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

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

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DefaultParser

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From source file:com.movielabs.availstool.AvailsTool.java

public static void main(String[] args) throws Exception {
    String fileName, outFile, sheetName;
    int sheetNum = -1;

    Logger log = LogManager.getLogger(AvailsTool.class.getName());
    log.info("Initializing logger");

    Options options = new Options();
    options.addOption(Opts.v.name(), false, "verbose mode");
    options.addOption(Opts.s.name(), true, "specify sheet");
    options.addOption(Opts.f.name(), true, "specify file name");
    options.addOption(Opts.o.name(), true, "specify output file name");
    options.addOption(Opts.sstoxml.name(), false, "convert avails spreadsheet to XML");
    options.addOption(Opts.xmltoss.name(), false, "convert avails XML to a spreadsheet");
    options.addOption(Opts.dumpsheet.name(), false, "dump a single sheet from a spreadsheet");
    options.addOption(Opts.dumpss.name(), false, "dump a spreadsheet file");
    options.addOption(Opts.wx.name(), false, "treat warning as fatal error");
    options.addOption(Opts.clean.name(), false, "clean up data entries");

    CommandLineParser cli = new DefaultParser();

    try {//from ww  w  .  j a  va  2 s. c  o m
        CommandLine cmd = cli.parse(options, args);
        boolean optToXML = cmd.hasOption(Opts.sstoxml.name());
        boolean optToSS = cmd.hasOption(Opts.xmltoss.name());
        boolean optDumpSS = cmd.hasOption(Opts.dumpss.name());
        boolean optDumpSheet = cmd.hasOption(Opts.dumpsheet.name());
        fileName = cmd.getOptionValue(Opts.f.name());
        sheetName = cmd.getOptionValue(Opts.s.name());
        boolean clean = cmd.hasOption(Opts.clean.name());
        boolean wx = cmd.hasOption(Opts.wx.name());
        boolean verbose = cmd.hasOption(Opts.v.name());
        AvailSS ss;
        AvailsSheet as;
        String message;

        if (sheetName != null) {
            Pattern pat = Pattern.compile("^\\d+$");
            Matcher m = pat.matcher(sheetName);
            if (m.matches())
                sheetNum = Integer.parseInt(sheetName);
        }

        if (fileName == null)
            throw new ParseException("input file not specified");

        if (!(optToXML | optToSS | optDumpSS | optDumpSheet))
            throw new ParseException("missing operation");

        if (optToXML) {
            if (optToSS | optDumpSS | optDumpSheet)
                throw new ParseException("more than one operation specified");
            outFile = cmd.getOptionValue(Opts.o.name());
            if (outFile == null)
                throw new ParseException("output file not specified");

            ss = new AvailSS(fileName, log, wx, clean);
            if (sheetNum < 0)
                as = ss.addSheet(sheetName);
            else
                as = ss.addSheet(sheetNum);
            message = "toXML file: " + fileName + " sheet: " + sheetName;
            log.info(message);
            if (verbose)
                System.out.println(message);
            log.info("Options: -clean:" + clean + "; -wx:" + wx + "; output file: " + outFile);
            String timeStamp = new SimpleDateFormat("yyyy.MM.dd.HH.mm.ss").format(new java.util.Date());
            String shortDesc = String.format("generated XML from %s:%s on %s", fileName, sheetName, timeStamp);
            as.makeXMLFile(outFile, shortDesc);
        } else if (optToSS) {
            if (optToXML | optDumpSS | optDumpSheet)
                throw new ParseException("more than one operation specified");
            // TODO implement this
            outFile = cmd.getOptionValue(Opts.o.name());
            if (outFile == null)
                throw new ParseException("output file not specified");
            AvailXML x = new AvailXML(fileName, log);
            x.makeSS(outFile);
        } else if (optDumpSS) {
            if (optToXML | optToSS | optDumpSheet)
                throw new ParseException("more than one operation specified");
            message = "dumping file: " + fileName;
            log.info(message);
            if (verbose)
                System.out.println(message);
            AvailSS.dumpFile(fileName);
        } else { // dumpSheet
            if (sheetName == null)
                throw new ParseException("sheet name not specified");
            message = "dumping file: " + fileName + " sheet: " + sheetName;
            log.info(message);
            if (verbose)
                System.out.println(message);
            ss = new AvailSS(fileName, log, wx, clean);
            if (sheetNum < 0)
                as = ss.addSheet(sheetName);
            else
                as = ss.addSheet(sheetNum);

            ss.dumpSheet(sheetName);
        }
    } catch (ParseException exp) {
        System.out.println("bad command line: " + exp.getMessage());
        usage();
        System.exit(-1);
    }
}

