Example usage for java.io File getAbsolutePath

List of usage examples for java.io File getAbsolutePath

Introduction

In this page you can find the example usage for java.io File getAbsolutePath.

Prototype

public String getAbsolutePath() 

Source Link

Document

Returns the absolute pathname string of this abstract pathname.

Usage

From source file:at.nonblocking.cliwix.cli.CliwixCliClient.java

public static void main(String[] args) throws Exception {
    Options options = null;/*from w  w w . java 2  s .  c o  m*/

    try {
        options = Options.parseArgs(args);
    } catch (CliwixCliClientArgumentException e) {
        if (debug)
            console.printStacktrace(e);
        console.printlnError("Error: Invalid arguments: " + e.getMessage());
        Options.printUsage();
        console.exit(EXIT_STATUS_FAIL);
        return;
    }

    if (options == null || Options.COMMAND_HELP.equals(options.getCommand())) {
        Options.printUsage();
        console.exit(0);
        return;
    }

    if (Options.COMMAND_CREATE_CONFIG.equals(options.getCommand())) {
        if (args.length < 2) {
            console.printlnError("Error: No config file location given!");
            console.exit(EXIT_STATUS_FAIL);
            return;
        }
        File configFile = new File(args[1]);
        options.copyDefaultPropertiesTo(configFile);
        console.println("Configuration saved under: " + configFile.getAbsolutePath());
        console.exit(0);
        return;
    }

    debug = options.isDebug();

    String cliwixServerUrl = options.getServerCliwixUrl();
    String username = options.getServerUsername();
    String password = options.getServerPassword();

    if (cliwixServerUrl == null) {
        console.printlnError("Error: Property server.cliwix.url is required!");
        console.exit(EXIT_STATUS_FAIL);
        return;
    }

    cookieManager.clear();

    //Login
    if (username != null && password != null) {
        JSONObject loginData = new JSONObject();
        loginData.put("username", username);
        loginData.put("password", password);
        JSONObject result = postJson(cliwixServerUrl, "/services/login", loginData);
        JSONObject loginResult = (JSONObject) result.get("loginResult");

        if (loginResult.get("succeeded") == Boolean.TRUE) {
            console.println("Login successful");
        } else {
            console.printlnError("Error: Login failed! Reason: " + loginData.get("errorMessage"));
            console.exit(EXIT_STATUS_FAIL);
            return;
        }

    } else if (username != null) {
        console.printlnError("Error: If -user is set -pass is required!");
        console.exit(EXIT_STATUS_FAIL);
        return;
    } else if (password != null) {
        console.printlnError("Error: If -pass is set -user is required!");
        console.exit(EXIT_STATUS_FAIL);
        return;
    }

    switch (options.getCommand()) {
    case Options.COMMAND_INFO:
        doInfo(cliwixServerUrl, options);
        break;
    case Options.COMMAND_EXPORT:
        doExport(cliwixServerUrl, options);
        break;
    case Options.COMMAND_IMPORT:
        doImport(cliwixServerUrl, options);
        break;
    default:
    case Options.COMMAND_HELP:
        Options.printUsage();
    }
}

From source file:com.joseflavio.unhadegato.Concentrador.java

/**
 * @param args [0] = Diretrio de configuraes.
 *///from   ww  w .  j ava  2  s.c  o  m
public static void main(String[] args) {

    log.info(Util.getMensagem("unhadegato.iniciando"));

    try {

        /***********************/

        if (args.length > 0) {
            if (!args[0].isEmpty()) {
                configuracao = new File(args[0]);
                if (!configuracao.isDirectory()) {
                    String msg = Util.getMensagem("unhadegato.diretorio.incorreto");
                    System.out.println(msg);
                    log.error(msg);
                    System.exit(1);
                }
            }
        }

        if (configuracao == null) {
            configuracao = new File(System.getProperty("user.home") + File.separator + "unhadegato");
            configuracao.mkdirs();
        }

        log.info(Util.getMensagem("unhadegato.diretorio.endereco", configuracao.getAbsolutePath()));

        /***********************/

        File confGeralArq = new File(configuracao, "unhadegato.conf");

        if (!confGeralArq.exists()) {
            try (InputStream is = Concentrador.class.getResourceAsStream("/unhadegato.conf");
                    OutputStream os = new FileOutputStream(confGeralArq);) {
                IOUtils.copy(is, os);
            }
        }

