List of usage examples for java.util Arrays toString
public static String toString(Object[] a)
From source file:deck36.storm.plan9.php.KittenRobbersTopology.java
public static void main(String[] args) throws Exception { String env = null;//from w ww . j a v a2 s.c om if (args != null && args.length > 0) { env = args[0]; } if (!"dev".equals(env)) if (!"prod".equals(env)) { System.out.println("Usage: $0 (dev|prod)\n"); System.exit(1); } // Topology config Config conf = new Config(); // Load parameters and add them to the Config Map configMap = YamlLoader.loadYamlFromResource("config_" + env + ".yml"); conf.putAll(configMap); log.info(JSONValue.toJSONString((conf))); // Set topology loglevel to DEBUG conf.put(Config.TOPOLOGY_DEBUG, JsonPath.read(conf, "$.deck36_storm.debug")); // Create Topology builder TopologyBuilder builder = new TopologyBuilder(); // if there are not special reasons, start with parallelism hint of 1 // and multiple tasks. By that, you can scale dynamically later on. int parallelism_hint = JsonPath.read(conf, "$.deck36_storm.default_parallelism_hint"); int num_tasks = JsonPath.read(conf, "$.deck36_storm.default_num_tasks"); String badgeName = KittenRobbersTopology.class.getSimpleName(); // construct command to invoke the external bolt implementation ArrayList<String> command = new ArrayList(15); // Add main execution program (php, hhvm, zend, ..) and parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.php.executor")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.executor_params")); // Add main command to be executed (app/console, the phar file, etc.) and global context parameters (environment etc.) command.add((String) JsonPath.read(conf, "$.deck36_storm.php.main")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.main_params")); // Add main route to be invoked and its parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.KittenRobbersFromOuterSpaceBolt.main")); List boltParams = (List<String>) JsonPath.read(conf, "$.deck36_storm.KittenRobbersFromOuterSpaceBolt.params"); if (boltParams != null) command.addAll(boltParams); // Log the final command log.info("Command to start bolt for KittenRobbersFromOuterSpace: " + Arrays.toString(command.toArray())); // Add constructed external bolt command to topology using MultilangAdapterBolt builder.setBolt("badge", new MultilangAdapterTickTupleBolt(command, (Integer) JsonPath.read(conf, "$.deck36_storm.KittenRobbersFromOuterSpaceBolt.robber_frequency"), "badge"), parallelism_hint).setNumTasks(num_tasks); builder.setBolt("rabbitmq_router", new Plan9RabbitMQRouterBolt( (String) JsonPath.read(conf, "$.deck36_storm.KittenRobbersFromOuterSpaceBolt.rabbitmq.target_exchange"), "KittenRobbers" // RabbitMQ routing key ), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("badge"); builder.setBolt("rabbitmq_producer", new Plan9RabbitMQPushBolt(), parallelism_hint).setNumTasks(num_tasks) .shuffleGrouping("rabbitmq_router"); if ("dev".equals(env)) { LocalCluster cluster = new LocalCluster(); cluster.submitTopology(badgeName + System.currentTimeMillis(), conf, builder.createTopology()); Thread.sleep(2000000); } if ("prod".equals(env)) { StormSubmitter.submitTopology(badgeName + "-" + System.currentTimeMillis(), conf, builder.createTopology()); } }
From source file:ms1quant.MS1Quant.java