From source file:com.act.lcms.db.io.LoadStandardIonAnalysisTableIntoDB.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 . jav  a  2  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(LoadStandardIonAnalysisTableIntoDB.class.getCanonicalName(), HELP_MESSAGE,
                opts, null, true);
        System.exit(1);
    }

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

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

    try (DB db = DB.openDBFromCLI(cl)) {
        db.getConn().setAutoCommit(false);

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

        for (Map<String, String> row : parser.getResults()) {
            Integer standardIonResultId = Integer.parseInt(row.get(
                    ExportStandardIonResultsFromDB.STANDARD_ION_HEADER_FIELDS.STANDARD_ION_RESULT_ID.name()));

            String dbValueOfMetlinIon = ExportStandardIonResultsFromDB.NULL_VALUE;
            StandardIonResult ionResult = StandardIonResult.getInstance().getById(db, standardIonResultId);
            if (ionResult.getManualOverrideId() != null) {
                // There is an existing manual override ion in the DB
                CuratedStandardMetlinIon curatedChemical = CuratedStandardMetlinIon.getBestMetlinIon(db,
                        ionResult.getManualOverrideId());
                dbValueOfMetlinIon = curatedChemical.getBestMetlinIon();
            }

            String manualPickOfMetlinIon = row
                    .get(ExportStandardIonResultsFromDB.STANDARD_ION_HEADER_FIELDS.MANUAL_PICK.name());

            // If the manual metlin ion pick row is not NULL and it is not the same as the value stored in the DB, then
            // we need to add a new entry to the curated metlin ion table.
            if (!manualPickOfMetlinIon.equals(ExportStandardIonResultsFromDB.NULL_VALUE)
                    && !manualPickOfMetlinIon.equals(dbValueOfMetlinIon)) {
                System.out.format("Manual override has been found, so updating the DB\n");
                // A manual entry was created.
                if (!MS1.VALID_MS1_IONS.contains(manualPickOfMetlinIon)) {
                    System.err.format("ERROR: found invalid chemical name: %s\n", manualPickOfMetlinIon);
                    System.exit(-1);
                }

                String note = row.get(ExportStandardIonResultsFromDB.STANDARD_ION_HEADER_FIELDS.NOTE.name());
                CuratedStandardMetlinIon result = CuratedStandardMetlinIon.insertCuratedStandardMetlinIonIntoDB(
                        db, LocalDateTime.now(CuratedStandardMetlinIon.utcDateTimeZone),
                        cl.getOptionValue(OPTION_AUTHOR), manualPickOfMetlinIon, note, standardIonResultId);

                if (result == null) {
                    System.err.format(
                            "WARNING: Could not insert curated entry to the curated metlin ion table\n",
                            manualPickOfMetlinIon);
                    System.exit(-1);
                } else {
                    StandardIonResult getIonResult = StandardIonResult.getInstance().getById(db,
                            standardIonResultId);
                    getIonResult.setManualOverrideId(result.getId());
                    if (!StandardIonResult.getInstance().update(db, getIonResult)) {
                        System.err.format(
                                "WARNING: Could not insert manual override id to the standard ion table\n",
                                manualPickOfMetlinIon);
                        System.exit(-1);
                    } else {
                        System.out.format(
                                "Successfully committed updates to the standard ion table and the curated metlin ion table\n");
                    }
                }
            }
        }

        db.getConn().commit();
    }
}

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

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    opts.addOption(Option.builder("b").argName("barcode").desc("The barcode of the plate to print").hasArg()
            .longOpt("barcode").build());
    opts.addOption(Option.builder("n").argName("name").desc("The name of the plate to print").hasArg()
            .longOpt("name").build());

    opts.addOption(Option.builder("o").argName("output file").desc(
            "An output file to which to write this plate's composition table (writes to stdout if omitted")
            .hasArg().longOpt("output-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 w  w.j  ava2 s.co  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());
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

