List of usage examples for java.util Arrays toString
public static String toString(Object[] a)
From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapCreator.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 w ww . java 2s . co 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); options.addOption(inputOpt); options.addOption(outputOpt); options.addOption(inClassOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME, new MapPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI sourceUri = URI.createFileURI(commandLine.getOptionValue(IN)); URI targetUri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(OUT))); Class<?> inClazz = KyanosMapCreator.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()); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME, PersistentResourceFactory.eINSTANCE); 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))); Resource targetResource = resourceSet.createResource(targetUri); Map<String, Object> saveOpts = new HashMap<String, Object>(); List<StoreOption> storeOptions = new ArrayList<StoreOption>(); storeOptions.add(MapResourceOptions.EStoreMapOption.AUTOCOMMIT); saveOpts.put(MapResourceOptions.STORE_OPTIONS, storeOptions); targetResource.save(saveOpts); LOG.log(Level.INFO, "Start moving elements"); targetResource.getContents().clear(); targetResource.getContents().addAll(sourceResource.getContents()); LOG.log(Level.INFO, "End moving elements"); LOG.log(Level.INFO, "Start saving"); targetResource.save(saveOpts); LOG.log(Level.INFO, "Saved"); if (targetResource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) targetResource); } else { targetResource.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()); e.printStackTrace(); } }
From source file:eqtlmappingpipeline.util.ModuleEqtlNeutrophilReplication.java
/** * @param args the command line arguments *///from ww w . j a v a2s. com public static void main(String[] args) throws IOException, LdCalculatorException { System.out.println(HEADER); System.out.println(); System.out.flush(); //flush to make sure header is before errors try { Thread.sleep(25); //Allows flush to complete } catch (InterruptedException ex) { } CommandLineParser parser = new PosixParser(); final CommandLine commandLine; try { commandLine = parser.parse(OPTIONS, args, true); } catch (ParseException ex) { System.err.println("Invalid command line arguments: " + ex.getMessage()); System.err.println(); new HelpFormatter().printHelp(" ", OPTIONS); System.exit(1); return; } final String[] genotypesBasePaths = commandLine.getOptionValues("g"); final RandomAccessGenotypeDataReaderFormats genotypeDataType; final String replicationQtlFilePath = commandLine.getOptionValue("e"); final String interactionQtlFilePath = commandLine.getOptionValue("i"); final String outputFilePath = commandLine.getOptionValue("o"); final double ldCutoff = Double.parseDouble(commandLine.getOptionValue("ld")); final int window = Integer.parseInt(commandLine.getOptionValue("w")); System.out.println("Genotype: " + Arrays.toString(genotypesBasePaths)); System.out.println("Interaction file: " + interactionQtlFilePath); System.out.println("Replication file: " + replicationQtlFilePath); System.out.println("Output: " + outputFilePath); System.out.println("LD: " + ldCutoff); System.out.println("Window: " + window); try { if (commandLine.hasOption("G")) { genotypeDataType = RandomAccessGenotypeDataReaderFormats .valueOf(commandLine.getOptionValue("G").toUpperCase()); } else { if (genotypesBasePaths[0].endsWith(".vcf")) { System.err.println( "Only vcf.gz is supported. Please see manual on how to do create a vcf.gz file."); System.exit(1); return; } try { genotypeDataType = RandomAccessGenotypeDataReaderFormats .matchFormatToPath(genotypesBasePaths[0]); } catch (GenotypeDataException e) { System.err .println("Unable to determine input 1 type based on specified path. Please specify -G"); System.exit(1); return; } } } catch (IllegalArgumentException e) { System.err.println("Error parsing --genotypesFormat \"" + commandLine.getOptionValue("G") + "\" is not a valid input data format"); System.exit(1); return; } final RandomAccessGenotypeData genotypeData; try { genotypeData = genotypeDataType.createFilteredGenotypeData(genotypesBasePaths, 100, null, null, null, 0.8); } catch (TabixFileNotFoundException e) { LOGGER.fatal("Tabix file not found for input data at: " + e.getPath() + "\n" + "Please see README on how to create a tabix file"); System.exit(1); return; } catch (IOException e) { LOGGER.fatal("Error reading input data: " + e.getMessage(), e); System.exit(1); return; } catch (IncompatibleMultiPartGenotypeDataException e) { LOGGER.fatal("Error combining the impute genotype data files: " + e.getMessage(), e); System.exit(1); return; } catch (GenotypeDataException e) { LOGGER.fatal("Error reading input data: " + e.getMessage(), e); System.exit(1); return; } ChrPosTreeMap<ArrayList<ReplicationQtl>> replicationQtls = new ChrPosTreeMap<>(); CSVReader replicationQtlReader = new CSVReader(new FileReader(replicationQtlFilePath), '\t'); replicationQtlReader.readNext();//skip header String[] replicationLine; while ((replicationLine = replicationQtlReader.readNext()) != null) { try { GeneticVariant variant = genotypeData.getSnpVariantByPos(replicationLine[REPLICATION_SNP_CHR_COL], Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL])); if (variant == null) { continue; } ReplicationQtl replicationQtl = new ReplicationQtl(replicationLine[REPLICATION_SNP_CHR_COL], Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL]), replicationLine[REPLICATION_GENE_COL], Double.parseDouble(replicationLine[REPLICATION_BETA_COL]), variant.getAlternativeAlleles().get(0).getAlleleAsString()); ArrayList<ReplicationQtl> posReplicationQtls = replicationQtls.get(replicationQtl.getChr(), replicationQtl.getPos()); if (posReplicationQtls == null) { posReplicationQtls = new ArrayList<>(); replicationQtls.put(replicationQtl.getChr(), replicationQtl.getPos(), posReplicationQtls); } posReplicationQtls.add(replicationQtl); } catch (Exception e) { System.out.println(Arrays.toString(replicationLine)); throw e; } } int interactionSnpNotInGenotypeData = 0; int noReplicationQtlsInWindow = 0; int noReplicationQtlsInLd = 0; int multipleReplicationQtlsInLd = 0; int replicationTopSnpNotInGenotypeData = 0; final CSVWriter outputWriter = new CSVWriter(new FileWriter(new File(outputFilePath)), '\t', '\0'); final String[] outputLine = new String[14]; int c = 0; outputLine[c++] = "Chr"; outputLine[c++] = "Pos"; outputLine[c++] = "SNP"; outputLine[c++] = "Gene"; outputLine[c++] = "Module"; outputLine[c++] = "DiscoveryZ"; outputLine[c++] = "ReplicationZ"; outputLine[c++] = "DiscoveryZCorrected"; outputLine[c++] = "ReplicationZCorrected"; outputLine[c++] = "DiscoveryAlleleAssessed"; outputLine[c++] = "ReplicationAlleleAssessed"; outputLine[c++] = "bestLd"; outputLine[c++] = "bestLd_dist"; outputLine[c++] = "nextLd"; outputWriter.writeNext(outputLine); HashSet<String> notFound = new HashSet<>(); CSVReader interactionQtlReader = new CSVReader(new FileReader(interactionQtlFilePath), '\t'); interactionQtlReader.readNext();//skip header String[] interactionQtlLine; while ((interactionQtlLine = interactionQtlReader.readNext()) != null) { String snp = interactionQtlLine[1]; String chr = interactionQtlLine[2]; int pos = Integer.parseInt(interactionQtlLine[3]); String gene = interactionQtlLine[4]; String alleleAssessed = interactionQtlLine[9]; String module = interactionQtlLine[12]; double discoveryZ = Double.parseDouble(interactionQtlLine[10]); GeneticVariant interactionQtlVariant = genotypeData.getSnpVariantByPos(chr, pos); if (interactionQtlVariant == null) { System.err.println("Interaction QTL SNP not found in genotype data: " + chr + ":" + pos); ++interactionSnpNotInGenotypeData; continue; } ReplicationQtl bestMatch = null; double bestMatchR2 = Double.NaN; Ld bestMatchLd = null; double nextBestR2 = Double.NaN; ArrayList<ReplicationQtl> sameSnpQtls = replicationQtls.get(chr, pos); if (sameSnpQtls != null) { for (ReplicationQtl sameSnpQtl : sameSnpQtls) { if (sameSnpQtl.getGene().equals(gene)) { bestMatch = sameSnpQtl; bestMatchR2 = 1; } } } NavigableMap<Integer, ArrayList<ReplicationQtl>> potentionalReplicationQtls = replicationQtls .getChrRange(chr, pos - window, true, pos + window, true); for (ArrayList<ReplicationQtl> potentialReplicationQtls : potentionalReplicationQtls.values()) { for (ReplicationQtl potentialReplicationQtl : potentialReplicationQtls) { if (!potentialReplicationQtl.getGene().equals(gene)) { continue; } GeneticVariant potentialReplicationQtlVariant = genotypeData .getSnpVariantByPos(potentialReplicationQtl.getChr(), potentialReplicationQtl.getPos()); if (potentialReplicationQtlVariant == null) { notFound.add(potentialReplicationQtl.getChr() + ":" + potentialReplicationQtl.getPos()); ++replicationTopSnpNotInGenotypeData; continue; } Ld ld = interactionQtlVariant.calculateLd(potentialReplicationQtlVariant); double r2 = ld.getR2(); if (r2 > 1) { r2 = 1; } if (bestMatch == null) { bestMatch = potentialReplicationQtl; bestMatchR2 = r2; bestMatchLd = ld; } else if (r2 > bestMatchR2) { bestMatch = potentialReplicationQtl; nextBestR2 = bestMatchR2; bestMatchR2 = r2; bestMatchLd = ld; } } } double replicationZ = Double.NaN; double replicationZCorrected = Double.NaN; double discoveryZCorrected = Double.NaN; String replicationAlleleAssessed = null; if (bestMatch != null) { replicationZ = bestMatch.getBeta(); replicationAlleleAssessed = bestMatch.getAssessedAllele(); if (pos != bestMatch.getPos()) { String commonHap = null; double commonHapFreq = -1; for (Map.Entry<String, Double> hapFreq : bestMatchLd.getHaplotypesFreq().entrySet()) { double