List of usage examples for org.apache.commons.cli Options Options
Options
From source file:com.github.zk1931.pulsefs.Main.java
public static void main(String[] args) throws Exception { // Options for command arguments. Options options = new Options(); Option port = OptionBuilder.withArgName("port").hasArg(true).isRequired(true).withDescription("port number") .create("port"); Option addr = OptionBuilder.withArgName("addr").hasArg(true).withDescription("addr (ip:port) for Zab.") .create("addr"); Option join = OptionBuilder.withArgName("join").hasArg(true).withDescription("the addr of server to join.") .create("join"); Option dir = OptionBuilder.withArgName("dir").hasArg(true).withDescription("the directory for logs.") .create("dir"); Option help = OptionBuilder.withArgName("h").hasArg(false).withLongOpt("help") .withDescription("print out usages.").create("h"); Option timeout = OptionBuilder.withArgName("timeout").hasArg(true) .withDescription("session timeout(seconds)").create("timeout"); options.addOption(port).addOption(addr).addOption(join).addOption(dir).addOption(timeout).addOption(help); CommandLineParser parser = new BasicParser(); CommandLine cmd;/* w w w .ja v a 2 s . c om*/ String usage = "./bin/pulsefs -port port [Options]"; try { cmd = parser.parse(options, args); if (cmd.hasOption("h")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(usage, options); return; } } catch (ParseException exp) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(usage, options); return; } PulseFSConfig config = new PulseFSConfig(); if (cmd.hasOption("addr")) { config.setServerId(cmd.getOptionValue("addr")); } if (cmd.hasOption("join")) { config.setJoinPeer(cmd.getOptionValue("join")); } if (cmd.hasOption("dir")) { config.setLogDir(cmd.getOptionValue("dir")); } if (cmd.hasOption("timeout")) { String sessionTimeout = cmd.getOptionValue("timeout"); config.setSessionTimeout(Integer.parseInt(sessionTimeout)); } if (cmd.hasOption("port")) { config.setPort(Integer.parseInt(cmd.getOptionValue("port"))); } Server server = new Server(config.getPort()); // Suppress "Server" header in HTTP response. for (Connector y : server.getConnectors()) { for (ConnectionFactory x : y.getConnectionFactories()) { if (x instanceof HttpConnectionFactory) { ((HttpConnectionFactory) x).getHttpConfiguration().setSendServerVersion(false); } } } PulseFS fs = new PulseFS(config); SessionFilter sessionFilter = new SessionFilter(fs); FilterHolder filters = new FilterHolder(sessionFilter); ServletContextHandler pulsefs = new ServletContextHandler(ServletContextHandler.SESSIONS); pulsefs.setContextPath(PulseFSConfig.PULSEFS_ROOT); pulsefs.setAllowNullPathInfo(true); pulsefs.addServlet(new ServletHolder(new PulseFSHandler(fs)), "/*"); pulsefs.addFilter(filters, "/*", EnumSet.of(DispatcherType.REQUEST)); ServletContextHandler servers = new ServletContextHandler(ServletContextHandler.SESSIONS); servers.setContextPath(PulseFSConfig.PULSEFS_SERVERS_PATH); // Redirects /pulsefs/servers to /pulsefs/servers/ servers.setAllowNullPathInfo(true); servers.addServlet(new ServletHolder(new PulseFSServersHandler(fs)), "/*"); servers.addFilter(filters, "/*", EnumSet.of(DispatcherType.REQUEST)); ServletContextHandler tree = new ServletContextHandler(ServletContextHandler.SESSIONS); tree.setContextPath("/"); tree.addServlet(new ServletHolder(new TreeHandler(fs)), "/*"); tree.addFilter(filters, "/*", EnumSet.of(DispatcherType.REQUEST)); ServletContextHandler sessions = new ServletContextHandler(ServletContextHandler.SESSIONS); sessions.setContextPath(PulseFSConfig.PULSEFS_SESSIONS_PATH); // Redirects /pulsefs/sessions to /pulsefs/sessions/ sessions.setAllowNullPathInfo(true); sessions.addServlet(new ServletHolder(new PulseFSSessionsHandler(fs)), "/*"); sessions.addFilter(filters, "/*", EnumSet.of(DispatcherType.REQUEST)); ContextHandlerCollection contexts = new ContextHandlerCollection(); contexts.setHandlers(new Handler[] { sessions, servers, pulsefs, tree }); server.setHandler(contexts); server.start(); server.join(); }
From source file:com.ikanow.infinit.e.core.CoreMain.java
/** * @param args//from ww w. j a v a 2 s. c o m * @throws ParseException * @throws IOException * @throws InterruptedException */ public static void main(String[] args) throws ParseException, IOException, InterruptedException { CommandLineParser cliParser = new BasicParser(); Options allOps = new Options(); // Common allOps.addOption("c", "config", true, "Configuration path"); allOps.addOption("g", "community", true, "Only run on one community"); // Harvest specific allOps.addOption("h", "harvest", false, "Run harvester"); allOps.addOption("l", "local", false, "(for debug: use dummy index)"); allOps.addOption("i", "source", true, "(for debug: use a single source)"); allOps.addOption("r", "reset", false, "Reset bad sources"); // Sync specific allOps.addOption("s", "sync", false, "Run synchronization"); allOps.addOption("f", "from", true, "String unix time (secs) from when to sync"); // Custom specifc allOps.addOption("p", "custom", false, "Run custom