Example usage for java.util.concurrent ExecutorService shutdown

List of usage examples for java.util.concurrent ExecutorService shutdown

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Introduction

In this page you can find the example usage for java.util.concurrent ExecutorService shutdown.

Prototype

void shutdown();

Source Link

Document

Initiates an orderly shutdown in which previously submitted tasks are executed, but no new tasks will be accepted.

Usage

From source file:eu.itesla_project.offline.mpi.Master.java

public static void main(String[] args) throws Exception {
    try {//w w  w  . jav a 2 s  .co m
        CommandLineParser parser = new GnuParser();
        CommandLine line = parser.parse(OPTIONS, args);

        Mode mode = Mode.valueOf(line.getOptionValue("mode"));
        String simulationDbName = line.hasOption("simulation-db-name")
                ? line.getOptionValue("simulation-db-name")
                : OfflineConfig.DEFAULT_SIMULATION_DB_NAME;
        String rulesDbName = line.hasOption("rules-db-name") ? line.getOptionValue("rules-db-name")
                : OfflineConfig.DEFAULT_RULES_DB_NAME;
        String metricsDbName = line.hasOption("metrics-db-name") ? line.getOptionValue("metrics-db-name")
                : OfflineConfig.DEFAULT_METRICS_DB_NAME;
        Path tmpDir = Paths.get(line.getOptionValue("tmp-dir"));
        Class<?> statisticsFactoryClass = Class.forName(line.getOptionValue("statistics-factory-class"));
        Path statisticsDbDir = Paths.get(line.getOptionValue("statistics-db-dir"));
        String statisticsDbName = line.getOptionValue("statistics-db-name");
        int coresPerRank = Integer.parseInt(line.getOptionValue("cores"));
        Path stdOutArchive = line.hasOption("stdout-archive") ? Paths.get(line.getOptionValue("stdout-archive"))
                : null;
        String workflowId = line.hasOption("workflow") ? line.getOptionValue("workflow") : null;

        MpiExecutorContext mpiExecutorContext = new MultiStateNetworkAwareMpiExecutorContext();
        ScheduledExecutorService scheduledExecutorService = Executors.newScheduledThreadPool(1);
        ExecutorService offlineExecutorService = MultiStateNetworkAwareExecutors
                .newSizeLimitedThreadPool("OFFLINE_POOL", 100);
        try {
            MpiStatisticsFactory statisticsFactory = statisticsFactoryClass
                    .asSubclass(MpiStatisticsFactory.class).newInstance();
            try (MpiStatistics statistics = statisticsFactory.create(statisticsDbDir, statisticsDbName)) {
                try (ComputationManager computationManager = new MpiComputationManager(tmpDir, statistics,
                        mpiExecutorContext, coresPerRank, false, stdOutArchive)) {
                    OfflineConfig config = OfflineConfig.load();
                    try (LocalOfflineApplication application = new LocalOfflineApplication(config,
                            computationManager, simulationDbName, rulesDbName, metricsDbName,
                            scheduledExecutorService, offlineExecutorService)) {
                        switch (mode) {
                        case ui:
                            application.await();
                            break;

                        case simulations: {
                            if (workflowId == null) {
                                workflowId = application.createWorkflow(null,
                                        OfflineWorkflowCreationParameters.load());
                            }
                            application.startWorkflowAndWait(workflowId, OfflineWorkflowStartParameters.load());
                        }
                            break;

                        case rules: {
                            if (workflowId == null) {
                                throw new RuntimeException("Workflow '" + workflowId + "' not found");
                            }
                            application.computeSecurityRulesAndWait(workflowId);
                        }
                            break;

                        default:
                            throw new IllegalArgumentException("Invalid mode " + mode);
                        }
                    }
                }
            }
        } finally {
            mpiExecutorContext.shutdown();
            offlineExecutorService.shutdown();
            scheduledExecutorService.shutdown();
            offlineExecutorService.awaitTermination(15, TimeUnit.MINUTES);
            scheduledExecutorService.awaitTermination(15, TimeUnit.MINUTES);
        }
    } catch (ParseException e) {
        System.err.println(e.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("master", OPTIONS, true);
        System.exit(-1);
    } catch (Throwable t) {
        LOGGER.error(t.toString(), t);
        System.exit(-1);
    }
}

