Example usage for java.io File isFile

List of usage examples for java.io File isFile

  1. HOME
  2. Java
  3. java
  4. java.io.*
  5. File
  6. isFile

Introduction

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

Prototype

public boolean isFile()

Source Link

Document

Tests whether the file denoted by this abstract pathname is a normal file.

Usage

From source file:net.mybox.mybox.Server.java

/**
 * Handle the command line args and instantiate the Server
 * @param args//from  ww w . j ava  2 s .c  o m
 */
public static void main(String args[]) {

    Options options = new Options();
    options.addOption("c", "config", true, "configuration file");
    //    options.addOption("d", "database", true, "accounts database file"); // TODO: handle in config?
    options.addOption("a", "apphome", true, "application home directory");
    options.addOption("h", "help", false, "show help screen");
    options.addOption("V", "version", false, "print the Mybox version");

    CommandLineParser line = new GnuParser();
    CommandLine cmd = null;

    try {
        cmd = line.parse(options, args);
    } catch (ParseException exp) {
        System.err.println(exp.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(Server.class.getName(), options);
        return;
    }

    if (cmd.hasOption("h")) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(Server.class.getName(), options);
        return;
    }

    if (cmd.hasOption("V")) {
        Client.printMessage("version " + Common.appVersion);
        return;
    }

    if (cmd.hasOption("a")) {
        String appHomeDir = cmd.getOptionValue("a");
        try {
            Common.updatePaths(appHomeDir);
        } catch (FileNotFoundException e) {
            printErrorExit(e.getMessage());
        }

        updatePaths();
    }

    String configFile = defaultConfigFile;
    //    String accountsDBfile = defaultAccountsDbFile;

    if (cmd.hasOption("c")) {
        configFile = cmd.getOptionValue("c");
    }

    File fileCheck = new File(configFile);
    if (!fileCheck.isFile())
        Server.printErrorExit("Config not found: " + configFile + "\nPlease run ServerSetup");

    //    if (cmd.hasOption("d")){
    //      accountsDBfile = cmd.getOptionValue("d");
    //    }
    //
    //    fileCheck = new File(accountsDBfile);
    //    if (!fileCheck.isFile())
    //      Server.printErrorExit("Error: account database not found " + accountsDBfile);

    Server server = new Server(configFile);
}

From source file:net.sf.mcf2pdf.Main.java

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

    Option o = OptionBuilder.hasArg().isRequired()
            .withDescription("Installation location of My CEWE Photobook. REQUIRED.").create('i');
    options.addOption(o);/*from  w w w.  jav  a 2s .c om*/
    options.addOption("h", false, "Prints this help and exits.");
    options.addOption("t", true, "Location of MCF temporary files.");
    options.addOption("w", true, "Location for temporary images generated during conversion.");
    options.addOption("r", true, "Sets the resolution to use for page rendering, in DPI. Default is 150.");
    options.addOption("n", true, "Sets the page number to render up to. Default renders all pages.");
    options.addOption("b", false, "Prevents rendering of binding between double pages.");
    options.addOption("x", false, "Generates only XSL-FO content instead of PDF content.");
    options.addOption("q", false, "Quiet mode - only errors are logged.");
    options.addOption("d", false, "Enables debugging logging output.");

    CommandLine cl;
    try {
        CommandLineParser parser = new PosixParser();
        cl = parser.parse(options, args);
    } catch (ParseException pe) {
        printUsage(options, pe);
        System.exit(3);
        return;
    }

    if (cl.hasOption("h")) {
        printUsage(options, null);
        return;
    }

    if (cl.getArgs().length != 2) {
        printUsage(options,
                new ParseException("INFILE and OUTFILE must be specified. Arguments were: " + cl.getArgList()));
        System.exit(3);
        return;
    }

    File installDir = new File(cl.getOptionValue("i"));
    if (!installDir.isDirectory()) {
        printUsage(options, new ParseException("Specified installation directory does not exist."));
        System.exit(3);
        return;
    }

    File tempDir = null;
    String sTempDir = cl.getOptionValue("t");
    if (sTempDir == null) {
        tempDir = new File(new File(System.getProperty("user.home")), ".mcf");
        if (!tempDir.isDirectory()) {
            printUsage(options, new ParseException("MCF temporary location not specified and default location "
                    + tempDir + " does not exist."));
            System.exit(3);
            return;
        }
    } else {
        tempDir = new File(sTempDir);
        if (!tempDir.isDirectory()) {
            printUsage(options, new ParseException("Specified temporary location does not exist."));
            System.exit(3);
            return;
        }
    }

    File mcfFile = new File(cl.getArgs()[0]);
    if (!mcfFile.isFile()) {
        printUsage(options, new ParseException("MCF input file does not exist."));
        System.exit(3);
        return;
    }
    mcfFile = mcfFile.getAbsoluteFile();

