Example usage for java.util.logging Level FINE

List of usage examples for java.util.logging Level FINE

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Introduction

In this page you can find the example usage for java.util.logging Level FINE.

Prototype

Level FINE

To view the source code for java.util.logging Level FINE.

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Document

FINE is a message level providing tracing information.

Usage

From source file:HTMLFormatter.java

public static void main(String args[]) throws Exception {
    LogManager lm = LogManager.getLogManager();
    Logger parentLogger, childLogger;
    FileHandler xml_handler = new FileHandler("log_output.xml");
    FileHandler html_handler = new FileHandler("log_output.html");
    parentLogger = Logger.getLogger("ParentLogger");
    childLogger = Logger.getLogger("ParentLogger.ChildLogger");

    lm.addLogger(parentLogger);//  w  ww .j  a  va 2  s  .  c o  m

    lm.addLogger(childLogger);

    parentLogger.setLevel(Level.WARNING);
    childLogger.setLevel(Level.ALL);
    xml_handler.setFormatter(new XMLFormatter());
    html_handler.setFormatter(new HTMLFormatter());

    parentLogger.addHandler(xml_handler);
    childLogger.addHandler(html_handler);

    childLogger.log(Level.FINE, "This is a fine log message");
    childLogger.log(Level.SEVERE, "This is a severe log message");
    xml_handler.close();
    html_handler.close();
}

From source file:ec.nbdemetra.ui.demo.ComponentsDemo.java

public static void main(String[] args) {
    new BasicSwingLauncher().content(ComponentsDemo.class).title("Components Demo").logLevel(Level.FINE)
            .launch();// w ww  .j ava  2s .c  om
}

From source file:org.schemaspy.Main.java

public static void main(String[] argv) throws Exception {
    Logger logger = Logger.getLogger(Main.class.getName());

    final AnnotationConfigApplicationContext applicationContext = new AnnotationConfigApplicationContext(
            "org.schemaspy.service");
    applicationContext.register(SchemaAnalyzer.class);

    if (argv.length == 1 && "-gui".equals(argv[0])) { // warning: serious temp hack
        new MainFrame().setVisible(true);
        return;//from w w  w  .j  av a 2 s .c  o m
    }

    SchemaAnalyzer analyzer = applicationContext.getBean(SchemaAnalyzer.class);

    int rc = 1;

    try {
        rc = analyzer.analyze(new Config(argv)) == null ? 1 : 0;
    } catch (ConnectionFailure couldntConnect) {
        logger.log(Level.WARNING, "Connection Failure", couldntConnect);
        rc = 3;
    } catch (EmptySchemaException noData) {
        logger.log(Level.WARNING, "Empty schema", noData);
        rc = 2;
    } catch (InvalidConfigurationException badConfig) {
        logger.info("");
        if (badConfig.getParamName() != null)
            logger.log(Level.WARNING, "Bad parameter specified for " + badConfig.getParamName());
        logger.log(Level.WARNING, "Bad config " + badConfig.getMessage());
        if (badConfig.getCause() != null && !badConfig.getMessage().endsWith(badConfig.getMessage()))
            logger.log(Level.WARNING, " caused by " + badConfig.getCause().getMessage());

        logger.log(Level.FINE, "Command line parameters: " + Arrays.asList(argv));
        logger.log(Level.FINE, "Invalid configuration detected", badConfig);
    } catch (ProcessExecutionException badLaunch) {
        logger.log(Level.WARNING, badLaunch.getMessage(), badLaunch);
    } catch (Exception exc) {
        logger.log(Level.SEVERE, exc.getMessage(), exc);
    }

    System.exit(rc);
}

From source file:ar.com.ergio.uncoma.cei.MiniPas.java

/**
 * @param args//  ww  w.  ja  v  a2 s.c  om
 * @throws IOException 
 */
@SuppressWarnings("static-access")
public static void main(String[] args) throws IOException {
    // Config logging system -- TODO improve this
    Handler console = new ConsoleHandler();
    ROOT_LOG.addHandler(console);

    // Create cmdline options - TODO - I18N
    final Options options = new Options();
    options.addOption(new Option("help", "Muestra este mensaje"));
    options.addOption(new Option("version", "Muestra la informaci\u00f3 de versi\u00f3n y termina"));
    options.addOption(new Option("debug", "Muestra informaci\u00f3n para depuraci\u00f3n"));
    options.addOption(
            OptionBuilder.withArgName("file").hasArg().withDescription("Archivo de log").create("logFile"));

    final CommandLineParser cmdlineParser = new GnuParser();
    final HelpFormatter formatter = new HelpFormatter();
    try {
        final CommandLine cmdline = cmdlineParser.parse(options, args);

        // Process command line args  -- TODO Improve this
        if (args.length == 0 || cmdline.hasOption("help")) {
            formatter.printHelp("minipas", options, true);
        } else if (cmdline.hasOption("version")) {
            System.out.println("MiniPas versi\u00f3n: 0.0.1");
        } else if (cmdline.hasOption("debug")) {
            ROOT_LOG.setLevel(Level.FINE);
        } else {
            ROOT_LOG.fine("Arguments: " + Arrays.toString(args));
            final Scanner scanner = new Scanner(args[0]);
            while (scanner.hasTokens()) {
                System.out.println(scanner.nextToken());
            }
        }

