List of usage examples for java.util HashSet HashSet
public HashSet()
From source file:de.citec.csra.elancsv.parser.SimpleParser.java
public static void main(String[] args) throws IOException, ParseException { Options opts = new Options(); opts.addOption("file", true, "Tab-separated ELAN export file to load."); opts.addOption("tier", true, "Tier to analyze. Optional: Append ::num to interpret annotations numerically."); opts.addOption("format", true, "How to read information from the file name. %V -> participant, %A -> annoatator, %C -> condition, e.g. \"%V - %A\""); opts.addOption("help", false, "Print this help and exit"); CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(opts, args); if (cmd.hasOption("help")) { helpExit(opts, "where OPTION includes:"); }/*from w w w.ja va 2 s.c o m*/ String infile = cmd.getOptionValue("file"); if (infile == null) { helpExit(opts, "Error: no file given."); } String format = cmd.getOptionValue("format"); if (format == null) { helpExit(opts, "Error: no format given."); } String tier = cmd.getOptionValue("tier"); if (tier == null) { helpExit(opts, "Error: no tier given."); } // TODO count values in annotations (e.g. search all robot occurrences) String[] tn = tier.split("::"); boolean numeric = false; if (tn.length == 2 && tn[1].equals("num")) { numeric = true; tier = tn[0]; } format = "^" + format + "$"; format = format.replaceFirst("%V", "(?<V>.*?)"); format = format.replaceFirst("%A", "(?<A>.*?)"); format = format.replaceFirst("%C", "(?<C>.*?)"); Pattern pa = Pattern.compile(format); Map<String, Participant> participants = new HashMap<>(); BufferedReader br = new BufferedReader(new FileReader(infile)); String line; int lineno = 0; while ((line = br.readLine()) != null) { String[] parts = line.split("\t"); lineno++; if (parts.length < 5) { System.err.println("WARNING: line '" + lineno + "' too short '" + line + "'"); continue; } Annotation a = new Annotation(Long.valueOf(parts[ElanFormat.START.field]), Long.valueOf(parts[ElanFormat.STOP.field]), Long.valueOf(parts[ElanFormat.DURATION.field]), parts[ElanFormat.VALUE.field]); String tname = parts[ElanFormat.TIER.field]; String file = parts[ElanFormat.FILE.field].replaceAll(".eaf", ""); Matcher m = pa.matcher(file); String vp = file; String condition = "?"; String annotator = "?"; String participantID = vp; if (m.find()) { vp = m.group("V"); if (format.indexOf("<A>") > 0) { annotator = m.group("A"); } if (format.indexOf("<C>") > 0) { condition = m.group("C"); } } participantID = vp + ";" + annotator; if (!participants.containsKey(participantID)) { participants.put(participantID, new Participant(vp, condition, annotator)); } Participant p = participants.get(participantID); if (!p.tiers.containsKey(tname)) { p.tiers.put(tname, new Tier(tname)); } p.tiers.get(tname).annotations.add(a); } Map<String, Map<String, Number>> values = new HashMap<>(); Set<String> rownames = new HashSet<>(); String allCountKey = "c: all values"; String allDurationKey = "d: all values"; String allMeanKey = "m: all values"; for (Map.Entry<String, Participant> e : participants.entrySet()) { // System.out.println(e); Tier t = e.getValue().tiers.get(tier); String participantID = e.getKey(); if (!values.containsKey(participantID)) { values.put(participantID, new HashMap<String, Number>()); } Map<String, Number> row = values.get(participantID); //participant id if (t != null) { row.put(allCountKey, 0l); row.put(allDurationKey, 0l); row.put(allMeanKey, 0l); for (Annotation a : t.annotations) { long countAll = (long) row.get(allCountKey) + 1; long durationAll = (long) row.get(allDurationKey) + a.duration; long meanAll = durationAll / countAll; row.put(allCountKey, countAll); row.put(allDurationKey, durationAll); row.put(allMeanKey, meanAll); if (!numeric) { String countKey = "c: " + a.value; String durationKey = "d: " + a.value; String meanKey = "m: " + a.value; if (!row.containsKey(countKey)) { row.put(countKey, 0l); } if (!row.containsKey(durationKey)) { row.put(durationKey, 0l); } if (!row.containsKey(meanKey)) { row.put(meanKey, 0d); } long count = (long) row.get(countKey) + 1; long duration = (long) row.get(durationKey) + a.duration; double mean = duration * 1.0 / count; row.put(countKey, count); row.put(durationKey, duration); row.put(meanKey, mean); rownames.add(countKey); rownames.add(durationKey); rownames.add(meanKey); } else { String countKey = "c: " + t.name; String sumKey = "s: " + t.name; String meanKey = "m: " + t.name; if (!row.containsKey(countKey)) { row.put(countKey, 0l); } if (!row.containsKey(sumKey)) { row.put(sumKey, 0d); } if (!row.containsKey(meanKey)) { row.put(meanKey, 0d); } double d = 0; try { d = Double.valueOf(a.value); } catch (NumberFormatException ex) { } long count = (long) row.get(countKey) + 1; double sum = (double) row.get(sumKey) + d; double mean = sum / count; row.put(countKey, count); row.put(sumKey, sum); row.put(meanKey, mean); rownames.add(countKey); rownames.add(sumKey); rownames.add(meanKey); } } } } ArrayList<String> list = new ArrayList(rownames); Collections.sort(list); StringBuilder