List of usage examples for java.util.concurrent Future get
V get() throws InterruptedException, ExecutionException;
From source file:com.yahoo.pulsar.testclient.PerformanceProducer.java
public static void main(String[] args) throws Exception { final Arguments arguments = new Arguments(); JCommander jc = new JCommander(arguments); jc.setProgramName("pulsar-perf-producer"); try {/* ww w.java 2s .c o m*/ jc.parse(args); } catch (ParameterException e) { System.out.println(e.getMessage()); jc.usage(); System.exit(-1); } if (arguments.help) { jc.usage(); System.exit(-1); } if (arguments.destinations.size() != 1) { System.out.println("Only one topic name is allowed"); jc.usage(); System.exit(-1); } if (arguments.confFile != null) { Properties prop = new Properties(System.getProperties()); prop.load(new FileInputStream(arguments.confFile)); if (arguments.serviceURL == null) { arguments.serviceURL = prop.getProperty("brokerServiceUrl"); } if (arguments.serviceURL == null) { arguments.serviceURL = prop.getProperty("webServiceUrl"); } // fallback to previous-version serviceUrl property to maintain backward-compatibility if (arguments.serviceURL == null) { arguments.serviceURL = prop.getProperty("serviceUrl", "http://localhost:8080/"); } if (arguments.authPluginClassName == null) { arguments.authPluginClassName = prop.getProperty("authPlugin", null); } if (arguments.authParams == null) { arguments.authParams = prop.getProperty("authParams", null); } } arguments.testTime = TimeUnit.SECONDS.toMillis(arguments.testTime); // Dump config variables ObjectMapper m = new ObjectMapper(); ObjectWriter w = m.writerWithDefaultPrettyPrinter(); log.info("Starting Pulsar perf producer with config: {}", w.writeValueAsString(arguments)); // Read payload data from file if needed byte payloadData[]; if (arguments.payloadFilename != null) { payloadData = Files.readAllBytes(Paths.get(arguments.payloadFilename)); } else { payloadData = new byte[arguments.msgSize]; } // Now processing command line arguments String prefixTopicName = arguments.destinations.get(0); List<Future<Producer>> futures = Lists.newArrayList(); EventLoopGroup eventLoopGroup; if (SystemUtils.IS_OS_LINUX) { eventLoopGroup = new EpollEventLoopGroup(Runtime.getRuntime().availableProcessors(), new DefaultThreadFactory("pulsar-perf-producer")); } else { eventLoopGroup = new NioEventLoopGroup(Runtime.getRuntime().availableProcessors(), new DefaultThreadFactory("pulsar-perf-producer")); } ClientConfiguration clientConf = new ClientConfiguration(); clientConf.setConnectionsPerBroker(arguments.maxConnections); clientConf.setStatsInterval(arguments.statsIntervalSeconds, TimeUnit.SECONDS); if (isNotBlank(arguments.authPluginClassName)) { clientConf.setAuthentication(arguments.authPluginClassName, arguments.authParams); } PulsarClient client = new PulsarClientImpl(arguments.serviceURL, clientConf, eventLoopGroup); ProducerConfiguration producerConf = new ProducerConfiguration(); producerConf.setSendTimeout(0, TimeUnit.SECONDS); producerConf.setCompressionType(arguments.compression); // enable round robin message routing if it is a partitioned topic producerConf.setMessageRoutingMode(MessageRoutingMode.RoundRobinPartition); if (arguments.batchTime > 0) { producerConf.setBatchingMaxPublishDelay(arguments.batchTime, TimeUnit.MILLISECONDS); producerConf.setBatchingEnabled(true); producerConf.setMaxPendingMessages(arguments.msgRate); } for (int i = 0; i < arguments.numTopics; i++) { String topic = (arguments.numTopics == 1) ? prefixTopicName : String.format("%s-%d", prefixTopicName, i); log.info("Adding {} publishers on destination {}", arguments.numProducers, topic); for (int j = 0; j < arguments.numProducers; j++) { futures.add(client.createProducerAsync(topic, producerConf)); } } final List<Producer> producers = Lists.newArrayListWithCapacity(futures.size()); for (Future<Producer> future : futures) { producers.add(future.get()); } log.info("Created {} producers", producers.size()); Runtime.getRuntime().addShutdownHook(new Thread() { public void run() { printAggregatedStats(); } }); Collections.shuffle(producers); AtomicBoolean isDone = new AtomicBoolean(); executor.submit(() -> { try { RateLimiter rateLimiter = RateLimiter.create(arguments.msgRate); long startTime = System.currentTimeMillis(); // Send messages on all topics/producers long totalSent = 0; while (true) { for (Producer producer : producers) { if (arguments.testTime > 0) { if (System.currentTimeMillis() - startTime > arguments.testTime) { log.info("------------------- DONE -----------------------"); printAggregatedStats(); isDone.set(true); Thread.sleep(5000); System.exit(0); } } if (arguments.numMessages > 0) { if (totalSent++ >= arguments.numMessages) { log.info("------------------- DONE -----------------------"); printAggregatedStats(); isDone.set(true); Thread.sleep(5000); System.exit(0); } } rateLimiter.acquire(); final long sendTime = System.nanoTime(); producer.sendAsync(payloadData).thenRun(() -> { messagesSent.increment(); bytesSent.add(payloadData.length); long latencyMicros = NANOSECONDS.toMicros(System.nanoTime() - sendTime); recorder.recordValue(latencyMicros); cumulativeRecorder.recordValue(latencyMicros); }).exceptionally(ex -> { log.warn("Write error on message", ex); System.exit(-1); return null; }); } } } catch (Throwable t) { log.error("Got error", t); } }); // Print report stats long oldTime = System.nanoTime(); Histogram reportHistogram = null; String statsFileName = "perf-producer-" + System.currentTimeMillis() + ".hgrm"; log.info("Dumping latency stats to {}", statsFileName); PrintStream histogramLog = new PrintStream(new FileOutputStream(statsFileName), false); HistogramLogWriter histogramLogWriter = new HistogramLogWriter(histogramLog); // Some log header bits histogramLogWriter.outputLogFormatVersion(); histogramLogWriter.outputLegend(); while (true) { try { Thread.sleep(10000); } catch (InterruptedException e) { break; } if (isDone.get()) { break; } long now = System.nanoTime(); double elapsed = (now - oldTime) / 1e9; double rate = messagesSent.sumThenReset() / elapsed; double throughput = bytesSent.sumThenReset() / elapsed / 1024 / 1024 * 8; reportHistogram = recorder.getIntervalHistogram(reportHistogram); log.info( "Throughput produced: {} msg/s --- {} Mbit/s --- Latency: mean: {} ms - med: {} - 95pct: {} - 99pct: {} - 99.9pct: {} - 99.99pct: {} - Max: {}", throughputFormat.format(rate), throughputFormat.format(throughput), dec.format(reportHistogram.getMean() / 1000.0), dec.format(reportHistogram.getValueAtPercentile(50) / 1000.0), dec.format(reportHistogram.getValueAtPercentile(95) / 1000.0), dec.format(reportHistogram.getValueAtPercentile(99) / 1000.0), dec.format(reportHistogram.getValueAtPercentile(99.9) / 1000.0), dec.format(reportHistogram.getValueAtPercentile(99.99) / 1000.0), dec.format(reportHistogram.getMaxValue() / 1000.0)); histogramLogWriter.outputIntervalHistogram(reportHistogram); reportHistogram.reset(); oldTime = now; } client.close(); }
From source file:com.utdallas.s3lab.smvhunter.monkey.MonkeyMe.java
/** * @param args/*from w w w .j a v a 2s. c o m*/ */ public static void main(String[] args) throws Exception { logger.info("start time ==== " + System.currentTimeMillis()); try { //load the adb location from the props file Properties props = new Properties(); props.load(new FileInputStream(new File("adb.props"))); //set the adb location WindowUpdate.adbLocation = props.getProperty("adb_location"); adbLocation = props.getProperty("adb_location"); //set root dir ROOT_DIRECTORY = props.getProperty("root_dir"); //completed txt completedFile = new File(ROOT_DIRECTORY + "tested.txt"); //db location for static analysis dbLocation = props.getProperty("db_location"); //location for smart input generation output smartInputLocation = props.getProperty("smart_input_location"); //udp dump location udpDumpLocation = props.getProperty("udp_dump_location"); //logcat dump location logCatLocation = props.getProperty("log_cat_location"); //strace output location straceOutputLocation = props.getProperty("strace_output_location"); //strace dump location straceDumpLocation = props.getProperty("strace_output_location"); //set x and y coords UIEnumerator.screenX = props.getProperty("x"); UIEnumerator.screenY = props.getProperty("y"); DeviceOfflineMonitor.START_EMULATOR = props.getProperty("restart"); //read output of static analysis readFromStaticAnalysisText(); logger.info("Read static analysis output"); readFromSmartInputText(); logger.info("Read smart input generation output"); //populate the queue with apps which are only present in the static analysis @SuppressWarnings("unchecked") final Set<? extends String> sslApps = new HashSet<String>( CollectionUtils.collect(FileUtils.readLines(new File(dbLocation)), new