/** * @param args the command line arguments MS1Quant parameterfile */// w w w .j a v a2 s . co m public static void main(String[] args) throws Exception { BufferedReader reader = null; try { System.out.println( "================================================================================================="); System.out.println("Umpire MS1 quantification and feature detection analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length < 3 || !args[1].startsWith("-mode")) { System.out .println("command : java -jar -Xmx10G MS1Quant.jar ms1quant.params -mode[1 or 2] [Option]"); System.out.println("\n-mode"); System.out.println("\t1:Single file mode--> mzXML_file PepXML_file"); System.out.println("\t\tEx: -mode1 file1.mzXML file1.pep.xml"); System.out.println( "\t2:Folder mode--> mzXML_Folder PepXML_Folder, all generated csv tables will be merged into a single csv file"); System.out.println("\t\tEx: -mode2 /data/mzxml/ /data/pepxml/"); System.out.println("\nOptions"); System.out.println( "\t-C\tNo of concurrent files to be processed (only for folder mode), Ex. -C5, default:1"); System.out.println("\t-p\tMinimum probability, Ex. -p0.9, default:0.9"); System.out.println("\t-ID\tDetect identified feature only"); System.out.println("\t-O\toutput folder, Ex. -O/data/"); return; } ConsoleLogger consoleLogger = new ConsoleLogger(); consoleLogger.SetConsoleLogger(Level.DEBUG); consoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "ms1quant_debug.log"); Logger logger = Logger.getRootLogger(); logger.debug("Command: " + Arrays.toString(args)); logger.info("MS1Quant version: " + UmpireInfo.GetInstance().Version); String parameterfile = args[0]; logger.info("Parameter file: " + parameterfile); File paramfile = new File(parameterfile); if (!paramfile.exists()) { logger.error("Parameter file " + paramfile.getAbsolutePath() + " cannot be found. The program will exit."); } reader = new BufferedReader(new FileReader(paramfile.getAbsolutePath())); String line = ""; InstrumentParameter param = new InstrumentParameter(InstrumentParameter.InstrumentType.TOF5600); int NoCPUs = 2; int NoFile = 1; param.DetermineBGByID = false; param.EstimateBG = true; //<editor-fold defaultstate="collapsed" desc="Read parameter file"> while ((line = reader.readLine()) != null) { if (!"".equals(line) && !line.startsWith("#")) { logger.info(line); //System.out.println(line); if (line.split("=").length < 2) { continue; } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); if (type.startsWith("para.")) { type = type.replace("para.", "SE."); } String value = line.split("=")[1].trim(); switch (type) { case "Thread": { NoCPUs = Integer.parseInt(value); break; } //<editor-fold defaultstate="collapsed" desc="instrument parameters"> case "SE.MS1PPM": { param.MS1PPM = Float.parseFloat(value); break; } case "SE.MS2PPM": { param.MS2PPM = Float.parseFloat(value); break; } case "SE.SN": { param.SNThreshold = Float.parseFloat(value); break; } case "SE.MS2SN": { param.MS2SNThreshold = Float.parseFloat(value); break; } case "SE.MinMSIntensity": { param.MinMSIntensity = Float.parseFloat(value); break; } case "SE.MinMSMSIntensity": { param.MinMSMSIntensity = Float.parseFloat(value); break; } case "SE.MinRTRange": { param.MinRTRange = Float.parseFloat(value); break; } case "SE.MaxNoPeakCluster": { param.MaxNoPeakCluster = Integer.parseInt(value); param.MaxMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinNoPeakCluster": { param.MinNoPeakCluster = Integer.parseInt(value); param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinMS2NoPeakCluster": { param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MaxCurveRTRange": { param.MaxCurveRTRange = Float.parseFloat(value); break; } case "SE.Resolution": { param.Resolution = Integer.parseInt(value); break; } case "SE.RTtol": { param.RTtol = Float.parseFloat(value); break; } case "SE.NoPeakPerMin": { param.NoPeakPerMin = Integer.parseInt(value); break; } case "SE.StartCharge": { param.StartCharge = Integer.parseInt(value); break; } case "SE.EndCharge": { param.EndCharge = Integer.parseInt(value); break; } case "SE.MS2StartCharge": { param.MS2StartCharge = Integer.parseInt(value); break; } case "SE.MS2EndCharge": { param.MS2EndCharge = Integer.parseInt(value); break; } case "SE.NoMissedScan": { param.NoMissedScan = Integer.parseInt(value); break; } case "SE.Denoise": { param.Denoise = Boolean.valueOf(value); break; } case "SE.EstimateBG": { param.EstimateBG = Boolean.valueOf(value); break; } case "SE.RemoveGroupedPeaks": { param.RemoveGroupedPeaks = Boolean.valueOf(value); break; } case "SE.MinFrag": { param.MinFrag = Integer.parseInt(value); break; } case "SE.IsoPattern": { param.IsoPattern = Float.valueOf(value); break; } case "SE.StartRT": { param.startRT = Float.valueOf(value); } case "SE.EndRT": { param.endRT = Float.valueOf(value); } //</editor-fold> } } } //</editor-fold> int mode = 1; if (args[1].equals("-mode2")) { mode = 2; } else if (args[1].equals("-mode1")) { mode = 1; } else { logger.error("-mode number not recongized. The program will exit."); } String mzXML = ""; String pepXML = ""; String mzXMLPath = ""; String pepXMLPath = ""; File mzXMLfile = null; File pepXMLfile = null; File mzXMLfolder = null; File pepXMLfolder = null; int idx = 0; if (mode == 1) { mzXML = args[2]; logger.info("Mode1 mzXML file: " + mzXML); mzXMLfile = new File(mzXML); if (!mzXMLfile.exists()) { logger.error("Mode1 mzXML file " + mzXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } pepXML = args[3]; logger.info("Mode1 pepXML file: " + pepXML); pepXMLfile = new File(pepXML); if (!pepXMLfile.exists()) { logger.error("Mode1 pepXML file " + pepXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } idx = 4; } else if (mode == 2) { mzXMLPath = args[2]; logger.info("Mode2 mzXML folder: " + mzXMLPath); mzXMLfolder = new File(mzXMLPath); if (!mzXMLfolder.exists()) { logger.error("Mode2 mzXML folder " + mzXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } pepXMLPath = args[3]; logger.info("Mode2 pepXML folder: " + pepXMLPath); pepXMLfolder = new File(pepXMLPath); if (!pepXMLfolder.exists()) { logger.error("Mode2 pepXML folder " + pepXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } idx = 4; } String outputfolder = ""; float MinProb = 0f; for (int i = idx; i < args.length; i++) { if (args[i].startsWith("-")) { if (args[i].equals("-ID")) { param.TargetIDOnly = true; logger.info("Detect ID feature only: true"); } if (args[i].startsWith("-O")) { outputfolder = args[i].substring(2); logger.info("Output folder: " + outputfolder); File outputfile = new File(outputfolder); if (!outputfolder.endsWith("\\") | outputfolder.endsWith("/")) { outputfolder += "/"; } if (!outputfile.exists()) { outputfile.mkdir(); } } if (args[i].startsWith("-C")) { try { NoFile = Integer.parseInt(args[i].substring(2)); logger.info("No of concurrent files: " + NoFile); } catch (Exception ex) { logger.error(args[i] + " is not a correct integer format, will process only one file at a time."); } } if (args[i].startsWith("-p")) { try { MinProb = Float.parseFloat(args[i].substring(2)); logger.info("probability threshold: " + MinProb); } catch (Exception ex) { logger.error(args[i] + " is not a correct format, will use 0 as threshold instead."); } } } } reader.close(); TandemParam tandemparam = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); PTMManager.GetInstance(); if (param.TargetIDOnly) { param.EstimateBG = false; param.ApexDelta = 1.5f; param.NoMissedScan = 10; param.MiniOverlapP = 0.2f; param.RemoveGroupedPeaks = false; param.CheckMonoIsotopicApex = false; param.DetectByCWT = false; param.FillGapByBK = false; param.IsoCorrThreshold = -1f; param.SmoothFactor = 3; } if (mode == 1) { logger.info("Processing " + mzXMLfile.getAbsolutePath() + "...."); long time = System.currentTimeMillis(); LCMSPeakMS1 LCMS1 = new LCMSPeakMS1(mzXMLfile.getAbsolutePath(), NoCPUs); LCMS1.SetParameter(param); LCMS1.Resume = false; if (!param.TargetIDOnly) { LCMS1.CreatePeakFolder(); } LCMS1.ExportPeakClusterTable = true; if (pepXMLfile.exists()) { tandemparam.InteractPepXMLPath = pepXMLfile.getAbsolutePath(); LCMS1.ParsePepXML(tandemparam, MinProb); logger.info("No. of PSMs included: " + LCMS1.IDsummary.PSMList.size()); logger.info("No. of Peptide ions included: " + LCMS1.IDsummary.GetPepIonList().size()); } if (param.TargetIDOnly) { LCMS1.SaveSerializationFile = false; } if (param.TargetIDOnly || !LCMS1.ReadPeakCluster()) { LCMS1.PeakClusterDetection(); } if (pepXMLfile.exists()) { LCMS1.AssignQuant(false); LCMS1.IDsummary.ExportPepID(outputfolder); } time = System.currentTimeMillis() - time; logger.info(LCMS1.ParentmzXMLName + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); LCMS1.BaseClearAllPeaks(); LCMS1.SetSpectrumParser(null); LCMS1.IDsummary = null; LCMS1 = null; System.gc(); } else if (mode == 2) { LCMSID IDsummary = new LCMSID("", "", ""); logger.info("Parsing all pepXML files in " + pepXMLPath + "...."); for (File file : pepXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("pep.xml") || file.getName().toLowerCase().endsWith("pepxml")) { PepXMLParser pepXMLParser = new PepXMLParser(IDsummary, file.getAbsolutePath(), MinProb); } } HashMap<String, LCMSID> LCMSIDMap = IDsummary.GetLCMSIDFileMap(); ExecutorService executorPool = null; executorPool = Executors.newFixedThreadPool(NoFile); logger.info("Processing all mzXML files in " + mzXMLPath + "...."); for (File file : mzXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("mzxml")) { LCMSID id = LCMSIDMap.get(FilenameUtils.getBaseName(file.getName())); if (id == null || id.PSMList == null) { logger.warn("No IDs found in :" + FilenameUtils.getBaseName(file.getName()) + ". Quantification for this file is skipped"); continue; } if (!id.PSMList.isEmpty()) { MS1TargetQuantThread thread = new MS1TargetQuantThread(file, id, NoCPUs, outputfolder, param); executorPool.execute(thread); } } } LCMSIDMap.clear(); LCMSIDMap = null; IDsummary = null; executorPool.shutdown(); try { executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); } catch (InterruptedException e) { logger.info("interrupted.."); } if (outputfolder == null | outputfolder.equals("")) { outputfolder = mzXMLPath; } logger.info("Merging PSM files.."); File output = new File(outputfolder); FileWriter writer = new FileWriter(output.getAbsolutePath() + "/PSM_merge.csv"); boolean header = false; for (File csvfile : output.listFiles()) { if (csvfile.getName().toLowerCase().endsWith("_psms.csv")) { BufferedReader outreader = new BufferedReader(new FileReader(csvfile)); String outline = outreader.readLine(); if (!header) { writer.write(outline + "\n"); header = true; } while ((outline = outreader.readLine()) != null) { writer.write(outline + "\n"); } outreader.close(); csvfile.delete(); } } writer.close(); } logger.info("MS1 quant module is complete."); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:com.cloudera.hts.utils.math.MyFunc2.java
public static void main(String[] args) { double[] x = { -5.0, -4.0, -3.0, -2.0, 0, 2, 3, 4 }; double[] y = { 21, 13, 7, 3, 1, 7, 13, 21 }; FunctionFitTest fitter = new FunctionFitTest(); ArrayList<WeightedObservedPoint> points = new ArrayList<WeightedObservedPoint>(); // Add points here; for instance, int i = 0;// w w w .j av a 2s . c o m for (double xc : x) { if (i < 1) { WeightedObservedPoint point = new WeightedObservedPoint(xc, y[i], 1.0); points.add(point); System.out.println(xc + " " + y[i]); } i++; } final double coeffs[] = fitter.fit(points); System.out.println(Arrays.toString(coeffs)); }
From source file:net.kahowell.xsd.fuzzer.XmlGenerator.java