f = hapFreq.getValue(); if (f > commonHapFreq) { commonHapFreq = f; commonHap = hapFreq.getKey(); } } String[] commonHapAlleles = StringUtils.split(commonHap, '/'); discoveryZCorrected = commonHapAlleles[0].equals(alleleAssessed) ? discoveryZ : discoveryZ * -1; replicationZCorrected = commonHapAlleles[1].equals(replicationAlleleAssessed) ? replicationZ : replicationZ * -1; } else { discoveryZCorrected = discoveryZ; replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) ? replicationZ : replicationZ * -1; } } c = 0; outputLine[c++] = chr; outputLine[c++] = String.valueOf(pos); outputLine[c++] = snp; outputLine[c++] = gene; outputLine[c++] = module; outputLine[c++] = String.valueOf(discoveryZ); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZ); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(discoveryZCorrected); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZCorrected); outputLine[c++] = alleleAssessed; outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.getAssessedAllele()); outputLine[c++] = String.valueOf(bestMatchR2); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(Math.abs(pos - bestMatch.getPos())); outputLine[c++] = String.valueOf(nextBestR2); outputWriter.writeNext(outputLine); } outputWriter.close(); for (String e : notFound) { System.err.println("Not found: " + e); } System.out.println("interactionSnpNotInGenotypeData: " + interactionSnpNotInGenotypeData); System.out.println("noReplicationQtlsInWindow: " + noReplicationQtlsInWindow); System.out.println("noReplicationQtlsInLd: " + noReplicationQtlsInLd); System.out.println("multipleReplicationQtlsInLd: " + multipleReplicationQtlsInLd); System.out.println("replicationTopSnpNotInGenotypeData: " + replicationTopSnpNotInGenotypeData); }
From source file:io.bfscan.clueweb12.MergeTermStatistics.java
/** * Dispatches command-line arguments to the tool via the <code>ToolRunner</code>. *//*ww w . ja v a 2 s .c o m*/ public static void main(String[] args) throws Exception { LOG.info("Running " + MergeTermStatistics.class.getCanonicalName() + " with args " + Arrays.toString(args)); ToolRunner.run(new MergeTermStatistics(), args); }
From source file:fr.inria.atlanmod.kyanos.benchmarks.ase2015.NeoEMFGraphQueryGetBranchStatements.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. ja va 2 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 optFileOpt = OptionBuilder.create(OPTIONS_FILE); optFileOpt.setArgName("FILE"); optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource"); optFileOpt.setArgs(1); options.addOption(inputOpt); options.addOption(inClassOpt); options.addOption(optFileOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, new BlueprintsPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = NeoEMFGraphQueryGetBranchStatements.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap() .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); if (commandLine.hasOption(OPTIONS_FILE)) { Properties properties = new Properties(); properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE)))); for (final Entry<Object, Object> entry : properties.entrySet()) { loadOpts.put((String) entry.getKey(), (String) entry.getValue()); } } // Add the LoadedObjectCounter store List<StoreOption> storeOptions = new ArrayList<StoreOption>(); // storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING); storeOptions.add(BlueprintsResourceOptions.EStoreGraphOption.AUTOCOMMIT); loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions); resource.load(loadOpts); { Runtime.getRuntime().gc(); long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}", MessageUtil.byteCountToDisplaySize(initialUsedMemory))); LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); Set<TextElement> list = ASE2015JavaQueries.getCommentsTagContent(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); Runtime.getRuntime().gc(); long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}", MessageUtil.byteCountToDisplaySize(finalUsedMemory))); LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}", MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { 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:deck36.storm.plan9.php.RecordBreakerBadgeTopology.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"); // Create Stream from RabbitMQ messages // bind new queue with name of the topology // to the main plan9 exchange (from properties config) // consuming only CBT-related events by using the rounting key 'cbt.