
    try {
        contentType = Plate.CONTENT_TYPE.valueOf(cl.getOptionValue("plate-type"));
    } catch (IllegalArgumentException e) {
        System.err.format("Unrecognized plate type '%s'\n", cl.getOptionValue("plate-type"));
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    DB db;
    if (cl.hasOption("db-url")) {
        db = new DB().connectToDB(cl.getOptionValue("db-url"));
    } else {
        Integer port = null;
        if (cl.getOptionValue("P") != null) {
            port = Integer.parseInt(cl.getOptionValue("P"));
        }
        db = new DB().connectToDB(cl.getOptionValue("H"), port, cl.getOptionValue("N"), cl.getOptionValue("u"),
                cl.getOptionValue("p"));
    }

    try {
        db.getConn().setAutoCommit(false);

        Plate p = Plate.getOrInsertFromPlateComposition(db, parser, contentType);

        switch (contentType) {
        case LCMS:
            List<LCMSWell> LCMSWells = LCMSWell.getInstance().insertFromPlateComposition(db, parser, p);
            for (LCMSWell LCMSWell : LCMSWells) {
                System.out.format("%d: %d x %d  %s  %s\n", LCMSWell.getId(), LCMSWell.getPlateColumn(),
                        LCMSWell.getPlateRow(), LCMSWell.getMsid(), LCMSWell.getComposition());
            }
            break;
        case STANDARD:
            List<StandardWell> standardWells = StandardWell.getInstance().insertFromPlateComposition(db, parser,
                    p);
            for (StandardWell standardWell : standardWells) {
                System.out.format("%d: %d x %d  %s\n", standardWell.getId(), standardWell.getPlateColumn(),
                        standardWell.getPlateRow(), standardWell.getChemical());
            }
            break;
        case DELIVERED_STRAIN:
            List<DeliveredStrainWell> deliveredStrainWells = DeliveredStrainWell.getInstance()
                    .insertFromPlateComposition(db, parser, p);
            for (DeliveredStrainWell deliveredStrainWell : deliveredStrainWells) {
                System.out.format("%d: %d x %d (%s) %s %s \n", deliveredStrainWell.getId(),
                        deliveredStrainWell.getPlateColumn(), deliveredStrainWell.getPlateRow(),
                        deliveredStrainWell.getWell(), deliveredStrainWell.getMsid(),
                        deliveredStrainWell.getComposition());
            }
            break;
        case INDUCTION:
            List<InductionWell> inductionWells = InductionWell.getInstance().insertFromPlateComposition(db,
                    parser, p);
            for (InductionWell inductionWell : inductionWells) {
                System.out.format("%d: %d x %d %s %s %s %d\n", inductionWell.getId(),
                        inductionWell.getPlateColumn(), inductionWell.getPlateRow(), inductionWell.getMsid(),
                        inductionWell.getComposition(), inductionWell.getChemical(), inductionWell.getGrowth());
            }
            break;
        case PREGROWTH:
            List<PregrowthWell> pregrowthWells = PregrowthWell.getInstance().insertFromPlateComposition(db,
                    parser, p);
            for (PregrowthWell pregrowthWell : pregrowthWells) {
                System.out.format("%d: %d x %d (%s @ %s) %s %s %d\n", pregrowthWell.getId(),
                        pregrowthWell.getPlateColumn(), pregrowthWell.getPlateRow(),
                        pregrowthWell.getSourcePlate(), pregrowthWell.getSourceWell(), pregrowthWell.getMsid(),
                        pregrowthWell.getComposition(), pregrowthWell.getGrowth());
            }
            break;
        case FEEDING_LCMS:
            List<FeedingLCMSWell> feedingLCMSWells = FeedingLCMSWell.getInstance()
                    .insertFromPlateComposition(db, parser, p);
            for (FeedingLCMSWell feedingLCMSWell : feedingLCMSWells) {
                System.out.format("%d: %d x %d (%s @ %s) %s %s %f\n", feedingLCMSWell.getId(),
                        feedingLCMSWell.getPlateColumn(), feedingLCMSWell.getPlateRow(),
                        feedingLCMSWell.getMsid(), feedingLCMSWell.getComposition(),
                        feedingLCMSWell.getExtract(), feedingLCMSWell.getChemical(),
                        feedingLCMSWell.getConcentration());
            }
            break;
        default:
            System.err.format("Unrecognized/unimplemented data type '%s'\n", contentType);
            break;
        }
        // If we didn't encounter an exception, commit the transaction.
        db.getConn().commit();
    } catch (Exception e) {
        System.err.format("Caught exception when trying to load plate composition, rolling back. %s\n",
                e.getMessage());
        db.getConn().rollback();
        throw (e);
    } finally {
        db.getConn().close();
    }

}