/** * Drives the application, parsing command-line arguments to determine * options./*w ww . jav a 2 s . co m*/ * * @param args command line args */ public static void main(String[] args) { try { setupLog4j(); CommandLine commandLine = parser.parse(ConsoleOptions.OPTIONS, args); if (commandLine.hasOption("d")) { Logger.getLogger("net.kahowell.xsd.fuzzer").setLevel(Level.DEBUG); } for (Option option : commandLine.getOptions()) { if (option.getValue() != null) { log.debug("Using " + option.getDescription() + ": " + option.getValue()); } else { log.debug("Using " + option.getDescription()); } } Injector injector = Guice.createInjector( Modules.override(Modules.combine(new DefaultGeneratorsModule(), new DefaultOptionsModule())) .with(new CommandLineArgumentsModule(commandLine))); log.debug(injector.getBindings()); XsdParser xsdParser = injector.getInstance(XsdParser.class); XmlOptions xmlOptions = injector .getInstance(Key.get(XmlOptions.class, Names.named("xml save options"))); XmlGenerator xmlGenerator = injector.getInstance(XmlGenerator.class); XmlGenerationOptions xmlGenerationOptions = injector.getInstance(XmlGenerationOptions.class); doPostModuleConfig(commandLine, xmlGenerationOptions, injector); ByteArrayOutputStream stream = new ByteArrayOutputStream(); XmlObject generatedXml = xsdParser.generateXml(commandLine.getOptionValue("root")); generatedXml.save(stream, xmlOptions); if (commandLine.hasOption("v")) { if (xsdParser.validate(stream)) { log.info("Valid XML file produced."); } else { log.info("Invalid XML file produced."); System.exit(4); } } xmlGenerator.showOrSave(stream); } catch (MissingOptionException e) { if (e.getMissingOptions().size() != 0) { System.err.println("Missing argument(s): " + Arrays.toString(e.getMissingOptions().toArray())); } helpFormatter.printHelp(XmlGenerator.class.getSimpleName(), ConsoleOptions.OPTIONS); System.exit(1); } catch (ParseException e) { helpFormatter.printHelp(XmlGenerator.class.getSimpleName(), ConsoleOptions.OPTIONS); System.exit(2); } catch (Exception e) { e.printStackTrace(); System.exit(3); } }
From source file:at.tuwien.ifs.somtoolbox.apps.helper.VectorFileSubsetGenerator.java
public static void main(String[] args) throws IOException, SOMToolboxException { // register and parse all options JSAPResult config = OptionFactory.parseResults(args, OPTIONS); String inputFileName = AbstractOptionFactory.getFilePath(config, "input"); String classInformationFileName = AbstractOptionFactory.getFilePath(config, "classInformationFile"); String outputFileName = AbstractOptionFactory.getFilePath(config, "output"); String[] keepClasses = config.getStringArray("classList"); boolean skipInstanceNames = false;// config.getBoolean("skipInstanceNames"); boolean skipInputsWithoutClass = false;// config.getBoolean("skipInputsWithoutClass"); boolean tabSeparatedClassFile = false;// config.getBoolean("tabSeparatedClassFile"); String inputFormat = config.getString("inputFormat"); if (inputFormat == null) { inputFormat = InputDataFactory.detectInputFormatFromExtension(inputFileName, "input"); }//ww w .j ava 2s . c o m String outputFormat = config.getString("outputFormat"); if (outputFormat == null) { outputFormat = InputDataFactory.detectInputFormatFromExtension(outputFileName, "output"); } InputData data = InputDataFactory.open(inputFormat, inputFileName); if (classInformationFileName != null) { SOMLibClassInformation classInfo = new SOMLibClassInformation(classInformationFileName); data.setClassInfo(classInfo); } if (data.classInformation() == null) { throw new SOMToolboxException("Need to provide a class information file."); } Logger.getLogger("at.tuwien.ifs.somtoolbox") .info("Retaining elements of classes: " + Arrays.toString(keepClasses)); ArrayList<InputDatum> subData = new ArrayList<InputDatum>(); for (int i = 0; i < data.numVectors(); i++) { InputDatum datum = data.getInputDatum(i); String className = data.classInformation().getClassName(datum.getLabel()); System.out.println(datum.getLabel() + "=>" + className); if (ArrayUtils.contains(keepClasses, className)) { subData.add(datum); } } InputData subset = new SOMLibSparseInputData(subData.toArray(new InputDatum[subData.size()]), data.classInformation()); InputDataWriter.write(outputFileName, subset, outputFormat, tabSeparatedClassFile, skipInstanceNames, skipInputsWithoutClass); }