#' String badgeName = RecordBreakerBadgeTopology.class.getSimpleName(); String rabbitQueueName = badgeName; // use topology class name as name for the queue String rabbitExchangeName = JsonPath.read(conf, "$.deck36_storm.RecordBreakerBolt.rabbitmq.exchange"); String rabbitRoutingKey = JsonPath.read(conf, "$.deck36_storm.RecordBreakerBolt.rabbitmq.routing_key"); // Get JSON deserialization scheme Scheme rabbitScheme = new SimpleJSONScheme(); // Setup a Declarator to configure exchange/queue/routing key RabbitMQDeclarator rabbitDeclarator = new RabbitMQDeclarator(rabbitExchangeName, rabbitQueueName, rabbitRoutingKey); // Create Configuration for the Spout ConnectionConfig connectionConfig = new ConnectionConfig( (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.host"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.port"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.user"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.pass"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.vhost"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.heartbeat")); ConsumerConfig spoutConfig = new ConsumerConfigBuilder().connection(connectionConfig).queue(rabbitQueueName) .prefetch((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")).requeueOnFail() .build(); // add global parameters to topology config - the RabbitMQSpout will read them from there conf.putAll(spoutConfig.asMap()); // For production, set the spout pending value to the same value as the RabbitMQ pre-fetch // see: https://github.com/ppat/storm-rabbitmq/blob/master/README.md if ("prod".equals(env)) { conf.put(Config.TOPOLOGY_MAX_SPOUT_PENDING, (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")); } // Add RabbitMQ spout to topology builder.setSpout("incoming", new RabbitMQSpout(rabbitScheme, rabbitDeclarator), parallelism_hint) .setNumTasks((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.spout_tasks")); // construct command to invoke the external bolt implementation ArrayList<String> command = new ArrayList(15); // Add main execution program (php, hhvm, zend, ..) and parameters command.add((String) JsonPath.read(conf, "$.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, "$.deck36_storm.php.main_params")); // create command to execute the RecordBreakerBolt ArrayList<String> recordBreakerBoltCommand = new ArrayList<String>(command); // Add main route to be invoked and its parameters recordBreakerBoltCommand.add((String) JsonPath.read(conf, "$.deck36_storm.RecordBreakerBolt.main")); List boltParams = (List<String>) JsonPath.read(conf, "$.deck36_storm.RecordBreakerBolt.params"); if (boltParams != null) recordBreakerBoltCommand.addAll(boltParams); // create command to execute the RecordMasterBolt ArrayList<String> recordMasterBoltCommand = new ArrayList<String>(command); // Add main route to be invoked and its parameters recordMasterBoltCommand.add((String) JsonPath.read(conf, "$.deck36_storm.RecordMasterBolt.main")); boltParams = (List<String>) JsonPath.read(conf, "$.deck36_storm.RecordMasterBolt.params"); if (boltParams != null) recordMasterBoltCommand.addAll(boltParams); // Log the final commands log.info("Command to start bolt for RecordBreaker badge: " + Arrays.toString(recordBreakerBoltCommand.toArray())); log.info("Command to start bolt for RecordMaster badge: " + Arrays.toString(recordMasterBoltCommand.toArray())); // Add constructed external bolt command to topology using MultilangAdapterBolt // The RecordBreaker reads the incoming messages from the game application, i.e. the "incoming" spout builder.setBolt("record_breaker", new MultilangAdapterBolt(recordBreakerBoltCommand, "badge"), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("incoming"); // The RecordMaster reads the badge messages generated by the RecordBreakerBolt builder.setBolt("record_master", new MultilangAdapterBolt(recordMasterBoltCommand, "badge"), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("record_breaker"); // the RabbitMQ router bolt can read messages from both, RecordBreakerBolt and RecordMasterBolt, // and forward those messages to the broker builder.setBolt("rabbitmq_router", new Plan9RabbitMQRouterBolt( (String) JsonPath.read(conf, "$.deck36_storm.RecordBreakerBolt.rabbitmq.target_exchange"), "RecordBreakerMaster" // RabbitMQ routing key ), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("record_breaker") .shuffleGrouping("record_master"); 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:de.upb.timok.run.GenericSmacPipeline.java
/** * @param args/*from ww w . jav a2 s. c om*/ * @throws IOException * @throws InterruptedException */ public static void main(String[] args) throws IOException, InterruptedException { final GenericSmacPipeline sp = new GenericSmacPipeline(); final JCommander jc = new JCommander(sp); System.out.println(Arrays.toString(args)); if (args.length < 4) { logger.error( "Please provide the following inputs: [inputFile] 1 1 [Random Seed] [Parameter Arguments..]"); jc.usage(); System.exit(1); } jc.parse(args); sp.dataString = args[0]; logger.info("Running Generic Pipeline with args" + Arrays.toString(args)); MasterSeed.setSeed(Long.parseLong(args[3])); // try { final PdttaExperimentResult result = sp.run(); final Path resultPath = Paths.get("result.csv"); if (!Files.exists(resultPath)) { Files.createFile(resultPath); } try (BufferedWriter bw = Files.newBufferedWriter(resultPath, StandardCharsets.UTF_8, StandardOpenOption.APPEND)) { bw.append(Arrays.toString(args) + "; " + result.toCsvString()); bw.append('\n'); } System.exit(0); // } catch (Exception e) { // logger.error("Unexpected exception with parameters" + Arrays.toString(args), e); // throw e; // } }
