Example usage for java.io File getName

List of usage examples for java.io File getName

Introduction

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

Prototype

public String getName() 

Source Link

Document

Returns the name of the file or directory denoted by this abstract pathname.

Usage

From source file:mil.tatrc.physiology.utilities.csv.plots.CSVPlotTool.java

public static void main(String[] args) {
    if (args.length < 1) {
        Log.fatal("Expected inputs : [results file path]");
        return;/* w w  w .j  a va 2  s  . c  om*/
    }
    File f = new File(args[0]);
    if (!f.exists()) {
        Log.fatal("Input file cannot be found");
        return;
    }
    String reportDir = "./graph_results/" + f.getName();
    reportDir = reportDir.substring(0, reportDir.lastIndexOf(".")) + "/";
    CSVPlotTool t = new CSVPlotTool();
    t.graphResults(args[0], reportDir);
}

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

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

    ActionUtils.setUpInitFileProperty();
    //        boolean success = ActionUtils.markActionChainBroken("Just Testing");        
    //        System.exit(success ? 0 : 1);
    ActionUtils.assertActionChainNotBroken();
    ActionUtils.assertEnvironmentSetupOk();
    ActionUtils.assertFileExists("~/.mvdb", "~/.mvdb missing. Existing.");
    ActionUtils.assertFileExists("~/.mvdb/status.InitCustomerData.complete",
            "300init-customer-data.sh not executed yet. Exiting");
    //This check is not required as data can be modified any number of times
    //ActionUtils.assertFileDoesNotExist("~/.mvdb/status.ModifyCustomerData.complete", "ModifyCustomerData already done. Start with 100init.sh if required. Exiting");

    ActionUtils.createMarkerFile("~/.mvdb/status.ExtractDBChanges.start", true);

    //String schemaDescription = "{ 'root' : [{'table' : 'orders', 'keyColumn' : 'order_id', 'updateTimeColumn' : 'update_time'}]}";

    String customerName = null;//from w w w . java  2 s. c om
    final CommandLineParser cmdLinePosixParser = new PosixParser();
    final Options posixOptions = constructPosixOptions();
    CommandLine commandLine;
    try {
        commandLine = cmdLinePosixParser.parse(posixOptions, args);
        if (commandLine.hasOption("customer")) {
            customerName = commandLine.getOptionValue("customer");
        }
    } catch (ParseException parseException) // checked exception
    {
        System.err.println(
                "Encountered exception while parsing using PosixParser:\n" + parseException.getMessage());
    }

    if (customerName == null) {
        System.err.println("Could not find customerName. Aborting...");
        System.exit(1);
    }

    ApplicationContext context = Top.getContext();

    final OrderDAO orderDAO = (OrderDAO) context.getBean("orderDAO");
    final ConfigurationDAO configurationDAO = (ConfigurationDAO) context.getBean("configurationDAO");
    final GenericDAO genericDAO = (GenericDAO) context.getBean("genericDAO");
    File snapshotDirectory = getSnapshotDirectory(configurationDAO, customerName);
    try {
        FileUtils.writeStringToFile(new File("/tmp/etl.extractdbchanges.directory.txt"),
                snapshotDirectory.getName(), false);
    } catch (IOException e) {
        e.printStackTrace();
        System.exit(1);
        return;
    }
    long currentTime = new Date().getTime();
    Configuration lastRefreshTimeConf = configurationDAO.find(customerName, "last-refresh-time");
    Configuration schemaDescriptionConf = configurationDAO.find(customerName, "schema-description");
    long lastRefreshTime = Long.parseLong(lastRefreshTimeConf.getValue());
    OrderJsonFileConsumer orderJsonFileConsumer = new OrderJsonFileConsumer(snapshotDirectory);
    Map<String, ColumnMetadata> metadataMap = orderDAO.findMetadata();
    //write file schema-orders.dat in snapshotDirectory
    genericDAO.fetchMetadata("orders", snapshotDirectory);
    //writes files: header-orders.dat, data-orders.dat in snapshotDirectory
    JSONObject json = new JSONObject(schemaDescriptionConf.getValue());
    JSONArray rootArray = json.getJSONArray("root");
    int length = rootArray.length();
    for (int i = 0; i < length; i++) {
        JSONObject jsonObject = rootArray.getJSONObject(i);
        String table = jsonObject.getString("table");
        String keyColumnName = jsonObject.getString("keyColumn");
        String updateTimeColumnName = jsonObject.getString("updateTimeColumn");
        System.out.println("table:" + table + ", keyColumn: " + keyColumnName + ", updateTimeColumn: "
                + updateTimeColumnName);
        genericDAO.fetchAll2(snapshotDirectory, new Timestamp(lastRefreshTime), table, keyColumnName,
                updateTimeColumnName);
    }

    //Unlikely failure
    //But Need to factor this into a separate task so that extraction does not have to be repeated. 
    //Extraction is an expensive task. 
    try {
        String sourceDirectoryAbsolutePath = snapshotDirectory.getAbsolutePath();