    File tempImages = new File(new File(System.getProperty("user.home")), ".mcf2pdf");
    if (cl.hasOption("w")) {
        tempImages = new File(cl.getOptionValue("w"));
        if (!tempImages.mkdirs() && !tempImages.isDirectory()) {
            printUsage(options,
                    new ParseException("Specified working dir does not exist and could not be created."));
            System.exit(3);
            return;
        }
    }

    int dpi = 150;
    if (cl.hasOption("r")) {
        try {
            dpi = Integer.valueOf(cl.getOptionValue("r")).intValue();
            if (dpi < 30 || dpi > 600)
                throw new IllegalArgumentException();
        } catch (Exception e) {
            printUsage(options,
                    new ParseException("Parameter for option -r must be an integer between 30 and 600."));
        }
    }

    int maxPageNo = -1;
    if (cl.hasOption("n")) {
        try {
            maxPageNo = Integer.valueOf(cl.getOptionValue("n")).intValue();
            if (maxPageNo < 0)
                throw new IllegalArgumentException();
        } catch (Exception e) {
            printUsage(options, new ParseException("Parameter for option -n must be an integer >= 0."));
        }
    }

    boolean binding = true;
    if (cl.hasOption("b")) {
        binding = false;
    }

    OutputStream finalOut;
    if (cl.getArgs()[1].equals("-"))
        finalOut = System.out;
    else {
        try {
            finalOut = new FileOutputStream(cl.getArgs()[1]);
        } catch (IOException e) {
            printUsage(options, new ParseException("Output file could not be created."));
            System.exit(3);
            return;
        }
    }

    // configure logging, if no system property is present
    if (System.getProperty("log4j.configuration") == null) {
        PropertyConfigurator.configure(Main.class.getClassLoader().getResource("log4j.properties"));

        Logger.getRootLogger().setLevel(Level.INFO);
        if (cl.hasOption("q"))
            Logger.getRootLogger().setLevel(Level.ERROR);
        if (cl.hasOption("d"))
            Logger.getRootLogger().setLevel(Level.DEBUG);
    }

    // start conversion to XSL-FO
    // if -x is specified, this is the only thing we do
    OutputStream xslFoOut;
    if (cl.hasOption("x"))
        xslFoOut = finalOut;
    else
        xslFoOut = new ByteArrayOutputStream();

    Log log = LogFactory.getLog(Main.class);

    try {
        new Mcf2FoConverter(installDir, tempDir, tempImages).convert(mcfFile, xslFoOut, dpi, binding,
                maxPageNo);
        xslFoOut.flush();

        if (!cl.hasOption("x")) {
            // convert to PDF
            log.debug("Converting XSL-FO data to PDF");
            byte[] data = ((ByteArrayOutputStream) xslFoOut).toByteArray();
            PdfUtil.convertFO2PDF(new ByteArrayInputStream(data), finalOut, dpi);
            finalOut.flush();
        }
    } catch (Exception e) {
        log.error("An exception has occured", e);
        System.exit(1);
        return;
    } finally {
        if (finalOut instanceof FileOutputStream) {
            try {
                finalOut.close();
            } catch (Exception e) {
            }
        }
    }
}

From source file:DIA_Umpire_Quant.DIA_Umpire_LCMSIDGen.java

/**
 * @param args the command line arguments
 *//*from w  w  w .ja  v  a 2  s  .  co m*/
public static void main(String[] args) throws FileNotFoundException, IOException, Exception {
    System.out.println(
            "=================================================================================================");
    System.out.println("DIA-Umpire LCMSID geneartor (version: " + UmpireInfo.GetInstance().Version + ")");
    if (args.length != 1) {
        System.out.println(
                "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_LCMSIDGen.jar diaumpire_module.params");
        return;
    }
    try {
        ConsoleLogger.SetConsoleLogger(Level.INFO);
        ConsoleLogger.SetFileLogger(Level.DEBUG,
                FilenameUtils.getFullPath(args[0]) + "diaumpire_lcmsidgen.log");
    } catch (Exception e) {
    }

    Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version);
    Logger.getRootLogger().info("Parameter file:" + args[0]);

    BufferedReader reader = new BufferedReader(new FileReader(args[0]));
    String line = "";
    String WorkFolder = "";
    int NoCPUs = 2;

    TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600);
    HashMap<String, File> AssignFiles = new HashMap<>();