processing server"); allOps.addOption("d", "dummy", true, "Use to keep temp unwanted options on the command line"); allOps.addOption("j", "jobtitle", true, "(for debug: run a single job)"); CommandLine cliOpts = cliParser.parse(allOps, args); Globals.setIdentity(com.ikanow.infinit.e.data_model.Globals.Identity.IDENTITY_SERVICE); if (cliOpts.hasOption("config")) { String configOverride = (String) cliOpts.getOptionValue("config"); Globals.overrideConfigLocation(configOverride); } //Set up logging java.io.File file = new java.io.File( com.ikanow.infinit.e.data_model.Globals.getLogPropertiesLocation() + ".xml"); if (file.exists()) { DOMConfigurator.configure(com.ikanow.infinit.e.data_model.Globals.getLogPropertiesLocation() + ".xml"); } else { PropertyConfigurator.configure(Globals.getLogPropertiesLocation()); } if (cliOpts.hasOption("harvest")) { if (SourceUtils.checkDbSyncLock()) { Thread.sleep(10000); // (wait 10s and then try again) System.exit(0); } String communityOverride = null; String sourceDebug = null; if (cliOpts.hasOption("local")) { ElasticSearchManager.setLocalMode(true); } if (cliOpts.hasOption("reset")) { SourceUtils.resetBadSources(); } if (cliOpts.hasOption("community")) { communityOverride = (String) cliOpts.getOptionValue("community"); } if (cliOpts.hasOption("source")) { sourceDebug = (String) cliOpts.getOptionValue("source"); } new HarvestThenProcessController() .startService(SourceUtils.getSourcesToWorkOn(communityOverride, sourceDebug, false, true)); } //TESTED else if (cliOpts.hasOption("sync")) { if (SourceUtils.checkDbSyncLock()) { Thread.sleep(10000); // (wait 10s and then try again) System.exit(0); } // Sync command line options: long nTimeOfLastCleanse_secs = 0; // (default) if (cliOpts.hasOption("from")) { try { nTimeOfLastCleanse_secs = Long.parseLong((String) cliOpts.getOptionValue("from")); } catch (NumberFormatException e) { System.out.println("From date is incorrect"); System.exit(-1); } } String communityOverride = null; String sourceDebug = null; if (cliOpts.hasOption("community")) { communityOverride = (String) cliOpts.getOptionValue("community"); } else if (cliOpts.hasOption("source")) { sourceDebug = (String) cliOpts.getOptionValue("source"); } SourceUtils.checkSourcesHaveHashes(communityOverride, sourceDebug); // (infrequently ie as part of sync, check all the sources have hashes, which the harvester depends on) new SynchronizationController().startService(nTimeOfLastCleanse_secs, SourceUtils.getSourcesToWorkOn(communityOverride, sourceDebug, true, true)); } //TESTED else if (cliOpts.hasOption("custom")) { String jobOverride = null; if (cliOpts.hasOption("jobtitle")) { jobOverride = (String) cliOpts.getOptionValue("jobtitle"); } CustomProcessingController customPxController = new CustomProcessingController(); customPxController.checkScheduledJobs(jobOverride); customPxController.checkRunningJobs(); customPxController.runThroughSavedQueues(); } else { //Test code for distribution: // boolean bSync = true; // LinkedList<SourcePojo> testSources = null; // LinkedList<SourcePojo> batchOfSources = null; // testSources = getSourcesToWorkOn(null, null, bSync, true); // System.out.println("Sources considered = " + testSources.size()); // // Grab a batch of sources // batchOfSources = getDistributedSourceList(testSources, null, false); // System.out.println("Sources left = " + testSources.size()); // System.out.println("Sources extracted = " + new com.google.gson.Gson().toJson(batchOfSources)); System.out.println( "com.ikanow.infinit.e.core.server [--config <config-dir>] [--harvest [<other options>]|--sync [<other options>]|--custom [<other options>]]"); System.exit(-1); } MongoApplicationLock.registerAppShutdown(); // (in case the saved queries are running, for some reason built in startup hook not running) }
From source file:com.redhat.poc.jdg.bankofchina.performance.TestCase531RemoteMultiThreads.java
public static void main(String[] args) throws Exception { CommandLine commandLine;//from w w w.j a v a2s. co m Options options = new Options(); options.addOption("n", true, "The read thread numbers option"); options.addOption("t", true, "The thread read times option"); BasicParser parser = new BasicParser(); parser.parse(options, args); commandLine = parser.parse(options, args); if (commandLine.getOptions().length > 0) { if (commandLine.hasOption("n")) { String numbers = commandLine.getOptionValue("n"); if (numbers != null && numbers.length() > 0) { readThreadNumbers = Integer.parseInt(numbers); } } if (commandLine.hasOption("t")) { String times = commandLine.getOptionValue("t"); if (times != null && times.length() > 0) { threadReadTimes = Integer.parseInt(times); } } } System.out.println(); System.out.println("%%%%%%%%% userid.csv %%%%%%%%%"); LoadUserIdList(); randomPoolSize = userIdList.size(); System.out.println( "%%%%%%%%% ? userid.csv , " + randomPoolSize + " ?? %%%%%%%%%"); randomPoolSizeByThread = randomPoolSize / readThreadNumbers; System.out.println(); System.out.println( "%%%%%%%%% ?, " + readThreadNumbers + " ,, ???, " + threadReadTimes + " ,?, ?(ms)," + new Date().getTime()); for (int i = 0; i < readThreadNumbers; i++) { new TestCase531RemoteMultiThreads(i * randomPoolSizeByThread).start(); } }