        File sourceRelativeDirectoryPath = getRelativeSnapShotDirectory(configurationDAO,
                sourceDirectoryAbsolutePath);
        String hdfsRoot = ActionUtils.getConfigurationValue(ConfigurationKeys.GLOBAL_CUSTOMER,
                ConfigurationKeys.GLOBAL_HDFS_ROOT);
        String targetDirectoryFullPath = hdfsRoot + "/data" + sourceRelativeDirectoryPath;

        ActionUtils.copyLocalDirectoryToHdfsDirectory(sourceDirectoryAbsolutePath, targetDirectoryFullPath);
        String dirName = snapshotDirectory.getName();
        ActionUtils.setConfigurationValue(customerName, ConfigurationKeys.LAST_COPY_TO_HDFS_DIRNAME, dirName);
    } catch (Throwable e) {
        e.printStackTrace();
        logger.error("Objects Extracted from database. But copy of snapshot directory<"
                + snapshotDirectory.getAbsolutePath() + "> to hdfs <" + ""
                + ">failed. Fix the problem and redo extract.", e);
        System.exit(1);
    }

    //Unlikely failure
    //But Need to factor this into a separate task so that extraction does not have to be repeated. 
    //Extraction is an expensive task. 
    String targetZip = null;
    try {
        File targetZipDirectory = new File(snapshotDirectory.getParent(), "archives");
        if (!targetZipDirectory.exists()) {
            boolean success = targetZipDirectory.mkdirs();
            if (success == false) {
                logger.error("Objects copied to hdfs. But able to create archive directory <"
                        + targetZipDirectory.getAbsolutePath() + ">. Fix the problem and redo extract.");
                System.exit(1);
            }
        }
        targetZip = new File(targetZipDirectory, snapshotDirectory.getName() + ".zip").getAbsolutePath();
        ActionUtils.zipFullDirectory(snapshotDirectory.getAbsolutePath(), targetZip);
    } catch (Throwable e) {
        e.printStackTrace();
        logger.error("Objects copied to hdfs. But zipping of snapshot directory<"
                + snapshotDirectory.getAbsolutePath() + "> to  <" + targetZip
                + ">failed. Fix the problem and redo extract.", e);
        System.exit(1);
    }

    //orderDAO.findAll(new Timestamp(lastRefreshTime), orderJsonFileConsumer);
    Configuration updateRefreshTimeConf = new Configuration(customerName, "last-refresh-time",
            String.valueOf(currentTime));
    configurationDAO.update(updateRefreshTimeConf, String.valueOf(lastRefreshTimeConf.getValue()));
    ActionUtils.createMarkerFile("~/.mvdb/status.ExtractDBChanges.complete", true);

}

From source file:bookChapter.theoretical.AnalyzeTheoreticalMSMSCalculation.java

/**
 *
 * @param args/*ww w.  j  a v a2s  .  c o m*/
 * @throws IOException
 * @throws FileNotFoundException
 * @throws ClassNotFoundException
 * @throws InterruptedException
 * @throws MzMLUnmarshallerException
 */
public static void main(String[] args) throws IOException, FileNotFoundException, ClassNotFoundException,
        IOException, InterruptedException, MzMLUnmarshallerException {
    Logger l = Logger.getLogger("AnalyzeTheoreticalMSMSCalculation");
    Date date = Calendar.getInstance().getTime();
    DateFormat formatter = new SimpleDateFormat("EEEE, dd MMMM yyyy, hh:mm:ss.SSS a");
    String now = formatter.format(date);
    l.log(Level.INFO, "Calculation starts at {0}", now);
    double precursorTolerance = ConfigHolder.getInstance().getDouble("precursor.tolerance"),
            fragmentTolerance = ConfigHolder.getInstance().getDouble("fragment.tolerance");
    String databaseName = ConfigHolder.getInstance().getString("database.name"),
            spectraName = ConfigHolder.getInstance().getString("spectra.name"),
            output = ConfigHolder.getInstance().getString("output");
    int correctionFactor = ConfigHolder.getInstance().getInt("correctionFactor");
    boolean theoFromAllCharges = ConfigHolder.getInstance().getBoolean("hasAllPossCharge");
    BufferedWriter bw = new BufferedWriter(new FileWriter(output));
    bw.write("SpectrumTitle" + "\t" + "PrecursorMZ" + "\t" + "PrecursorCharge" + "\t" + "Observed Mass (M+H)"
            + "\t" + "AndromedaLikeScore" + "\t" + "SequestLikeScore" + "\t" + "PeptideByAndromedaLikeScore"
            + "\t" + "PeptideBySequestLikeScore" + "\t" + "LevenshteinDistance" + "\t" + "TotalScoredPeps"
            + "\t" + "isCorrectMatchByAndromedaLike" + "\t" + "isCorrectMatchBySequestLikeScore" + "\n");
    l.info("Getting database entries");
    // first load all sequences into the memory 
    HashSet<DBEntry> dbEntries = getDBEntries(databaseName);
    // for every spectrum-calculate both score...
    // now convert to binExperimental spectrum
    int num = 0;
    SpectrumFactory fct = SpectrumFactory.getInstance();
    num = 0;
    File f = new File(spectraName);
    if (spectraName.endsWith(".mgf")) {
        fct.addSpectra(f, new WaitingHandlerCLIImpl());
        l.log(Level.INFO, "Spectra scoring starts at {0}", now);
        for (String title : fct.getSpectrumTitles(f.getName())) {
            num++;
            MSnSpectrum ms = (MSnSpectrum) fct.getSpectrum(f.getName(), title);
            // here calculate all except this is an empty spectrum...
            if (ms.getPeakList().size() > 2) {
                // to check a spectrum with negative values..
                String text = result(ms, precursorTolerance, dbEntries, fragmentTolerance, correctionFactor,
                        theoFromAllCharges);
                if (!text.isEmpty()) {
                    bw.write(text);
                }
            }
            if (num % 500 == 0) {
                l.info("Running " + num + " spectra." + Calendar.getInstance().getTime());
            }
        }
    }
    l.info("Program finished at " + Calendar.getInstance().getTime());