    //<editor-fold defaultstate="collapsed" desc="Reading parameter file">
    while ((line = reader.readLine()) != null) {
        line = line.trim();
        Logger.getRootLogger().info(line);
        if (!"".equals(line) && !line.startsWith("#")) {
            //System.out.println(line);
            if (line.equals("==File list begin")) {
                do {
                    line = reader.readLine();
                    line = line.trim();
                    if (line.equals("==File list end")) {
                        continue;
                    } else if (!"".equals(line)) {
                        File newfile = new File(line);
                        if (newfile.exists()) {
                            AssignFiles.put(newfile.getAbsolutePath(), newfile);
                        } else {
                            Logger.getRootLogger().info("File: " + newfile + " does not exist.");
                        }
                    }
                } while (!line.equals("==File list end"));
            }
            if (line.split("=").length < 2) {
                continue;
            }
            String type = line.split("=")[0].trim();
            String value = line.split("=")[1].trim();
            switch (type) {
            case "Path": {
                WorkFolder = value;
                break;
            }
            case "path": {
                WorkFolder = value;
                break;
            }
            case "Thread": {
                NoCPUs = Integer.parseInt(value);
                break;
            }
            case "DecoyPrefix": {
                if (!"".equals(value)) {
                    tandemPara.DecoyPrefix = value;
                }
                break;
            }
            case "PeptideFDR": {
                tandemPara.PepFDR = Float.parseFloat(value);
                break;
            }
            }
        }
    }
    //</editor-fold>

    //Initialize PTM manager using compomics library
    PTMManager.GetInstance();

    //Generate DIA file list
    ArrayList<DIAPack> FileList = new ArrayList<>();

    File folder = new File(WorkFolder);
    if (!folder.exists()) {
        Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found.");
        System.exit(1);
    }
    for (final File fileEntry : folder.listFiles()) {
        if (fileEntry.isFile()
                && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml")
                        | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")
                && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml")
                && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) {
            AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry);
        }
        if (fileEntry.isDirectory()) {
            for (final File fileEntry2 : fileEntry.listFiles()) {
                if (fileEntry2.isFile()
                        && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml")
                                | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                        && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")
                        && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml")
                        && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) {
                    AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2);
                }
            }
        }
    }

    Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size());
    for (File fileEntry : AssignFiles.values()) {
        Logger.getRootLogger().info(fileEntry.getAbsolutePath());
    }

    //process each DIA file to genearate untargeted identifications
    for (File fileEntry : AssignFiles.values()) {
        String mzXMLFile = fileEntry.getAbsolutePath();
        if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) {
            long time = System.currentTimeMillis();

            DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs);
            FileList.add(DiaFile);
            Logger.getRootLogger().info(
                    "=================================================================================================");
            Logger.getRootLogger().info("Processing " + mzXMLFile);
            if (!DiaFile.LoadDIASetting()) {
                Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete");
                System.exit(1);
            }
            if (!DiaFile.LoadParams()) {
                Logger.getRootLogger().info("Loading parameters failed, job is incomplete");
                System.exit(1);
            }
            Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "....");

            DiaFile.ParsePepXML(tandemPara, null);
            DiaFile.BuildStructure();
            if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) {
                Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete");
                System.exit(1);
            }
            DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster();
            //Generate mapping between index of precursor feature and pseudo MS/MS scan index 
            DiaFile.GenerateClusterScanNomapping();
            //Doing quantification
            DiaFile.AssignQuant();
            DiaFile.ClearStructure();

            DiaFile.IDsummary.ReduceMemoryUsage();
            time = System.currentTimeMillis() - time;
            Logger.getRootLogger().info(mzXMLFile + " processed time:"
                    + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time),
                            TimeUnit.MILLISECONDS.toMinutes(time)
                                    - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)),
                            TimeUnit.MILLISECONDS.toSeconds(time)
                                    - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time))));
        }
        Logger.getRootLogger().info("Job done");
        Logger.getRootLogger().info(
                "=================================================================================================");
    }
}

From source file:gemlite.core.commands.WServer.java

public static void main(String[] args2) throws Exception {
    String[] defaultArgs = new String[] { "D:/work/data/Gemlite-demo/target/Gemlite-demo-0.0.1-SNAPSHOT.war",
            "8082", "/" };
    defaultArgs = args2 == null || args2.length == 0 ? defaultArgs : args2;
    ServerConfigHelper.initConfig();//from  w ww .  j  av  a2 s. c om
    ServerConfigHelper.initLog4j("classpath:log4j2-server.xml");
    ServerConfigHelper.setProperty("bind-address", ServerConfigHelper.getConfig(ITEMS.BINDIP));
    int port = 8080;
    String contextPath = "/";
    String warPath = "";
    if (defaultArgs.length < 1) {
        LogUtil.getCoreLog().error(
                "Start error,plelase Start Ws server like this : java gemlite.core.command.WServer /home/ws.war");
        return;
    }

    warPath = defaultArgs[0];
    File file = new File(warPath);
    if (!file.exists()) {
        LogUtil.getCoreLog().error("Error input:" + defaultArgs[0] + " war path is not existing!");
        return;
    }
    if (!file.isFile()) {
        LogUtil.getCoreLog().error("Error input:" + defaultArgs[0] + " war path is not a valid file!");
        return;
    }

    if (defaultArgs.length > 1) {
        port = NumberUtils.toInt(defaultArgs[1]);
        if (port <= 0 || port >= 65535) {
            LogUtil.getCoreLog().error(
                    "Port Error:" + defaultArgs[1] + ",not a valid port , make sure port>0 and port<65535");
            return;
        }
    }