        Properties confGeral = new Properties();

        try (FileInputStream fis = new FileInputStream(confGeralArq)) {
            confGeral.load(fis);
        }

        String prop_porta = confGeral.getProperty("porta");
        String prop_porta_segura = confGeral.getProperty("porta.segura");
        String prop_seg_pri = confGeral.getProperty("seguranca.privada");
        String prop_seg_pri_senha = confGeral.getProperty("seguranca.privada.senha");
        String prop_seg_pri_tipo = confGeral.getProperty("seguranca.privada.tipo");
        String prop_seg_pub = confGeral.getProperty("seguranca.publica");
        String prop_seg_pub_senha = confGeral.getProperty("seguranca.publica.senha");
        String prop_seg_pub_tipo = confGeral.getProperty("seguranca.publica.tipo");

        if (StringUtil.tamanho(prop_porta) == 0)
            prop_porta = "8885";
        if (StringUtil.tamanho(prop_porta_segura) == 0)
            prop_porta_segura = "8886";
        if (StringUtil.tamanho(prop_seg_pri) == 0)
            prop_seg_pri = "servidor.jks";
        if (StringUtil.tamanho(prop_seg_pri_senha) == 0)
            prop_seg_pri_senha = "123456";
        if (StringUtil.tamanho(prop_seg_pri_tipo) == 0)
            prop_seg_pri_tipo = "JKS";
        if (StringUtil.tamanho(prop_seg_pub) == 0)
            prop_seg_pub = "cliente.jks";
        if (StringUtil.tamanho(prop_seg_pub_senha) == 0)
            prop_seg_pub_senha = "123456";
        if (StringUtil.tamanho(prop_seg_pub_tipo) == 0)
            prop_seg_pub_tipo = "JKS";

        /***********************/

        File seg_pri = new File(prop_seg_pri);
        if (!seg_pri.isAbsolute())
            seg_pri = new File(configuracao.getAbsolutePath() + File.separator + prop_seg_pri);

        if (seg_pri.exists()) {
            System.setProperty("javax.net.ssl.keyStore", seg_pri.getAbsolutePath());
            System.setProperty("javax.net.ssl.keyStorePassword", prop_seg_pri_senha);
            System.setProperty("javax.net.ssl.keyStoreType", prop_seg_pri_tipo);
        }

        File seg_pub = new File(prop_seg_pub);
        if (!seg_pub.isAbsolute())
            seg_pub = new File(configuracao.getAbsolutePath() + File.separator + prop_seg_pub);

        if (seg_pub.exists()) {
            System.setProperty("javax.net.ssl.trustStore", seg_pub.getAbsolutePath());
            System.setProperty("javax.net.ssl.trustStorePassword", prop_seg_pub_senha);
            System.setProperty("javax.net.ssl.trustStoreType", prop_seg_pub_tipo);
        }

        /***********************/

        new Thread() {

            File arquivo = new File(configuracao, "copaibas.conf");

            long ultimaData = -1;

            @Override
            public void run() {

                while (true) {

                    long data = arquivo.lastModified();

                    if (data > ultimaData) {
                        executarCopaibas(arquivo);
                        ultimaData = data;
                    }

                    try {
                        Thread.sleep(5 * 1000);
                    } catch (InterruptedException e) {
                        return;
                    }

                }

            }

        }.start();

        /***********************/

        log.info(Util.getMensagem("unhadegato.conexao.esperando"));

        log.info(Util.getMensagem("copaiba.porta.normal.abrindo", prop_porta));
        Portal portal1 = new Portal(new SocketServidor(Integer.parseInt(prop_porta), false, true));

        log.info(Util.getMensagem("copaiba.porta.segura.abrindo", prop_porta_segura));
        Portal portal2 = new Portal(new SocketServidor(Integer.parseInt(prop_porta_segura), true, true));

        portal1.start();
        portal2.start();

        portal1.join();

        /***********************/

    } catch (Exception e) {

        log.error(e.getMessage(), e);

    } finally {

        for (CopaibaGerenciador gerenciador : gerenciadores.values())
            gerenciador.encerrar();
        gerenciadores.clear();
        gerenciadores = null;