From source file:Gen.java
public static void main(String[] args) throws Exception { try {/*from ww w. j a v a2 s. com*/ File[] files = null; if (System.getProperty("dir") != null && !System.getProperty("dir").equals("")) { files = new File(System.getProperty("dir")).listFiles(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toUpperCase().endsWith(".XML"); }; }); } else { String fileName = System.getProperty("file") != null && !System.getProperty("file").equals("") ? System.getProperty("file") : "rjmap.xml"; files = new File[] { new File(fileName) }; } log.info("files : " + Arrays.toString(files)); if (files == null || files.length == 0) { log.info("no files to parse"); System.exit(0); } boolean formatsource = true; if (System.getProperty("formatsource") != null && !System.getProperty("formatsource").equals("") && System.getProperty("formatsource").equalsIgnoreCase("false")) { formatsource = false; } GEN_ROOT = System.getProperty("outputdir"); if (GEN_ROOT == null || GEN_ROOT.equals("")) { GEN_ROOT = new File(files[0].getAbsolutePath()).getParent() + FILE_SEPARATOR + "distrib"; } GEN_ROOT = new File(GEN_ROOT).getAbsolutePath().replace('\\', '/'); if (GEN_ROOT.endsWith("/")) GEN_ROOT = GEN_ROOT.substring(0, GEN_ROOT.length() - 1); System.out.println("GEN ROOT:" + GEN_ROOT); MAPPING_JAR_NAME = System.getProperty("mappingjar") != null && !System.getProperty("mappingjar").equals("") ? System.getProperty("mappingjar") : "mapping.jar"; if (!MAPPING_JAR_NAME.endsWith(".jar")) MAPPING_JAR_NAME += ".jar"; GEN_ROOT_SRC = GEN_ROOT + FILE_SEPARATOR + "src"; GEN_ROOT_LIB = GEN_ROOT + FILE_SEPARATOR + ""; DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance(); domFactory.setNamespaceAware(true); domFactory.setValidating(false); DocumentBuilder documentBuilder = domFactory.newDocumentBuilder(); for (int f = 0; f < files.length; ++f) { log.info("parsing file : " + files[f]); Document document = documentBuilder.parse(files[f]); Vector<Node> initNodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "scripts"), "initScript", initNodes); for (int i = 0; i < initNodes.size(); ++i) { NamedNodeMap attrs = initNodes.elementAt(i).getAttributes(); boolean embed = attrs.getNamedItem("embed") != null && attrs.getNamedItem("embed").getNodeValue().equalsIgnoreCase("true"); StringBuffer vbuffer = new StringBuffer(); if (attrs.getNamedItem("inline") != null) { vbuffer.append(attrs.getNamedItem("inline").getNodeValue()); vbuffer.append('\n'); } else { String fname = attrs.getNamedItem("name").getNodeValue(); if (!fname.startsWith("\\") && !fname.startsWith("/") && fname.toCharArray()[1] != ':') { String path = files[f].getAbsolutePath(); path = path.substring(0, path.lastIndexOf(FILE_SEPARATOR)); fname = new File(path + FILE_SEPARATOR + fname).getCanonicalPath(); } vbuffer.append(Utils.getFileAsStringBuffer(fname)); } initScriptBuffer.append(vbuffer); if (embed) embedScriptBuffer.append(vbuffer); } Vector<Node> packageInitNodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "scripts"), "packageScript", packageInitNodes); for (int i = 0; i < packageInitNodes.size(); ++i) { NamedNodeMap attrs = packageInitNodes.elementAt(i).getAttributes(); String packageName = attrs.getNamedItem("package").getNodeValue(); if (packageName.equals("")) packageName = "rGlobalEnv"; if (!packageName.endsWith("Function")) packageName += "Function"; if (packageEmbedScriptHashMap.get(packageName) == null) { packageEmbedScriptHashMap.put(packageName, new StringBuffer()); } StringBuffer vbuffer = packageEmbedScriptHashMap.get(packageName); // if (!packageName.equals("rGlobalEnvFunction")) { // vbuffer.append("library("+packageName.substring(0,packageName.lastIndexOf("Function"))+")\n"); // } if (attrs.getNamedItem("inline") != null) { vbuffer.append(attrs.getNamedItem("inline").getNodeValue() + "\n"); initScriptBuffer.append(attrs.getNamedItem("inline").getNodeValue() + "\n"); } else { String fname = attrs.getNamedItem("name").getNodeValue(); if (!fname.startsWith("\\") && !fname.startsWith("/") && fname.toCharArray()[1] != ':') { String path = files[f].getAbsolutePath(); path = path.substring(0, path.lastIndexOf(FILE_SEPARATOR)); fname = new File(path + FILE_SEPARATOR + fname).getCanonicalPath(); } StringBuffer fileBuffer = Utils.getFileAsStringBuffer(fname); vbuffer.append(fileBuffer); initScriptBuffer.append(fileBuffer); } } Vector<Node> functionsNodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "functions"), "function", functionsNodes); for (int i = 0; i < functionsNodes.size(); ++i) { NamedNodeMap attrs = functionsNodes.elementAt(i).getAttributes(); String functionName = attrs.getNamedItem("name").getNodeValue(); boolean forWeb = attrs.getNamedItem("forWeb") != null && attrs.getNamedItem("forWeb").getNodeValue().equalsIgnoreCase("true"); String signature = (attrs.getNamedItem("signature") == null ? "" : attrs.getNamedItem("signature").getNodeValue() + ","); String renameTo = (attrs.getNamedItem("renameTo") == null ? null : attrs.getNamedItem("renameTo").getNodeValue()); HashMap<String, FAttributes> sigMap = Globals._functionsToPublish.get(functionName); if (sigMap == null) { sigMap = new HashMap<String, FAttributes>(); Globals._functionsToPublish.put(functionName, sigMap); if (attrs.getNamedItem("returnType") == null) { _functionsVector.add(new String[] { functionName }); } else { _functionsVector.add( new String[] { functionName, attrs.getNamedItem("returnType").getNodeValue() }); } } sigMap.put(signature, new FAttributes(renameTo, forWeb)); if (forWeb) _webPublishingEnabled = true; } if (System.getProperty("targetjdk") != null && !System.getProperty("targetjdk").equals("") && System.getProperty("targetjdk").compareTo("1.5") < 0) { if (_webPublishingEnabled || (System.getProperty("ws.r.api") != null && System.getProperty("ws.r.api").equalsIgnoreCase("true"))) { log.info("be careful, web publishing disabled beacuse target JDK<1.5"); } _webPublishingEnabled = false; } else { if (System.getProperty("ws.r.api") == null || System.getProperty("ws.r.api").equals("") || !System.getProperty("ws.r.api").equalsIgnoreCase("false")) { _webPublishingEnabled = true; } if (_webPublishingEnabled && System.getProperty("java.version").compareTo("1.5") < 0) { log.info("be careful, web publishing disabled beacuse a JDK<1.5 is in use"); _webPublishingEnabled = false; } } Vector<Node> s4Nodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "s4classes"), "class", s4Nodes); if (s4Nodes.size() > 0) { String formalArgs = ""; String signature = ""; for (int i = 0; i < s4Nodes.size(); ++i) { NamedNodeMap attrs = s4Nodes.elementAt(i).getAttributes(); String s4Name = attrs.getNamedItem("name").getNodeValue(); formalArgs += "p" + i + (i == s4Nodes.size() - 1 ? "" : ","); signature += "'" + s4Name + "'" + (i == s4Nodes.size() - 1 ? "" : ","); } String genBeansScriptlet = "setGeneric('" + PUBLISH_S4_HEADER + "', function(" + formalArgs + ") standardGeneric('" + PUBLISH_S4_HEADER + "'));" + "setMethod('" + PUBLISH_S4_HEADER + "', signature(" + signature + ") , function(" + formalArgs + ") { })"; initScriptBuffer.append(genBeansScriptlet); _functionsVector.add(new String[] { PUBLISH_S4_HEADER, "numeric" }); } } if (!new File(GEN_ROOT_LIB).exists()) regenerateDir(GEN_ROOT_LIB); else { clean(GEN_ROOT_LIB, true); } for (int i = 0; i < rwebservicesScripts.length; ++i) DirectJNI.getInstance().getRServices().sourceFromResource(rwebservicesScripts[i]); String lastStatus = DirectJNI.getInstance().runR(new ExecutionUnit() { public void run(Rengine e) { DirectJNI.getInstance().toggleMarker(); DirectJNI.getInstance().sourceFromBuffer(initScriptBuffer.toString()); log.info(" init script status : " + DirectJNI.getInstance().cutStatusSinceMarker()); for (int i = 0; i < _functionsVector.size(); ++i) { String[] functionPair = _functionsVector.elementAt(i); log.info("dealing with : " + functionPair[0]); regenerateDir(GEN_ROOT_SRC); String createMapStr = "createMap("; boolean isGeneric = e.rniGetBoolArrayI( e.rniEval(e.rniParse("isGeneric(\"" + functionPair[0] + "\")", 1), 0))[0] == 1; log.info("is Generic : " + isGeneric); if (isGeneric) { createMapStr += functionPair[0]; } else { createMapStr += "\"" + functionPair[0] + "\""; } createMapStr += ", outputDirectory=\"" + GEN_ROOT_SRC .substring(0, GEN_ROOT_SRC.length() - "/src".length()).replace('\\', '/') + "\""; createMapStr += ", typeMode=\"robject\""; createMapStr += (functionPair.length == 1 || functionPair[1] == null || functionPair[1].trim().equals("") ? "" : ", S4DefaultTypedSig=TypedSignature(returnType=\"" + functionPair[1] + "\")"); createMapStr += ")"; log.info("------------------------------------------"); log.info("-- createMapStr=" + createMapStr); DirectJNI.getInstance().toggleMarker(); e.rniEval(e.rniParse(createMapStr, 1), 0); String createMapStatus = DirectJNI.getInstance().cutStatusSinceMarker(); log.info(" createMap status : " + createMapStatus); log.info("------------------------------------------"); deleteDir(GEN_ROOT_SRC + "/org/kchine/r/rserviceJms"); compile(GEN_ROOT_SRC); jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar", null); URL url = null; try { url = new URL( "jar:file:" + (GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar") .replace('\\', '/') + "!