    if (defaultArgs.length > 2) {
        contextPath += StringUtils.replace(defaultArgs[2], "/", "");
    }

    try {
        // jetty_home
        String jetty_home = ServerConfigHelper.getConfig(ITEMS.GS_WORK) + File.separator + "jetty_home";
        jetty_home += File.separator + StringUtils.replace(contextPath, "/", "") + port;
        File jfile = new File(jetty_home);
        jfile.mkdirs();
        System.setProperty("jetty.home", jetty_home);
        String jetty_logs = jetty_home + File.separator + "logs" + File.separator;
        File logsFile = new File(jetty_logs);
        logsFile.mkdirs();
        System.setProperty("jetty.logs", jetty_logs);

        Server server = new Server();
        HttpConfiguration config = new HttpConfiguration();
        ServerConnector connector = new ServerConnector(server, new HttpConnectionFactory(config));
        connector.setReuseAddress(true);
        connector.setIdleTimeout(30000);
        connector.setPort(port);
        server.addConnector(connector);

        WebAppContext webapp = new WebAppContext();
        webapp.setContextPath(contextPath);
        webapp.setWar(warPath);
        String tmpStr = jetty_home + File.separator + "webapps" + File.separator;
        File tmpDir = new File(tmpStr);
        tmpDir.mkdirs();
        webapp.setTempDirectory(tmpDir);

        // ???
        // webapp.setExtraClasspath(extrapath);
        webapp.setParentLoaderPriority(true);

        // ?Log
        RequestLogHandler requestLogHandler = new RequestLogHandler();
        NCSARequestLog requestLog = new NCSARequestLog(
                jetty_logs + File.separator + "jetty-yyyy_mm_dd.request.log");
        requestLog.setRetainDays(30);
        requestLog.setAppend(true);
        requestLog.setExtended(false);
        requestLog.setLogTimeZone(TimeZone.getDefault().getID());
        requestLogHandler.setRequestLog(requestLog);
        webapp.setHandler(requestLogHandler);

        ContextHandler ch = webapp.getServletContext().getContextHandler();
        ch.setLogger(new Slf4jLog("gemlite.coreLog"));
        server.setHandler(webapp);
        server.start();

        System.out.println("-----------------------------------------------------");
        LogUtil.getCoreLog().info("Ws Server started,You can visite -> http://"
                + ServerConfigHelper.getConfig(ITEMS.BINDIP) + ":" + port + contextPath);

        server.join();

    } catch (Exception e) {
        LogUtil.getCoreLog().error("Ws Server error:", e);
    }
}

From source file:net.sf.mpaxs.test.ImpaxsExecution.java

/**
 *
 * @param args//w  ww.j  a  v a2s  . c o  m
 */
public static void main(String[] args) {
    Options options = new Options();
    Option[] optionArray = new Option[] {
            OptionBuilder.withArgName("nhosts").hasArg()
                    .withDescription("Number of hosts for parallel processing").create("n"),
            OptionBuilder.withArgName("mjobs").hasArg().withDescription("Number of jobs to run in parallel")
                    .create("m"),
            OptionBuilder.withArgName("runmode").hasArg()
                    .withDescription("The mode in which to operate: one of <ALL,LOCAL,DISTRIBUTED>")
                    .create("r"), //            OptionBuilder.withArgName("gui").
            //            withDescription("Create gui for distributed execution").create("g")
    };
    for (Option opt : optionArray) {
        options.addOption(opt);
    }
    if (args.length == 0) {
        HelpFormatter hf = new HelpFormatter();
        hf.printHelp(StartUp.class.getCanonicalName(), options, true);
        System.exit(1);
    }
    GnuParser gp = new GnuParser();
    int nhosts = 1;
    int mjobs = 10;
    boolean gui = false;
    Mode mode = Mode.ALL;
    try {
        CommandLine cl = gp.parse(options, args);
        if (cl.hasOption("n")) {
            nhosts = Integer.parseInt(cl.getOptionValue("n"));
        }
        if (cl.hasOption("m")) {
            mjobs = Integer.parseInt(cl.getOptionValue("m"));
        }
        if (cl.hasOption("r")) {
            mode = Mode.valueOf(cl.getOptionValue("r"));
        }
        //            if (cl.hasOption("g")) {
        //                gui = true;
        //            }
    } catch (Exception ex) {
        Logger.getLogger(StartUp.class.getName()).log(Level.SEVERE, null, ex);
        HelpFormatter hf = new HelpFormatter();
        hf.printHelp(StartUp.class.getCanonicalName(), options, true);
        System.exit(1);
    }