    }

}

From source file:com.faces.controller.util.FaceRecognitionUtils.java

public static void main(String[] args) {
    String path = "H:\\MyWork\\facerecognition\\javacv-02385ce192fb\\facerecExample_ORL\\Cambridge_FaceDB\\s42\\";
    List<String> listOfimages = new ArrayList<>();

    File dir = new File(path);

    File[] arrFile = dir.listFiles();
    for (File file : arrFile) {
        listOfimages.add(file.getAbsolutePath());
    }//from   w  w  w  . ja v  a 2  s  . co m

    FaceRecognitionUtils utils = new FaceRecognitionUtils();
    utils.storeTraningData(1, listOfimages);

    listOfimages.clear();
    String path1 = "H:\\MyWork\\facerecognition\\javacv-02385ce192fb\\facerecExample_ORL\\Cambridge_FaceDB\\s41\\";
    listOfimages.add(path1 + File.separator + "35.jpg");

    utils.recognizeStudent(1, listOfimages);

}

From source file:com.act.lcms.v2.TraceIndexExtractor.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 .  ja v a2s  .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(TraceIndexExtractor.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

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

    // Not enough memory available?  We're gonna need a bigger heap.
    long maxMemory = Runtime.getRuntime().maxMemory();
    if (maxMemory < 1 << 34) { // 16GB
        String msg = StringUtils.join(
                String.format(
                        "You have run this class with a maximum heap size of less than 16GB (%d to be exact). ",
                        maxMemory),
                "There is no way this process will complete with that much space available. ",
                "Crank up your heap allocation with -Xmx and try again.", "");
        throw new RuntimeException(msg);
    }

    File inputFile = new File(cl.getOptionValue(OPTION_SCAN_FILE));
    if (!inputFile.exists()) {
        System.err.format("Cannot find input scan file at %s\n", inputFile.getAbsolutePath());
        HELP_FORMATTER.printHelp(TraceIndexExtractor.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    File rocksDBFile = new File(cl.getOptionValue(OPTION_INDEX_PATH));
    if (rocksDBFile.exists()) {
        System.err.format("Index file at %s already exists--remove and retry\n", rocksDBFile.getAbsolutePath());
        HELP_FORMATTER.printHelp(TraceIndexExtractor.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    List<Double> targetMZs = new ArrayList<>();
    try (BufferedReader reader = new BufferedReader(new FileReader(cl.getOptionValue(OPTION_TARGET_MASSES)))) {
        String line;
        while ((line = reader.readLine()) != null) {
            targetMZs.add(Double.valueOf(line));
        }
    }

    TraceIndexExtractor extractor = new TraceIndexExtractor();
    extractor.processScan(targetMZs, inputFile, rocksDBFile);
}

From source file:fi.uta.infim.usaproxyreportgenerator.App.java

/**
 * Entry point.//w  w w .  j av a 2s .  c om
 * @param args command line arguments
 */
public static void main(String[] args) {
    printLicense();
    System.out.println();

    try {
        // Command line arguments
        cli = parser.parse(cliOptions, args);
    } catch (org.apache.commons.cli.ParseException e) {
        System.err.println(e.getMessage());
        printHelp();
        return;
    }

    File outputDir;
    // Use CWD if output dir is not supplied
    outputDir = new File(cli.getOptionValue("outputDir", "."));

    // Set up the browsing data provider that mines the log entries for 
    // visualizable data.
    setupDataProvider();

    // Output CLI options, so that the user sees what is happening
    System.out.println("Output directory: " + outputDir.getAbsolutePath());
    System.out.println("Data provider class: " + dataProviderClass.getCanonicalName());

    UsaProxyLogParser parser = new UsaProxyLogParser();
    UsaProxyLog log;
    try {
        String filenames[] = cli.getArgs();
        if (filenames.length == 0) {
            throw new IndexOutOfBoundsException();
        }