    bw.close();
}

From source file:apps.quantification.LearnQuantificationSVMPerf.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = LearnQuantificationSVMPerf.class.getName()
            + " [OPTIONS] <path to svm_perf_learn> <path to svm_perf_classify> <trainingIndexDirectory> <outputDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("f");
    OptionBuilder.withDescription("Number of folds");
    OptionBuilder.withLongOpt("f");
    OptionBuilder.isRequired(true);//from w  w w. ja  v  a  2 s . co  m
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("c");
    OptionBuilder.withDescription("The c value for svm_perf (default 0.01)");
    OptionBuilder.withLongOpt("c");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("t");
    OptionBuilder.withDescription("Path for temporary files");
    OptionBuilder.withLongOpt("t");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("l");
    OptionBuilder.withDescription("The loss function to optimize (default 2):\n"
            + "               0  Zero/one loss: 1 if vector of predictions contains error, 0 otherwise.\n"
            + "               1  F1: 100 minus the F1-score in percent.\n"
            + "               2  Errorrate: Percentage of errors in prediction vector.\n"
            + "               3  Prec/Rec Breakeven: 100 minus PRBEP in percent.\n"
            + "               4  Prec@p: 100 minus precision at p in percent.\n"
            + "               5  Rec@p: 100 minus recall at p in percent.\n"
            + "               10  ROCArea: Percentage of swapped pos/neg pairs (i.e. 100 - ROCArea).");
    OptionBuilder.withLongOpt("l");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("w");
    OptionBuilder.withDescription("Choice of structural learning algorithm (default 9):\n"
            + "               0: n-slack algorithm described in [2]\n"
            + "               1: n-slack algorithm with shrinking heuristic\n"
            + "               2: 1-slack algorithm (primal) described in [5]\n"
            + "               3: 1-slack algorithm (dual) described in [5]\n"
            + "               4: 1-slack algorithm (dual) with constraint cache [5]\n"
            + "               9: custom algorithm in svm_struct_learn_custom.c");
    OptionBuilder.withLongOpt("w");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("p");
    OptionBuilder.withDescription("The value of p used by the prec@p and rec@p loss functions (default 0)");
    OptionBuilder.withLongOpt("p");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("v");
    OptionBuilder.withDescription("Verbose output");
    OptionBuilder.withLongOpt("v");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("s");
    OptionBuilder.withDescription("Don't delete temporary training file in svm_perf format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmPerfLearnerCustomizer classificationLearnerCustomizer = null;
    SvmPerfClassifierCustomizer classificationCustomizer = null;

    int folds = -1;

    GnuParser parser = new GnuParser();
    String[] remainingArgs = null;
    try {
        CommandLine line = parser.parse(options, args);

        remainingArgs = line.getArgs();

        classificationLearnerCustomizer = new SvmPerfLearnerCustomizer(remainingArgs[0]);
        classificationCustomizer = new SvmPerfClassifierCustomizer(remainingArgs[1]);

        folds = Integer.parseInt(line.getOptionValue("f"));

        if (line.hasOption("c"))
            classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c")));

        if (line.hasOption("w"))
            classificationLearnerCustomizer.setW(Integer.parseInt(line.getOptionValue("w")));

        if (line.hasOption("p"))
            classificationLearnerCustomizer.setP(Integer.parseInt(line.getOptionValue("p")));

        if (line.hasOption("l"))
            classificationLearnerCustomizer.setL(Integer.parseInt(line.getOptionValue("l")));

        if (line.hasOption("v"))
            classificationLearnerCustomizer.printSvmPerfOutput(true);

        if (line.hasOption("s"))
            classificationLearnerCustomizer.setDeleteTrainingFiles(false);

        if (line.hasOption("t")) {
            classificationLearnerCustomizer.setTempPath(line.getOptionValue("t"));
            classificationCustomizer.setTempPath(line.getOptionValue("t"));
        }

    } catch (Exception exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    assert (classificationLearnerCustomizer != null);

    if (remainingArgs.length != 4) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    String indexFile = remainingArgs[2];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String outputPath = remainingArgs[3];

    SvmPerfLearner classificationLearner = new SvmPerfLearner();

    classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(indexPath, false);
    fssm.open();