    } catch (ParseException e) {
        formatter.printHelp("minipas", options, true);
    }
}

From source file:de.fosd.jdime.Main.java

/**
 * Perform a merge operation on the input files or directories.
 *
 * @param args/*from   w  w w . j a  va 2 s  .  c  o m*/
 *         command line arguments
 */
public static void main(String[] args) {

    try {
        run(args);
    } catch (AbortException e) {

        if (e.getCause() != null) {
            LOG.log(Level.SEVERE, e.getCause(), () -> "Aborting the merge.");
        } else {
            System.err.println(e.getMessage());
            LOG.log(Level.FINE, e, () -> "Aborting the merge.");
        }

        System.exit(EXIT_ABORTED);
    } catch (Throwable e) {
        LOG.log(Level.SEVERE, e, () -> "Uncaught exception.");
        System.exit(EXIT_FAILURE);
    }
}

From source file:com.archivas.clienttools.arcmover.cli.ManagedCLIJob.java

@SuppressWarnings({ "UseOfSystemOutOrSystemErr" })
public static void main(String args[]) {
    if (LOG.isLoggable(Level.FINE)) {
        StringBuffer sb = new StringBuffer();
        sb.append("Program Arguments").append(NEWLINE);
        for (int i = 0; i < args.length; i++) {
            sb.append("    ").append(i).append(": ").append(args[i]);
            sb.append(NEWLINE);/*  w  w w. j  a v a  2 s .  c  om*/
        }
        LOG.log(Level.FINE, sb.toString());
    }

    ConfigurationHelper.validateLaunchOK();

    ManagedCLIJob arcCmd = null;
    try {
        if (args[0].equals("copy")) {
            arcCmd = new ArcCopy(args, 2);
        } else if (args[0].equals("delete")) {
            arcCmd = new ArcDelete(args, 2);
        } else if (args[0].equals("metadata")) {
            arcCmd = new ArcMetadata(args, 2);
        } else {
            throw new RuntimeException("Unsupported operation: " + args[0]);
        }

        arcCmd.parseArgs();

        if (arcCmd.shouldPrintHelp()) {
            System.out.println(arcCmd.helpScreen());
        } else {
            arcCmd.execute(new PrintWriter(System.out), new PrintWriter(System.err));
        }
    } catch (ParseException e) {
        System.out.println("Error: " + e.getMessage());
        System.out.println();
        System.out.println(arcCmd.helpScreen());
        arcCmd.setExitCode(EXIT_CODE_OPTION_PARSE_ERROR);
    } catch (Exception e) {
        LOG.log(Level.SEVERE, e.getMessage(), e);
        System.out.println();
        System.err.println("Job failed.  " + e.getMessage());
        if (arcCmd != null) {
            arcCmd.setExitCode(EXIT_CODE_DM_ERROR);
        }
    } finally {
        if (arcCmd != null) {
            arcCmd.exit();
        }
    }
}

From source file:MailHandlerDemo.java

/**
 * Runs the demo./*from   w  w w. j  av  a 2  s  .  c o m*/
 *
 * @param args the command line arguments
 * @throws IOException if there is a problem.
 */
public static void main(String[] args) throws IOException {
    List<String> l = Arrays.asList(args);
    if (l.contains("/?") || l.contains("-?") || l.contains("-help")) {
        LOGGER.info("Usage: java MailHandlerDemo " + "[[-all] | [-body] | [-custom] | [-debug] | [-low] "
                + "| [-simple] | [-pushlevel] | [-pushfilter] " + "| [-pushnormal] | [-pushonly]] " + "\n\n"
                + "-all\t\t: Execute all demos.\n" + "-body\t\t: An email with all records and only a body.\n"
                + "-custom\t\t: An email with attachments and dynamic names.\n"
                + "-debug\t\t: Output basic debug information about the JVM " + "and log configuration.\n"
                + "-low\t\t: Generates multiple emails due to low capacity." + "\n"
                + "-simple\t\t: An email with all records with body and " + "an attachment.\n"
                + "-pushlevel\t: Generates high priority emails when the"
                + " push level is triggered and normal priority when " + "flushed.\n"
                + "-pushFilter\t: Generates high priority emails when the "
                + "push level and the push filter is triggered and normal " + "priority emails when flushed.\n"
                + "-pushnormal\t: Generates multiple emails when the "
                + "MemoryHandler push level is triggered.  All generated "
                + "email are sent as normal priority.\n" + "-pushonly\t: Generates multiple emails when the "
                + "MemoryHandler push level is triggered.  Generates high "
                + "priority emails when the push level is triggered and " + "normal priority when flushed.\n");
    } else {
        final boolean debug = init(l); //may create log messages.
        try {
            LOGGER.log(Level.FINEST, "This is the finest part of the demo.",
                    new MessagingException("Fake JavaMail issue."));
            LOGGER.log(Level.FINER, "This is the finer part of the demo.",
                    new NullPointerException("Fake bug."));
            LOGGER.log(Level.FINE, "This is the fine part of the demo.");
            LOGGER.log(Level.CONFIG, "Logging config file is {0}.", getConfigLocation());
            LOGGER.log(Level.INFO, "Your temp directory is {0}, " + "please wait...", getTempDir());

            try { //Waste some time for the custom formatter.
                Thread.sleep(3L * 1000L);
            } catch (InterruptedException ex) {
                Thread.currentThread().interrupt();
            }