From source file:fr.inria.atlanmod.kyanos.benchmarks.XmiTraverser.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input model"); inputOpt.setArgs(1);//from ww w .jav a 2 s . c om inputOpt.setRequired(true); Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS); inClassOpt.setArgName("CLASS"); inClassOpt.setDescription("FQN of EPackage implementation class"); inClassOpt.setArgs(1); inClassOpt.setRequired(true); options.addOption(inputOpt); options.addOption(inClassOpt); CommandLineParser parser = new PosixParser(); try { CommandLine commandLine = parser.parse(options, args); URI uri = URI.createFileURI(commandLine.getOptionValue(IN)); Class<?> inClazz = XmiTraverser.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("xmi", new XMIResourceFactoryImpl()); resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("zxmi", new XMIResourceFactoryImpl()); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); resource.load(loadOpts); LOG.log(Level.INFO, "Start counting"); int count = 0; long begin = System.currentTimeMillis(); for (Iterator<EObject> iterator = resource.getAllContents(); iterator.hasNext(); iterator .next(), count++) ; long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End counting"); LOG.log(Level.INFO, MessageFormat.format("Resource {0} contains {1} elements", uri, count)); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); resource.unload(); } catch (ParseException e) { MessageUtil.showError(e.toString()); MessageUtil.showError("Current arguments: " + Arrays.toString(args)); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("java -jar <this-file.jar>", options, true); } catch (Throwable e) { MessageUtil.showError(e.toString()); } }
From source file:io.anserini.embeddings.WordEmbeddingDictionary.java
public static void main(String[] args) throws Exception { WordEmbeddingDictionary.Args dictionaryArgs = new WordEmbeddingDictionary.Args(); CmdLineParser parser = new CmdLineParser(dictionaryArgs, ParserProperties.defaults().withUsageWidth(90)); try {// www. jav a 2 s.c om parser.parseArgument(args); } catch (CmdLineException e) { System.err.println(e.getMessage()); parser.printUsage(System.err); System.err.println("Example: " + WordEmbeddingDictionary.class.getSimpleName() + parser.printExample(OptionHandlerFilter.REQUIRED)); return; } WordEmbeddingDictionary index = new WordEmbeddingDictionary(dictionaryArgs.index); if (!dictionaryArgs.term.isEmpty()) { System.out.println(Arrays.toString(index.getEmbeddingVector(dictionaryArgs.term))); } }
From source file:drpc.KMeansDrpcQuery.java
public static void main(final String[] args) throws IOException, TException, DRPCExecutionException, DecoderException, ClassNotFoundException { if (args.length < 3) { System.err.println("Where are the arguments? args -- DrpcServer DrpcFunctionName folder"); return;//from w ww. jav a 2 s . co m } final DRPCClient client = new DRPCClient(args[0], 3772, 1000000 /*timeout*/); final Queue<String> featureFiles = new ArrayDeque<String>(); SpoutUtils.listFilesForFolder(new File(args[2]), featureFiles); Scanner scanner = new Scanner(featureFiles.peek()); int i = 0; while (scanner.hasNextLine() && i++ < 10) { List<Map<String, List<Double>>> dict = SpoutUtils.pythonDictToJava(scanner.nextLine()); for (Map<String, List<Double>> map : dict) { i++; Double[] features = map.get("chi2").toArray(new Double[0]); Double[] moreFeatures = map.get("chi1").toArray(new Double[0]); Double[] rmsd = map.get("rmsd").toArray(new Double[0]); Double[] both = (Double[]) ArrayUtils.addAll(features, moreFeatures); String parameters = serializeFeatureVector(ArrayUtils.toPrimitive(both)); String centroidsSerialized = runQuery(args[1], parameters, client); Gson gson = new Gson(); Object[] deserialized = gson.fromJson(centroidsSerialized, Object[].class); for (Object obj : deserialized) { // result we get is of the form List<result> List l = ((List) obj); centroidsSerialized = (String) l.get(0); String[] centroidSerializedArrays = centroidsSerialized .split(MlStormClustererQuery.KmeansClustererQuery.CENTROID_DELIM); List<double[]> centroids = new ArrayList<double[]>(); for (String centroid : centroidSerializedArrays) { centroids.add(MlStormFeatureVectorUtils.deserializeToFeatureVector(centroid)); } double[] rmsdPrimitive = ArrayUtils.toPrimitive(both); double[] rmsdKmeans = new double[centroids.size()]; for (int k = 0; k < centroids.size(); k++) { System.out.println("centroid -- " + Arrays.toString(centroids.get(k))); double[] centroid = centroids.get(k); rmsdKmeans[k] = computeRootMeanSquare(centroid); } System.out.println("1 rmsd original -- " + Arrays.toString(rmsd)); System.out.println("2 rmsd k- Means -- " + Arrays.toString(rmsdKmeans)); System.out.println(); } } } client.close(); }
From source file:fr.inria.atlanmod.kyanos.benchmarks.CdoTraverser.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input CDO resource directory"); inputOpt.setArgs(1);//from w w w . ja v a2 s .com inputOpt.setRequired(true); Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS); inClassOpt.setArgName("CLASS"); inClassOpt.setDescription("FQN of EPackage implementation class"); inClassOpt.setArgs(1); inClassOpt.setRequired(true); Option repoOpt = OptionBuilder.create(REPO_NAME); repoOpt.setArgName("REPO_NAME"); repoOpt.setDescription("CDO Repository name"); repoOpt.setArgs(1); repoOpt.setRequired(true); options.addOption(inputOpt); options.addOption(inClassOpt); options.addOption(repoOpt); CommandLineParser parser = new PosixParser(); try { CommandLine commandLine = parser.parse(options, args); String repositoryDir = commandLine.getOptionValue(IN); String repositoryName = commandLine.getOptionValue(REPO_NAME); Class<?> inClazz = CdoTraverser.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); EmbeddedCDOServer server = new EmbeddedCDOServer(repositoryDir, repositoryName); try { server.run(); CDOSession session = server.openSession(); CDOTransaction transaction = session.openTransaction(); Resource resource = transaction.getRootResource(); LOG.log(Level.INFO, "Start counting"); int count = 0; long begin = System.currentTimeMillis(); for (Iterator<EObject> iterator = resource.getAllContents(); iterator.hasNext(); iterator .next(), count++) ; long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End counting"); LOG.log(Level.INFO, MessageFormat.format("Resource {0} contains {1} elements", resource.getURI(), count)); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); transaction.close(); session.close(); } finally { server.stop(); } } catch (ParseException e) { MessageUtil.showError(e.toString()); MessageUtil.showError("Current arguments: " + Arrays.toString(args)); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("java -jar <this-file.jar>", options, true); } catch (Throwable e) { MessageUtil.showError(e.toString()); } }
From source file:org.mitre.mpf.rest.client.Main.java