    IIndex training = TroveReadWriteHelper.readIndex(fssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    final TextualProgressBar progressBar = new TextualProgressBar("Learning the quantifiers");

    IOperationStatusListener status = new IOperationStatusListener() {

        @Override
        public void operationStatus(double percentage) {
            progressBar.signal((int) percentage);
        }
    };

    QuantificationLearner quantificationLearner = new QuantificationLearner(folds, classificationLearner,
            classificationLearnerCustomizer, classificationCustomizer, ClassificationMode.PER_CATEGORY,
            new LogisticFunction(), status);

    IQuantifier[] quantifiers = quantificationLearner.learn(training);

    File executableFile = new File(classificationLearnerCustomizer.getSvmPerfLearnPath());
    IDataManager classifierDataManager = new SvmPerfDataManager(new SvmPerfClassifierCustomizer(
            executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_perf_classify"));
    String description = "_SVMPerf_C-" + classificationLearnerCustomizer.getC() + "_W-"
            + classificationLearnerCustomizer.getW() + "_L-" + classificationLearnerCustomizer.getL();
    if (classificationLearnerCustomizer.getL() == 4 || classificationLearnerCustomizer.getL() == 5)
        description += "_P-" + classificationLearnerCustomizer.getP();
    if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0)
        description += "_" + classificationLearnerCustomizer.getAdditionalParameters();
    String quantifierPrefix = indexName + "_Quantifier-" + folds + description;

    FileSystemStorageManager fssmo = new FileSystemStorageManager(
            outputPath + File.separatorChar + quantifierPrefix, true);
    fssmo.open();
    QuantificationLearner.write(quantifiers, fssmo, classifierDataManager);
    fssmo.close();

    BufferedWriter bfs = new BufferedWriter(
            new FileWriter(outputPath + File.separatorChar + quantifierPrefix + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = quantificationLearner.getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = quantificationLearner.getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = quantificationLearner.getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = quantificationLearner.getScaledFPRs();

    ContingencyTableSet contingencyTableSet = quantificationLearner.getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = training.getCategoryDB().getCategoryName(cat);
        ContingencyTable contingencyTable = contingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = quantifierPrefix + "\ttrain\tsimple\t" + catName + "\t" + cat + "\t"
                + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t"
                + contingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n";
        bfs.write(line);
        line = quantifierPrefix + "\ttrain\tscaled\t" + catName + "\t" + cat + "\t" + contingencyTable.tp()
                + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn()
                + "\t" + scaledTPR + "\t" + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}

From source file:dependencies.DependencyResolving.java

/**
 * @param args the command line arguments
 *///from  w ww  . j av a 2s . c  o m
public static void main(String[] args) {
    // TODO code application logic here
    JSONParser parser = new JSONParser(); //we use JSONParser in order to be able to read from JSON file
    try { //here we declare the file reader and define the path to the file dependencies.json
        Object obj = parser.parse(new FileReader(
                "C:\\Users\\Vladimir\\Documents\\NetBeansProjects\\DependenciesResolving\\src\\dependencies\\dependencies.json"));
        JSONObject project = (JSONObject) obj; //a JSON object containing all the data in the .json file
        JSONArray dependencies = (JSONArray) project.get("dependencies"); //get array of objects with key "dependencies"
        System.out.print("We need to install the following dependencies: ");
        Iterator<String> iterator = dependencies.iterator(); //define an iterator over the array "dependencies"
        while (iterator.hasNext()) {
            System.out.println(iterator.next());
        } //on the next line we declare another object, which parses a Parser object and reads from all_packages.json
        Object obj2 = parser.parse(new FileReader(
                "C:\\Users\\Vladimir\\Documents\\NetBeansProjects\\DependenciesResolving\\src\\dependencies\\all_packages.json"));
        JSONObject tools = (JSONObject) obj2; //a JSON object containing all thr data in the file all_packages.json
        for (int i = 0; i < dependencies.size(); i++) {
            if (tools.containsKey(dependencies.get(i))) {
                System.out.println(
                        "In order to install " + dependencies.get(i) + ", we need the following programs:");
                JSONArray temporaryArray = (JSONArray) tools.get(dependencies.get(i)); //a temporary JSON array in which we store the keys and values of the dependencies
                for (i = 0; i < temporaryArray.size(); i++) {
                    System.out.println(temporaryArray.get(i));
                }
                ArrayList<Object> arraysOfJsonData = new ArrayList<Object>(); //an array in which we will store the keys of the objects, after we use the values and won't need them anymore
                for (i = 0; i < temporaryArray.size(); i++) {
                    System.out.println("Installing " + temporaryArray.get(i));
                }
                while (!temporaryArray.isEmpty()) {

                    for (Object element : temporaryArray) {

                        if (tools.containsKey(element)) {
                            JSONArray secondaryArray = (JSONArray) tools.get(element); //a temporary array within the scope of the if-statement
                            if (secondaryArray.size() != 0) {
                                System.out.println("In order to install " + element + ", we need ");
                            }
                            for (i = 0; i < secondaryArray.size(); i++) {
                                System.out.println(secondaryArray.get(i));
                            }