        // Interpret remaining cli args as file names
        System.out.print("Parsing log file... ");
        log = parser.parseFilesByName(Arrays.asList(filenames));
        System.out.println("done.");
    } catch (IOException ioe) {
        System.err.println("Error opening log file: " + ioe.getMessage());
        printHelp();
        return;
    } catch (ParseException pe) {
        System.err.println("Error parsing log file.");
        printHelp();
        return;
    } catch (IndexOutOfBoundsException e) {
        System.err.println("Please supply a file name.");
        printHelp();
        return;
    } catch (NoSuchElementException e) {
        System.err.println("Error opening log file: " + e.getMessage());
        printHelp();
        return;
    }

    setupJsonConfig(); // Set up JSON processors

    // Iterate over sessions and generate a report for each one.
    for (UsaProxySession s : log.getSessions()) {
        System.out.print("Generating report for session " + s.getSessionID() + "... ");
        try {
            generateHTMLReport(s, outputDir);
            System.out.println("done.");
        } catch (IOException e) {
            System.err.println(
                    "I/O error generating report for session id " + s.getSessionID() + ": " + e.getMessage());
            System.err.println("Skipping.");
        } catch (TemplateException e) {
            System.err.println(
                    "Error populating template for session id " + s.getSessionID() + ": " + e.getMessage());
            System.err.println("Skipping.");
        }
    }
}

From source file:hk.idv.kenson.jrconsole.Console.java

/**
 * @param args//from   w ww.  j  a v  a 2  s.c o m
 */
public static void main(String[] args) {
    try {
        Map<String, Object> params = Console.parseArgs(args);
        if (params.containsKey("help")) {
            printUsage();
            return;
        }
        if (params.containsKey("version")) {
            System.err.println("Version: " + VERSION);
            return;
        }
        if (params.containsKey("debug")) {
            for (String key : params.keySet())
                log.info("\"" + key + "\" => \"" + params.get(key) + "\"");
            return;
        }

        checkParam(params);
        stepCompile(params);
        JasperReport jasper = stepLoadReport(params);
        JasperPrint print = stepFill(jasper, params);
        InputStream stream = stepExport(print, params);

        File output = new File(params.get("output").toString());
        FileOutputStream fos = new FileOutputStream(output);
        copy(stream, fos);

        fos.close();
        stream.close();
        System.out.println(output.getAbsolutePath()); //Output the report path for pipe
    } catch (IllegalArgumentException ex) {
        printUsage();
        System.err.println("Error: " + ex.getMessage());
        ex.printStackTrace();
    } catch (RuntimeException ex) {
        throw ex;
    } catch (Exception ex) {
        throw new RuntimeException("Unexpected exception", ex);
    }
}

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

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

    try (DB db = DB.openDBFromCLI(cl)) {
        List<String> chemicalNames = new ArrayList<>();
        if (cl.hasOption(OPTION_CONSTRUCT)) {
            // Extract the chemicals in the pathway and their product masses, then look up info on those chemicals
            List<Pair<ChemicalAssociatedWithPathway, Double>> productMasses = Utils
                    .extractMassesForChemicalsAssociatedWithConstruct(db, cl.getOptionValue(OPTION_CONSTRUCT));

            for (Pair<ChemicalAssociatedWithPathway, Double> pair : productMasses) {
                chemicalNames.add(pair.getLeft().getChemical());
            }
        }

        if (cl.hasOption(OPTION_CHEMICALS)) {
            chemicalNames.addAll(Arrays.asList(cl.getOptionValues(OPTION_CHEMICALS)));
        }

        if (chemicalNames.size() == 0) {
            System.err.format("No chemicals can be found from the input query.\n");
            System.exit(-1);
        }

        List<String> standardIonHeaderFields = new ArrayList<String>() {
            {
                add(STANDARD_ION_HEADER_FIELDS.CHEMICAL.name());
                add(STANDARD_ION_HEADER_FIELDS.BEST_ION_FROM_ALGO.name());
                add(STANDARD_ION_HEADER_FIELDS.MANUAL_PICK.name());
                add(STANDARD_ION_HEADER_FIELDS.AUTHOR.name());
                add(STANDARD_ION_HEADER_FIELDS.DIAGNOSTIC_PLOTS.name());
                add(STANDARD_ION_HEADER_FIELDS.NOTE.name());
            }
        };

        String outAnalysis;
        if (cl.hasOption(OPTION_OUTPUT_PREFIX)) {
            outAnalysis = cl.getOptionValue(OPTION_OUTPUT_PREFIX) + "." + TSV_FORMAT;
        } else {
            outAnalysis = String.join("-", chemicalNames) + "." + TSV_FORMAT;
        }

        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);
        }

        String plottingDirectory = cl.getOptionValue(OPTION_PLOTTING_DIR);