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

    if (!cl.hasOption("b") && !cl.hasOption("n")) {
        System.err.format("Must specify either plate barcode or plate name.");
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
    }

    DB db = null;
    try {
        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"));
        }

        Writer writer = null;
        if (cl.hasOption("o")) {
            writer = new FileWriter(cl.getOptionValue("o"));
        } else {
            writer = new OutputStreamWriter(System.out);
        }

        PlateCompositionWriter cw = new PlateCompositionWriter();
        if (cl.hasOption("b")) {
            cw.writePlateCompositionByBarcode(db, cl.getOptionValue("b"), writer);
        } else if (cl.hasOption("n")) {
            cw.writePlateCompositionByName(db, cl.getOptionValue("n"), writer);
        }

        writer.close();
    } finally {
        if (db != null) {
            db.close();
        }
    }
}

From source file:com.blackducksoftware.integration.hubdiff.HubDiff.java

public static void main(String[] args) throws IOException, IllegalArgumentException, EncryptionException,
        HubIntegrationException, JSONException {
    Options options = new Options();
    Option optUrl1 = new Option("h1", "hub-url-1", true,
            "the base url to the hub. Example: http://int-hub01.dc1.lan:8080");
    Option optUsername1 = new Option("u1", "username-1", true, "the username for your hub instance");
    Option optPassword1 = new Option("p1", "password-1", true,
            "the password for your hub instance and username");
    Option optUrl2 = new Option("h2", "hub-url-2", true,
            "the base url to the hub. Example: http://int-auto.dc1.lan:9000");
    Option optUsername2 = new Option("u2", "username-2", true, "the username for your hub instance");
    Option optPassword2 = new Option("p2", "password-2", true,
            "the password for your hub instance and username");
    Option optOutputFile = new Option("o", "output", true, "the file path to your output file");

    optUrl1.setRequired(true);/*www  . jav  a 2 s.c  o  m*/
    optUsername1.setRequired(true);
    optPassword1.setRequired(true);
    optUsername2.setRequired(true);
    optUrl1.setRequired(true);
    optPassword2.setRequired(true);
    optOutputFile.setRequired(false);

    // Add options to collection
    options.addOption(optUrl1);
    options.addOption(optUsername1);
    options.addOption(optPassword1);
    options.addOption(optUrl2);
    options.addOption(optUsername2);
    options.addOption(optPassword2);
    options.addOption(optOutputFile);

    // Parse the arguments array for the options
    CommandLineParser cliParser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine optionParser;
    try {
        optionParser = cliParser.parse(options, args);
    } catch (ParseException e) {
        formatter.printHelp("hub-model-generator", options);
        log.error(e.getMessage());
        System.exit(1);
        return;
    }

    // Read arguments
    String url1 = optionParser.getOptionValue("hub-url-1");
    String username1 = optionParser.getOptionValue("username-1");
    String password1 = optionParser.getOptionValue("password-1");
    String url2 = optionParser.getOptionValue("hub-url-2");
    String username2 = optionParser.getOptionValue("username-2");
    String password2 = optionParser.getOptionValue("password-2");
    String outputFilePath = optionParser.getOptionValue("output");

    HubServerConfigBuilder configBuilder = new HubServerConfigBuilder();
    configBuilder.setHubUrl(url1);
    configBuilder.setUsername(username1);
    configBuilder.setPassword(password1);
    HubServerConfig config1 = configBuilder.build();

    HubServerConfigBuilder configBuilder2 = new HubServerConfigBuilder();
    configBuilder2.setHubUrl(url2);
    configBuilder2.setUsername(username2);
    configBuilder2.setPassword(password2);
    HubServerConfig config2 = configBuilder2.build();

    HubDiff hubDiff = new HubDiff(config1, config2);
    hubDiff.printDiff(System.out);

    if (outputFilePath != null) {
        File outputFile = new File(outputFilePath);
        hubDiff.writeDiffAsCSV(outputFile);
    }
}