From source file:com.redhat.poc.jdg.bankofchina.performance.TestCase532RemoteMultiThreads.java
public static void main(String[] args) throws Exception { CommandLine commandLine;// w ww .j a v a 2 s .c om Options options = new Options(); options.addOption("n", true, "The read thread numbers option"); options.addOption("t", true, "The thread read times option"); BasicParser parser = new BasicParser(); parser.parse(options, args); commandLine = parser.parse(options, args); if (commandLine.getOptions().length > 0) { if (commandLine.hasOption("n")) { String numbers = commandLine.getOptionValue("n"); if (numbers != null && numbers.length() > 0) { writeThreadNumbers = Integer.parseInt(numbers); } } if (commandLine.hasOption("t")) { String times = commandLine.getOptionValue("t"); if (times != null && times.length() > 0) { threadWriteTimes = Integer.parseInt(times); } } } System.out.println(); System.out.println("%%%%%%%%% userid.csv %%%%%%%%%"); LoadUserIdList(); randomPoolSize = userIdList.size(); System.out.println( "%%%%%%%%% ? userid.csv , " + randomPoolSize + " ?? %%%%%%%%%"); randomPoolSizeByThread = randomPoolSize / writeThreadNumbers; System.out.println(); System.out.println( "%%%%%%%%% ?, " + writeThreadNumbers + ", , ??, " + threadWriteTimes + ", ?, ?(ms)," + new Date().getTime()); for (int i = 0; i < writeThreadNumbers; i++) { new TestCase532RemoteMultiThreads(i * randomPoolSizeByThread).start(); } }
From source file:apps.LuceneIndexer.java
public static void main(String[] args) { Options options = new Options(); options.addOption("i", null, true, "input file"); options.addOption("o", null, true, "output directory"); options.addOption("r", null, true, "optional output TREC-format QREL file"); options.addOption("bm25_b", null, true, "BM25 parameter: b"); options.addOption("bm25_k1", null, true, "BM25 parameter: k1"); options.addOption("bm25fixed", null, false, "use the fixed BM25 similarity"); Joiner commaJoin = Joiner.on(','); Joiner spaceJoin = Joiner.on(' '); options.addOption("source_type", null, true, "document source type: " + commaJoin.join(SourceFactory.getDocSourceList())); // If you increase this value, you may need to modify the following line in *.sh file // export MAVEN_OPTS="-Xms8192m -server" double ramBufferSizeMB = 1024 * 8; // 8 GB CommandLineParser parser = new org.apache.commons.cli.GnuParser(); IndexWriter indexWriter = null;//from w w w .j a va2s. c o m BufferedWriter qrelWriter = null; int docNum = 0; try { CommandLine cmd = parser.parse(options, args); String inputFileName = null, outputDirName = null, qrelFileName = null; if (cmd.hasOption("i")) { inputFileName = cmd.getOptionValue("i"); } else { Usage("Specify 'input file'", options); } if (cmd.hasOption("o")) { outputDirName = cmd.getOptionValue("o"); } else { Usage("Specify 'index directory'", options); } if (cmd.hasOption("r")) { qrelFileName = cmd.getOptionValue("r"); } String sourceName = cmd.getOptionValue("source_type"); if (sourceName == null) Usage("Specify document source type", options); if (qrelFileName != null) qrelWriter = new BufferedWriter(new FileWriter(qrelFileName)); File outputDir = new File(outputDirName); if (!outputDir.exists()) { if (!outputDir.mkdirs()) { System.out.println("couldn't create " + outputDir.getAbsolutePath()); System.exit(1); } } if (!outputDir.isDirectory()) { System.out.println(outputDir.getAbsolutePath() + " is not a directory!"); System.exit(1); } if (!outputDir.canWrite()) { System.out.println("Can't write to " + outputDir.getAbsolutePath()); System.exit(1); } boolean useFixedBM25 = cmd.hasOption("bm25fixed"); float bm25_k1 = UtilConst.BM25_K1_DEFAULT, bm25_b = UtilConst.BM25_B_DEFAULT; if (cmd.hasOption("bm25_k1")) { try { bm25_k1 = Float.parseFloat(cmd.getOptionValue("bm25_k1")); } catch (NumberFormatException e) { Usage("Wrong format for 'bm25_k1'", options); } } if (cmd.hasOption("bm25_b")) { try { bm25_b = Float.parseFloat(cmd.getOptionValue("bm25_b")); } catch (NumberFormatException e) { Usage("Wrong format for 'bm25_b'", options); } } EnglishAnalyzer analyzer = new EnglishAnalyzer(); FSDirectory indexDir = FSDirectory.open(Paths.get(outputDirName)); IndexWriterConfig indexConf = new IndexWriterConfig(analyzer); /* OpenMode.CREATE creates a new index or overwrites an existing one. https://lucene.apache.org/core/6_0_0/core/org/apache/lucene/index/IndexWriterConfig.OpenMode.html#CREATE */ indexConf.setOpenMode(OpenMode.CREATE); indexConf.setRAMBufferSizeMB(ramBufferSizeMB); System.out.println(String.format("BM25 parameters k1=%f b=%f ", bm25_k1, bm25_b)); if (useFixedBM25) { System.out.println(String.format("Using fixed BM25Simlarity, k1=%f b=%f", bm25_k1, bm25_b)); indexConf.setSimilarity(new BM25SimilarityFix(bm25_k1, bm25_b)); } else { System.out.println(String.format("Using Lucene BM25Similarity, k1=%f b=%f", bm25_k1, bm25_b)); indexConf.setSimilarity(new