            LOGGER.log(Level.WARNING, "This is a warning.",
                    new FileNotFoundException("Fake file chooser issue."));
            LOGGER.log(Level.SEVERE, "The end of the demo.", new IOException("Fake access denied issue."));
        } finally {
            closeHandlers();
        }

        //Force parse errors.  This does have side effects.
        if (debug && getConfigLocation() != null) {
            LogManager.getLogManager().readConfiguration();
        }
    }
}

From source file:com.frostvoid.trekwar.server.TrekwarServer.java

public static void main(String[] args) {
    // load language
    try {//w w w .j  a va2s.  c  om
        lang = new Language(Language.ENGLISH);
    } catch (IOException ioe) {
        System.err.println("FATAL ERROR: Unable to load language file!");
        System.exit(1);
    }

    System.out.println(lang.get("trekwar_server") + " " + VERSION);
    System.out.println("==============================================".substring(0,
            lang.get("trekwar_server").length() + 1 + VERSION.length()));

    // Handle parameters
    Options options = new Options();
    options.addOption(OptionBuilder.withArgName("file").withLongOpt("galaxy").hasArg()
            .withDescription("the galaxy file to load").create("g")); //"g", "galaxy", true, "the galaxy file to load");
    options.addOption(OptionBuilder.withArgName("port number").withLongOpt("port").hasArg()
            .withDescription("the port number to bind to (default 8472)").create("p"));
    options.addOption(OptionBuilder.withArgName("number").withLongOpt("save-interval").hasArg()
            .withDescription("how often (in turns) to save the galaxy to disk (default: 5)").create("s"));
    options.addOption(OptionBuilder.withArgName("log level").withLongOpt("log").hasArg()
            .withDescription("sets the log level: ALL, FINEST, FINER, FINE, CONFIG, INFO, WARNING, SEVERE, OFF")
            .create("l"));
    options.addOption("h", "help", false, "prints this help message");

    CommandLineParser cliParser = new BasicParser();

    try {
        CommandLine cmd = cliParser.parse(options, args);
        String portStr = cmd.getOptionValue("p");
        String galaxyFileStr = cmd.getOptionValue("g");
        String saveIntervalStr = cmd.getOptionValue("s");
        String logLevelStr = cmd.getOptionValue("l");

        if (cmd.hasOption("h")) {
            HelpFormatter help = new HelpFormatter();
            help.printHelp("TrekwarServer", options);
            System.exit(0);
        }

        if (cmd.hasOption("g") && galaxyFileStr != null) {
            galaxyFileName = galaxyFileStr;
        } else {
            throw new ParseException("galaxy file not specified");
        }

        if (cmd.hasOption("p") && portStr != null) {
            port = Integer.parseInt(portStr);
            if (port < 1 || port > 65535) {
                throw new NumberFormatException(lang.get("port_number_out_of_range"));
            }
        } else {
            port = 8472;
        }

        if (cmd.hasOption("s") && saveIntervalStr != null) {
            saveInterval = Integer.parseInt(saveIntervalStr);
            if (saveInterval < 1 || saveInterval > 100) {
                throw new NumberFormatException("Save Interval out of range (1-100)");
            }
        } else {
            saveInterval = 5;
        }

        if (cmd.hasOption("l") && logLevelStr != null) {
            if (logLevelStr.equalsIgnoreCase("finest")) {
                LOG.setLevel(Level.FINEST);
            } else if (logLevelStr.equalsIgnoreCase("finer")) {
                LOG.setLevel(Level.FINER);
            } else if (logLevelStr.equalsIgnoreCase("fine")) {
                LOG.setLevel(Level.FINE);
            } else if (logLevelStr.equalsIgnoreCase("config")) {
                LOG.setLevel(Level.CONFIG);
            } else if (logLevelStr.equalsIgnoreCase("info")) {
                LOG.setLevel(Level.INFO);
            } else if (logLevelStr.equalsIgnoreCase("warning")) {
                LOG.setLevel(Level.WARNING);
            } else if (logLevelStr.equalsIgnoreCase("severe")) {
                LOG.setLevel(Level.SEVERE);
            } else if (logLevelStr.equalsIgnoreCase("off")) {
                LOG.setLevel(Level.OFF);
            } else if (logLevelStr.equalsIgnoreCase("all")) {
                LOG.setLevel(Level.ALL);
            } else {
                System.err.println("ERROR: invalid log level: " + logLevelStr);
                System.err.println("Run again with -h flag to see valid log level values");
                System.exit(1);
            }
        } else {
            LOG.setLevel(Level.INFO);
        }
        // INIT LOGGING
        try {
            LOG.setUseParentHandlers(false);
            initLogging();
        } catch (IOException ex) {
            System.err.println("Unable to initialize logging to file");
            System.err.println(ex);
            System.exit(1);
        }

    } catch (Exception ex) {
        System.err.println("ERROR: " + ex.getMessage());
        System.err.println("use -h for help");
        System.exit(1);
    }

    LOG.log(Level.INFO, "Trekwar2 server " + VERSION + " starting up");