                            for (Object o : secondaryArray) {

                                arraysOfJsonData.add(o);
                                //here we create a file with the installed dependency
                                File file = new File(
                                        "C:\\Users\\Vladimir\\Documents\\NetBeansProjects\\DependenciesResolving\\src\\dependencies\\installed_modules\\"
                                                + o);
                                if (file.createNewFile()) {
                                    System.out.println(file.getName() + " is installed!");
                                } else {
                                }
                            }
                            secondaryArray.clear();
                        }
                    }
                    temporaryArray.clear();
                    for (i = 0; i < arraysOfJsonData.size(); i++) {
                        temporaryArray.add(arraysOfJsonData.get(i));
                    }
                    arraysOfJsonData.clear();
                }
            }
        }
        Set<String> keys = tools.keySet(); // here we define a set of keys of the objects in all_packages.json
        for (String s : keys) {
            File file = new File(
                    "C:\\Users\\Vladimir\\Documents\\NetBeansProjects\\DependenciesResolving\\src\\dependencies\\installed_modules\\"
                            + s);
            if (file.createNewFile()) {
                System.out.println(file.getName() + " is installed.");
            } else {
            }
        }
    } catch (IOException ex) {
        Logger.getLogger(DependencyResolving.class.getName()).log(Level.SEVERE, null, ex);
    } catch (ParseException ex) {
        Logger.getLogger(DependencyResolving.class.getName()).log(Level.SEVERE, null, ex);
    }
}

From source file:com.p2p.peercds.cli.TorrentMain.java

/**
 * Torrent reader and creator.//from  www . j  ava2  s.co  m
 *
 * <p>
 * You can use the {@code main()} function of this class to read or create
 * torrent files. See usage for details.
 * </p>
 *
 */
public static void main(String[] args) {
    BasicConfigurator.configure(new ConsoleAppender(new PatternLayout("%-5p: %m%n")));

    CmdLineParser parser = new CmdLineParser();
    CmdLineParser.Option help = parser.addBooleanOption('h', "help");
    CmdLineParser.Option filename = parser.addStringOption('t', "torrent");
    CmdLineParser.Option create = parser.addBooleanOption('c', "create");
    CmdLineParser.Option announce = parser.addStringOption('a', "announce");

    try {
        parser.parse(args);
    } catch (CmdLineParser.OptionException oe) {
        System.err.println(oe.getMessage());
        usage(System.err);
        System.exit(1);
    }

    // Display help and exit if requested
    if (Boolean.TRUE.equals((Boolean) parser.getOptionValue(help))) {
        usage(System.out);
        System.exit(0);
    }

    String filenameValue = (String) parser.getOptionValue(filename);
    if (filenameValue == null) {
        usage(System.err, "Torrent file must be provided!");
        System.exit(1);
    }

    Boolean createFlag = (Boolean) parser.getOptionValue(create);

    //For repeated announce urls
    @SuppressWarnings("unchecked")
    Vector<String> announceURLs = (Vector<String>) parser.getOptionValues(announce);

    String[] otherArgs = parser.getRemainingArgs();

    if (Boolean.TRUE.equals(createFlag) && (otherArgs.length != 1 || announceURLs.isEmpty())) {
        usage(System.err,
                "Announce URL and a file or directory must be " + "provided to create a torrent file!");
        System.exit(1);
    }

    OutputStream fos = null;
    try {
        if (Boolean.TRUE.equals(createFlag)) {
            if (filenameValue != null) {
                fos = new FileOutputStream(filenameValue);
            } else {
                fos = System.out;
            }

            //Process the announce URLs into URIs
            List<URI> announceURIs = new ArrayList<URI>();
            for (String url : announceURLs) {
                announceURIs.add(new URI(url));
            }

            //Create the announce-list as a list of lists of URIs
            //Assume all the URI's are first tier trackers
            List<List<URI>> announceList = new ArrayList<List<URI>>();
            announceList.add(announceURIs);

            File source = new File(otherArgs[0]);
            if (!source.exists() || !source.canRead()) {
                throw new IllegalArgumentException(
                        "Cannot access source file or directory " + source.getName());
            }

            String creator = String.format("%s (ttorrent)", System.getProperty("user.name"));

            Torrent torrent = null;
            if (source.isDirectory()) {
                File[] files = source.listFiles(Constants.hiddenFilesFilter);
                Arrays.sort(files);
                torrent = Torrent.create(source, Arrays.asList(files), announceList, creator);
            } else {
                torrent = Torrent.create(source, announceList, creator);

            }

            torrent.save(fos);
        } else {
            Torrent.load(new File(filenameValue), true);
        }
    } catch (Exception e) {
        logger.error("{}", e.getMessage(), e);
        System.exit(2);
    } finally {
        if (fos != System.out) {
            IOUtils.closeQuietly(fos);
        }
    }
}