/"); } catch (Exception ex) { ex.printStackTrace(); } DirectJNI.generateMaps(url, true); } } }); log.info(lastStatus); log.info(DirectJNI._rPackageInterfacesHash); regenerateDir(GEN_ROOT_SRC); for (int i = 0; i < _functionsVector.size(); ++i) { unjar(GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar", GEN_ROOT_SRC); } regenerateRPackageClass(true); generateS4BeanRef(); if (formatsource) applyJalopy(GEN_ROOT_SRC); compile(GEN_ROOT_SRC); for (String k : DirectJNI._rPackageInterfacesHash.keySet()) { Rmic rmicTask = new Rmic(); rmicTask.setProject(_project); rmicTask.setTaskName("rmic_packages"); rmicTask.setClasspath(new Path(_project, GEN_ROOT_SRC)); rmicTask.setBase(new File(GEN_ROOT_SRC)); rmicTask.setClassname(k + "ImplRemote"); rmicTask.init(); rmicTask.execute(); } // DirectJNI._rPackageInterfacesHash=new HashMap<String, // Vector<Class<?>>>(); // DirectJNI._rPackageInterfacesHash.put("org.bioconductor.packages.rGlobalEnv.rGlobalEnvFunction",new // Vector<Class<?>>()); if (_webPublishingEnabled) { jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar", null); URL url = new URL( "jar:file:" + (GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar").replace('\\', '/') + "!/"); ClassLoader cl = new URLClassLoader(new URL[] { url }, Globals.class.getClassLoader()); for (String className : DirectJNI._rPackageInterfacesHash.keySet()) { if (cl.loadClass(className + "Web").getDeclaredMethods().length == 0) continue; log.info("######## " + className); WsGen wsgenTask = new WsGen(); wsgenTask.setProject(_project); wsgenTask.setTaskName("wsgen"); FileSet rjb_fileSet = new FileSet(); rjb_fileSet.setProject(_project); rjb_fileSet.setDir(new File(".")); rjb_fileSet.setIncludes("RJB.jar"); DirSet src_dirSet = new DirSet(); src_dirSet.setDir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/")); Path classPath = new Path(_project); classPath.addFileset(rjb_fileSet); classPath.addDirset(src_dirSet); wsgenTask.setClasspath(classPath); wsgenTask.setKeep(true); wsgenTask.setDestdir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/")); wsgenTask.setResourcedestdir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/")); wsgenTask.setSei(className + "Web"); wsgenTask.init(); wsgenTask.execute(); } new File(GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar").delete(); } embedRScripts(); HashMap<String, String> marker = new HashMap<String, String>(); marker.put("RJBMAPPINGJAR", "TRUE"); Properties props = new Properties(); props.put("PACKAGE_NAMES", PoolUtils.objectToHex(DirectJNI._packageNames)); props.put("S4BEANS_MAP", PoolUtils.objectToHex(DirectJNI._s4BeansMapping)); props.put("S4BEANS_REVERT_MAP", PoolUtils.objectToHex(DirectJNI._s4BeansMappingRevert)); props.put("FACTORIES_MAPPING", PoolUtils.objectToHex(DirectJNI._factoriesMapping)); props.put("S4BEANS_HASH", PoolUtils.objectToHex(DirectJNI._s4BeansHash)); props.put("R_PACKAGE_INTERFACES_HASH", PoolUtils.objectToHex(DirectJNI._rPackageInterfacesHash)); props.put("ABSTRACT_FACTORIES", PoolUtils.objectToHex(DirectJNI._abstractFactories)); new File(GEN_ROOT_SRC + "/" + "maps").mkdirs(); FileOutputStream fos = new FileOutputStream(GEN_ROOT_SRC + "/" + "maps/rjbmaps.xml"); props.storeToXML(fos, null); fos.close(); jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + MAPPING_JAR_NAME, marker); if (_webPublishingEnabled) genWeb(); DirectJNI._mappingClassLoader = null; } finally { System.exit(0); } }
From source file:fr.inria.atlanmod.kyanos.benchmarks.ase2015.NeoEMFGraphQueryGrabats09.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);//w ww . j a v a2 s . co m 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 optFileOpt = OptionBuilder.create(OPTIONS_FILE); optFileOpt.setArgName("FILE"); optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource"); optFileOpt.setArgs(1); options.addOption(inputOpt); options.addOption(inClassOpt); options.addOption(optFileOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, new BlueprintsPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = NeoEMFGraphQueryGrabats09.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap() .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); if (commandLine.hasOption(OPTIONS_FILE)) { Properties properties = new Properties(); properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE)))); for (final Entry<Object, Object> entry : properties.entrySet()) { loadOpts.put((String) entry.getKey(), (String) entry.getValue()); } } // Add the LoadedObjectCounter store List<StoreOption> storeOptions = new ArrayList<StoreOption>(); // storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING); storeOptions.add(BlueprintsResourceOptions.EStoreGraphOption.AUTOCOMMIT); loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions); resource.load(loadOpts); { Runtime.getRuntime().gc(); long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}", MessageUtil.byteCountToDisplaySize(initialUsedMemory))); LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); EList<ClassDeclaration> list = ASE2015JavaQueries.grabats09(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); Runtime.getRuntime().gc(); long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}", MessageUtil.byteCountToDisplaySize(finalUsedMemory))); LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}", MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { 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:fr.inria.atlanmod.kyanos.benchmarks.ase2015.NeoEMFMapQueryGrabats09.