    String version;
    try {
        version = net.sf.mpaxs.api.Version.getVersion();
        System.out.println("Running mpaxs " + version);
        File computeHostJarLocation = new File(System.getProperty("user.dir"), "mpaxs.jar");
        if (!computeHostJarLocation.exists() || !computeHostJarLocation.isFile()) {
            throw new IOException("Could not locate mpaxs.jar in " + System.getProperty("user.dir"));
        }
        final PropertiesConfiguration cfg = new PropertiesConfiguration();
        //set default execution type
        cfg.setProperty(ConfigurationKeys.KEY_EXECUTION_MODE, ExecutionType.DRMAA);
        //set location of compute host jar
        cfg.setProperty(ConfigurationKeys.KEY_PATH_TO_COMPUTEHOST_JAR, computeHostJarLocation);
        //do not exit to console when master server shuts down
        cfg.setProperty(ConfigurationKeys.KEY_MASTER_SERVER_EXIT_ON_SHUTDOWN, false);
        //limit the number of used compute hosts
        cfg.setProperty(ConfigurationKeys.KEY_MAX_NUMBER_OF_CHOSTS, nhosts);
        cfg.setProperty(ConfigurationKeys.KEY_NATIVE_SPEC, "");
        cfg.setProperty(ConfigurationKeys.KEY_GUI_MODE, gui);
        cfg.setProperty(ConfigurationKeys.KEY_SILENT_MODE, true);
        cfg.setProperty(ConfigurationKeys.KEY_SCHEDULE_WAIT_TIME, "500");
        final int maxJobs = mjobs;
        final int maxThreads = nhosts;
        final Mode runMode = mode;
        printMessage("Run mode: " + runMode);
        Executors.newSingleThreadExecutor().submit(new Runnable() {
            @Override
            public void run() {
                if (runMode == Mode.ALL || runMode == Mode.LOCAL) {
                    printMessage("Running Within VM Execution");
                    /*
                     * LOCAL within VM execution
                     */
                    WithinVmExecution lhe = new WithinVmExecution(maxJobs, maxThreads);
                    try {
                        Logger.getLogger(ImpaxsExecution.class.getName()).log(Level.INFO,
                                "Sum is: " + lhe.call());
                    } catch (Exception ex) {
                        Logger.getLogger(ImpaxsExecution.class.getName()).log(Level.SEVERE, null, ex);
                    }
                }

                if (runMode == Mode.ALL || runMode == Mode.DISTRIBUTED) {
                    printMessage("Running Distributed Host RMI Execution");
                    /*
                     * Grid Engine (DRMAA API) or local host distributed RMI execution
                     */
                    DistributedRmiExecution de = new DistributedRmiExecution(cfg, maxJobs);
                    try {
                        Logger.getLogger(ImpaxsExecution.class.getName()).log(Level.INFO,
                                "Sum is: " + de.call());
                    } catch (Exception ex) {
                        Logger.getLogger(ImpaxsExecution.class.getName()).log(Level.SEVERE, null, ex);
                    }
                }
                System.exit(0);
            }
        });
    } catch (IOException ex) {
        Logger.getLogger(ImpaxsExecution.class.getName()).log(Level.SEVERE, null, ex);
    }
}

From source file:edu.ucla.cs.scai.swim.qa.ontology.dbpedia.tipicality.Test.java

public static void main(String[] args) throws IOException, ClassNotFoundException {
    String path = DBpediaOntology.DBPEDIA_CSV_FOLDER;
    if (args != null && args.length > 0) {
        path = args[0];/*www.j  av  a 2  s  .c  om*/
        if (!path.endsWith("/")) {
            path = path + "/";
        }
    }

    stopAttributes.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#type");
    stopAttributes.add("http://www.w3.org/2002/07/owl#sameAs");
    stopAttributes.add("http://dbpedia.org/ontology/wikiPageRevisionID");
    stopAttributes.add("http://dbpedia.org/ontology/wikiPageID");
    stopAttributes.add("http://purl.org/dc/elements/1.1/description");
    stopAttributes.add("http://dbpedia.org/ontology/thumbnail");
    stopAttributes.add("http://dbpedia.org/ontology/type");

    try (ObjectInputStream ois = new ObjectInputStream(new FileInputStream(path + "counts.bin"))) {
        categories = (HashSet<String>) ois.readObject();
        attributes = (HashSet<String>) ois.readObject();
        categoryCount = (HashMap<String, Integer>) ois.readObject();
        attributeCount = (HashMap<String, Integer>) ois.readObject();
        categoryAttributeCount = (HashMap<String, HashMap<String, Integer>>) ois.readObject();
        attributeCategoryCount = (HashMap<String, HashMap<String, Integer>>) ois.readObject();
    }

    System.out.println(categories.size() + " categories found");
    System.out.println(attributes.size() + " attributes found");

    n = 0;
    for (Map.Entry<String, Integer> e : categoryCount.entrySet()) {
        n += e.getValue();
    }

    System.out.println(n);