Transformer() { @Override public Object transform(Object input) { //get app file name String temp = StringUtils.substringBefore(input.toString(), " "); return StringUtils.substringAfterLast(temp, "/"); } })); Collection<File> fileList = FileUtils.listFiles(new File(ROOT_DIRECTORY), new String[] { "apk" }, false); CollectionUtils.filter(fileList, new Predicate() { @Override public boolean evaluate(Object object) { return sslApps.contains(StringUtils.substringAfterLast(object.toString(), "/")); } }); apkQueue = new LinkedBlockingDeque<File>(fileList); logger.info("finished listing files from the root directory"); try { //populate the tested apk list completedApps.addAll(FileUtils.readLines(completedFile)); } catch (Exception e) { //pass except logger.info("No tested.txt file found"); //create new file if (completedFile.createNewFile()) { logger.info("tested.txt created in root directory"); } else { logger.info("tested.txt file could not be created"); } } //get the executors for managing the emulators executors = Executors.newCachedThreadPool(); //set the devicemonitor exec DeviceOfflineMonitor.exec = executors; final List<Future<?>> futureList = new ArrayList<Future<?>>(); //start the offline device monitor (emulator management thread) logger.info("Starting Device Offline Monitor Thread"); executors.submit(new DeviceOfflineMonitor()); //get ADB backend object for device change listener AdbBackend adb = new AdbBackend(); //register for device change and wait for events //once event is received, start the MonkeyMe thread MonkeyDeviceChangeListener deviceChangeListener = new MonkeyDeviceChangeListener(executors, futureList); AndroidDebugBridge.addDeviceChangeListener(deviceChangeListener); logger.info("Listening to changes in devices (emulators)"); //wait for the latch to come down //this means that all the apks have been processed cdl.await(); logger.info("Finished testing all apps waiting for threads to join"); //now wait for every thread to finish for (Future<?> future : futureList) { future.get(); } logger.info("All threads terminated"); //stop listening for device update AndroidDebugBridge.removeDeviceChangeListener(deviceChangeListener); //stop the debug bridge AndroidDebugBridge.terminate(); //stop offline device monitor DeviceOfflineMonitor.stop = true; logger.info("adb and listeners terminated"); } finally { logger.info("Executing this finally"); executors.shutdownNow(); } logger.info("THE END!!"); }
From source file:meme.singularsyntax.benchmark.Benchmark.java
public static void main(String[] argv) { Application app = new Application(argv); app.getThreadPool().prestartAllCoreThreads(); int rejectedTasks = 0; long begTicks = System.currentTimeMillis(); long endTicks; for (int seconds = 0; seconds < app.getRunTime(); seconds++) { try {/*from ww w. j av a2 s.co m*/ for (int requests = 0; requests < app.getRequestsPerSecond(); requests++) { Task task = new Task(app.getComputeSteps(), app.getServiceDispatch()); try { app.getCompletionService().submit(task); } catch (RejectedExecutionException e) { rejectedTasks++; } } Thread.sleep(1000L); } catch (InterruptedException ignored) { } } int remaining = (app.getRequestsPerSecond() * app.getRunTime()) - rejectedTasks; while (remaining > 0) { try { Future<byte[]> future = app.getCompletionService().take(); if (!app.isQuiet()) System.out.println(toHexString(future.get())); remaining--; } catch (InterruptedException e) { // ignored } catch (ExecutionException e) { System.err.println(e.getMessage()); } } endTicks = System.currentTimeMillis(); System.out.printf("Finished processing in %d msec\n", endTicks - begTicks); System.out.println("Thread Pool Statistics:"); System.out.println(" Active Count: " + app.getThreadPool().getActiveCount()); System.out.println(" Completed Task Count: " + app.getThreadPool().getCompletedTaskCount()); System.out.println(" Core Pool Size: " + app.getThreadPool().getCorePoolSize()); System.out.println(" Largest Pool Size: " + app.getThreadPool().getLargestPoolSize()); System.out.println(" Maximum Pool Size: " + app.getThreadPool().getMaximumPoolSize()); System.out.println(" Pool Size: " + app.getThreadPool().getPoolSize()); System.out.println(" Task Count: " + app.getThreadPool().getTaskCount()); System.out.println(" Rejected Tasks: " + rejectedTasks); app.getRandomByteService().shutdown(); app.getThreadPool().shutdown(); }