        TSVWriter<String, String> resultsWriter = new TSVWriter<>(standardIonHeaderFields);
        resultsWriter.open(new File(outAnalysis));

        // For each chemical, create a TSV row and a corresponding diagnostic plot
        for (String chemicalName : chemicalNames) {
            List<String> graphLabels = new ArrayList<>();
            List<Double> yMaxList = new ArrayList<>();

            String outData = plottingDirectory + "/" + chemicalName + ".data";
            String outImg = plottingDirectory + "/" + chemicalName + ".pdf";

            // For each diagnostic plot, open a new file stream.
            try (FileOutputStream fos = new FileOutputStream(outData)) {

                List<StandardIonResult> getResultByChemicalName = StandardIonResult.getByChemicalName(db,
                        chemicalName);

                if (getResultByChemicalName != null && getResultByChemicalName.size() > 0) {

                    // PART 1: Get the best metlin ion across all standard ion results for a given chemical
                    String bestGlobalMetlinIon = AnalysisHelper
                            .scoreAndReturnBestMetlinIonFromStandardIonResults(getResultByChemicalName,
                                    new HashMap<>(), true, true);

                    // PART 2: Plot all the graphs related to the chemical. The plots are structured as follows:
                    //
                    // Page 1: All graphs (water, MeOH, Yeast) for Global ion picked (best ion among ALL standard ion runs for
                    // the given chemical) by the algorithm
                    // Page 2: All graphs for M+H
                    // Page 3: All graphs for Local ions picked (best ion within a SINGLE standard ion run) + negative controls
                    // for Yeast.
                    //
                    // Each page is demarcated by a blank graph.

                    // Arrange results based on media
                    Map<String, List<StandardIonResult>> categories = StandardIonResult
                            .categorizeListOfStandardWellsByMedia(db, getResultByChemicalName);

                    // This set contains all the best metlin ions corresponding to all the standard ion runs.
                    Set<String> bestLocalIons = new HashSet<>();
                    bestLocalIons.add(bestGlobalMetlinIon);
                    bestLocalIons.add(DEFAULT_ION);

                    for (StandardIonResult result : getResultByChemicalName) {
                        bestLocalIons.add(result.getBestMetlinIon());
                    }

                    // We sort the best local ions are follows:
                    // 1) Global best ion spectra 2) M+H spectra 3) Local best ion spectra
                    List<String> bestLocalIonsArray = new ArrayList<>(bestLocalIons);
                    Collections.sort(bestLocalIonsArray, new Comparator<String>() {
                        @Override
                        public int compare(String o1, String o2) {
                            if (o1.equals(bestGlobalMetlinIon) && !o2.equals(bestGlobalMetlinIon)) {
                                return -1;
                            } else if (o1.equals(DEFAULT_ION) && !o2.equals(bestGlobalMetlinIon)) {
                                return -1;
                            } else {
                                return 1;
                            }
                        }
                    });

                    // This variable stores the index of the array at which all the remaining spectra are contained in one
                    // page. This happens right after the M+H ion spectra.
                    Integer combineAllSpectraIntoPageThreeFromIndex = 0;
                    for (int i = 0; i < bestLocalIonsArray.size(); i++) {
                        if (bestLocalIonsArray.get(i).equals(DEFAULT_ION)) {
                            combineAllSpectraIntoPageThreeFromIndex = i + 1;
                        }
                    }

                    for (int i = 0; i < bestLocalIonsArray.size(); i++) {

                        String ion = bestLocalIonsArray.get(i);
                        for (Map.Entry<String, List<StandardIonResult>> mediaToListOfIonResults : categories
                                .entrySet()) {

                            for (StandardIonResult result : mediaToListOfIonResults.getValue()) {

                                // For every standard ion result, we plot the best global metlin ion and M+H. These plots are in the
                                // pages 1 and 2. For all page 3 (aka miscellaneous spectra), we only plot the best local ion
                                // corresponding to it's spectra and not some other graph's spectra. In the below condition,
                                // we reach the page 3 case with not the same best ion as the spectra, in which case we just continue
                                // and not draw anything on the page.
                                if (i >= combineAllSpectraIntoPageThreeFromIndex
                                        && !(result.getBestMetlinIon().equals(ion))) {
                                    continue;
                                }

                                StandardWell positiveWell = StandardWell.getInstance().getById(db,
                                        result.getStandardWellId());
                                String positiveControlChemical = positiveWell.getChemical();