    HashMap<String, ArrayList<Pair>> sortedCategoryAttributes = new HashMap<>();

    for (String category : categories) {
        //System.out.println(category);
        //System.out.println("-----------");
        ArrayList<Pair> attributesRank = new ArrayList<Pair>();
        Integer c = categoryCount.get(category);
        if (c == null || c == 0) {
            continue;
        }
        HashMap<String, Integer> thisCategoryAttributeCount = categoryAttributeCount.get(category);
        for (Map.Entry<String, Integer> e : thisCategoryAttributeCount.entrySet()) {
            attributesRank.add(new Pair(e.getKey(), 1.0 * e.getValue() / c));
        }
        Collections.sort(attributesRank);
        for (Pair p : attributesRank) {
            //System.out.println("A:" + p.getS() + "\t" + p.getP());
        }
        //System.out.println("===============================");
        sortedCategoryAttributes.put(category, attributesRank);
    }

    for (String attribute : attributes) {
        //System.out.println(attribute);
        //System.out.println("-----------");
        ArrayList<Pair> categoriesRank = new ArrayList<>();
        Integer a = attributeCount.get(attribute);
        if (a == null || a == 0) {
            continue;
        }
        HashMap<String, Integer> thisAttributeCategoryCount = attributeCategoryCount.get(attribute);
        for (Map.Entry<String, Integer> e : thisAttributeCategoryCount.entrySet()) {
            categoriesRank.add(new Pair(e.getKey(), 1.0 * e.getValue() / a));
        }
        Collections.sort(categoriesRank);
        for (Pair p : categoriesRank) {
            //System.out.println("C:" + p.getS() + "\t" + p.getP());
        }
        //System.out.println("===============================");
    }

    HashMap<Integer, Integer> histogram = new HashMap<>();
    histogram.put(0, 0);
    histogram.put(1, 0);
    histogram.put(2, 0);
    histogram.put(Integer.MAX_VALUE, 0);

    int nTest = 0;

    if (args != null && args.length > 0) {
        path = args[0];
        if (!path.endsWith("/")) {
            path = path + "/";
        }
    }

    for (File f : new File(path).listFiles()) {
        if (f.isFile() && f.getName().endsWith(".csv")) {
            String category = f.getName().replaceFirst("\\.csv", "");
            System.out.println("Category: " + category);
            ArrayList<HashSet<String>> entities = extractEntities(f, 2);
            for (HashSet<String> attributesOfThisEntity : entities) {
                nTest++;
                ArrayList<String> rankedCategories = rankedCategories(attributesOfThisEntity);
                boolean found = false;
                for (int i = 0; i < rankedCategories.size() && !found; i++) {
                    if (rankedCategories.get(i).equals(category)) {
                        Integer count = histogram.get(i);
                        if (count == null) {
                            histogram.put(i, 1);
                        } else {
                            histogram.put(i, count + 1);
                        }
                        found = true;
                    }
                }
                if (!found) {
                    histogram.put(Integer.MAX_VALUE, histogram.get(Integer.MAX_VALUE) + 1);
                }
            }
            System.out.println("Tested entities: " + nTest);
            System.out.println("1: " + histogram.get(0));
            System.out.println("2: " + histogram.get(1));
            System.out.println("3: " + histogram.get(2));
            System.out.println("+3: " + (nTest - histogram.get(2) - histogram.get(1) - histogram.get(0)
                    - histogram.get(Integer.MAX_VALUE)));
            System.out.println("NF: " + histogram.get(Integer.MAX_VALUE));
        }
    }
}

From source file:eu.fbk.utils.lsa.util.AnvurDev.java

public static void main(String[] args) throws Exception {
    String logConfig = System.getProperty("log-config");
    if (logConfig == null) {
        logConfig = "log-config.txt";
    }/*from   www  .  j  a  v a 2 s  .co m*/

    PropertyConfigurator.configure(logConfig);

    if (args.length != 8) {
        System.out.println(args.length);
        System.out.println(
                "Usage: java -mx2G eu.fbk.utils.lsa.util.AnvurDev root-lsa-en root-lsa-it threshold-lsa size-lsa dim-lsa idf-lsa in-file-tsv fields-tsv\n\n");
        System.exit(1);
    }

    //
    DecimalFormat dec = new DecimalFormat("#.00");

    File enUt = new File(args[0] + "-Ut");
    File enSk = new File(args[0] + "-S");
    File enr = new File(args[0] + "-row");
    File enc = new File(args[0] + "-col");
    File endf = new File(args[0] + "-df");
    File itUt = new File(args[1] + "-Ut");
    File itSk = new File(args[1] + "-S");
    File itr = new File(args[1] + "-row");
    File itc = new File(args[1] + "-col");
    File itdf = new File(args[1] + "-df");

    double threshold = Double.parseDouble(args[2]);
    int size = Integer.parseInt(args[3]);
    int dim = Integer.parseInt(args[4]);
    boolean rescaleIdf = Boolean.parseBoolean(args[5]);