public static void main(String[] args) throws RestClientException, IOException, InterruptedException { System.out.println("Starting rest-client!"); //not necessary for localhost, but left if a proxy configuration is needed //System.setProperty("http.proxyHost",""); //System.setProperty("http.proxyPort",""); String currentDirectory;/*from w w w. ja v a 2 s . com*/ currentDirectory = System.getProperty("user.dir"); System.out.println("Current working directory : " + currentDirectory); String username = "mpf"; String password = "mpf123"; byte[] encodedBytes = Base64.encodeBase64((username + ":" + password).getBytes()); String base64 = new String(encodedBytes); System.out.println("encodedBytes " + base64); final String mpfAuth = "Basic " + base64; RequestInterceptor authorize = new RequestInterceptor() { @Override public void intercept(HttpRequestBase request) { request.addHeader("Authorization", mpfAuth /*credentials*/); } }; //RestClient client = RestClient.builder().requestInterceptor(authorize).build(); CustomRestClient client = (CustomRestClient) CustomRestClient.builder() .restClientClass(CustomRestClient.class).requestInterceptor(authorize).build(); //getAvailableWorkPipelineNames String url = "http://localhost:8080/workflow-manager/rest/pipelines"; Map<String, String> params = new HashMap<String, String>(); List<String> availableWorkPipelines = client.get(url, params, new TypeReference<List<String>>() { }); System.out.println("availableWorkPipelines size: " + availableWorkPipelines.size()); System.out.println(Arrays.toString(availableWorkPipelines.toArray())); //processMedia JobCreationRequest jobCreationRequest = new JobCreationRequest(); URI uri = Paths.get(currentDirectory, "/trunk/workflow-manager/src/test/resources/samples/meds/aa/S001-01-t10_01.jpg").toUri(); jobCreationRequest.getMedia().add(new JobCreationMediaData(uri.toString())); uri = Paths.get(currentDirectory, "/trunk/workflow-manager/src/test/resources/samples/meds/aa/S008-01-t10_01.jpg").toUri(); jobCreationRequest.getMedia().add(new JobCreationMediaData(uri.toString())); jobCreationRequest.setExternalId("external id"); //get first DLIB pipeline String firstDlibPipeline = availableWorkPipelines.stream() //.peek(pipepline -> System.out.println("will filter - " + pipepline)) .filter(pipepline -> pipepline.startsWith("DLIB")).findFirst().get(); System.out.println("found firstDlibPipeline: " + firstDlibPipeline); jobCreationRequest.setPipelineName(firstDlibPipeline); //grabbed from 'rest/pipelines' - see #1 //two optional params jobCreationRequest.setBuildOutput(true); //jobCreationRequest.setPriority(priority); //will be set to 4 (default) if not set JobCreationResponse jobCreationResponse = client.customPostObject( "http://localhost:8080/workflow-manager/rest/jobs", jobCreationRequest, JobCreationResponse.class); System.out.println("jobCreationResponse job id: " + jobCreationResponse.getJobId()); System.out.println("\n---Sleeping for 10 seconds to let the job process---\n"); Thread.sleep(10000); //getJobStatus url = "http://localhost:8080/workflow-manager/rest/jobs"; // /status"; params = new HashMap<String, String>(); //OPTIONAL //params.put("v", "") - no versioning currently implemented //id is now a path var - if not set, all job info will returned url = url + "/" + Long.toString(jobCreationResponse.getJobId()); SingleJobInfo jobInfo = client.get(url, params, SingleJobInfo.class); System.out.println("jobInfo id: " + jobInfo.getJobId()); //getSerializedOutput String jobIdToGetOutputStr = Long.toString(jobCreationResponse.getJobId()); url = "http://localhost:8080/workflow-manager/rest/jobs/" + jobIdToGetOutputStr + "/output/detection"; params = new HashMap<String, String>(); //REQUIRED - job id is now a path var and required for this endpoint String serializedOutput = client.getAsString(url, params); System.out.println("serializedOutput: " + serializedOutput); }