BM25Similarity(bm25_k1, bm25_b)); } indexWriter = new IndexWriter(indexDir, indexConf); DocumentSource inpDocSource = SourceFactory.createDocumentSource(sourceName, inputFileName); DocumentEntry inpDoc = null; TextCleaner textCleaner = new TextCleaner(null); while ((inpDoc = inpDocSource.next()) != null) { ++docNum; Document luceneDoc = new Document(); ArrayList<String> cleanedToks = textCleaner.cleanUp(inpDoc.mDocText); String cleanText = spaceJoin.join(cleanedToks); // System.out.println(inpDoc.mDocId); // System.out.println(cleanText); // System.out.println("=============================="); luceneDoc.add(new StringField(UtilConst.FIELD_ID, inpDoc.mDocId, Field.Store.YES)); luceneDoc.add(new TextField(UtilConst.FIELD_TEXT, cleanText, Field.Store.YES)); indexWriter.addDocument(luceneDoc); if (inpDoc.mIsRel != null && qrelWriter != null) { saveQrelOneEntry(qrelWriter, inpDoc.mQueryId, inpDoc.mDocId, inpDoc.mIsRel ? MAX_GRADE : 0); } if (docNum % 1000 == 0) System.out.println(String.format("Indexed %d documents", docNum)); } } catch (ParseException e) { e.printStackTrace(); Usage("Cannot parse arguments" + e, options); } catch (Exception e) { System.err.println("Terminating due to an exception: " + e); System.exit(1); } finally { System.out.println(String.format("Indexed %d documents", docNum)); try { if (null != indexWriter) indexWriter.close(); if (null != qrelWriter) qrelWriter.close(); } catch (IOException e) { System.err.println("IO exception: " + e); e.printStackTrace(); } } }
From source file:microbiosima.SelectiveMicrobiosima.java
/** * @param args/* w ww . java 2 s . co m*/ * the command line arguments * @throws java.io.FileNotFoundException * @throws java.io.UnsupportedEncodingException */ public static void main(String[] args) throws FileNotFoundException, UnsupportedEncodingException { int populationSize = 500;//Integer.parseInt(parameters[1]); int microSize = 1000;//Integer.parseInt(parameters[2]); int numberOfSpecies = 150;//Integer.parseInt(parameters[3]); int numberOfGeneration = 10000; int Ngene = 10; int numberOfObservation = 100; int numberOfReplication = 10; double Ngenepm = 5; double pctEnv = 0; double pctPool = 0; double msCoeff = 1; double hsCoeff = 1; boolean HMS_or_TMS = true; Options options = new Options(); Option help = new Option("h", "help", false, "print this message"); Option version = new Option("v", "version", false, "print the version information and exit"); options.addOption(help); options.addOption(version); options.addOption(Option.builder("o").longOpt("obs").hasArg().argName("OBS") .desc("Number generation for observation [default: 100]").build()); options.addOption(Option.builder("r").longOpt("rep").hasArg().argName("REP") .desc("Number of replication [default: 1]").build()); Builder C = Option.builder("c").longOpt("config").numberOfArgs(6).argName("Pop Micro Spec Gen") .desc("Four Parameters in the following orders: " + "(1) population size, (2) microbe size, (3) number of species, (4) number of generation, (5) number of total traits, (6)number of traits per microbe" + " [default: 500 1000 150 10000 10 5]"); options.addOption(C.build()); HelpFormatter formatter = new HelpFormatter(); String syntax = "microbiosima pctEnv pctPool"; String header = "\nSimulates the evolutionary and ecological dynamics of microbiomes within a population of hosts.\n\n" + "required arguments:\n" + " pctEnv Percentage of environmental acquisition\n" + " pctPool Percentage of pooled environmental component\n" + " msCoeff Parameter related to microbe selection strength\n" + " hsCoeff Parameter related to host selection strength\n" + " HMS_or_TMS String HMS or TMS to specify host-mediated or trait-mediated microbe selection\n" + "\noptional arguments:\n"; String footer = "\n"; formatter.setWidth(80); CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); String[] pct_config = cmd.getArgs(); if (cmd.hasOption("h") || args.length == 0) { formatter.printHelp(syntax, header, options, footer, true); System.exit(0); } if (cmd.hasOption("v")) { System.out.println("Microbiosima " + VERSION); System.exit(0); } if (pct_config.length != 5) { System.out.println( "ERROR! Required exactly five argumennts for pct_env, pct_pool, msCoeff, hsCoeff and HMS_or_TMS. It got " + pct_config.length + ": " + Arrays.toString(pct_config)); formatter.printHelp(syntax, header, options, footer, true); System.exit(3); } else { pctEnv = Double.parseDouble(pct_config[0]); pctPool = Double.parseDouble(pct_config[1]); msCoeff = Double.parseDouble(pct_config[2]); hsCoeff = Double.parseDouble(pct_config[3]); if (pct_config[4].equals("HMS")) HMS_or_TMS = true; if (pct_config[4].equals("TMS")) HMS_or_TMS = false; if (pctEnv < 0 || pctEnv > 1) { System.out.println( "ERROR: pctEnv (Percentage of environmental acquisition) must be between 0 and 1 (pctEnv=" + pctEnv + ")! EXIT"); System.exit(3); } if (pctPool < 0 || pctPool > 1) { System.out.println( "ERROR: pctPool (Percentage of pooled environmental component must) must be between 0 and 1 (pctPool=" + pctPool + ")! EXIT"); System.exit(3); } if (msCoeff < 1) { System.out.println( "ERROR: msCoeff (parameter related to microbe selection strength) must be not less than 1 (msCoeff=" + msCoeff + ")! EXIT"); System.exit(3); } if (hsCoeff < 1) { System.out.println( "ERROR: hsCoeff (parameter related to host selection strength) must be not less than 1 (hsCoeff=" + hsCoeff + ")! EXIT"); System.exit(3); } if (!