    // LOAD GALAXY
    File galaxyFile = new File(galaxyFileName);
    if (galaxyFile.exists()) {
        try {
            long timer = System.currentTimeMillis();
            LOG.log(Level.INFO, "Loading galaxy file {0}", galaxyFileName);
            ObjectInputStream ois = new ObjectInputStream(new FileInputStream(galaxyFile));
            galaxy = (Galaxy) ois.readObject();
            timer = System.currentTimeMillis() - timer;
            LOG.log(Level.INFO, "Galaxy file loaded in {0} ms", timer);
            ois.close();
        } catch (IOException ioe) {
            LOG.log(Level.SEVERE, "IO error while trying to load galaxy file", ioe);
        } catch (ClassNotFoundException cnfe) {
            LOG.log(Level.SEVERE, "Unable to find class while loading galaxy", cnfe);
        }
    } else {
        System.err.println("Error: file " + galaxyFileName + " not found");
        System.exit(1);
    }

    // if turn == 0 (start of game), execute first turn to update fog of war.
    if (galaxy.getCurrentTurn() == 0) {
        TurnExecutor.executeTurn(galaxy);
    }

    LOG.log(Level.INFO, "Current turn  : {0}", galaxy.getCurrentTurn());
    LOG.log(Level.INFO, "Turn speed    : {0} seconds", galaxy.getTurnSpeed() / 1000);
    LOG.log(Level.INFO, "Save Interval : {0}", saveInterval);
    LOG.log(Level.INFO, "Users / max   : {0} / {1}",
            new Object[] { galaxy.getUserCount(), galaxy.getMaxUsers() });

    // START SERVER
    try {
        server = new ServerSocket(port);
        LOG.log(Level.INFO, "Server listening on port {0}", port);
    } catch (BindException be) {
        LOG.log(Level.SEVERE, "Error: Unable to bind to port {0}", port);
        System.err.println(be);
        System.exit(1);
    } catch (IOException ioe) {
        LOG.log(Level.SEVERE, "Error: IO error while binding to port {0}", port);
        System.err.println(ioe);
        System.exit(1);
    }

    galaxy.startup();

    Thread timerThread = new Thread(new Runnable() {

        @Override
        @SuppressWarnings("SleepWhileInLoop")
        public void run() {
            while (true) {
                try {
                    Thread.sleep(1000);
                    // && galaxy.getLoggedInUsers().size() > 0 will make server pause when nobody is logged in (TESTING)
                    if (System.currentTimeMillis() > galaxy.nextTurnDate) {
                        StringBuffer loggedInUsers = new StringBuffer();
                        for (User u : galaxy.getLoggedInUsers()) {
                            loggedInUsers.append(u.getUsername()).append(", ");
                        }

                        long time = TurnExecutor.executeTurn(galaxy);
                        LOG.log(Level.INFO, "Turn {0} executed in {1} ms",
                                new Object[] { galaxy.getCurrentTurn(), time });
                        LOG.log(Level.INFO, "Logged in users: " + loggedInUsers.toString());
                        LOG.log(Level.INFO,
                                "====================================================================================");

                        if (galaxy.getCurrentTurn() % saveInterval == 0) {
                            saveGalaxy();
                        }

                        galaxy.lastTurnDate = System.currentTimeMillis();
                        galaxy.nextTurnDate = galaxy.lastTurnDate + galaxy.turnSpeed;
                    }

                } catch (InterruptedException e) {
                    LOG.log(Level.SEVERE, "Error in main server loop, interrupted", e);
                }
            }
        }
    });
    timerThread.start();

    // ACCEPT CONNECTIONS AND DELEGATE TO CLIENT SESSIONS
    while (true) {
        Socket clientConnection;
        try {
            clientConnection = server.accept();
            ClientSession c = new ClientSession(clientConnection, galaxy);
            Thread t = new Thread(c);
            t.start();
        } catch (IOException ex) {
            LOG.log(Level.SEVERE, "IO Exception while trying to handle incoming client connection", ex);
        }
    }
}

From source file:baldrickv.s3streamingtool.S3StreamingTool.java

public static void main(String args[]) throws Exception {
    BasicParser p = new BasicParser();

    Options o = getOptions();//from   w  w w  .ja  v a 2 s .c o m

    CommandLine cl = p.parse(o, args);

    if (cl.hasOption('h')) {
        HelpFormatter hf = new HelpFormatter();
        hf.setWidth(80);

        StringBuilder sb = new StringBuilder();

        sb.append("\n");
        sb.append("Upload:\n");
        sb.append("    -u -r creds -s 50M -b my_bucket -f hda1.dump -t 10\n");
        sb.append("Download:\n");
        sb.append("    -d -r creds -s 50M -b my_bucket -f hda1.dump -t 10\n");
        sb.append("Upload encrypted:\n");
        sb.append("    -u -r creds -z -k secret_key -s 50M -b my_bucket -f hda1.dump -t 10\n");
        sb.append("Download encrypted:\n");
        sb.append("    -d -r creds -z -k secret_key -s 50M -b my_bucket -f hda1.dump -t 10\n");
        sb.append("Cleanup in-progress multipart uploads\n");
        sb.append("    -c -r creds -b my_bucket\n");
        System.out.println(sb.toString());