From source file:cmd.freebase2rdf.java

public static void main(String[] args) throws Exception {
    if (args.length != 2) {
        usage();//from w ww  .  j a va 2 s. c o m
    }
    File input = new File(args[0]);
    if (!input.exists())
        error("File " + input.getAbsolutePath() + " does not exist.");
    if (!input.canRead())
        error("Cannot read file " + input.getAbsolutePath());
    if (!input.isFile())
        error("Not a file " + input.getAbsolutePath());
    File output = new File(args[1]);
    if (output.exists())
        error("Output file " + output.getAbsolutePath()
                + " already exists, this program do not override existing files.");
    if (output.canWrite())
        error("Cannot write file " + output.getAbsolutePath());
    if (output.isDirectory())
        error("Not a file " + output.getAbsolutePath());
    if (!output.getName().endsWith(".nt.gz"))
        error("Output filename should end with .nt.gz, this is the only format supported.");

    BufferedReader in = new BufferedReader(
            new InputStreamReader(new BZip2CompressorInputStream(new FileInputStream(input))));
    BufferedOutputStream out = new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(output)));
    String line;

    ProgressLogger progressLogger = new ProgressLogger(log, "lines", 100000, 1000000);
    progressLogger.start();
    Freebase2RDF freebase2rdf = null;
    try {
        freebase2rdf = new Freebase2RDF(out);
        while ((line = in.readLine()) != null) {
            freebase2rdf.send(line);
            progressLogger.tick();
        }
    } finally {
        if (freebase2rdf != null)
            freebase2rdf.close();
    }
    print(log, progressLogger);
}

From source file:com.bluexml.tools.miscellaneous.Translate.java

/**
 * @param args/*from w ww. ja v a  2  s  . c o m*/
 */
public static void main(String[] args) {
    System.out.println("Translate.main() 1");
    Console console = System.console();

    System.out.println("give path to folder that contains properties files");
    Scanner scanIn = new Scanner(System.in);

    try {
        // TODO Auto-generated method stub
        String sWhatever;

        System.out.println("Translate.main() 2");
        sWhatever = scanIn.nextLine();
        System.out.println("Translate.main() 3");

        System.out.println(sWhatever);

        File inDir = new File(sWhatever);

        FilenameFilter filter = new FilenameFilter() {

            public boolean accept(File arg0, String arg1) {
                return arg1.endsWith("properties");
            }
        };
        File[] listFiles = inDir.listFiles(filter);
        for (File file : listFiles) {

            prapareFileToTranslate(file, inDir);

        }

        System.out.println("please translate text files and press enter");
        String readLine = scanIn.nextLine();
        System.out.println("Translate.main() 4");
        for (File file : listFiles) {

            File values = new File(file.getParentFile(), file.getName() + ".txt");
            writeBackValues(values, file);
            values.delete();
        }
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } finally {
        scanIn.close();
    }

}

From source file:Pathway2RDFv2.java

public static void main(String[] args) throws ParserConfigurationException, SAXException, IOException,
        ServiceException, ClassNotFoundException, IDMapperException, ParseException {

    int softwareVersion = 0;
    int schemaVersion = 0;
    int latestRevision = 0;

    BioDataSource.init();//from   w  ww  . jav a 2 s.  c o m
    Class.forName("org.bridgedb.rdb.IDMapperRdb");
    File dir = new File("/Users/andra/Downloads/bridge");
    File[] bridgeDbFiles = dir.listFiles();
    IDMapperStack mapper = new IDMapperStack();
    for (File bridgeDbFile : bridgeDbFiles) {
        System.out.println(bridgeDbFile.getAbsolutePath());
        mapper.addIDMapper("idmapper-pgdb:" + bridgeDbFile.getAbsolutePath());
    }

    Model bridgeDbmodel = ModelFactory.createDefaultModel();
    InputStream in = new FileInputStream("/tmp/BioDataSource.ttl");
    bridgeDbmodel.read(in, "", "TURTLE");

    WikiPathwaysClient client = new WikiPathwaysClient(
            new URL("http://www.wikipathways.org/wpi/webservice/webservice.php"));

    basicCalls.printMemoryStatus();

    //Map wikipathway organisms to NCBI organisms
    HashMap<String, String> organismTaxonomy = wpRelatedCalls.getOrganismsTaxonomyMapping();
    //HashMap<String, String> miriamSources = new HashMap<String, String>();
    //      HashMap<String, Str ing> miriamLinks = basicCalls.getMiriamUriBridgeDb();

    //Document wikiPathwaysDom = basicCalls.openXmlFile(args[0]);
    Document wikiPathwaysDom = basicCalls.openXmlFile("/tmp/WpGPML.xml");

    //initiate the Jena model to be populated
    Model model = ModelFactory.createDefaultModel();
    Model voidModel = ModelFactory.createDefaultModel();

    voidModel.setNsPrefix("xsd", XSD.getURI());
    voidModel.setNsPrefix("void", Void.getURI());
    voidModel.setNsPrefix("wprdf", "http://rdf.wikipathways.org/");
    voidModel.setNsPrefix("pav", Pav.getURI());
    voidModel.setNsPrefix("prov", Prov.getURI());
    voidModel.setNsPrefix("dcterms", DCTerms.getURI());
    voidModel.setNsPrefix("biopax", Biopax_level3.getURI());
    voidModel.setNsPrefix("gpml", Gpml.getURI());
    voidModel.setNsPrefix("wp", Wp.getURI());
    voidModel.setNsPrefix("foaf", FOAF.getURI());
    voidModel.setNsPrefix("hmdb", "http://identifiers.org/hmdb/");
    voidModel.setNsPrefix("freq", Freq.getURI());
    voidModel.setNsPrefix("dc", DC.getURI());
    setModelPrefix(model);