(pct_config[4].equals("HMS") || pct_config[4].equals("TMS"))) { System.out.println( "ERROR: HMS_or_TMS (parameter specifying host-mediated or trait-mediated selection) must be either 'HMS' or 'TMS' (HMS_or_TMS=" + pct_config[4] + ")! EXIT"); System.exit(3); } } if (cmd.hasOption("config")) { String[] configs = cmd.getOptionValues("config"); populationSize = Integer.parseInt(configs[0]); microSize = Integer.parseInt(configs[1]); numberOfSpecies = Integer.parseInt(configs[2]); numberOfGeneration = Integer.parseInt(configs[3]); Ngene = Integer.parseInt(configs[4]); Ngenepm = Double.parseDouble(configs[5]); if (Ngenepm > Ngene) { System.out.println( "ERROR: number of traits per microbe must not be greater than number of total traits! EXIT"); System.exit(3); } } if (cmd.hasOption("obs")) { numberOfObservation = Integer.parseInt(cmd.getOptionValue("obs")); } if (cmd.hasOption("rep")) { numberOfReplication = Integer.parseInt(cmd.getOptionValue("rep")); } } catch (ParseException e) { e.printStackTrace(); System.exit(3); } StringBuilder sb = new StringBuilder(); sb.append("Configuration Summary:").append("\n\tPopulation size: ").append(populationSize) .append("\n\tMicrobe size: ").append(microSize).append("\n\tNumber of species: ") .append(numberOfSpecies).append("\n\tNumber of generation: ").append(numberOfGeneration) .append("\n\tNumber generation for observation: ").append(numberOfObservation) .append("\n\tNumber of replication: ").append(numberOfReplication) .append("\n\tNumber of total traits: ").append(Ngene).append("\n\tNumber of traits per microbe: ") .append(Ngenepm).append("\n"); System.out.println(sb.toString()); double[] environment = new double[numberOfSpecies]; for (int i = 0; i < numberOfSpecies; i++) { environment[i] = 1 / (double) numberOfSpecies; } int[] fitnessToHost = new int[Ngene]; int[] fitnessToMicrobe = new int[Ngene]; for (int rep = 0; rep < numberOfReplication; rep++) { String prefix = "" + (rep + 1) + "_"; String sufix; if (HMS_or_TMS) sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_HMS" + msCoeff + ".txt"; else sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_TMS" + msCoeff + ".txt"; System.out.println("Output 5 result files in the format of: " + prefix + "[****]" + sufix); try { PrintWriter file1 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "gamma_diversity" + sufix))); PrintWriter file2 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "alpha_diversity" + sufix))); PrintWriter file3 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "beta_diversity" + sufix))); PrintWriter file4 = new PrintWriter(new BufferedWriter(new FileWriter(prefix + "sum" + sufix))); PrintWriter file5 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "inter_generation_distance" + sufix))); PrintWriter file6 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "environment_population_distance" + sufix))); PrintWriter file7 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "host_fitness" + sufix))); PrintWriter file8 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "cos_theta" + sufix))); PrintWriter file9 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "host_fitness_distribution" + sufix))); PrintWriter file10 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "microbiome_fitness_distribution" + sufix))); PrintWriter file11 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "bacteria_contents" + sufix))); PrintWriter file12 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "individual_bacteria_contents" + sufix))); for (int i = 0; i < Ngene; i++) { fitnessToMicrobe[i] = MathUtil.getNextInt(2) - 1; fitnessToHost[i] = MathUtil.getNextInt(2) - 1; } MathUtil.setSeed(rep % numberOfReplication); SelectiveSpeciesRegistry ssr = new SelectiveSpeciesRegistry(numberOfSpecies, Ngene, Ngenepm, msCoeff, fitnessToHost, fitnessToMicrobe); MathUtil.setSeed(); SelectivePopulation population = new SelectivePopulation(microSize, environment, populationSize, pctEnv, pctPool, 0, 0, ssr, hsCoeff, HMS_or_TMS); while (population.getNumberOfGeneration() < numberOfGeneration) { population.sumSpecies(); if (population.getNumberOfGeneration() % numberOfObservation == 0) { //file1.print(population.gammaDiversity(false)); //file2.print(population.alphaDiversity(false)); //file1.print("\t"); //file2.print("\t"); file1.println(population.gammaDiversity(true)); file2.println(population.alphaDiversity(true)); //file3.print(population.betaDiversity(true)); //file3.print("\t"); file3.println(population.BrayCurtis(true)); file4.println(population.printOut()); file5.println(population.interGenerationDistance()); file6.println(population.environmentPopulationDistance()); file7.print(population.averageHostFitness()); file7.print("\t"); file7.println(population.varianceHostFitness()); file8.println(population.cosOfMH()); file9.println(population.printOutHFitness()); file10.println(population.printOutMFitness()); file11.println(population.printBacteriaContents()); } population.getNextGen(); } for (SelectiveIndividual host : population.getIndividuals()) { file12.println(host.printBacteriaContents()); } file1.close(); file2.close(); file3.close(); file4.close(); file5.close(); file6.close(); file7.close(); file8.close(); file9.close(); file10.close(); file11.close(); file12.close(); } catch (IOException e) { e.printStackTrace(); } } }