                                ScanData<StandardWell> encapsulatedDataForPositiveControl = AnalysisHelper
                                        .getScanDataForWell(db, lcmsDir, positiveWell, positiveControlChemical,
                                                positiveControlChemical);

                                Set<String> singletonSet = Collections.singleton(ion);
                                String additionalInfo = generateAdditionalLabelInformation(positiveWell, result,
                                        ion);

                                List<String> labels = AnalysisHelper
                                        .writeScanData(fos, lcmsDir, MAX_INTENSITY,
                                                encapsulatedDataForPositiveControl, false, false, singletonSet)
                                        .stream().map(label -> label + additionalInfo)
                                        .collect(Collectors.toList());

                                yMaxList.add(encapsulatedDataForPositiveControl.getMs1ScanResults()
                                        .getMaxIntensityForIon(ion));

                                List<String> negativeLabels = null;
                                // Only do the negative control in the miscellaneous page (page 3) and if the well is in yeast media.
                                if (mediaToListOfIonResults.getKey()
                                        .equals(StandardWell.MEDIA_TYPE.YEAST.name())
                                        && (i >= combineAllSpectraIntoPageThreeFromIndex
                                                && (result.getBestMetlinIon().equals(ion)))) {
                                    //TODO: Change the representative negative well to one that displays the highest noise in the future.
                                    // For now, we just use the first index among the negative wells.
                                    int representativeIndex = 0;
                                    StandardWell representativeNegativeControlWell = StandardWell.getInstance()
                                            .getById(db, result.getNegativeWellIds().get(representativeIndex));

                                    ScanData encapsulatedDataForNegativeControl = AnalysisHelper
                                            .getScanDataForWell(db, lcmsDir, representativeNegativeControlWell,
                                                    positiveWell.getChemical(),
                                                    representativeNegativeControlWell.getChemical());

                                    String negativePlateAdditionalInfo = generateAdditionalLabelInformation(
                                            representativeNegativeControlWell, null, null);

                                    negativeLabels = AnalysisHelper.writeScanData(fos, lcmsDir, MAX_INTENSITY,
                                            encapsulatedDataForNegativeControl, false, false, singletonSet)
                                            .stream().map(label -> label + negativePlateAdditionalInfo)
                                            .collect(Collectors.toList());

                                    yMaxList.add(encapsulatedDataForNegativeControl.getMs1ScanResults()
                                            .getMaxIntensityForIon(ion));
                                }

                                graphLabels.addAll(labels);

                                if (negativeLabels != null) {
                                    graphLabels.addAll(negativeLabels);
                                }
                            }
                        }

                        // Add a blank graph to demarcate pages.
                        if (i < combineAllSpectraIntoPageThreeFromIndex) {
                            graphLabels.addAll(AnalysisHelper.writeScanData(fos, lcmsDir, 0.0, BLANK_SCAN,
                                    false, false, new HashSet<>()));
                            yMaxList.add(0.0d);
                        }
                    }

                    // We need to pass the yMax values as an array to the Gnuplotter.
                    Double fontScale = null;
                    if (cl.hasOption(FONT_SCALE)) {
                        try {
                            fontScale = Double.parseDouble(cl.getOptionValue(FONT_SCALE));
                        } catch (IllegalArgumentException e) {
                            System.err.format("Argument for font-scale must be a floating point number.\n");
                            System.exit(1);
                        }
                    }

                    Double[] yMaxes = yMaxList.toArray(new Double[yMaxList.size()]);
                    Gnuplotter plotter = fontScale == null ? new Gnuplotter() : new Gnuplotter(fontScale);
                    plotter.plot2D(outData, outImg, graphLabels.toArray(new String[graphLabels.size()]), "time",
                            null, "intensity", "pdf", null, null, yMaxes, outImg + ".gnuplot");

                    Map<String, String> row = new HashMap<>();
                    row.put(STANDARD_ION_HEADER_FIELDS.CHEMICAL.name(), chemicalName);
                    row.put(STANDARD_ION_HEADER_FIELDS.BEST_ION_FROM_ALGO.name(), bestGlobalMetlinIon);
                    row.put(STANDARD_ION_HEADER_FIELDS.DIAGNOSTIC_PLOTS.name(), outImg);

                    resultsWriter.append(row);
                    resultsWriter.flush();
                }
            }
        }

        resultsWriter.flush();
        resultsWriter.close();
    }
}

From source file:de.ingrid.iplug.AdminServer.java

/**
 * To start the admin web server from the commandline. 
 * @param args The server port and the web app folder. 
 * @throws Exception Something goes wrong.
 *//*from   w ww.  j av  a2s  .  co  m*/
public static void main(String[] args) throws Exception {