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 . jav a 2s . c o m*/ 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 optFileOpt = OptionBuilder.create(OPTIONS_FILE); optFileOpt.setArgName("FILE"); optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource"); optFileOpt.setArgs(1); options.addOption(inputOpt); options.addOption(inClassOpt); options.addOption(optFileOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME, new MapPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = NeoEMFMapQueryGrabats09.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); if (commandLine.hasOption(OPTIONS_FILE)) { Properties properties = new Properties(); properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE)))); for (final Entry<Object, Object> entry : properties.entrySet()) { loadOpts.put((String) entry.getKey(), (String) entry.getValue()); } } // Add the LoadedObjectCounter store List<StoreOption> storeOptions = new ArrayList<StoreOption>(); // storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING); storeOptions.add(MapResourceOptions.EStoreMapOption.AUTOCOMMIT); storeOptions.add(PersistentResourceOptions.EStoreOption.ESTRUCUTRALFEATURE_CACHING); storeOptions.add(PersistentResourceOptions.EStoreOption.IS_SET_CACHING); storeOptions.add(PersistentResourceOptions.EStoreOption.SIZE_CACHING); loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions); resource.load(loadOpts); { Runtime.getRuntime().gc(); long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}", MessageUtil.byteCountToDisplaySize(initialUsedMemory))); LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); EList<ClassDeclaration> list = ASE2015JavaQueries.grabats09(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); Runtime.getRuntime().gc(); long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}", MessageUtil.byteCountToDisplaySize(finalUsedMemory))); LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}", MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { 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:fr.inria.atlanmod.kyanos.benchmarks.ase2015.NeoEMFMapQueryGetBranchStatements.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 ww . j a v a 2s.co m*/ 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 optFileOpt = OptionBuilder.create(OPTIONS_FILE); optFileOpt.setArgName("FILE"); optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource"); optFileOpt.setArgs(1); options.addOption(inputOpt); options.addOption(inClassOpt); options.addOption(optFileOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME, new MapPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = NeoEMFMapQueryGetBranchStatements.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); if (commandLine.hasOption(OPTIONS_FILE)) { Properties properties = new Properties(); properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE)))); for (final Entry<Object, Object> entry : properties.entrySet()) { loadOpts.put((String) entry.getKey(), (String) entry.getValue()); } } // Add the LoadedObjectCounter store List<StoreOption> storeOptions = new ArrayList<StoreOption>(); // storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING); storeOptions.add(MapResourceOptions.EStoreMapOption.AUTOCOMMIT); storeOptions.add(PersistentResourceOptions.EStoreOption.ESTRUCUTRALFEATURE_CACHING); storeOptions.add(PersistentResourceOptions.EStoreOption.IS_SET_CACHING); storeOptions.add(PersistentResourceOptions.EStoreOption.SIZE_CACHING); loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions); resource.load(loadOpts); { Runtime.getRuntime().gc(); long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}", MessageUtil.byteCountToDisplaySize(initialUsedMemory))); LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); Set<TextElement> list = ASE2015JavaQueries.getCommentsTagContent(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); Runtime.getRuntime().gc(); long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}", MessageUtil.byteCountToDisplaySize(finalUsedMemory))); LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}", MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { 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()); } }