        hf.printHelp("See above", o);

        return;
    }

    int n = 0;
    if (cl.hasOption('d'))
        n++;
    if (cl.hasOption('u'))
        n++;
    if (cl.hasOption('c'))
        n++;
    if (cl.hasOption('m'))
        n++;

    if (n != 1) {
        System.err.println("Must specify at exactly one of -d, -u, -c or -m");
        System.exit(-1);
    }

    if (cl.hasOption('m')) {
        //InputStream in = new java.io.BufferedInputStream(System.in,1024*1024*2);
        InputStream in = System.in;
        System.out.println(TreeHashGenerator.calculateTreeHash(in));
        return;
    }

    require(cl, 'b');

    if (cl.hasOption('d') || cl.hasOption('u')) {
        require(cl, 'f');
    }
    if (cl.hasOption('z')) {
        require(cl, 'k');
    }

    AWSCredentials creds = null;

    if (cl.hasOption('r')) {
        creds = Utils.loadAWSCredentails(cl.getOptionValue('r'));
    } else {
        if (cl.hasOption('i') && cl.hasOption('e')) {
            creds = new BasicAWSCredentials(cl.getOptionValue('i'), cl.getOptionValue('e'));
        } else {

            System.out.println("Must specify either credential file (-r) or AWS key ID and secret (-i and -e)");
            System.exit(-1);
        }
    }

    S3StreamConfig config = new S3StreamConfig();
    config.setEncryption(false);
    if (cl.hasOption('z')) {
        config.setEncryption(true);
        config.setSecretKey(Utils.loadSecretKey(cl.getOptionValue("k")));
    }

    if (cl.hasOption("encryption-mode")) {
        config.setEncryptionMode(cl.getOptionValue("encryption-mode"));
    }
    config.setS3Bucket(cl.getOptionValue("bucket"));
    if (cl.hasOption("file")) {
        config.setS3File(cl.getOptionValue("file"));
    }

    if (cl.hasOption("threads")) {
        config.setIOThreads(Integer.parseInt(cl.getOptionValue("threads")));
    }

    if (cl.hasOption("blocksize")) {
        String s = cl.getOptionValue("blocksize");
        s = s.toUpperCase();
        int multi = 1;

        int end = 0;
        while ((end < s.length()) && (s.charAt(end) >= '0') && (s.charAt(end) <= '9')) {
            end++;
        }
        int size = Integer.parseInt(s.substring(0, end));

        if (end < s.length()) {
            String m = s.substring(end);
            if (m.equals("K"))
                multi = 1024;
            else if (m.equals("M"))
                multi = 1048576;
            else if (m.equals("G"))
                multi = 1024 * 1024 * 1024;
            else if (m.equals("KB"))
                multi = 1024;
            else if (m.equals("MB"))
                multi = 1048576;
            else if (m.equals("GB"))
                multi = 1024 * 1024 * 1024;
            else {
                System.out.println("Unknown suffix on block size.  Only K,M and G understood.");
                System.exit(-1);
            }

        }
        size *= multi;
        config.setBlockSize(size);
    }

    Logger.getLogger("").setLevel(Level.FINE);

    S3StreamingDownload.log.setLevel(Level.FINE);
    S3StreamingUpload.log.setLevel(Level.FINE);

    config.setS3Client(new AmazonS3Client(creds));
    config.setGlacierClient(new AmazonGlacierClient(creds));
    config.getGlacierClient().setEndpoint("glacier.us-west-2.amazonaws.com");

    if (cl.hasOption("glacier")) {
        config.setGlacier(true);
        config.setStorageInterface(new StorageGlacier(config.getGlacierClient()));
    } else {
        config.setStorageInterface(new StorageS3(config.getS3Client()));
    }
    if (cl.hasOption("bwlimit")) {
        config.setMaxBytesPerSecond(Double.parseDouble(cl.getOptionValue("bwlimit")));

    }

    if (cl.hasOption('c')) {
        if (config.getGlacier()) {
            GlacierCleanupMultipart.cleanup(config);
        } else {
            S3CleanupMultipart.cleanup(config);
        }
        return;
    }
    if (cl.hasOption('d')) {
        config.setOutputStream(System.out);
        S3StreamingDownload.download(config);
        return;
    }
    if (cl.hasOption('u')) {
        config.setInputStream(System.in);
        S3StreamingUpload.upload(config);
        return;
    }

}

From source file:tuit.java

@SuppressWarnings("ConstantConditions")
public static void main(String[] args) {
    System.out.println(licence);//from   ww w  .j a  v  a  2s.c  o  m
    //Declare variables
    File inputFile;
    File outputFile;
    File tmpDir;
    File blastnExecutable;
    File properties;
    File blastOutputFile = null;
    //
    TUITPropertiesLoader tuitPropertiesLoader;
    TUITProperties tuitProperties;
    //
    String[] parameters = null;
    //
    Connection connection = null;
    MySQL_Connector mySQL_connector;
    //
    Map<Ranks, TUITCutoffSet> cutoffMap;
    //
    BLASTIdentifier blastIdentifier = null;
    //
    RamDb ramDb = null;