From source file:edu.cornell.med.icb.R.RUtils.java

public static void main(final String[] args) throws ParseException, ConfigurationException {
    final Options options = new Options();

    final Option helpOption = new Option("h", "help", false, "Print this message");
    options.addOption(helpOption);//from w  w w . j  a  va 2 s  . c o  m

    final Option startupOption = new Option(Mode.startup.name(), Mode.startup.name(), false,
            "Start Rserve process");
    final Option shutdownOption = new Option(Mode.shutdown.name(), Mode.shutdown.name(), false,
            "Shutdown Rserve process");
    final Option validateOption = new Option(Mode.validate.name(), Mode.validate.name(), false,
            "Validate that Rserve processes are running");

    final OptionGroup optionGroup = new OptionGroup();
    optionGroup.addOption(startupOption);
    optionGroup.addOption(shutdownOption);
    optionGroup.addOption(validateOption);
    optionGroup.setRequired(true);
    options.addOptionGroup(optionGroup);

    final Option portOption = new Option("port", "port", true,
            "Use specified port to communicate with the Rserve process");
    portOption.setArgName("port");
    portOption.setType(int.class);
    options.addOption(portOption);

    final Option hostOption = new Option("host", "host", true,
            "Communicate with the Rserve process on the given host");
    hostOption.setArgName("hostname");
    hostOption.setType(String.class);
    options.addOption(hostOption);

    final Option userOption = new Option("u", "username", true, "Username to send to the Rserve process");
    userOption.setArgName("username");
    userOption.setType(String.class);
    options.addOption(userOption);

    final Option passwordOption = new Option("p", "password", true, "Password to send to the Rserve process");
    passwordOption.setArgName("password");
    passwordOption.setType(String.class);
    options.addOption(passwordOption);

    final Option configurationOption = new Option("c", "configuration", true,
            "Configuration file or url to read from");
    configurationOption.setArgName("configuration");
    configurationOption.setType(String.class);
    options.addOption(configurationOption);

    final Parser parser = new BasicParser();
    final CommandLine commandLine;
    try {
        commandLine = parser.parse(options, args);
    } catch (ParseException e) {
        usage(options);
        throw e;
    }

    int exitStatus = 0;
    if (commandLine.hasOption("h")) {
        usage(options);
    } else {
        Mode mode = null;
        for (final Mode potentialMode : Mode.values()) {
            if (commandLine.hasOption(potentialMode.name())) {
                mode = potentialMode;
                break;
            }
        }

        final ExecutorService threadPool = Executors.newCachedThreadPool();

        if (commandLine.hasOption("configuration")) {
            final String configurationFile = commandLine.getOptionValue("configuration");
            LOG.info("Reading configuration from " + configurationFile);
            XMLConfiguration configuration;
            try {
                final URL configurationURL = new URL(configurationFile);
                configuration = new XMLConfiguration(configurationURL);
            } catch (MalformedURLException e) {
                // resource is not a URL: attempt to get the resource from a file
                LOG.debug("Configuration is not a valid url");
                configuration = new XMLConfiguration(configurationFile);
            }

            configuration.setValidating(true);
            final int numberOfRServers = configuration.getMaxIndex("RConfiguration.RServer") + 1;
            boolean failed = false;
            for (int i = 0; i < numberOfRServers; i++) {
                final String server = "RConfiguration.RServer(" + i + ")";
                final String host = configuration.getString(server + "[@host]");
                final int port = configuration.getInt(server + "[@port]",
                        RConfigurationUtils.DEFAULT_RSERVE_PORT);
                final String username = configuration.getString(server + "[@username]");
                final String password = configuration.getString(server + "[@password]");
                final String command = configuration.getString(server + "[@command]", DEFAULT_RSERVE_COMMAND);

                if (executeMode(mode, threadPool, host, port, username, password, command) != 0) {
                    failed = true; // we have other hosts to check so keep a failed state
                }
            }
            if (failed) {
                exitStatus = 3;
            }
        } else {
            final String host = commandLine.getOptionValue("host", "localhost");
            final int port = Integer.valueOf(commandLine.getOptionValue("port", "6311"));
            final String username = commandLine.getOptionValue("username");
            final String password = commandLine.getOptionValue("password");

            exitStatus = executeMode(mode, threadPool, host, port, username, password, null);
        }
        threadPool.shutdown();
    }

    System.exit(exitStatus);
}

From source file:cloudworker.RemoteWorker.java

public static void main(String[] args) throws Exception {
    //Command interpreter
    CommandLineInterface cmd = new CommandLineInterface(args);
    final int poolSize = Integer.parseInt(cmd.getOptionValue("s"));
    long idle_time = Long.parseLong(cmd.getOptionValue("i")); //idle time = 60 sec

    init();//  w  w w. ja v  a  2 s. c  om
    System.out.println("Initialized one remote worker.\n");

    //Create thread pool
    ExecutorService threadPool = Executors.newFixedThreadPool(poolSize);
    BlockingExecutor blockingPool = new BlockingExecutor(threadPool, poolSize);