From source file:com.act.biointerpretation.desalting.ChemicalDesalter.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.  j a v  a2  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(ReactionDesalter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    ChemicalDesalter runner = new ChemicalDesalter();
    String outAnalysis = cl.getOptionValue(OPTION_OUTPUT_PREFIX);
    if (cl.hasOption(OPTION_INCHI_INPUT_LIST)) {
        File inputFile = new File(cl.getOptionValue(OPTION_INCHI_INPUT_LIST));
        if (!inputFile.exists()) {
            System.err.format("Cannot find input file at %s\n", inputFile.getAbsolutePath());
            HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts,
                    null, true);
            System.exit(1);
        }
        runner.exampleChemicalsList(outAnalysis, inputFile);
    }
}

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

public static void main(String[] args) {
    try {//  ww  w.j  a 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("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("BasicNVTest.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("proxy")) {
            proxySetting = line.getOptionValue("proxy");
        }

        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
                + "***   (\"3G Busy\" is one of NV's built-in network profiles. A network profile specifies the         ***"
                + newLine
                + "***   network traffic behavior, including latency, packet loss, and incoming/outgoing bandwidth.   ***"
                + newLine
                + "***   Network profiles are used to emulate traffic over real-world networks.)                      ***"
                + 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.                                                       ***"
                + newLine
                + "***                                                                                                ***"
                + newLine
                + "***   You can view the actual steps of this sample in the BasicNVTest.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                                                                *****/
        printPartDescription("------    Part 4 - Stop the NV test");
        stopTest();
        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.lcms.db.io.report.IonAnalysisInterchangeModelOperations.java

public static void main(String[] args) throws IOException {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*  w  ww.j av  a2s . c  o m*/
    }

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

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(IonAnalysisInterchangeModelOperations.class.getCanonicalName(), HELP_MESSAGE,
                opts, null, true);
        System.exit(1);
    }

    if (cl.hasOption(OPTION_LOG_DISTRIBUTION)) {
        IonAnalysisInterchangeModel model = new IonAnalysisInterchangeModel();
        model.loadResultsFromFile(new File(cl.getOptionValue(OPTION_INPUT_FILE)));
        Map<Pair<Double, Double>, Integer> rangeToCount = model
                .computeLogFrequencyDistributionOfMoleculeCountToMetric(
                        IonAnalysisInterchangeModel.METRIC.valueOf(cl.getOptionValue(OPTION_LOG_DISTRIBUTION)));

        try (BufferedWriter predictionWriter = new BufferedWriter(
                new FileWriter(new File(OPTION_OUTPUT_FILE)))) {
            for (Map.Entry<Pair<Double, Double>, Integer> entry : rangeToCount.entrySet()) {
                String value = String.format("%f,%d", entry.getKey().getLeft(), entry.getValue());
                predictionWriter.write(value);
                predictionWriter.newLine();
            }
        }
    }
}

From source file:com.act.lcms.db.io.PrintConstructInfo.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 . jav  a 2 s. co 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;
    }

    File lcmsDir = new File(cl.getOptionValue(OPTION_DIRECTORY));
    if (!lcmsDir.isDirectory()) {
        System.err.format("File at %s is not a directory\n", lcmsDir.getAbsolutePath());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    try (DB db = DB.openDBFromCLI(cl)) {
        System.out.print("Loading/updating LCMS scan files into DB\n");
        ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir);

        String construct = cl.getOptionValue(OPTION_CONSTRUCT);
        List<LCMSWell> lcmsWells = LCMSWell.getInstance().getByConstructID(db, construct);
        Collections.sort(lcmsWells, new Comparator<LCMSWell>() {
            @Override
            public int compare(LCMSWell o1, LCMSWell o2) {
                return o1.getId().compareTo(o2.getId());
            }
        });

        Set<String> uniqueMSIDs = new HashSet<>();
        Map<Integer, Plate> platesById = new HashMap<>();

        System.out.format("\n\n-- Construct %s --\n\n", construct);