    CommandLineParser parser = new GnuParser();
    Options options = new Options();

    options.addOption(tuit.IN, "input<file>", true, "Input file (currently fasta-formatted only)");
    options.addOption(tuit.OUT, "output<file>", true, "Output file (in " + tuit.TUIT_EXT + " format)");
    options.addOption(tuit.P, "prop<file>", true, "Properties file (XML formatted)");
    options.addOption(tuit.V, "verbose", false, "Enable verbose output");
    options.addOption(tuit.B, "blast_output<file>", true, "Perform on a pre-BLASTed output");
    options.addOption(tuit.DEPLOY, "deploy", false, "Deploy the taxonomic databases");
    options.addOption(tuit.UPDATE, "update", false, "Update the taxonomic databases");
    options.addOption(tuit.USE_DB, "usedb", false, "Use RDBMS instead of RAM-based taxonomy");

    Option option = new Option(tuit.REDUCE, "reduce", true,
            "Pack identical (100% similar sequences) records in the given sample file");
    option.setArgs(Option.UNLIMITED_VALUES);
    options.addOption(option);
    option = new Option(tuit.COMBINE, "combine", true,
            "Combine a set of given reduction files into an HMP Tree-compatible taxonomy");
    option.setArgs(Option.UNLIMITED_VALUES);
    options.addOption(option);
    options.addOption(tuit.NORMALIZE, "normalize", false,
            "If used in combination with -combine ensures that the values are normalized by the root value");

    HelpFormatter formatter = new HelpFormatter();

    try {

        //Get TUIT directory
        final File tuitDir = new File(
                new File(tuit.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath())
                        .getParent());
        final File ramDbFile = new File(tuitDir, tuit.RAM_DB);

        //Setup logger
        Log.getInstance().setLogName("tuit.log");

        //Read command line
        final CommandLine commandLine = parser.parse(options, args, true);

        //Check if the REDUCE option is on
        if (commandLine.hasOption(tuit.REDUCE)) {

            final String[] fileList = commandLine.getOptionValues(tuit.REDUCE);
            for (String s : fileList) {
                final Path path = Paths.get(s);
                Log.getInstance().log(Level.INFO, "Processing " + path.toString() + "...");
                final NucleotideFastaSequenceReductor nucleotideFastaSequenceReductor = NucleotideFastaSequenceReductor
                        .fromPath(path);
                ReductorFileOperator.save(nucleotideFastaSequenceReductor,
                        path.resolveSibling(path.getFileName().toString() + ".rdc"));
            }

            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }

        //Check if COMBINE is on
        if (commandLine.hasOption(tuit.COMBINE)) {
            final boolean normalize = commandLine.hasOption(tuit.NORMALIZE);
            final String[] fileList = commandLine.getOptionValues(tuit.COMBINE);
            //TODO: implement a test for format here

            final List<TreeFormatter.TreeFormatterFormat.HMPTreesOutput> hmpTreesOutputs = new ArrayList<>();
            final TreeFormatter treeFormatter = TreeFormatter
                    .newInstance(new TreeFormatter.TuitLineTreeFormatterFormat());
            for (String s : fileList) {
                final Path path = Paths.get(s);
                Log.getInstance().log(Level.INFO, "Merging " + path.toString() + "...");
                treeFormatter.loadFromPath(path);
                final TreeFormatter.TreeFormatterFormat.HMPTreesOutput output = TreeFormatter.TreeFormatterFormat.HMPTreesOutput
                        .newInstance(treeFormatter.toHMPTree(normalize), s.substring(0, s.indexOf(".")));
                hmpTreesOutputs.add(output);
                treeFormatter.erase();
            }
            final Path destination;
            if (commandLine.hasOption(OUT)) {
                destination = Paths.get(commandLine.getOptionValue(tuit.OUT));
            } else {
                destination = Paths.get("merge.tcf");
            }
            CombinatorFileOperator.save(hmpTreesOutputs, treeFormatter, destination);
            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }

        if (!commandLine.hasOption(tuit.P)) {
            throw new ParseException("No properties file option found, exiting.");
        } else {
            properties = new File(commandLine.getOptionValue(tuit.P));
        }

        //Load properties
        tuitPropertiesLoader = TUITPropertiesLoader.newInstanceFromFile(properties);
        tuitProperties = tuitPropertiesLoader.getTuitProperties();

        //Create tmp directory and blastn executable
        tmpDir = new File(tuitProperties.getTMPDir().getPath());
        blastnExecutable = new File(tuitProperties.getBLASTNPath().getPath());

        //Check for deploy
        if (commandLine.hasOption(tuit.DEPLOY)) {
            if (commandLine.hasOption(tuit.USE_DB)) {
                NCBITablesDeployer.fastDeployNCBIDatabasesFromNCBI(connection, tmpDir);
            } else {
                NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile);
            }

            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }
        //Check for update
        if (commandLine.hasOption(tuit.UPDATE)) {
            if (commandLine.hasOption(tuit.USE_DB)) {
                NCBITablesDeployer.updateDatabasesFromNCBI(connection, tmpDir);
            } else {
                //No need to specify a different way to update the database other than just deploy in case of the RAM database
                NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile);
            }
            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }

        //Connect to the database
        if (commandLine.hasOption(tuit.USE_DB)) {
            mySQL_connector = MySQL_Connector.newDefaultInstance(
                    "jdbc:mysql://" + tuitProperties.getDBConnection().getUrl().trim() + "/",
                    tuitProperties.getDBConnection().getLogin().trim(),
                    tuitProperties.getDBConnection().getPassword().trim());
            mySQL_connector.connectToDatabase();
            connection = mySQL_connector.getConnection();
        } else {
            //Probe for ram database

            if (ramDbFile.exists() && ramDbFile.canRead()) {
                Log.getInstance().log(Level.INFO, "Loading RAM taxonomic map...");
                try {
                    ramDb = RamDb.loadSelfFromFile(ramDbFile);
                } catch (IOException ie) {
                    if (ie instanceof java.io.InvalidClassException)
                        throw new IOException("The RAM-based taxonomic database needs to be updated.");
                }

            } else {
                Log.getInstance().log(Level.SEVERE,
                        "The RAM database either has not been deployed, or is not accessible."
                                + "Please use the --deploy option and check permissions on the TUIT directory. "
                                + "If you were looking to use the RDBMS as a taxonomic reference, plese use the -usedb option.");
                return;
            }
        }

        if (commandLine.hasOption(tuit.B)) {
            blastOutputFile = new File(commandLine.getOptionValue(tuit.B));
            if (!blastOutputFile.exists() || !blastOutputFile.canRead()) {
                throw new Exception("BLAST output file either does not exist, or is not readable.");
            } else if (blastOutputFile.isDirectory()) {
                throw new Exception("BLAST output file points to a directory.");
            }
        }
        //Check vital parameters
        if (!commandLine.hasOption(tuit.IN)) {
            throw new ParseException("No input file option found, exiting.");
        } else {
            inputFile = new File(commandLine.getOptionValue(tuit.IN));
            Log.getInstance().setLogName(inputFile.getName().split("\\.")[0] + ".tuit.log");
        }
        //Correct the output file option if needed
        if (!commandLine.hasOption(tuit.OUT)) {
            outputFile = new File((inputFile.getPath()).split("\\.")[0] + tuit.TUIT_EXT);
        } else {
            outputFile = new File(commandLine.getOptionValue(tuit.OUT));
        }

        //Adjust the output level
        if (commandLine.hasOption(tuit.V)) {
            Log.getInstance().setLevel(Level.FINE);
            Log.getInstance().log(Level.INFO, "Using verbose output for the log");
        } else {
            Log.getInstance().setLevel(Level.INFO);
        }
        //Try all files
        if (inputFile != null) {
            if (!inputFile.exists() || !inputFile.canRead()) {
                throw new Exception("Input file either does not exist, or is not readable.");
            } else if (inputFile.isDirectory()) {
                throw new Exception("Input file points to a directory.");
            }
        }

        if (!properties.exists() || !properties.canRead()) {
            throw new Exception("Properties file either does not exist, or is not readable.");
        } else if (properties.isDirectory()) {
            throw new Exception("Properties file points to a directory.");
        }

        //Create blast parameters
        final StringBuilder stringBuilder = new StringBuilder();
        for (Database database : tuitProperties.getBLASTNParameters().getDatabase()) {
            stringBuilder.append(database.getUse());
            stringBuilder.append(" ");//Gonna insert an extra space for the last database
        }
        String remote;
        String entrez_query;
        if (tuitProperties.getBLASTNParameters().getRemote().getDelegate().equals("yes")) {
            remote = "-remote";
            entrez_query = "-entrez_query";
            parameters = new String[] { "-db", stringBuilder.toString(), remote, entrez_query,
                    tuitProperties.getBLASTNParameters().getEntrezQuery().getValue(), "-evalue",
                    tuitProperties.getBLASTNParameters().getExpect().getValue() };
        } else {
            if (!commandLine.hasOption(tuit.B)) {
                if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase()
                        .startsWith("NOT")
                        || tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase()
                                .startsWith("ALL")) {
                    parameters = new String[] { "-db", stringBuilder.toString(), "-evalue",
                            tuitProperties.getBLASTNParameters().getExpect().getValue(), "-negative_gilist",
                            TUITFileOperatorHelper.restrictToEntrez(tmpDir,
                                    tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()
                                            .toUpperCase().replace("NOT", "OR"))
                                    .getAbsolutePath(),
                            "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() };
                } else if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase()
                        .equals("")) {
                    parameters = new String[] { "-db", stringBuilder.toString(), "-evalue",
                            tuitProperties.getBLASTNParameters().getExpect().getValue(), "-num_threads",
                            tuitProperties.getBLASTNParameters().getNumThreads().getValue() };
                } else {
                    parameters = new String[] { "-db", stringBuilder.toString(), "-evalue",
                            tuitProperties.getBLASTNParameters().getExpect().getValue(),
                            /*"-gilist", TUITFileOperatorHelper.restrictToEntrez(
                            tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()).getAbsolutePath(),*/ //TODO remove comment!!!!!
                            "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() };
                }
            }
        }
        //Prepare a cutoff Map
        if (tuitProperties.getSpecificationParameters() != null
                && tuitProperties.getSpecificationParameters().size() > 0) {
            cutoffMap = new HashMap<Ranks, TUITCutoffSet>(tuitProperties.getSpecificationParameters().size());
            for (SpecificationParameters specificationParameters : tuitProperties
                    .getSpecificationParameters()) {
                cutoffMap.put(Ranks.valueOf(specificationParameters.getCutoffSet().getRank()),
                        TUITCutoffSet.newDefaultInstance(
                                Double.parseDouble(
                                        specificationParameters.getCutoffSet().getPIdentCutoff().getValue()),
                                Double.parseDouble(specificationParameters.getCutoffSet()
                                        .getQueryCoverageCutoff().getValue()),
                                Double.parseDouble(
                                        specificationParameters.getCutoffSet().getAlpha().getValue())));
            }
        } else {
            cutoffMap = new HashMap<Ranks, TUITCutoffSet>();
        }
        final TUITFileOperatorHelper.OutputFormat format;
        if (tuitProperties.getBLASTNParameters().getOutputFormat().getFormat().equals("rdp")) {
            format = TUITFileOperatorHelper.OutputFormat.RDP_FIXRANK;
        } else {
            format = TUITFileOperatorHelper.OutputFormat.TUIT;
        }