    //Get queue url
    GetQueueUrlResult urlResult = sqs.getQueueUrl("JobQueue");
    String jobQueueUrl = urlResult.getQueueUrl();

    // Receive messages
    //System.out.println("Receiving messages from JobQueue.\n");

    //...Check idle state
    boolean terminate = false;
    boolean startClock = true;
    long start_time = 0, end_time;

    JSONParser parser = new JSONParser();
    Runtime runtime = Runtime.getRuntime();
    String task_id = null;
    boolean runAnimoto = false;

    while (!terminate || idle_time == 0) {
        while (getQueueSize(sqs, jobQueueUrl) > 0) {

            //Batch retrieving messages
            ReceiveMessageRequest receiveMessageRequest = new ReceiveMessageRequest().withQueueUrl(jobQueueUrl)
                    .withMaxNumberOfMessages(10);

            List<Message> messages = sqs.receiveMessage(receiveMessageRequest).getMessages();

            for (Message message : messages) {
                //System.out.println("  Message");
                //                  System.out.println("    MessageId:     " + message.getMessageId());
                //                  System.out.println("    ReceiptHandle: " + message.getReceiptHandle());
                //                  System.out.println("    MD5OfBody:     " + message.getMD5OfBody());
                //System.out.println("    Body:          " + message.getBody());

                //Get task
                String messageBody = message.getBody();
                JSONObject json = (JSONObject) parser.parse(messageBody);

                task_id = json.get("task_id").toString();
                String task = json.get("task").toString();

                try {
                    //Check duplicate task
                    dynamoDB.addTask(task_id, task);

                    //Execute task, will be blocked if no more thread is currently available 
                    blockingPool.submitTask(new Animoto(task_id, task, sqs));

                    // Delete the message
                    String messageRecieptHandle = message.getReceiptHandle();
                    sqs.deleteMessage(new DeleteMessageRequest(jobQueueUrl, messageRecieptHandle));
                } catch (ConditionalCheckFailedException ccf) {
                    //DO something...
                }

            }

            startClock = true;

        }

        //Start clock to measure idle time
        if (startClock) {
            startClock = false;
            start_time = System.currentTimeMillis();
        } else {
            end_time = System.currentTimeMillis();
            long elapsed_time = (end_time - start_time) / 1000;
            if (elapsed_time > idle_time) {
                terminate = true;
            }
        }
    }

    //System.out.println();

    threadPool.shutdown();
    // Wait until all threads are finished
    while (!threadPool.isTerminated()) {

    }

    //Terminate running instance
    cleanUpInstance();

}

From source file:de.huberlin.wbi.cuneiform.cmdline.main.Main.java

public static void main(String[] args)
        throws IOException, ParseException, InterruptedException, NotDerivableException {

    CommandLine cmd;// w w  w . jav  a  2  s  .  c o m
    Options opt;
    BaseRepl repl;
    BaseCreActor cre;
    Path sandbox;
    ExecutorService executor;
    TicketSrcActor ticketSrc;
    JsonSummary summary;
    Path summaryPath;
    Log statLog;
    int nthread;
    Path workDir;

    statLog = LogFactory.getLog("statLogger");

    executor = Executors.newCachedThreadPool();
    try {

        opt = getOptions();
        cmd = parse(args, opt);
        config(cmd);

        if (cmd.hasOption('h')) {

            System.out.println("CUNEIFORM - A Functional Workflow Language\nversion " + BaseRepl.LABEL_VERSION
                    + " build " + BaseRepl.LABEL_BUILD);
            new HelpFormatter().printHelp("java -jar cuneiform.jar [OPTION]*", opt);

            return;
        }

        if (cmd.hasOption('r'))
            Invocation.putLibPath(ForeignLambdaExpr.LANGID_R, cmd.getOptionValue('r'));

        if (cmd.hasOption('y'))
            Invocation.putLibPath(ForeignLambdaExpr.LANGID_PYTHON, cmd.getOptionValue('y'));

        if (cmd.hasOption('l'))
            sandbox = Paths.get(cmd.getOptionValue("l"));
        else
            sandbox = Paths.get(System.getProperty("user.home")).resolve(".cuneiform");

        sandbox = sandbox.toAbsolutePath();

        if (cmd.hasOption('c'))
            LocalThread.deleteIfExists(sandbox);

        if (cmd.hasOption('t'))
            nthread = Integer.valueOf(cmd.getOptionValue('t'));
        else
            nthread = Runtime.getRuntime().availableProcessors();

        if (cmd.hasOption('w'))
            workDir = Paths.get(cmd.getOptionValue('w'));
        else
            workDir = Paths.get(System.getProperty("user.dir"));