header = new StringBuilder("ID;Annotator;"); header.append(allCountKey); header.append(";"); header.append(allDurationKey); header.append(";"); header.append(allMeanKey); header.append(";"); for (String l : list) { header.append(l); header.append(";"); } System.out.println(header); for (Map.Entry<String, Map<String, Number>> e : values.entrySet()) { StringBuilder row = new StringBuilder(e.getKey()); row.append(";"); if (e.getValue().containsKey(allCountKey)) { row.append(e.getValue().get(allCountKey)); } else { row.append("0"); } row.append(";"); if (e.getValue().containsKey(allDurationKey)) { row.append(e.getValue().get(allDurationKey)); } else { row.append("0"); } row.append(";"); if (e.getValue().containsKey(allMeanKey)) { row.append(e.getValue().get(allMeanKey)); } else { row.append("0"); } row.append(";"); for (String l : list) { if (e.getValue().containsKey(l)) { row.append(e.getValue().get(l)); } else { row.append("0"); } row.append(";"); } System.out.println(row); } }
From source file:com.lightboxtechnologies.spectrum.SequenceFileExport.java
public static void main(String[] args) throws Exception { final Configuration conf = new Configuration(); final String[] otherArgs = new GenericOptionsParser(conf, args).getRemainingArgs(); String imageID;/*from w ww .ja v a 2 s.com*/ String outpath; String friendlyname; final Set<String> exts = new HashSet<String>(); if ("-f".equals(otherArgs[0])) { if (otherArgs.length != 4) { die(); } // load extensions from file final Path extpath = new Path(otherArgs[1]); InputStream in = null; try { in = extpath.getFileSystem(conf).open(extpath); Reader r = null; try { r = new InputStreamReader(in); BufferedReader br = null; try { br = new BufferedReader(r); String line; while ((line = br.readLine()) != null) { exts.add(line.trim().toLowerCase()); } br.close(); } finally { IOUtils.closeQuietly(br); } r.close(); } finally { IOUtils.closeQuietly(r); } in.close(); } finally { IOUtils.closeQuietly(in); } imageID = otherArgs[2]; friendlyname = otherArgs[3]; outpath = otherArgs[4]; } else { if (otherArgs.length < 3) { die(); } // read extensions from trailing args imageID = otherArgs[0]; friendlyname = otherArgs[1]; outpath = otherArgs[2]; // lowercase all file extensions for (int i = 2; i < otherArgs.length; ++i) { exts.add(otherArgs[i].toLowerCase()); } } conf.setStrings("extensions", exts.toArray(new String[exts.size()])); final Job job = SKJobFactory.createJobFromConf(imageID, friendlyname, "SequenceFileExport", conf); job.setJarByClass(SequenceFileExport.class); job.setMapperClass(SequenceFileExportMapper.class); job.setNumReduceTasks(0); job.setOutputKeyClass(BytesWritable.class); job.setOutputValueClass(MapWritable.class); job.setInputFormatClass(FsEntryHBaseInputFormat.class); FsEntryHBaseInputFormat.setupJob(job, imageID); job.setOutputFormatClass(SequenceFileOutputFormat.class); SequenceFileOutputFormat.setOutputCompressionType(job, SequenceFile.CompressionType.BLOCK); FileOutputFormat.setOutputPath(job, new Path(outpath)); System.exit(job.waitForCompletion(true) ? 0 : 1); }
From source file:com.ibm.zurich.Main.java
public static void main(String[] args) throws NoSuchAlgorithmException, IOException { Option help = new Option(HELP, "print this message"); Option version = new Option(VERSION, "print the version information"); Options options = new Options(); Option useCurve = Option.builder(USECURVE).hasArg().argName("curve") .desc("Specify the BN Curve. Options: " + curveOptions()).build(); Option isskeygen = Option.builder(IKEYGEN).numberOfArgs(3).argName("ipk><isk><RL") .desc("Generate Issuer key pair and empty revocation list and store it in files").build(); Option join1 = Option.builder(JOIN1).numberOfArgs(3).argName("ipk><authsk><msg1") .desc("Create an authenticator secret key and perform the first step of the join protocol").build(); Option join2 = Option.builder(JOIN2).numberOfArgs(4).argName("ipk><isk><msg1><msg2") .desc("Complete the join protocol").build(); Option verify = Option.builder(VERIFY).numberOfArgs(5).argName("ipk><sig><krd><appId><RL") .desc("Verify a signature").build(); Option sign = Option.builder(SIGN).numberOfArgs(6).argName("ipk><authsk><msg2><appId><krd><sig") .desc("create a signature").build(); options.addOption(help);/*from w ww . j ava 2 s. co m*/ options.addOption(version); options.addOption(useCurve); options.addOption(isskeygen); options.addOption(sign); options.addOption(verify); options.addOption(join1); options.addOption(join2); HelpFormatter formatter = new HelpFormatter(); CommandLineParser parser = new DefaultParser(); //FIXME Choose a proper instantiation of SecureRandom depending on the platform SecureRandom random = new SecureRandom(); Base64.Encoder encoder = Base64.getUrlEncoder(); Base64.Decoder decoder = Base64.getUrlDecoder(); try { CommandLine line = parser.parse(options, args); BNCurveInstantiation instantiation = null; BNCurve curve = null; if (line.hasOption(HELP) || line.getOptions().length == 0) { formatter.printHelp(USAGE, options); } else if (line.hasOption(VERSION)) { System.out.println("Version " + Main.class.getPackage().getImplementationVersion()); } else if (line.hasOption(USECURVE)) { instantiation = BNCurveInstantiation.valueOf(line.getOptionValue(USECURVE)); curve = new BNCurve(instantiation); } else { System.out.println("Specify the curve to use."); return; } if (line.hasOption(IKEYGEN)) { String[] optionValues = line.getOptionValues(IKEYGEN); // Create secret key IssuerSecretKey sk = Issuer.createIssuerKey(curve, random); // Store pk writeToFile((new IssuerPublicKey(curve, sk, random)).toJSON(curve), optionValues[0]); // Store sk writeToFile(sk.toJson(curve), optionValues[1]); // Create empty revocation list and store HashSet<BigInteger> rl = new HashSet<BigInteger>(); writeToFile(Verifier.revocationListToJson(rl, curve), optionValues[2]); } else if (line.hasOption(SIGN)) { //("ipk><authsk><msg2><appId><krd><sig") String[] optionValues = line.getOptionValues(SIGN); IssuerPublicKey ipk = new IssuerPublicKey(curve, readStringFromFile(optionValues[0])); BigInteger authsk = curve.bigIntegerFromB(decoder.decode(readFromFile(optionValues[1]))); JoinMessage2 msg2 = new JoinMessage2(curve, readStringFromFile(optionValues[2])); // setup a new authenticator Authenticator auth = new Authenticator(curve, ipk, authsk); auth.EcDaaJoin1(curve.getRandomModOrder(random)); if (auth.EcDaaJoin2(msg2)) { EcDaaSignature sig = auth.EcDaaSign(optionValues[3]); // Write krd to file writeToFile(sig.krd, optionValues[4]); // Write signature to file writeToFile(sig.encode(curve), optionValues[5]); System.out.println("Signature written to " + optionValues[5]); } else { System.out.println("JoinMsg2 invalid"); } } else if (line.hasOption(VERIFY)) { Verifier ver = new Verifier(curve); String[] optionValues = line.getOptionValues(VERIFY); String pkFile = optionValues[0]; String sigFile = optionValues[1]; String krdFile = optionValues[2]; String appId = optionValues[3]; String rlPath = optionValues[4]; byte[] krd = Files.readAllBytes(Paths.get(krdFile)); IssuerPublicKey pk = new IssuerPublicKey(curve, readStringFromFile(pkFile)); EcDaaSignature sig = new EcDaaSignature(Files.readAllBytes(Paths.get(sigFile)), krd, curve); boolean valid = ver.verify(sig, appId, pk, Verifier.revocationListFromJson(readStringFromFile(rlPath), curve)); System.out.println("Signature is " + (valid ? "valid." : "invalid.")); } else if (line.hasOption(JOIN1)) { String[] optionValues = line.getOptionValues(JOIN1); IssuerPublicKey ipk = new IssuerPublicKey(curve, readStringFromFile(optionValues[0])); // Create authenticator key BigInteger sk = curve.getRandomModOrder(random); writeToFile(encoder.encodeToString(curve.bigIntegerToB(sk)), optionValues[1]); Authenticator auth = new Authenticator(curve, ipk, sk); JoinMessage1 msg1 = auth.EcDaaJoin1(curve.getRandomModOrder(random)); writeToFile(msg1.toJson(curve), optionValues[2]); } else if (line.hasOption(JOIN2)) { String[] optionValues = line.getOptionValues(JOIN2); // create issuer with the specified key IssuerPublicKey pk = new IssuerPublicKey(curve, readStringFromFile(optionValues[0])); IssuerSecretKey sk = new IssuerSecretKey(curve, readStringFromFile(optionValues[1])); Issuer iss = new Issuer(curve, sk, pk); JoinMessage1 msg1 = new JoinMessage1(curve, readStringFromFile(optionValues[2])); // Note that we do not check for nonce freshness. JoinMessage2 msg2 = iss.EcDaaIssuerJoin(msg1, false); if (msg2 == null) { System.out.println("Join message invalid."); } else { System.out.println("Join message valid, msg2 written to file."); writeToFile(msg2.toJson(curve), optionValues[3]); } } } catch (ParseException e) { System.out.println("Error parsing input."); e.printStackTrace(); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }
From source file:com.netflix.genie.client.sample.ClusterServiceSampleClient.java
/** * Main for running client code.//w w w .jav a 2 s . c o m * * @param args program arguments * @throws Exception On issue. */ public static void main(final String[] args) throws Exception { // Initialize Eureka, if it is being used // LOG.info("Initializing Eureka"); // ClusterServiceClient.initEureka("test"); LOG.info("Initializing list of Genie servers"); ConfigurationManager.getConfigInstance().setProperty("genie2Client.ribbon.listOfServers", "localhost:7001"); LOG.info("Initializing ApplicationServiceClient"); final ApplicationServiceClient appClient = ApplicationServiceClient.getInstance(); final Application app1 = appClient.createApplication( ApplicationServiceSampleClient.getSampleApplication(ApplicationServiceSampleClient.ID)); LOG.info("Created application:"); LOG.info(app1.toString()); final Application app2 = appClient.createApplication( ApplicationServiceSampleClient.getSampleApplication(ApplicationServiceSampleClient.ID + "2")); LOG.info("Created application:"); LOG.info(app2.toString()); LOG.info("Initializing CommandServiceClient"); final CommandServiceClient commandClient = CommandServiceClient.getInstance(); LOG.info("Creating command pig13_mr2"); final Command command1 = commandClient .createCommand(CommandServiceSampleClient.createSampleCommand(CommandServiceSampleClient.ID)); commandClient.setApplicationForCommand(command1.getId(), app1); LOG.info("Created command:"); LOG.info(command1.toString()); final List<Command> commands = new ArrayList<>(); commands.add(command1); LOG.info("Initializing ClusterConfigServiceClient"); final ClusterServiceClient clusterClient = ClusterServiceClient.getInstance(); LOG.info("Creating new cluster configuration"); final Cluster cluster1 = clusterClient.createCluster(createSampleCluster(ID)); clusterClient.addCommandsToCluster(cluster1.getId(), commands); LOG.info("Cluster config created with id: " + cluster1.getId()); LOG.info(cluster1.toString()); LOG.info("Getting cluster config by id"); final Cluster cluster2 = clusterClient.getCluster(cluster1.getId()); LOG.info(cluster2.toString()); LOG.info("Getting clusterConfigs using specified filter criteria"); final Multimap<String, String> params = ArrayListMultimap.create(); params.put("name", NAME); params.put("adHoc", "false"); params.put("test", "true"); params.put("limit", "3"); final List<Cluster> clusters = clusterClient.getClusters(params); if (clusters != null && !clusters.isEmpty()) { for (final Cluster cluster : clusters) { LOG.info(cluster.toString()); } } else { LOG.info("No clusters found for parameters"); } LOG.info("Configurations for cluster with id " + cluster1.getId()); final Set<String> configs = clusterClient.getConfigsForCluster(cluster1.getId()); for (final String config : configs) { LOG.info("Config = " + config); } LOG.info("Adding configurations to cluster with id " + cluster1.getId()); final Set<String> newConfigs = new HashSet<>(); newConfigs.add("someNewConfigFile"); newConfigs.add("someOtherNewConfigFile"); final Set<String> configs2 = clusterClient.addConfigsToCluster(cluster1.getId(), newConfigs); for (final String config : configs2) { LOG.info("Config = " + config); } LOG.info("Updating set of configuration files associated with id " + cluster1.getId()); //This should remove the original config leaving only the two in this set final Set<String> configs3 = clusterClient.updateConfigsForCluster(cluster1.getId(), newConfigs); for (final String config : configs3) { LOG.info("Config = " + config); } /**************** Begin tests for tag Api's *********************/ LOG.info("Get tags for cluster with id " + cluster1.getId()); final Set<String> tags = cluster1.getTags(); for (final String tag : tags) { LOG.info("Tag = " + tag); } LOG.info("Adding tags to cluster with id " + cluster1.getId()); final Set<String> newTags = new HashSet<>(); newTags.add("tag1"); newTags.add("tag2"); final Set<String> tags2 = clusterClient.addTagsToCluster(cluster1.getId(), newTags); for (final String tag : tags2) { LOG.info("Tag = " + tag); } LOG.info("Updating set of tags associated with id " + cluster1.getId()); //This should remove the original config leaving only the two in this set final Set<String> tags3 = clusterClient.updateTagsForCluster(cluster1.getId(), newTags); for (final String tag : tags3) { LOG.info("Tag = " + tag); } LOG.info("Deleting one tag from the cluster with id " + cluster1.getId()); //This should remove the "tag3" from the tags final Set<String> tags5 = clusterClient.removeTagForCluster(cluster1.getId(), "tag1"); for (final String tag : tags5) { //Shouldn't print anything LOG.info("Tag = " + tag); } LOG.info("Deleting all the tags from the cluster with id " + cluster1.getId()); //This should remove the original config leaving only the two in this set final Set<String> tags4 = clusterClient.removeAllTagsForCluster(cluster1.getId()); for (final String tag : tags4) { //Shouldn't print anything LOG.info("Config = " + tag); } /********************** End tests for tag Api's **********************/ LOG.info("Commands for cluster with id " + cluster1.getId()); final List<Command> commands1 = clusterClient.getCommandsForCluster(cluster1.getId()); for (final Command command : commands1) { LOG.info("Command = " + command); } LOG.info("Adding commands to cluster with id " + cluster1.getId()); final List<Command> newCmds = new ArrayList<>(); newCmds.add(commandClient.createCommand(CommandServiceSampleClient.createSampleCommand(ID + "something"))); newCmds.add(commandClient.createCommand(CommandServiceSampleClient.createSampleCommand(null))); final List<Command> commands2 = clusterClient.addCommandsToCluster(cluster1.getId(), newCmds); for (final Command command : commands2) { LOG.info("Command = " + command); } LOG.info("Updating set of commands files associated with id " + cluster1.getId()); //This should remove the original config leaving only the two in this set final List<Command> commands3 = clusterClient.updateCommandsForCluster(cluster1.getId(), newCmds); for (final Command command : commands3) { LOG.info("Command = " + command); } LOG.info("Deleting the command from the cluster with id " + ID + "something"); final Set<Command> commands4 = clusterClient.removeCommandForCluster(cluster1.getId(), ID + "something"); for (final Command command : commands4) { LOG.info("Command = " + command); } LOG.info("Deleting all the commands from the command with id " + command1.getId()); final List<Command> commands5 = clusterClient.removeAllCommandsForCluster(cluster1.getId()); for (final Command command : commands5) { //Shouldn't print anything LOG.info("Command = " + command); } LOG.info("Updating existing cluster config"); cluster2.setStatus(ClusterStatus.TERMINATED); final Cluster cluster3 = clusterClient.updateCluster(cluster2.getId(), cluster2); LOG.info("Cluster updated:"); LOG.info(cluster3.toString()); LOG.info("Deleting cluster config using id"); final Cluster cluster4 = clusterClient.deleteCluster(cluster1.getId()); LOG.info("Deleted cluster config with id: " + cluster1.getId()); LOG.info(cluster4.toString()); LOG.info("Deleting command config using id"); final Command command5 = commandClient.deleteCommand(command1.getId()); LOG.info("Deleted command config with id: " + command1.getId()); LOG.info(command5.toString()); LOG.info("Deleting commands in newCmd"); for (final Command cmd : newCmds) { commandClient.deleteCommand(cmd.getId()); } LOG.info("Deleting application config using id"); final Application app3 = appClient.deleteApplication(app1.getId()); LOG.info("Deleted application config with id: " + app1.getId()); LOG.info(app3.toString()); LOG.info("Deleting application config using id"); final Application app4 = appClient.deleteApplication(app2.getId()); LOG.info("Deleted application config with id: " + app2.getId()); LOG.info(app4.toString()); LOG.info("Done"); }
From source file:org.jaqpot.core.elastic.ElasticSearchWriter.java
License:asdf
public static void main(String... args) throws IOException { User u = UserBuilder.builder("jack.sparrow").setHashedPassword(UUID.randomUUID().toString()) .setMail("jack.sparrow@gmail.com").setMaxBibTeX(17680).setMaxFeatures(12678).setMaxModels(9999) .setName("Jack Sparrow").setMaxSubstances(1000).setMaxWeeklyPublishedFeatures(345) .setMaxWeeklyPublishedModels(67).setMaxWeeklyPublishedSubstances(5).setMaxParallelTasks(10).build(); //u.setId(null); BibTeX b = BibTeXBuilder.builder("WhaTevEr14").setAbstract("asdf").setAddress("sdfsdfsd") .setAnnotation("slkfsdlf").setAuthor("a").setBibType(BibTeX.BibTYPE.Article).setBookTitle("t6hdth") .setChapter("uthjsdfbkjs").setCopyright("sdfsdf").setCrossref("other").setEdition("234234") .setEditor("me").setISBN("23434234").setISSN("10010231230").setJournal("haha").setKey("lalala") .setKeywords("This is a set of keywords").setNumber("1").setPages("101-123") .setSeries("Some series").setTitle("Lololo").setURL("http://some.url.ch/").setVolume("100") .setYear("2010").build(); ROG rog = new ROG(false); Model m = rog.nextModel();/*from w ww . j av a2s . c om*/ m = new ModelMetaStripper(m).strip(); Feature f = new Feature(); f.setId("456"); Set<String> ontClasses = new HashSet<>(); ontClasses.add("ot:Feature"); ontClasses.add("ot:NumericFeature"); f.setOntologicalClasses(ontClasses); f.setMeta(MetaInfoBuilder.builder().addComments("this is a comment", "and a second one") .addTitles("My first feature", "a nice feature").addSubjects("feature of the day").build()); f.setUnits("mJ"); ElasticSearchWriter writer = new ElasticSearchWriter(b); InetSocketTransportAddress addrOpenTox = new InetSocketTransportAddress("147.102.82.32", 49101); InetSocketTransportAddress addrLocal = new InetSocketTransportAddress("localhost", 9300); writer.client = new TransportClient() //.addTransportAddress(addrLocal) .addTransportAddress(addrOpenTox); ObjectMapper om = new ObjectMapper(); om.enable(SerializationFeature.INDENT_OUTPUT); writer.om = om; System.out.println("http://147.102.82.32:49234/jaqpot/" + XmlNameExtractor.extractName(writer.entity.getClass()) + "/" + writer.index()); }
From source file:com.act.lcms.db.io.PrintConstructInfo.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());//from w w w.j a va2s. c o m } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } File lcmsDir = new File(cl.getOptionValue(OPTION_DIRECTORY)); if (!lcmsDir.isDirectory()) { System.err.format("File at %s is not a directory\n", lcmsDir.getAbsolutePath()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } try (DB db = DB.openDBFromCLI(cl)) { System.out.print("Loading/updating LCMS scan files into DB\n"); ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir); String construct = cl.getOptionValue(OPTION_CONSTRUCT); List<LCMSWell> lcmsWells = LCMSWell.getInstance().getByConstructID(db, construct); Collections.sort(lcmsWells, new Comparator<LCMSWell>() { @Override public int compare(LCMSWell o1, LCMSWell o2) { return o1.getId().compareTo(o2.getId()); } }); Set<String> uniqueMSIDs = new HashSet<>(); Map<Integer, Plate> platesById = new HashMap<>(); System.out.format("\n\n-- Construct %s --\n\n", construct); List<ChemicalAssociatedWithPathway> pathwayChems = ChemicalAssociatedWithPathway.getInstance() .getChemicalsAssociatedWithPathwayByConstructId(db, construct); System.out.print("Chemicals associated with pathway:\n"); System.out.format(" %-8s%-15s%-45s\n", "index", "kind", "chemical"); for (ChemicalAssociatedWithPathway chem : pathwayChems) { System.out.format(" %-8d%-15s%-45s\n", chem.getIndex(), chem.getKind(), chem.getChemical()); } System.out.print("\nLCMS wells:\n"); System.out.format(" %-15s%-6s%-15s%-15s%-15s\n", "barcode", "well", "msid", "fed", "lcms_count"); for (LCMSWell well : lcmsWells) { uniqueMSIDs.add(well.getMsid()); Plate p = platesById.get(well.getPlateId()); if (p == null) { // TODO: migrate Plate to be a subclass of BaseDBModel. p = Plate.getPlateById(db, well.getPlateId()); platesById.put(p.getId(), p); } String chem = well.getChemical(); List<ScanFile> scanFiles = ScanFile.getScanFileByPlateIDRowAndColumn(db, p.getId(), well.getPlateRow(), well.getPlateColumn()); System.out.format(" %-15s%-6s%-15s%-15s%-15d\n", p.getBarcode(), well.getCoordinatesString(), well.getMsid(), chem == null || chem.isEmpty() ? "--" : chem, scanFiles.size()); System.out.flush(); } List<Integer> plateIds = Arrays.asList(platesById.keySet().toArray(new Integer[platesById.size()])); Collections.sort(plateIds); System.out.print("\nAppears in plates:\n"); for (Integer id : plateIds) { Plate p = platesById.get(id); System.out.format(" %s: %s\n", p.getBarcode(), p.getName()); } List<String> msids = Arrays.asList(uniqueMSIDs.toArray(new String[uniqueMSIDs.size()])); Collections.sort(msids); System.out.format("\nMSIDS: %s\n", StringUtils.join(msids, ", ")); Set<String> availableNegativeControls = new HashSet<>(); for (Map.Entry<Integer, Plate> entry : platesById.entrySet()) { List<LCMSWell> wells = LCMSWell.getInstance().getByPlateId(db, entry.getKey()); for (LCMSWell well : wells) { if (!construct.equals(well.getComposition())) { availableNegativeControls.add(well.getComposition()); } } } // Print available standards for each step w/ plate barcodes and coordinates. System.out.format("\nAvailable Standards:\n"); Map<Integer, Plate> plateCache = new HashMap<>(); for (ChemicalAssociatedWithPathway chem : pathwayChems) { List<StandardWell> matchingWells = StandardWell.getInstance().getStandardWellsByChemical(db, chem.getChemical()); for (StandardWell well : matchingWells) { if (!plateCache.containsKey(well.getPlateId())) { Plate p = Plate.getPlateById(db, well.getPlateId()); plateCache.put(p.getId(), p); } } Map<Integer, List<StandardWell>> standardWellsByPlateId = new HashMap<>(); for (StandardWell well : matchingWells) { List<StandardWell> plateWells = standardWellsByPlateId.get(well.getPlateId()); if (plateWells == null) { plateWells = new ArrayList<>(); standardWellsByPlateId.put(well.getPlateId(), plateWells); } plateWells.add(well); } List<Pair<String, Integer>> plateBarcodes = new ArrayList<>(plateCache.size()); for (Plate p : plateCache.values()) { if (p.getBarcode() == null) { plateBarcodes.add(Pair.of("(no barcode)", p.getId())); } else { plateBarcodes.add(Pair.of(p.getBarcode(), p.getId())); } } Collections.sort(plateBarcodes); System.out.format(" %s:\n", chem.getChemical()); for (Pair<String, Integer> barcodePair : plateBarcodes) { // TODO: hoist this whole sorting/translation step into a utility class. List<StandardWell> wells = standardWellsByPlateId.get(barcodePair.getRight()); if (wells == null) { // Don't print plates that don't apply to this chemical, which can happen because we're caching the plates. continue; } Collections.sort(wells, new Comparator<StandardWell>() { @Override public int compare(StandardWell o1, StandardWell o2) { int c = o1.getPlateRow().compareTo(o2.getPlateRow()); if (c != 0) return c; return o1.getPlateColumn().compareTo(o2.getPlateColumn()); } }); List<String> descriptions = new ArrayList<>(wells.size()); for (StandardWell well : wells) { descriptions.add(String.format("%s in %s%s", well.getCoordinatesString(), well.getMedia(), well.getConcentration() == null ? "" : String.format(" c. %f", well.getConcentration()))); } System.out.format(" %s: %s\n", barcodePair.getLeft(), StringUtils.join(descriptions, ", ")); } } List<String> negativeControlStrains = Arrays .asList(availableNegativeControls.toArray(new String[availableNegativeControls.size()])); Collections.sort(negativeControlStrains); System.out.format("\nAvailable negative controls: %s\n", StringUtils.join(negativeControlStrains, ",")); System.out.print("\n----------\n"); System.out.print("\n\n"); } }
From source file:hyperloglog.tools.HyperLogLogCLI.java