    String usage = "<serverPort> <webappFolder>";
    if ((args.length == 0) && (args.length != 4) && (args.length != 6)) {
        System.err.println(usage);
        return;
    }

    Map arguments = readParameters(args);
    File plugDescriptionFile = new File(PLUG_DESCRIPTION);
    if (arguments.containsKey("--plugdescription")) {
        plugDescriptionFile = new File((String) arguments.get("--plugdescription"));
    }
    File communicationProperties = new File(COMMUNICATION_PROPERTES);
    if (arguments.containsKey("--descriptor")) {
        communicationProperties = new File((String) arguments.get("--descriptor"));
    }

    int port = Integer.parseInt(args[0]);
    File webFolder = new File(args[1]);

    //push init params for all contexts (e.g. step1 and step2)
    HashMap hashMap = new HashMap();
    hashMap.put("plugdescription.xml", plugDescriptionFile.getAbsolutePath());
    hashMap.put("communication.xml", communicationProperties.getAbsolutePath());

    WebContainer container = startWebContainer(hashMap, port, webFolder, false, null);
    container.join();
}

From source file:avantssar.aslanpp.testing.Tester.java

public static void main(String[] args) {

    Debug.initLog(LogLevel.INFO);//from ww w .j av a  2 s .  co m

    TesterCommandLineOptions options = new TesterCommandLineOptions();
    try {
        options.getParser().parseArgument(args);
        options.ckeckAtEnd();
    } catch (CmdLineException ex) {
        reportException("Inconsistent options.", ex, System.err);
        options.showShortHelp(System.err);
        return;
    }

    if (options.isShowHelp()) {
        options.showLongHelp(System.out);
        return;
    }

    ASLanPPConnectorImpl translator = new ASLanPPConnectorImpl();

    if (options.isShowVersion()) {
        System.out.println(translator.getFullTitleLine());
        return;
    }

    ISpecificationBundleProvider sbp;
    File realInDir;
    if (options.isLibrary()) {
        if (options.getHornClausesLevel() != HornClausesLevel.ALL) {
            System.out.println("When checking the internal library we output all Horn clauses.");
            options.setHornClausesLevel(HornClausesLevel.ALL);
        }
        if (!options.isStripOutput()) {
            System.out.println(
                    "When checking the internal library, the ouput is stripped of comments and line information.");
            options.setStripOutput(true);
        }
        File modelsDir = new File(FilenameUtils.concat(options.getOut().getAbsolutePath(), "_models"));
        try {
            FileUtils.forceMkdir(modelsDir);
        } catch (IOException e1) {
            System.out.println("Failed to create models folder: " + e1.getMessage());
            Debug.logger.error("Failed to create models folder.", e1);
        }
        realInDir = modelsDir;
        sbp = new LibrarySpecificationsProvider(modelsDir.getAbsolutePath());
    } else {
        realInDir = options.getIn();
        sbp = new DiskSpecificationsProvider(options.getIn().getAbsolutePath());
    }

    System.setProperty(EntityManager.ASLAN_ENVVAR, sbp.getASLanPath());
    // try {
    // EntityManager.loadASLanPath();
    // }
    // catch (IOException e) {
    // System.out.println("Exception while reloading ASLANPATH: " +
    // e.getMessage());
    // Debug.logger.error("Exception while loading ASLANPATH.", e);
    // }

    try {
        bm = BackendsManager.instance();
        if (bm != null) {
            for (IBackendRunner br : bm.getBackendRunners()) {
                System.out.println(br.getFullDescription());
                if (br.getTimeout() > finalTimeout) {
                    finalTimeout = br.getTimeout();
                }
            }
        }
    } catch (IOException e) {
        System.out.println("Failed to load backends: " + e);
    }