    //Populate void.ttl
    Calendar now = Calendar.getInstance();
    Literal nowLiteral = voidModel.createTypedLiteral(now);
    Literal titleLiteral = voidModel.createLiteral("WikiPathways-RDF VoID Description", "en");
    Literal descriptionLiteral = voidModel
            .createLiteral("This is the VoID description for a WikiPathwyas-RDF dataset.", "en");
    Resource voidBase = voidModel.createResource("http://rdf.wikipathways.org/");
    Resource identifiersOrg = voidModel.createResource("http://identifiers.org");
    Resource wpHomeBase = voidModel.createResource("http://www.wikipathways.org/");
    Resource authorResource = voidModel
            .createResource("http://semantics.bigcat.unimaas.nl/figshare/search_author.php?author=waagmeester");
    Resource apiResource = voidModel
            .createResource("http://www.wikipathways.org/wpi/webservice/webservice.php");
    Resource mainDatadump = voidModel.createResource("http://rdf.wikipathways.org/wpContent.ttl.gz");
    Resource license = voidModel.createResource("http://creativecommons.org/licenses/by/3.0/");
    Resource instituteResource = voidModel.createResource("http://dbpedia.org/page/Maastricht_University");
    voidBase.addProperty(RDF.type, Void.Dataset);
    voidBase.addProperty(DCTerms.title, titleLiteral);
    voidBase.addProperty(DCTerms.description, descriptionLiteral);
    voidBase.addProperty(FOAF.homepage, wpHomeBase);
    voidBase.addProperty(DCTerms.license, license);
    voidBase.addProperty(Void.uriSpace, voidBase);
    voidBase.addProperty(Void.uriSpace, identifiersOrg);
    voidBase.addProperty(Pav.importedBy, authorResource);
    voidBase.addProperty(Pav.importedFrom, apiResource);
    voidBase.addProperty(Pav.importedOn, nowLiteral);
    voidBase.addProperty(Void.dataDump, mainDatadump);
    voidBase.addProperty(Voag.frequencyOfChange, Freq.Irregular);
    voidBase.addProperty(Pav.createdBy, authorResource);
    voidBase.addProperty(Pav.createdAt, instituteResource);
    voidBase.addLiteral(Pav.createdOn, nowLiteral);
    voidBase.addProperty(DCTerms.subject, Biopax_level3.Pathway);
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/ncbigene/2678"));
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/pubmed/15215856"));
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/hmdb/HMDB02005"));
    voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://rdf.wikipathways.org/WP15"));
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/obo.chebi/17242"));

    for (String organism : organismTaxonomy.values()) {
        voidBase.addProperty(DCTerms.subject,
                voidModel.createResource("http://dbpedia.org/page/" + organism.replace(" ", "_")));
    }
    voidBase.addProperty(Void.vocabulary, Biopax_level3.NAMESPACE);
    voidBase.addProperty(Void.vocabulary, voidModel.createResource(Wp.getURI()));
    voidBase.addProperty(Void.vocabulary, voidModel.createResource(Gpml.getURI()));
    voidBase.addProperty(Void.vocabulary, FOAF.NAMESPACE);
    voidBase.addProperty(Void.vocabulary, Pav.NAMESPACE);
    //Custom Properties
    String baseUri = "http://rdf.wikipathways.org/";
    NodeList pathwayElements = wikiPathwaysDom.getElementsByTagName("Pathway");

    //BioDataSource.init();
    for (int i = 0; i < pathwayElements.getLength(); i++) {
        Model pathwayModel = createPathwayModel();
        String wpId = pathwayElements.item(i).getAttributes().getNamedItem("identifier").getTextContent();
        String revision = pathwayElements.item(i).getAttributes().getNamedItem("revision").getTextContent();
        String pathwayOrganism = "";
        if (pathwayElements.item(i).getAttributes().getNamedItem("Organism") != null)
            pathwayOrganism = pathwayElements.item(i).getAttributes().getNamedItem("Organism").getTextContent()
                    .trim();
        if (Integer.valueOf(revision) > latestRevision) {
            latestRevision = Integer.valueOf(revision);
        }
        File f = new File("/tmp/" + args[0] + "/" + wpId + "_r" + revision + ".ttl");
        System.out.println(f.getName());
        if (!f.exists()) {

            Resource voidPwResource = wpRelatedCalls.addVoidTriples(voidModel, voidBase,
                    pathwayElements.item(i), client);
            Resource pwResource = wpRelatedCalls.addPathwayLevelTriple(pathwayModel, pathwayElements.item(i),
                    organismTaxonomy);