        List<ChemicalAssociatedWithPathway> pathwayChems = ChemicalAssociatedWithPathway.getInstance()
                .getChemicalsAssociatedWithPathwayByConstructId(db, construct);
        System.out.print("Chemicals associated with pathway:\n");
        System.out.format("  %-8s%-15s%-45s\n", "index", "kind", "chemical");
        for (ChemicalAssociatedWithPathway chem : pathwayChems) {
            System.out.format("  %-8d%-15s%-45s\n", chem.getIndex(), chem.getKind(), chem.getChemical());
        }

        System.out.print("\nLCMS wells:\n");
        System.out.format("  %-15s%-6s%-15s%-15s%-15s\n", "barcode", "well", "msid", "fed", "lcms_count");
        for (LCMSWell well : lcmsWells) {
            uniqueMSIDs.add(well.getMsid());

            Plate p = platesById.get(well.getPlateId());
            if (p == null) {
                // TODO: migrate Plate to be a subclass of BaseDBModel.
                p = Plate.getPlateById(db, well.getPlateId());
                platesById.put(p.getId(), p);
            }

            String chem = well.getChemical();
            List<ScanFile> scanFiles = ScanFile.getScanFileByPlateIDRowAndColumn(db, p.getId(),
                    well.getPlateRow(), well.getPlateColumn());

            System.out.format("  %-15s%-6s%-15s%-15s%-15d\n", p.getBarcode(), well.getCoordinatesString(),
                    well.getMsid(), chem == null || chem.isEmpty() ? "--" : chem, scanFiles.size());
            System.out.flush();
        }

        List<Integer> plateIds = Arrays.asList(platesById.keySet().toArray(new Integer[platesById.size()]));
        Collections.sort(plateIds);
        System.out.print("\nAppears in plates:\n");
        for (Integer id : plateIds) {
            Plate p = platesById.get(id);
            System.out.format("  %s: %s\n", p.getBarcode(), p.getName());
        }

        List<String> msids = Arrays.asList(uniqueMSIDs.toArray(new String[uniqueMSIDs.size()]));
        Collections.sort(msids);
        System.out.format("\nMSIDS: %s\n", StringUtils.join(msids, ", "));

        Set<String> availableNegativeControls = new HashSet<>();
        for (Map.Entry<Integer, Plate> entry : platesById.entrySet()) {
            List<LCMSWell> wells = LCMSWell.getInstance().getByPlateId(db, entry.getKey());
            for (LCMSWell well : wells) {
                if (!construct.equals(well.getComposition())) {
                    availableNegativeControls.add(well.getComposition());
                }
            }
        }

        // Print available standards for each step w/ plate barcodes and coordinates.
        System.out.format("\nAvailable Standards:\n");
        Map<Integer, Plate> plateCache = new HashMap<>();
        for (ChemicalAssociatedWithPathway chem : pathwayChems) {
            List<StandardWell> matchingWells = StandardWell.getInstance().getStandardWellsByChemical(db,
                    chem.getChemical());
            for (StandardWell well : matchingWells) {
                if (!plateCache.containsKey(well.getPlateId())) {
                    Plate p = Plate.getPlateById(db, well.getPlateId());
                    plateCache.put(p.getId(), p);
                }
            }
            Map<Integer, List<StandardWell>> standardWellsByPlateId = new HashMap<>();
            for (StandardWell well : matchingWells) {
                List<StandardWell> plateWells = standardWellsByPlateId.get(well.getPlateId());
                if (plateWells == null) {
                    plateWells = new ArrayList<>();
                    standardWellsByPlateId.put(well.getPlateId(), plateWells);
                }
                plateWells.add(well);
            }
            List<Pair<String, Integer>> plateBarcodes = new ArrayList<>(plateCache.size());
            for (Plate p : plateCache.values()) {
                if (p.getBarcode() == null) {
                    plateBarcodes.add(Pair.of("(no barcode)", p.getId()));
                } else {
                    plateBarcodes.add(Pair.of(p.getBarcode(), p.getId()));
                }
            }
            Collections.sort(plateBarcodes);
            System.out.format("  %s:\n", chem.getChemical());
            for (Pair<String, Integer> barcodePair : plateBarcodes) {
                // TODO: hoist this whole sorting/translation step into a utility class.
                List<StandardWell> wells = standardWellsByPlateId.get(barcodePair.getRight());
                if (wells == null) {
                    // Don't print plates that don't apply to this chemical, which can happen because we're caching the plates.
                    continue;
                }
                Collections.sort(wells, new Comparator<StandardWell>() {
                    @Override
                    public int compare(StandardWell o1, StandardWell o2) {
                        int c = o1.getPlateRow().compareTo(o2.getPlateRow());
                        if (c != 0)
                            return c;
                        return o1.getPlateColumn().compareTo(o2.getPlateColumn());
                    }
                });
                List<String> descriptions = new ArrayList<>(wells.size());
                for (StandardWell well : wells) {
                    descriptions.add(String.format("%s in %s%s", well.getCoordinatesString(), well.getMedia(),
                            well.getConcentration() == null ? ""
                                    : String.format(" c. %f", well.getConcentration())));
                }
                System.out.format("    %s: %s\n", barcodePair.getLeft(), StringUtils.join(descriptions, ", "));
            }
        }