    LSM enLsm = new LSM(enUt, enSk, enr, enc, endf, dim, rescaleIdf);
    LSM itLsm = new LSM(itUt, itSk, itr, itc, itdf, dim, rescaleIdf);

    File in = new File(args[6]);

    if (in.isFile()) {
        run(enLsm, itLsm, args[6], args[7]);
    } else if (in.isDirectory()) {
        FolderScanner fs = new FolderScanner(in);
        fs.setFiler(new TsvFilter());
        int count = 0;
        while (fs.hasNext()) {
            Object[] files = fs.next();
            System.out.println((count++) + " : " + files.length);
            for (int i = 0; i < files.length; i++) {

                String name = ((File) files[i]).getAbsolutePath();
                System.out.println(name);
                run(enLsm, itLsm, name, args[7]);
            } // end for i
        } // end while
    }

}

From source file:eu.fbk.utils.lsa.util.AnvurTest.java

public static void main(String[] args) throws Exception {
    String logConfig = System.getProperty("log-config");
    if (logConfig == null) {
        logConfig = "log-config.txt";
    }//from  w  ww  .j a  v a2 s  . co m

    PropertyConfigurator.configure(logConfig);

    if (args.length != 8) {
        System.out.println(args.length);
        System.out.println(
                "Usage: java -mx2G eu.fbk.utils.lsa.util.AnvurTest root-lsa-en root-lsa-it threshold-lsa size-lsa dim-lsa idf-lsa in-file-tsv fields-tsv\n\n");
        System.exit(1);
    }

    //
    DecimalFormat dec = new DecimalFormat("#.00");

    File enUt = new File(args[0] + "-Ut");
    File enSk = new File(args[0] + "-S");
    File enr = new File(args[0] + "-row");
    File enc = new File(args[0] + "-col");
    File endf = new File(args[0] + "-df");
    File itUt = new File(args[1] + "-Ut");
    File itSk = new File(args[1] + "-S");
    File itr = new File(args[1] + "-row");
    File itc = new File(args[1] + "-col");
    File itdf = new File(args[1] + "-df");

    double threshold = Double.parseDouble(args[2]);
    int size = Integer.parseInt(args[3]);
    int dim = Integer.parseInt(args[4]);
    boolean rescaleIdf = Boolean.parseBoolean(args[5]);

    LSM enLsm = new LSM(enUt, enSk, enr, enc, endf, dim, rescaleIdf);
    LSM itLsm = new LSM(itUt, itSk, itr, itc, itdf, dim, rescaleIdf);

    File in = new File(args[6]);

    if (in.isFile()) {
        run(enLsm, itLsm, args[6], args[7]);
    } else if (in.isDirectory()) {
        FolderScanner fs = new FolderScanner(in);
        fs.setFiler(new TsvFilter());
        int count = 0;
        while (fs.hasNext()) {
            Object[] files = fs.next();
            System.out.println((count++) + " : " + files.length);
            for (int i = 0; i < files.length; i++) {

                String name = ((File) files[i]).getAbsolutePath();
                System.out.println(name);
                run(enLsm, itLsm, name, args[7]);
            } // end for i
        } // end while
    }

}

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

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*w ww .j a va2 s  . c  o  m*/
    }

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

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

    File inputFile = new File(cl.getOptionValue(OPTION_INPUT_FILE));
    if (!inputFile.isFile()) {
        System.err.format("No input file at: %s\n", inputFile.getAbsolutePath());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_FILE));
    if (outputFile.exists()) {
        System.err.format("WARNING: output file at %s already exists\n", outputFile.getAbsolutePath());
    }

    /* Sometimes the InChIs might not appear in the input file (like in regression results).  Instead a corpus of
     * names and InChIs can be specified in a separate file and looked up as molecules are read/visualized.  The join
     * field is the key on which the InChI for a given row in the input file is found. */
    File inchiSourceFile = null;
    if (cl.hasOption(OPTION_INCHI_SOURCE)) {
        inchiSourceFile = new File(cl.getOptionValue(OPTION_INCHI_SOURCE));
        boolean err = false;
        if (!inchiSourceFile.isFile()) {
            System.err.format("No inchi source file at: %s\n", inchiSourceFile.getAbsolutePath());
            err = true;
        }
        if (!cl.hasOption(OPTION_INCHI_SOURCE_JOIN_FIELD)) {
            System.err.format("Must specify a join field when using an inchi source file.\n");
            err = true;
        }
        if (err) {
            HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts,
                    null, true);
            System.exit(1);
        }
    }

    SurfactantLabeler surfactantLabeler = new SurfactantLabeler();
    surfactantLabeler.runAnalysis(cl.getOptionValue(OPTION_LICENSE_FILE), inputFile, outputFile,
            inchiSourceFile, cl.getOptionValue(OPTION_INCHI_SOURCE_JOIN_FIELD));
}