public static void main(String[] args) { Options options = new Options(); addOptions(options);/*from ww w .jav a2s .co m*/ CommandLineParser parser = new BasicParser(); CommandLine cli = null; long n = 0; long seed = 123; EncodingType enc = EncodingType.SPARSE; int p = 14; int hb = 64; boolean bitPack = true; boolean noBias = true; int unique = -1; String filePath = null; BufferedReader br = null; String outFile = null; String inFile = null; FileOutputStream fos = null; DataOutputStream out = null; FileInputStream fis = null; DataInputStream in = null; try { cli = parser.parse(options, args); if (!(cli.hasOption('n') || cli.hasOption('f') || cli.hasOption('d'))) { System.out.println("Example usage: hll -n 1000 " + "<OR> hll -f /tmp/input.txt " + "<OR> hll -d -i /tmp/out.hll"); usage(options); return; } if (cli.hasOption('n')) { n = Long.parseLong(cli.getOptionValue('n')); } if (cli.hasOption('e')) { String value = cli.getOptionValue('e'); if (value.equals(EncodingType.DENSE.name())) { enc = EncodingType.DENSE; } } if (cli.hasOption('p')) { p = Integer.parseInt(cli.getOptionValue('p')); if (p < 4 && p > 16) { System.out.println("Warning! Out-of-range value specified for p. Using to p=14."); p = 14; } } if (cli.hasOption('h')) { hb = Integer.parseInt(cli.getOptionValue('h')); } if (cli.hasOption('c')) { noBias = Boolean.parseBoolean(cli.getOptionValue('c')); } if (cli.hasOption('b')) { bitPack = Boolean.parseBoolean(cli.getOptionValue('b')); } if (cli.hasOption('f')) { filePath = cli.getOptionValue('f'); br = new BufferedReader(new FileReader(new File(filePath))); } if (filePath != null && cli.hasOption('n')) { System.out.println("'-f' (input file) specified. Ignoring -n."); } if (cli.hasOption('s')) { if (cli.hasOption('o')) { outFile = cli.getOptionValue('o'); fos = new FileOutputStream(new File(outFile)); out = new DataOutputStream(fos); } else { System.err.println("Specify output file. Example usage: hll -s -o /tmp/out.hll"); usage(options); return; } } if (cli.hasOption('d')) { if (cli.hasOption('i')) { inFile = cli.getOptionValue('i'); fis = new FileInputStream(new File(inFile)); in = new DataInputStream(fis); } else { System.err.println("Specify input file. Example usage: hll -d -i /tmp/in.hll"); usage(options); return; } } // return after deserialization if (fis != null && in != null) { long start = System.currentTimeMillis(); HyperLogLog deserializedHLL = HyperLogLogUtils.deserializeHLL(in); long end = System.currentTimeMillis(); System.out.println(deserializedHLL.toString()); System.out.println("Count after deserialization: " + deserializedHLL.count()); System.out.println("Deserialization time: " + (end - start) + " ms"); return; } // construct hll and serialize it if required HyperLogLog hll = HyperLogLog.builder().enableBitPacking(bitPack).enableNoBias(noBias).setEncoding(enc) .setNumHashBits(hb).setNumRegisterIndexBits(p).build(); if (br != null) { Set<String> hashset = new HashSet<String>(); String line; while ((line = br.readLine()) != null) { hll.addString(line); hashset.add(line); } n = hashset.size(); } else { Random rand = new Random(seed); for (int i = 0; i < n; i++) { if (unique < 0) { hll.addLong(rand.nextLong()); } else { int val = rand.nextInt(unique); hll.addLong(val); } } } long estCount = hll.count(); System.out.println("Actual count: " + n); System.out.println(hll.toString()); System.out.println("Relative error: " + HyperLogLogUtils.getRelativeError(n, estCount) + "%"); if (fos != null && out != null) { long start = System.currentTimeMillis(); HyperLogLogUtils.serializeHLL(out, hll); long end = System.currentTimeMillis(); System.out.println("Serialized hyperloglog to " + outFile); System.out.println("Serialized size: " + out.size() + " bytes"); System.out.println("Serialization time: " + (end - start) + " ms"); out.close(); } } catch (ParseException e) { System.err.println("Invalid parameter."); usage(options); } catch (NumberFormatException e) { System.err.println("Invalid type for parameter."); usage(options); } catch (FileNotFoundException e) { System.err.println("Specified file not found."); usage(options); } catch (IOException e) { System.err.println("Exception occured while reading file."); usage(options); } }
From source file:com.mfalaize.zipdiff.Main.java
/** * The command line interface to zipdiff utility * * @param args The command line parameters *//*from ww w . j a v a 2s . co m*/ public static void main(String[] args) { CommandLineParser parser = new DefaultParser(); try { CommandLine line = parser.parse(options, args); String filename1; String filename2; filename1 = line.getOptionValue(OPTION_FILE1); filename2 = line.getOptionValue(OPTION_FILE2); File f1 = new File(filename1); File f2 = new File(filename2); checkFile(f1); checkFile(f2); System.out.println("File 1 = " + f1); System.out.println("File 2 = " + f2); DifferenceCalculator calc = new DifferenceCalculator(f1, f2); String regularExpression; // todo - calc.setFilenamesToIgnore(); if (line.hasOption(OPTION_COMPARE_CRC_VALUES)) { calc.setCompareCRCValues(true); } else { calc.setCompareCRCValues(false); } if (line.hasOption(OPTION_IGNORE_CVS_FILES)) { calc.setIgnoreCVSFiles(true); } else { calc.setIgnoreCVSFiles(false); } if (line.hasOption(OPTION_COMPARE_TIMESTAMPS)) { calc.setIgnoreTimestamps(false); } else { calc.setIgnoreTimestamps(true); } if (line.hasOption(OPTION_REGEX)) { regularExpression = line.getOptionValue(OPTION_REGEX); Set<String> regexSet = new HashSet<String>(); regexSet.add(regularExpression); calc.setFilenameRegexToIgnore(regexSet); } boolean exitWithErrorOnDiff = false; if (line.hasOption(OPTION_EXIT_WITH_ERROR_ON_DIFF)) { exitWithErrorOnDiff = true; } Differences d = calc.getDifferences(); if (line.hasOption(OPTION_OUTPUT_FILE)) { String outputFilename = line.getOptionValue(OPTION_OUTPUT_FILE); writeOutputFile(outputFilename, d); } if (d.hasDifferences()) { if (line.hasOption(OPTION_VERBOSE)) { System.out.println(d); System.out.println(d.getFilename1() + " and " + d.getFilename2() + " are different."); } if (exitWithErrorOnDiff) { System.exit(EXITCODE_DIFF); } } else { System.out.println("No differences found."); } } catch (ParseException pex) { System.err.println(pex.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Main [options] ", options); System.exit(EXITCODE_ERROR); } catch (Exception ex) { ex.printStackTrace(); System.exit(EXITCODE_ERROR); } }