        List<String> negativeControlStrains = Arrays
                .asList(availableNegativeControls.toArray(new String[availableNegativeControls.size()]));
        Collections.sort(negativeControlStrains);
        System.out.format("\nAvailable negative controls: %s\n", StringUtils.join(negativeControlStrains, ","));
        System.out.print("\n----------\n");
        System.out.print("\n\n");
    }
}

From source file:com.dustindoloff.s3websitedeploy.Main.java

public static void main(final String[] args) {
    final Options options = buildOptions();
    final CommandLineParser parser = new DefaultParser();
    final CommandLine commandLine;
    try {//from w ww.j  av  a  2 s .c  o m
        commandLine = parser.parse(options, args);
    } catch (final ParseException e) {
        System.out.println(e.getMessage());
        new HelpFormatter().printHelp("s3WebsiteDeploy", options);
        System.exit(1);
        return;
    }

    final File websiteZip = new File(commandLine.getOptionValue(ARG_WEBSITE_ZIP));
    final String s3Bucket = commandLine.getOptionValue(ARG_BUCKET);
    final String awsAccessKey = commandLine.getOptionValue(ARG_AWS_ACCESS_KEY);
    final String awsSecretKey = commandLine.getOptionValue(ARG_AWS_SECRET_KEY);

    final ZipFile zipFile = getAsValidZip(websiteZip);
    if (zipFile == null) {
        System.out.println("Invalid zip file passed in");
        System.exit(2);
        return;
    }

    System.out.println("Running S3 Website Deploy");

    final AmazonS3 s3Client = new AmazonS3Client(new BasicAWSCredentials(awsAccessKey, awsSecretKey));

    final Region bucketRegion = getBucketRegion(s3Client, s3Bucket);

    if (bucketRegion == null) {
        System.out.println("Unable to get the region for the bucket.");
        System.exit(3);
        return;
    }

    s3Client.setRegion(bucketRegion);

    if (!emptyBucket(s3Client, s3Bucket)) {
        System.out.println("Unable to upload to empty bucket.");
        System.exit(4);
        return;
    }

    if (!upload(s3Client, s3Bucket, zipFile)) {
        System.out.println("Unable to upload to S3.");
        System.exit(5);
        return;
    }

    System.out.println("Deployment Complete");
}

From source file:eu.freme.bpt.Main.java

public static void main(String[] args) {
    final List<String> services = new ArrayList<>();
    for (EService eService : EService.values()) {
        services.add(eService.getName());
    }//w w w.j  a v a  2 s  . c  o  m

    Pair<EService, String[]> serviceAndArgs = extractService(args, services);

    EService service = serviceAndArgs.getName();

    // create options that will be parsed from the args
    /////// General BPT options ///////
    Option helpOption = new Option("h", "help", false, "Prints this message");
    Option inputOption = Option.builder("if").longOpt("input-file").argName("input file").desc(
            "The input file or directory to process. In case of a directory, each file in that directory is processed. "
                    + "If not given, standard in is used.")
            .hasArg().build();
    Option outputOption = Option.builder("od").longOpt("output-dir").argName("output dir")
            .desc("The output directory. If not given, output is written to standard out.").hasArg().build();
    Option propertiesOption = Option.builder("prop").longOpt("properties").argName("properties file")
            .desc("The properties file that contains configuration of the tool.").hasArg().build();