From source file:io.aos.protocol.http.httpcommon.FluentAsync.java
public static void main(String... args) throws Exception { // Use pool of two threads ExecutorService threadpool = Executors.newFixedThreadPool(2); Async async = Async.newInstance().use(threadpool); Request[] requests = new Request[] { Request.Get("http://www.google.com/"), Request.Get("http://www.yahoo.com/"), Request.Get("http://www.apache.com/"), Request.Get("http://www.apple.com/") }; Queue<Future<Content>> queue = new LinkedList<Future<Content>>(); // Execute requests asynchronously for (final Request request : requests) { Future<Content> future = async.execute(request, new FutureCallback<Content>() { public void failed(final Exception ex) { System.out.println(ex.getMessage() + ": " + request); }/* www. ja v a 2 s . c o m*/ public void completed(final Content content) { System.out.println("Request completed: " + request); } public void cancelled() { } }); queue.add(future); } while (!queue.isEmpty()) { Future<Content> future = queue.remove(); try { future.get(); } catch (ExecutionException ex) { } } System.out.println("Done"); threadpool.shutdown(); }
From source file:interoperabilite.webservice.fluent.FluentAsync.java
public static void main(String[] args) throws Exception { // Use pool of two threads ExecutorService threadpool = Executors.newFixedThreadPool(2); Async async = Async.newInstance().use(threadpool); Request[] requests = new Request[] { Request.Get("http://www.google.com/"), Request.Get("http://www.yahoo.com/"), Request.Get("http://www.apache.com/"), Request.Get("http://www.apple.com/") }; Queue<Future<Content>> queue = new LinkedList<Future<Content>>(); // Execute requests asynchronously for (final Request request : requests) { Future<Content> future = async.execute(request, new FutureCallback<Content>() { @Override// w w w. ja v a2 s . co m public void failed(final Exception ex) { System.out.println(ex.getMessage() + ": " + request); } @Override public void completed(final Content content) { System.out.println("Request completed: " + request); } @Override public void cancelled() { } }); queue.add(future); } while (!queue.isEmpty()) { Future<Content> future = queue.remove(); try { future.get(); } catch (ExecutionException ex) { } } System.out.println("Done"); threadpool.shutdown(); }
From source file:tuit.java
@SuppressWarnings("ConstantConditions") public static void main(String[] args) { System.out.println(licence);/*from w w w . j a v a2 s .co 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..."); } }
From source file:org.jaqpot.core.service.client.jpdi.JPDIClientFactory.java
public static void main(String[] args) throws IOException, InterruptedException, ExecutionException { CloseableHttpAsyncClient asyncClient = HttpAsyncClientBuilder.create().build(); asyncClient.start();/* w ww. j a v a 2 s . c o m*/ HttpGet request = new HttpGet("http://www.google.com"); request.addHeader("Accept", "text/html"); Future f = asyncClient.execute(request, new FutureCallback<HttpResponse>() { @Override public void completed(HttpResponse t) { System.out.println("completed"); try { String result = new BufferedReader(new InputStreamReader(t.getEntity().getContent())).lines() .collect(Collectors.joining("\n")); System.out.println(result); } catch (IOException ex) { Logger.getLogger(JPDIClientFactory.class.getName()).log(Level.SEVERE, null, ex); } catch (UnsupportedOperationException ex) { Logger.getLogger(JPDIClientFactory.class.getName()).log(Level.SEVERE, null, ex); } } @Override public void failed(Exception excptn) { System.out.println("failed"); } @Override public void cancelled() { System.out.println("cancelled"); } }); f.get(); asyncClient.close(); }
From source file:Main.java
public static <T extends Number> Long sum(List<Future<T>> list) throws InterruptedException, ExecutionException { long sum = 0; for (Future<T> each : list) { sum += each.get().longValue(); }//from w w w . jav a 2s. c o m return sum; }
From source file:Main.java
public static <T> T waitOnFuture(Future<T> future) { try {//w w w . ja va2 s. c o m return future.get(); } catch (ExecutionException ee) { throw new RuntimeException(ee); } catch (InterruptedException ie) { throw new AssertionError(ie); } }
From source file:Main.java
private static <T> T waitForCallableResult(Future<T> future) throws Exception { try {//from w ww. j ava 2 s . co m return future.get(); } finally { future.cancel(true); } }