From source file:cosmos.example.BuildingPermitsExample.java

public static void main(String[] args) throws Exception {
    BuildingPermitsExample example = new BuildingPermitsExample();
    new JCommander(example, args);

    File inputFile = new File(example.fileName);

    Preconditions.checkArgument(inputFile.exists() && inputFile.isFile() && inputFile.canRead(),
            "Expected " + example.fileName + " to be a readable file");

    String zookeepers;//from w w  w .  j  av a2s.  c om
    String instanceName;
    Connector connector;
    MiniAccumuloCluster mac = null;
    File macDir = null;

    // Use the MiniAccumuloCluster is requested
    if (example.useMiniAccumuloCluster) {
        macDir = Files.createTempDir();
        String password = "password";
        MiniAccumuloConfig config = new MiniAccumuloConfig(macDir, password);
        config.setNumTservers(1);

        mac = new MiniAccumuloCluster(config);
        mac.start();

        zookeepers = mac.getZooKeepers();
        instanceName = mac.getInstanceName();

        ZooKeeperInstance instance = new ZooKeeperInstance(instanceName, zookeepers);
        connector = instance.getConnector("root", new PasswordToken(password));
    } else {
        // Otherwise connect to a running instance
        zookeepers = example.zookeepers;
        instanceName = example.instanceName;

        ZooKeeperInstance instance = new ZooKeeperInstance(instanceName, zookeepers);
        connector = instance.getConnector(example.username, new PasswordToken(example.password));
    }

    // Instantiate an instance of Cosmos
    Cosmos cosmos = new CosmosImpl(zookeepers);

    // Create a definition for the data we want to load
    Store id = Store.create(connector, new Authorizations(), AscendingIndexIdentitySet.create());

    // Register the definition with Cosmos so it can track its progress.
    cosmos.register(id);

    // Load all of the data from our inputFile
    LoadBuildingPermits loader = new LoadBuildingPermits(cosmos, id, inputFile);
    loader.run();

    // Finalize the SortableResult which will prevent future writes to the data set
    cosmos.finalize(id);

    // Flush the ingest traces to the backend so we can see the results;
    id.sendTraces();

    // Get back the Set of Columns that we've ingested.
    Set<Column> schema = Sets.newHashSet(cosmos.columns(id));

    log.debug("\nColumns: " + schema);

    Iterator<Column> iter = schema.iterator();
    while (iter.hasNext()) {
        Column c = iter.next();
        // Remove the internal ID field and columns that begin with CONTRACTOR_
        if (c.equals(LoadBuildingPermits.ID) || c.name().startsWith("CONTRACTOR_")) {
            iter.remove();
        }
    }

    Iterable<Index> indices = Iterables.transform(schema, new Function<Column, Index>() {

        @Override
        public Index apply(Column col) {
            return Index.define(col);
        }

    });

    // Ensure that we have locality groups set as we expect
    log.info("Ensure locality groups are set");
    id.optimizeIndices(indices);

    // Compact down the data for this SortableResult    
    log.info("Issuing compaction for relevant data");
    id.consolidate();

    final int numTopValues = 10;

    // Walk through each column in the result set
    for (Column c : schema) {
        Stopwatch sw = new Stopwatch();
        sw.start();

        // Get the number of times we've seen each value in a given column
        CloseableIterable<Entry<RecordValue<?>, Long>> groupingsInColumn = cosmos.groupResults(id, c);

        log.info(c.name() + ":");

        // Iterate over the counts, collecting the top N values in each column
        TreeMap<Long, RecordValue<?>> topValues = Maps.newTreeMap();

        for (Entry<RecordValue<?>, Long> entry : groupingsInColumn) {
            if (topValues.size() == numTopValues) {
                Entry<Long, RecordValue<?>> least = topValues.pollFirstEntry();

                if (least.getKey() < entry.getValue()) {
                    topValues.put(entry.getValue(), entry.getKey());
                } else {
                    topValues.put(least.getKey(), least.getValue());
                }
            } else if (topValues.size() < numTopValues) {
                topValues.put(entry.getValue(), entry.getKey());
            }
        }

        for (Long key : topValues.descendingKeySet()) {
            log.info(topValues.get(key).value() + " occurred " + key + " times");
        }

        sw.stop();

        log.info("Took " + sw.toString() + " to run query.\n");
    }

    log.info("Deleting records");

    // Delete the records we've ingested
    if (!example.useMiniAccumuloCluster) {
        // Because I'm lazy and don't want to wait around to run the BatchDeleter when we're just going
        // to rm -rf the directory in a few secs.
        cosmos.delete(id);
    }

    // And shut down Cosmos
    cosmos.close();

    log.info("Cosmos stopped");

    // If we were using MAC, also stop that
    if (example.useMiniAccumuloCluster && null != mac) {
        mac.stop();
        if (null != macDir) {
            FileUtils.deleteDirectory(macDir);
        }
    }
}