From source file:com.hortonworks.registries.storage.tool.TablesInitializer.java
public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption(Option.builder("s").numberOfArgs(1).longOpt(OPTION_SCRIPT_ROOT_PATH) .desc("Root directory of script path").build()); options.addOption(Option.builder("c").numberOfArgs(1).longOpt(OPTION_CONFIG_FILE_PATH) .desc("Config file path").build()); options.addOption(Option.builder("m").numberOfArgs(1).longOpt(OPTION_MYSQL_JAR_URL_PATH) .desc("Mysql client jar url to download").build()); options.addOption(Option.builder().hasArg(false).longOpt(OPTION_EXECUTE_CREATE_TABLE) .desc("Execute 'create table' script").build()); options.addOption(Option.builder().hasArg(false).longOpt(OPTION_EXECUTE_DROP_TABLE) .desc("Execute 'drop table' script").build()); options.addOption(Option.builder().hasArg(false).longOpt(OPTION_EXECUTE_CHECK_CONNECTION) .desc("Check the connection for configured data source").build()); CommandLineParser parser = new BasicParser(); CommandLine commandLine = parser.parse(options, args); if (!commandLine.hasOption(OPTION_CONFIG_FILE_PATH) || !commandLine.hasOption(OPTION_SCRIPT_ROOT_PATH)) { usage(options);//from w w w .ja v a 2 s .c om System.exit(1); } // either create or drop should be specified, not both boolean executeCreate = commandLine.hasOption(OPTION_EXECUTE_CREATE_TABLE); boolean executeDrop = commandLine.hasOption(OPTION_EXECUTE_DROP_TABLE); boolean checkConnection = commandLine.hasOption(OPTION_EXECUTE_CHECK_CONNECTION); boolean moreThanOneOperationIsSpecified = executeCreate == executeDrop ? executeCreate : checkConnection; boolean noOperationSpecified = !(executeCreate || executeDrop || checkConnection); if (moreThanOneOperationIsSpecified) { System.out.println( "Only one operation can be execute at once, please select 'create' or 'drop', or 'check-connection'."); System.exit(1); } else if (noOperationSpecified) { System.out.println( "One of 'create', 'drop', 'check-connection' operation should be specified to execute."); System.exit(1); } String confFilePath = commandLine.getOptionValue(OPTION_CONFIG_FILE_PATH); String scriptRootPath = commandLine.getOptionValue(OPTION_SCRIPT_ROOT_PATH); String mysqlJarUrl = commandLine.getOptionValue(OPTION_MYSQL_JAR_URL_PATH); StorageProviderConfiguration storageProperties; try { Map<String, Object> conf = Utils.readConfig(confFilePath); StorageProviderConfigurationReader confReader = new StorageProviderConfigurationReader(); storageProperties = confReader.readStorageConfig(conf); } catch (IOException e) { System.err.println("Error occurred while reading config file: " + confFilePath); System.exit(1); throw new IllegalStateException("Shouldn't reach here"); } String bootstrapDirPath = null; try { bootstrapDirPath = System.getProperty("bootstrap.dir"); MySqlDriverHelper.downloadMySQLJarIfNeeded(storageProperties, bootstrapDirPath, mysqlJarUrl); } catch (Exception e) { System.err.println("Error occurred while downloading MySQL jar. bootstrap dir: " + bootstrapDirPath); System.exit(1); throw new IllegalStateException("Shouldn't reach here"); } try { SQLScriptRunner sqlScriptRunner = new SQLScriptRunner(storageProperties); try { sqlScriptRunner.initializeDriver(); } catch (ClassNotFoundException e) { System.err.println( "Driver class is not found in classpath. Please ensure that driver is in classpath."); System.exit(1); } if (checkConnection) { if (!sqlScriptRunner.checkConnection()) { System.exit(1); } } else if (executeDrop) { doExecuteDrop(sqlScriptRunner, storageProperties, scriptRootPath); } else { // executeCreate doExecuteCreate(sqlScriptRunner, storageProperties, scriptRootPath); } } catch (IOException e) { System.err.println("Error occurred while reading script file. Script root path: " + scriptRootPath); System.exit(1); } }
From source file:edu.umd.ujjwalgoel.AnalyzePMI.java
@SuppressWarnings({ "static-access" })
public static void main(String[] args) {
Options options = new Options();
options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
CommandLine cmdline = null;//from ww w. j ava2 s .co m
CommandLineParser parser = new GnuParser();
try {
cmdline = parser.parse(options, args);
} catch (ParseException exp) {
System.err.println("Error parsing command line: " + exp.getMessage());
System.exit(-1);
}
if (!cmdline.hasOption(INPUT)) {
System.out.println("args: " + Arrays.toString(args));
HelpFormatter formatter = new HelpFormatter();
formatter.setWidth(120);