        workDir = workDir.toAbsolutePath();

        switch (platform) {

        case PLATFORM_LOCAL:

            if (!Files.exists(sandbox))
                Files.createDirectories(sandbox);

            cre = new LocalCreActor(sandbox, workDir, nthread);
            break;

        case PLATFORM_HTCONDOR:

            if (!Files.exists(sandbox))
                Files.createDirectories(sandbox);

            if (cmd.hasOption('m')) { // MAX_TRANSFER SIZE
                String maxTransferSize = cmd.getOptionValue('m');
                try {
                    cre = new CondorCreActor(sandbox, maxTransferSize);
                } catch (Exception e) {
                    System.out.println("INVALID '-m' option value: " + maxTransferSize
                            + "\n\nCUNEIFORM - A Functional Workflow Language\nversion "
                            + BaseRepl.LABEL_VERSION + " build " + BaseRepl.LABEL_BUILD);
                    new HelpFormatter().printHelp("java -jar cuneiform.jar [OPTION]*", opt);

                    return;
                }
            } else {
                cre = new CondorCreActor(sandbox);
            }

            break;

        default:
            throw new RuntimeException("Platform not recognized.");
        }

        executor.submit(cre);
        ticketSrc = new TicketSrcActor(cre);
        executor.submit(ticketSrc);
        executor.shutdown();

        switch (format) {

        case FORMAT_CF:

            if (cmd.hasOption("i"))
                repl = new InteractiveRepl(ticketSrc, statLog);
            else
                repl = new CmdlineRepl(ticketSrc, statLog);
            break;

        case FORMAT_DAX:
            repl = new DaxRepl(ticketSrc, statLog);
            break;

        default:
            throw new RuntimeException("Format not recognized.");
        }

        if (cmd.hasOption("i")) {

            // run in interactive mode
            BaseRepl.run(repl);

            return;
        }

        // run in quiet mode

        if (inputFileVector.length > 0)

            for (Path f : inputFileVector)
                repl.interpret(readFile(f));

        else
            repl.interpret(readStdIn());

        Thread.sleep(3 * Actor.DELAY);
        while (repl.isBusy())
            Thread.sleep(Actor.DELAY);

        if (cmd.hasOption("s")) {

            summary = new JsonSummary(ticketSrc.getRunId(), sandbox, repl.getAns());
            summaryPath = Paths.get(cmd.getOptionValue("s"));
            summaryPath = summaryPath.toAbsolutePath();
            try (BufferedWriter writer = Files.newBufferedWriter(summaryPath, Charset.forName("UTF-8"))) {

                writer.write(summary.toString());
            }

        }

    } finally {
        executor.shutdownNow();
    }

}

From source file:tuit.java

@SuppressWarnings("ConstantConditions")
public static void main(String[] args) {
    System.out.println(licence);//from  ww  w.  j ava 2s . c om
    //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...");
    }
}

From source file:Main.java

static void awaitTermination(ExecutorService threadPool) {
    threadPool.shutdown();
    try {//from w w w.  ja  va2  s  . c  o m
        threadPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
    } catch (InterruptedException e) {
        e.printStackTrace();
    }
}

From source file:ReplaceWorker.java

private static void awaitTermination(ExecutorService threadPool) {
    try {/*from  w ww  . j  a  v  a2 s .  c  o  m*/
        threadPool.shutdown();
        boolean awaitTermination = threadPool.awaitTermination(1, TimeUnit.SECONDS);
        System.out.println("terminted successfull: " + awaitTermination);
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:Main.java

public static void stop(ExecutorService executor) {
    try {//from w w w . j a v  a2s  . c om
        executor.shutdown();
        executor.awaitTermination(60, TimeUnit.SECONDS);
    } catch (InterruptedException e) {
        e.printStackTrace();
    }
}

From source file:Main.java

public static void stop(ExecutorService executor) {
    try {// ww w  .  j ava2  s  .  co  m
        executor.shutdown();
        executor.awaitTermination(5, TimeUnit.SECONDS);
    } catch (InterruptedException e) {
        System.err.println("termination interrupted");
    } finally {
        if (!executor.isTerminated()) {
            System.err.println("killing non-finished tasks");
        }
        executor.shutdownNow();
    }
}

From source file:Main.java

public static void stop(ExecutorService executor) {
    try {/*w ww. j  a va2  s . c o m*/
        executor.shutdown();
        executor.awaitTermination(60, TimeUnit.SECONDS);
    } catch (InterruptedException e) {
        System.err.println("termination interrupted");
    } finally {
        if (!executor.isTerminated()) {
            System.err.println("killing non-finished tasks");
        }
        executor.shutdownNow();
    }
}