            // Get the comments
            NodeList commentElements = ((Element) pathwayElements.item(i)).getElementsByTagName("Comment");
            wpRelatedCalls.addCommentTriples(pathwayModel, pwResource, commentElements, wpId, revision);
            // Get the Groups
            NodeList groupElements = ((Element) pathwayElements.item(i)).getElementsByTagName("Group");
            for (int n = 0; n < groupElements.getLength(); n++) {
                wpRelatedCalls.addGroupTriples(pathwayModel, pwResource, groupElements.item(n), wpId, revision);
            }
            // Get all the Datanodes
            NodeList dataNodesElement = ((Element) pathwayElements.item(i)).getElementsByTagName("DataNode");
            for (int j = 0; j < dataNodesElement.getLength(); j++) {
                wpRelatedCalls.addDataNodeTriples(pathwayModel, pwResource, dataNodesElement.item(j), wpId,
                        revision, bridgeDbmodel, mapper);
            }
            // Get all the lines
            NodeList linesElement = ((Element) pathwayElements.item(i)).getElementsByTagName("Line");
            for (int k = 0; k < linesElement.getLength(); k++) {
                wpRelatedCalls.addLineTriples(pathwayModel, pwResource, linesElement.item(k), wpId, revision);
            }
            //Get all the labels
            NodeList labelsElement = ((Element) pathwayElements.item(i)).getElementsByTagName("Label");
            for (int l = 0; l < labelsElement.getLength(); l++) {
                wpRelatedCalls.addLabelTriples(pathwayModel, pwResource, labelsElement.item(l), wpId, revision);
            }
            NodeList referenceElements = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:PublicationXref");
            for (int m = 0; m < referenceElements.getLength(); m++) {
                wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements.item(m), wpId,
                        revision);
            }
            NodeList referenceElements2 = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:publicationXref");
            for (int m = 0; m < referenceElements2.getLength(); m++) {
                wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements2.item(m), wpId,
                        revision);
            }
            NodeList referenceElements3 = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:PublicationXRef");
            for (int m = 0; m < referenceElements3.getLength(); m++) {
                wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements3.item(m), wpId,
                        revision);
            }

            NodeList ontologyElements = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:openControlledVocabulary");
            for (int n = 0; n < ontologyElements.getLength(); n++) {
                wpRelatedCalls.addPathwayOntologyTriples(pathwayModel, pwResource, ontologyElements.item(n));
            }
            System.out.println(wpId);
            basicCalls.saveRDF2File(pathwayModel, "/tmp/" + args[0] + "/" + wpId + "_r" + revision + ".ttl",
                    "TURTLE");

            model.add(pathwayModel);
            pathwayModel.removeAll();
        }
    }
    Date myDate = new Date();
    SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd");
    String myDateString = sdf.format(myDate);
    FileUtils.writeStringToFile(new File("latestVersion.txt"),
            "v" + schemaVersion + "." + softwareVersion + "." + latestRevision + "_" + myDateString);
    basicCalls.saveRDF2File(model, "/tmp/wpContent_v" + schemaVersion + "." + softwareVersion + "."
            + latestRevision + "_" + myDateString + ".ttl", "TURTLE");
    basicCalls.saveRDF2File(voidModel, "/tmp/void.ttl", "TURTLE");
}

From source file:com.hp.test.framework.Utlis.java

public static void main(String ar[]) throws IOException {

    ArrayList<String> runs_list = new ArrayList<String>();
    String basepath = replacelogs();
    String path = basepath + "ATU Reports\\Results";
    File directory = new File(path);
    File[] subdirs = directory.listFiles((FileFilter) DirectoryFileFilter.DIRECTORY);
    for (File dir : subdirs) {
        log.info("Directory: " + dir.getName());
        runs_list.add(dir.getName());//from   w w  w .j a  v  a 2  s  . c  o m
    }

    Map<String, List<String>> runCounts = GetCountsrunsWise(runs_list, path);

    int success = replaceCounts(runCounts, path);

    if (success == 0) {
        File SourceFile = new File(path + "\\lineChart_temp.js");
        File RenameFile = new File(path + "\\lineChart.js");

        renameOriginalFile(SourceFile, RenameFile);

        File SourceFile1 = new File(path + "\\barChart_temp.js");
        File RenameFile1 = new File(path + "\\barChart.js");

        renameOriginalFile(SourceFile1, RenameFile1);

        String Reports_path = basepath + "ATU Reports\\";
        int LatestRun = Utlis.getLastRun(Reports_path);
        Utlis.getpaths(Reports_path + "\\Results\\Run_" + String.valueOf(LatestRun));
        try {
            Utlis.replaceMainTable(false, new File(Reports_path + "index.html"));
            Utlis.replaceMainTable(true, new File(Reports_path + "results\\" + "ConsolidatedPage.html"));
            Utlis.replaceMainTable(true,
                    new File(Reports_path + "Results\\Run_" + String.valueOf(LatestRun) + "CurrentRun.html"));

            fileList.add(
                    new File(Reports_path + "\\Results\\Run_" + String.valueOf(LatestRun) + "CurrentRun.html"));
            for (File f : fileList) {
                Utlis.replaceMainTable(true, f);
            }

        } catch (Exception ex) {
            log.error("Error in updating Report format" + ex.getMessage());
        }
    }

}