        try (TUITFileOperator<NucleotideFasta> nucleotideFastaTUITFileOperator = NucleotideFastaTUITFileOperator
                .newInstance(format, cutoffMap);) {
            nucleotideFastaTUITFileOperator.setInputFile(inputFile);
            nucleotideFastaTUITFileOperator.setOutputFile(outputFile);
            final String cleanupString = tuitProperties.getBLASTNParameters().getKeepBLASTOuts().getKeep();
            final boolean cleanup;
            if (cleanupString.equals("no")) {
                Log.getInstance().log(Level.INFO, "Temporary BLAST files will be deleted.");
                cleanup = true;
            } else {
                Log.getInstance().log(Level.INFO, "Temporary BLAST files will be kept.");
                cleanup = false;
            }
            //Create blast identifier
            ExecutorService executorService = Executors.newSingleThreadExecutor();
            if (commandLine.hasOption(tuit.USE_DB)) {

                if (blastOutputFile == null) {
                    blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromFileOperator(tmpDir,
                            blastnExecutable, parameters, nucleotideFastaTUITFileOperator, connection,
                            cutoffMap,
                            Integer.parseInt(
                                    tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                            cleanup);

                } else {
                    try {
                        blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromBLASTOutput(
                                nucleotideFastaTUITFileOperator, connection, cutoffMap, blastOutputFile,
                                Integer.parseInt(
                                        tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                                cleanup);

                    } catch (JAXBException e) {
                        Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName()
                                + ", please check input. The file must be XML formatted.");
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }

            } else {
                if (blastOutputFile == null) {
                    blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromFileOperator(tmpDir,
                            blastnExecutable, parameters, nucleotideFastaTUITFileOperator, cutoffMap,
                            Integer.parseInt(
                                    tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                            cleanup, ramDb);

                } else {
                    try {
                        blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromBLASTOutput(
                                nucleotideFastaTUITFileOperator, cutoffMap, blastOutputFile,
                                Integer.parseInt(
                                        tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                                cleanup, ramDb);

                    } catch (JAXBException e) {
                        Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName()
                                + ", please check input. The file must be XML formatted.");
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
            }
            Future<?> runnableFuture = executorService.submit(blastIdentifier);
            runnableFuture.get();
            executorService.shutdown();
        }
    } catch (ParseException pe) {
        Log.getInstance().log(Level.SEVERE, (pe.getMessage()));
        formatter.printHelp("tuit", options);
    } catch (SAXException saxe) {
        Log.getInstance().log(Level.SEVERE, saxe.getMessage());
    } catch (FileNotFoundException fnfe) {
        Log.getInstance().log(Level.SEVERE, fnfe.getMessage());
    } catch (TUITPropertyBadFormatException tpbfe) {
        Log.getInstance().log(Level.SEVERE, tpbfe.getMessage());
    } catch (ClassCastException cce) {
        Log.getInstance().log(Level.SEVERE, cce.getMessage());
    } catch (JAXBException jaxbee) {
        Log.getInstance().log(Level.SEVERE,
                "The properties file is not well formatted. Please ensure that the XML is consistent with the io.properties.dtd schema.");
    } catch (ClassNotFoundException cnfe) {
        //Probably won't happen unless the library deleted from the .jar
        Log.getInstance().log(Level.SEVERE, cnfe.getMessage());
        //cnfe.printStackTrace();
    } catch (SQLException sqle) {
        Log.getInstance().log(Level.SEVERE,
                "A database communication error occurred with the following message:\n" + sqle.getMessage());
        //sqle.printStackTrace();
        if (sqle.getMessage().contains("Access denied for user")) {
            Log.getInstance().log(Level.SEVERE, "Please use standard database login: "
                    + NCBITablesDeployer.login + " and password: " + NCBITablesDeployer.password);
        }
    } catch (Exception e) {
        Log.getInstance().log(Level.SEVERE, e.getMessage());
        e.printStackTrace();
    } finally {
        if (connection != null) {
            try {
                connection.close();
            } catch (SQLException sqle) {
                Log.getInstance().log(Level.SEVERE, "Problem closing the database connection: " + sqle);
            }
        }
        Log.getInstance().log(Level.FINE, "Task done, exiting...");
    }
}