    Options options = new Options().addOption(helpOption).addOption(inputOption).addOption(outputOption)
            .addOption(propertiesOption);

    /////// Common service options ///////
    Option informatOption = Option.builder("f").longOpt("informat").argName("FORMAT")
            .desc("The format of the input document(s). Defaults to 'turtle'").hasArg().build();
    Option outformatOption = Option.builder("o").longOpt("outformat").argName("FORMAT")
            .desc("The desired output format of the service. Defaults to 'turtle'").hasArg().build();
    options.addOption(informatOption).addOption(outformatOption);

    /////// Service specific options ///////
    if (service != null) {
        switch (service) {
        case E_TRANSLATION:
            ETranslation.addOptions(options);
            break;
        case E_ENTITY:
            EEntity.addOptions(options);
            break;
        case E_LINK:
            ELink.addOptions(options);
            break;
        case E_TERMINOLOGY:
            ETerminology.addOptions(options);
            break;
        case PIPELINING:
            Pipelining.addOptions(options);
            break;
        case E_PUBLISHING:
            // TODO !
        default:
            logger.warn("Unknown service {}. Skipping!", service);
            break;
        }
    } else {
        ETranslation.addOptions(options);
        EEntity.addOptions(options);
        ELink.addOptions(options);
        ETerminology.addOptions(options);
        Pipelining.addOptions(options);
    }

    CommandLine commandLine = null;
    int exitValue;
    try {
        CommandLineParser parser = new DefaultParser();
        commandLine = parser.parse(options, serviceAndArgs.getValue());
        exitValue = 0;
    } catch (ParseException e) {
        System.err.println(e.getMessage());
        exitValue = 1;
    }
    if ((exitValue != 0) || commandLine.hasOption("h") || service == null) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(132);
        formatter.printHelp("java -jar <this jar file> <e-service> ", options, true);
        System.exit(exitValue);
    }

    logger.debug("Commandline successfully parsed!");

    try {
        BPT batchProcessingTool = new BPT();
        if (commandLine.hasOption("prop")) {
            batchProcessingTool.loadProperties(commandLine.getOptionValue("prop"));
        }
        if (commandLine.hasOption("if")) {
            batchProcessingTool.setInput(commandLine.getOptionValue("if"));
        }
        if (commandLine.hasOption("od")) {
            batchProcessingTool.setOutput(commandLine.getOptionValue("od"));
        }
        if (commandLine.hasOption('f')) {
            batchProcessingTool.setInFormat(Format.valueOf(commandLine.getOptionValue('f').replace('-', '_')));
        }
        if (commandLine.hasOption('o')) {
            batchProcessingTool.setOutFormat(Format.valueOf(commandLine.getOptionValue('o').replace('-', '_')));
        }

        switch (service) {
        case E_TRANSLATION:
            batchProcessingTool.eTranslation(commandLine.getOptionValue("source-lang"),
                    commandLine.getOptionValue("target-lang"), commandLine.getOptionValue("system"),
                    commandLine.getOptionValue("domain"), commandLine.getOptionValue("key"));
            break;
        case E_ENTITY:
            batchProcessingTool.eEntity(commandLine.getOptionValue("language"),
                    commandLine.getOptionValue("dataset"), commandLine.getOptionValue("mode"));
            break;
        case E_LINK:
            batchProcessingTool.eLink(commandLine.getOptionValue("templateid"));
            break;
        case E_TERMINOLOGY:
            batchProcessingTool.eTerminology(commandLine.getOptionValue("source-lang"),
                    commandLine.getOptionValue("target-lang"), commandLine.getOptionValue("collection"),
                    commandLine.getOptionValue("domain"), commandLine.getOptionValue("key"),
                    commandLine.getOptionValue("mode"));
            break;
        case PIPELINING:
            batchProcessingTool.pipelining(commandLine.getOptionValue("templateid"));
            break;
        case E_PUBLISHING:
        default:
            logger.error("Unknown service {}. Aborting!", service);
            System.exit(3);
        }
    } catch (Exception e) {
        logger.error("Cannot handle input or output. Reason: ", e);
        System.exit(2);
    }
}