formatter.printHelp(AnalyzePMI.class.getName(), options);
ToolRunner.printGenericCommandUsage(System.out);
System.exit(-1);
}
String inputPath = cmdline.getOptionValue(INPUT);
System.out.println("input path: " + inputPath);
BufferedReader br = null;
int countPairs = 0;
List<PairOfWritables<PairOfStrings, FloatWritable>> pmis = new ArrayList<PairOfWritables<PairOfStrings, FloatWritable>>();
List<PairOfWritables<PairOfStrings, FloatWritable>> cloudPmis = new ArrayList<PairOfWritables<PairOfStrings, FloatWritable>>();
List<PairOfWritables<PairOfStrings, FloatWritable>> lovePmis = new ArrayList<PairOfWritables<PairOfStrings, FloatWritable>>();
PairOfWritables<PairOfStrings, FloatWritable> highestPMI = null;
PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI = null;
PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI2 = null;
PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI3 = null;
PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI = null;
PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI2 = null;
PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI3 = null;
try {
FileSystem fs = FileSystem.get(new Configuration());
FileStatus[] status = fs.listStatus(new Path(inputPath));
//PairOfStrings pair = new PairOfStrings();
for (int i = 0; i < status.length; i++) {
br = new BufferedReader(new InputStreamReader(fs.open(status[i].getPath())));
String line = br.readLine();
while (line != null) {
String[] words = line.split("\\t");
float value = Float.parseFloat(words[1].trim());
String[] wordPair = words[0].replaceAll("\\(", "").replaceAll("\\)", "").split(",");
PairOfStrings pair = new PairOfStrings();
pair.set(wordPair[0].trim(), wordPair[1].trim());
if (wordPair[0].trim().equals("cloud")) {
PairOfWritables<PairOfStrings, FloatWritable> cloudPmi = new PairOfWritables<PairOfStrings, FloatWritable>();
cloudPmi.set(pair, new FloatWritable(value));
cloudPmis.add(cloudPmi);
if ((highestCloudPMI == null)
|| (highestCloudPMI.getRightElement().compareTo(cloudPmi.getRightElement()) < 0)) {
highestCloudPMI = cloudPmi;
} else if ((highestCloudPMI2 == null)
|| (highestCloudPMI2.getRightElement().compareTo(cloudPmi.getRightElement()) < 0)) {
highestCloudPMI2 = cloudPmi;
} else if ((highestCloudPMI3 == null)
|| (highestCloudPMI3.getRightElement().compareTo(cloudPmi.getRightElement()) < 0)) {
highestCloudPMI3 = cloudPmi;
}
}
if (wordPair[0].trim().equals("love")) {
PairOfWritables<PairOfStrings, FloatWritable> lovePmi = new PairOfWritables<PairOfStrings, FloatWritable>();
lovePmi.set(pair, new FloatWritable(value));
lovePmis.add(lovePmi);
if ((highestLovePMI == null)
|| (highestLovePMI.getRightElement().compareTo(lovePmi.getRightElement()) < 0)) {
highestLovePMI = lovePmi;
} else if ((highestLovePMI2 == null)
|| (highestLovePMI2.getRightElement().compareTo(lovePmi.getRightElement()) < 0)) {
highestLovePMI2 = lovePmi;
} else if ((highestLovePMI3 == null)
|| (highestLovePMI3.getRightElement().compareTo(lovePmi.getRightElement()) < 0)) {
highestLovePMI3 = lovePmi;
}
}
PairOfWritables<PairOfStrings, FloatWritable> pmi = new PairOfWritables<PairOfStrings, FloatWritable>();
pmi.set(pair, new FloatWritable(value));
pmis.add(pmi);
if (highestPMI == null) {
highestPMI = pmi;
} else if (highestPMI.getRightElement().compareTo(pmi.getRightElement()) < 0) {
highestPMI = pmi;
}
countPairs++;
line = br.readLine();
}
}
} catch (Exception ex) {
System.out.println("ERROR" + ex.getMessage());
}
/*Collections.sort(pmis, new Comparator<PairOfWritables<PairOfStrings, FloatWritable>>() {
public int compare(PairOfWritables<PairOfStrings, FloatWritable> e1,
PairOfWritables<PairOfStrings, FloatWritable> e2) {
/*if (e2.getRightElement().compareTo(e1.getRightElement()) == 0) {
return e1.getLeftElement().getLeftElement().compareTo(e2.getLeftElement().getLeftElement());
}
return e2.getRightElement().compareTo(e1.getRightElement());
}
});
Collections.sort(cloudPmis, new Comparator<PairOfWritables<PairOfStrings, FloatWritable>>() {
public int compare(PairOfWritables<PairOfStrings, FloatWritable> e1,
PairOfWritables<PairOfStrings, FloatWritable> e2) {
if (e2.getRightElement().compareTo(e1.getRightElement()) == 0) {
return e1.getLeftElement().getLeftElement().compareTo(e2.getLeftElement().getLeftElement());
}
return e2.getRightElement().compareTo(e1.getRightElement());
}
});
Collections.sort(lovePmis, new Comparator<PairOfWritables<PairOfStrings, FloatWritable>>() {
public int compare(PairOfWritables<PairOfStrings, FloatWritable> e1,
PairOfWritables<PairOfStrings, FloatWritable> e2) {
if (e2.getRightElement().compareTo(e1.getRightElement()) == 0) {
return e1.getLeftElement().getLeftElement().compareTo(e2.getLeftElement().getLeftElement());
}
return e2.getRightElement().compareTo(e1.getRightElement());
}
});
PairOfWritables<PairOfStrings, FloatWritable> highestPMI = pmis.get(0);
PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI = cloudPmis.get(0); PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI2 = cloudPmis.get(1);
PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI3 = cloudPmis.get(2);
PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI = lovePmis.get(0); PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI2 = lovePmis.get(1);
PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI3 = lovePmis.get(2);*/
System.out.println("Total Distinct Pairs : " + countPairs);
System.out.println("Pair with highest PMI : (" + highestPMI.getLeftElement().getLeftElement() + ", "
+ highestPMI.getLeftElement().getRightElement());
System.out
.println("Word with highest PMI with Cloud : " + highestCloudPMI.getLeftElement().getRightElement()
+ " with value : " + highestCloudPMI.getRightElement().get());
System.out.println(
"Word with second highest PMI with Cloud : " + highestCloudPMI2.getLeftElement().getRightElement()
+ " with value : " + highestCloudPMI2.getRightElement().get());
System.out.println(
"Word with third highest PMI with Cloud : " + highestCloudPMI3.getLeftElement().getRightElement()
+ " with value : " + highestCloudPMI3.getRightElement().get());
System.out.println("Word with highest PMI with Love : " + highestLovePMI.getLeftElement().getRightElement()
+ " with value : " + highestLovePMI.getRightElement().get());
System.out.println(
"Word with second highest PMI with Love : " + highestLovePMI2.getLeftElement().getRightElement()
+ " with value : " + highestLovePMI2.getRightElement().get());
System.out.println(
"Word with third highest PMI with Love : " + highestLovePMI3.getLeftElement().getRightElement()
+ " with value : " + highestLovePMI3.getRightElement().get());
}
From source file:fr.inria.atlanmod.kyanos.benchmarks.MorsaTraverser.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input Kyanos resource directory"); inputOpt.setArgs(1);//from w w w . j a va 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.createURI("morsa://" + commandLine.getOptionValue(IN)); Class<?> inClazz = MorsaTraverser.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put("morsa", new MorsaResourceFactoryImpl(new MongoDBMorsaBackendFactory())); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); loadOpts.put(IMorsaResource.OPTION_SERVER_URI, "localhost"); loadOpts.put(IMorsaResource.OPTION_MAX_SAVE_CACHE_SIZE, 30000); loadOpts.put(IMorsaResource.OPTION_DEMAND_LOAD, false); // loadOpts.put(IMorsaResource.OPTION_CACHE_POLICY, FIFOEObjectCachePolicy.class.getName()); // loadOpts.put(IMorsaResource.OPTION_MAX_CACHE_SIZE, 30000); // loadOpts.put(IMorsaResource.OPTION_CACHE_FLUSH_FACTOR, 0.3f); // loadOpts.put(IMorsaResource.OPTION_DEMAND_LOAD_STRATEGY, IMorsaResource.OPTION_SINGLE_LOAD_STRATEGY); // loadOpts.put(IMorsaResource.OPTION_DEMAND_LOAD, true); 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))); } 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:fr.inria.atlanmod.kyanos.benchmarks.CdoCreator.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input file"); inputOpt.setArgs(1);//from ww w . j av a 2 s . c o m inputOpt.setRequired(true); Option outputOpt = OptionBuilder.create(OUT); outputOpt.setArgName("OUTPUT"); outputOpt.setDescription("Output directory"); outputOpt.setArgs(1); outputOpt.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(outputOpt); options.addOption(inClassOpt); options.addOption(repoOpt); CommandLineParser parser = new PosixParser(); try { CommandLine commandLine = parser.parse(options, args); URI sourceUri = URI.createFileURI(commandLine.getOptionValue(IN)); String outputDir = commandLine.getOptionValue(OUT); String repositoryName = commandLine.getOptionValue(REPO_NAME); Class<?> inClazz = CdoCreator.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 sourceResource = resourceSet.createResource(sourceUri); Map<String, Object> loadOpts = new HashMap<String, Object>(); if ("zxmi".equals(sourceUri.fileExtension())) { loadOpts.put(XMIResource.OPTION_ZIP, Boolean.TRUE); } Runtime.getRuntime().gc(); long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); LOG.log(Level.INFO, MessageFormat.format("Used memory before loading: {0}", MessageUtil.byteCountToDisplaySize(initialUsedMemory))); LOG.log(Level.INFO, "Loading source resource"); sourceResource.load(loadOpts); LOG.log(Level.INFO, "Source resource loaded"); Runtime.getRuntime().gc(); long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); LOG.log(Level.INFO, MessageFormat.format("Used memory after loading: {0}", MessageUtil.byteCountToDisplaySize(finalUsedMemory))); LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}", MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory))); EmbeddedCDOServer server = new EmbeddedCDOServer(outputDir, repositoryName); try { server.run(); CDOSession session = server.openSession(); CDOTransaction transaction = session.openTransaction(); transaction.getRootResource().getContents().clear(); LOG.log(Level.INFO, "Start moving elements"); transaction.getRootResource().getContents().addAll(sourceResource.getContents()); LOG.log(Level.INFO, "End moving elements"); LOG.log(Level.INFO, "Commiting"); transaction.commit(); LOG.log(Level.INFO, "Commit done"); 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()); } }