From source file:autocorrelator.apps.SDFGroovy.java
public static void main(String[] args) throws Exception { long start = System.currentTimeMillis(); // create command line Options object Options options = new Options(); Option opt = new Option("in", true, "input sd file"); options.addOption(opt);//from w ww.j av a 2 s. c om opt = new Option("out", true, "output file for return value true or null"); options.addOption(opt); opt = new Option("falseOut", true, "output file for return value false"); options.addOption(opt); opt = new Option("c", true, "groovy script line"); options.addOption(opt); opt = new Option("f", true, "groovy script file"); options.addOption(opt); opt = new Option("exception", true, "exception handling (Default: stop)"); options.addOption(opt); opt = new Option("h", false, "print help message"); options.addOption(opt); CommandLineParser parser = new BasicParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { exitWithHelp(e.getMessage(), options); } if (!cmd.hasOption("c") && !cmd.hasOption("f")) exitWithHelp("-c or -f must be given!", options); if (cmd.hasOption("c") && cmd.hasOption("f")) exitWithHelp("Only one of -c or -f may be given!", options); String groovyStrg; if (cmd.hasOption("c")) groovyStrg = cmd.getOptionValue("c"); else groovyStrg = fileToString(cmd.getOptionValue("f")); Set<String> inFileds = new HashSet<String>(); Set<String> outFields = new HashSet<String>(); Script script = getGroovyScript(groovyStrg, inFileds, outFields); if (cmd.hasOption("h")) { callScriptHelp(script); exitWithHelp("", options); } if (!cmd.hasOption("in") || !cmd.hasOption("out")) { callScriptHelp(script); exitWithHelp("-in and -out must be given", options); } String[] scriptArgs = cmd.getArgs(); String inFile = cmd.getOptionValue("in"); String outFile = cmd.getOptionValue("out"); String falseOutFile = cmd.getOptionValue("falseOut"); EXCEPTIONHandling eHandling = EXCEPTIONHandling.stop; if (cmd.hasOption("exception")) eHandling = EXCEPTIONHandling.getByName(cmd.getOptionValue("exception")); callScriptInit(script, scriptArgs); oemolistream ifs = new oemolistream(inFile); oemolostream ofs = new oemolostream(outFile); oemolostream falseOFS = null; if (falseOutFile != null) falseOFS = new oemolostream(falseOutFile); OEMolBase mol = new OEGraphMol(); int iCounter = 0; int oCounter = 0; int foCounter = 0; while (oechem.OEReadMolecule(ifs, mol)) { iCounter++; Binding binding = getFieldBindings(mol, inFileds, outFields); script.setBinding(binding); boolean printToTrue = true; boolean printToFalse = true; try { Object ret = script.run(); if (ret == null || !(ret instanceof Boolean)) { printToFalse = false; } else if (((Boolean) ret).booleanValue()) { printToFalse = false; } else // ret = false { printToTrue = false; } setOutputFields(mol, binding, outFields); } catch (Exception e) { switch (eHandling) { case stop: throw e; case printToTrue: printToFalse = false; System.err.println(e.getMessage()); break; case printToFalse: printToTrue = false; System.err.println(e.getMessage()); break; case dropRecord: printToTrue = false; printToFalse = false; System.err.println(e.getMessage()); break; default: assert false; break; } } if (printToTrue) { oechem.OEWriteMolecule(ofs, mol); oCounter++; } if (falseOFS != null && printToFalse) { oechem.OEWriteMolecule(falseOFS, mol); foCounter++; } } System.err.printf("SDFGroovy: Input %d, output %d,%d structures in %dsec\n", iCounter, oCounter, foCounter, (System.currentTimeMillis() - start) / 1000); if (falseOFS != null) falseOFS.close(); ofs.close(); ifs.close(); mol.delete(); }
From source file:dhbw.clippinggorilla.external.twitter.TwitterUtils.java
public static void main(String[] args) { Set<String> includedTagsSet = new HashSet<>(); Set<String> excludedTagsSet = new HashSet<>(); LocalDateTime date;// w w w .java 2 s. c om includedTagsSet.add("bmw, mercedes"); includedTagsSet.add("Audi, toyota"); includedTagsSet.add("merkel"); includedTagsSet.add("dat boi, pepe"); includedTagsSet.add("dhbw"); includedTagsSet.add("VW Golf"); Query query = queryBuilder(includedTagsSet, LocalDateTime.of(2017, 5, 1, 0, 0)); QueryResult result = searchTweets(query); for (Status status : result.getTweets()) { System.out.println("@" + status.getUser().getScreenName() + ":" + status.getText()); for (MediaEntity mediaEntity : status.getMediaEntities()) { System.out.println(mediaEntity.getType()); } System.out.println("_________________________________________________"); } }