    int threadsCount = 50;
    if (options.getThreads() > 0) {
        threadsCount = options.getThreads();
    }
    System.out.println("Will launch " + threadsCount
            + " threads in parallel (+ will show that a thread starts, - that a thread ends).");
    TranslationReport rep = new TranslationReport(
            bm != null ? bm.getBackendRunners() : new ArrayList<IBackendRunner>(), options.getOut());
    long startTime = System.currentTimeMillis();
    int specsCount = 0;
    pool = Executors.newFixedThreadPool(threadsCount);
    for (ITestTask task : sbp) {
        doTest(rep, task, realInDir, options.getOut(), translator, options, System.err);
        specsCount++;
    }
    pool.shutdown();
    String reportFile = FilenameUtils.concat(options.getOut().getAbsolutePath(), "index.html");
    try {
        while (!pool.awaitTermination(finalTimeout, TimeUnit.SECONDS)) {
        }
    } catch (InterruptedException e) {
        Debug.logger.error("Interrupted while waiting for pool termination.", e);
        System.out.println("Interrupted while waiting for pool termination: " + e.getMessage());
        System.out.println("The report may be incomplete.");
    }
    long endTime = System.currentTimeMillis();
    long duration = (endTime - startTime) / 1000;
    System.out.println();
    System.out.println(specsCount + " specifications checked in " + duration + " seconds.");
    rep.report(reportFile);
    System.out.println("You can find an overview report at '" + reportFile + "'.");
}

From source file:io.werval.cli.DamnSmallDevShell.java

public static void main(String[] args) {
    Options options = declareOptions();/*ww  w.j a  v  a 2  s.co  m*/

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

        // Handle --help
        if (cmd.hasOption("help")) {
            PrintWriter out = new PrintWriter(System.out);
            printHelp(options, out);
            out.flush();
            System.exit(0);
        }

        // Handle --version
        if (cmd.hasOption("version")) {
            System.out.print(String.format(
                    "Werval CLI v%s\n" + "Git commit: %s%s, built on: %s\n" + "Java version: %s, vendor: %s\n"
                            + "Java home: %s\n" + "Default locale: %s, platform encoding: %s\n"
                            + "OS name: %s, version: %s, arch: %s\n",
                    VERSION, COMMIT, (DIRTY ? " (DIRTY)" : ""), DATE, System.getProperty("java.version"),
                    System.getProperty("java.vendor"), System.getProperty("java.home"),
                    Locale.getDefault().toString(), System.getProperty("file.encoding"),
                    System.getProperty("os.name"), System.getProperty("os.version"),
                    System.getProperty("os.arch")));
            System.out.flush();
            System.exit(0);
        }

        // Debug
        final boolean debug = cmd.hasOption('d');

        // Temporary directory
        final File tmpDir = new File(cmd.getOptionValue('t', "build" + separator + "devshell.tmp"));
        if (debug) {
            System.out.println("Temporary directory set to '" + tmpDir.getAbsolutePath() + "'.");
        }

        // Handle commands
        @SuppressWarnings("unchecked")
        List<String> commands = cmd.getArgList();
        if (commands.isEmpty()) {
            commands = Collections.singletonList("start");
        }
        if (debug) {
            System.out.println("Commands to be executed: " + commands);
        }
        Iterator<String> commandsIterator = commands.iterator();
        while (commandsIterator.hasNext()) {
            String command = commandsIterator.next();
            switch (command) {
            case "new":
                System.out.println(LOGO);
                newCommand(commandsIterator.hasNext() ? commandsIterator.next() : "werval-application", cmd);
                break;
            case "clean":
                cleanCommand(debug, tmpDir);
                break;
            case "devshell":
                System.out.println(LOGO);
                devshellCommand(debug, tmpDir, cmd);
                break;
            case "start":
                System.out.println(LOGO);
                startCommand(debug, tmpDir, cmd);
                break;
            case "secret":
                secretCommand();
                break;
            default:
                PrintWriter out = new PrintWriter(System.err);
                System.err.println("Unknown command: '" + command + "'");
                printHelp(options, out);
                out.flush();
                System.exit(1);
                break;
            }
        }
    } catch (IllegalArgumentException | ParseException | IOException ex) {
        PrintWriter out = new PrintWriter(System.err);
        printHelp(options, out);
        out.flush();
        System.exit(1);
    } catch (WervalException ex) {
        ex.printStackTrace(System.err);
        System.err.flush();
        System.exit(1);
    }
}