List of usage examples for java.util HashSet HashSet
public HashSet()
From source file:com.github.brandtg.switchboard.FileLogAggregator.java
/** Main. */ public static void main(String[] args) throws Exception { Options opts = new Options(); opts.addOption("h", "help", false, "Prints help message"); opts.addOption("f", "file", true, "File to output aggregated logs to"); opts.addOption("s", "separator", true, "Line separator in log"); CommandLine cli = new GnuParser().parse(opts, args); if (cli.getArgs().length == 0 || cli.hasOption("help")) { new HelpFormatter().printHelp("usage: [opts] sourceHost:port ...", opts); System.exit(1);//from w ww .j a va 2s.co m } // Parse sources Set<InetSocketAddress> sources = new HashSet<>(); for (int i = 0; i < cli.getArgs().length; i++) { String[] tokens = cli.getArgs()[i].split(":"); sources.add(new InetSocketAddress(tokens[0], Integer.valueOf(tokens[1]))); } // Parse output stream OutputStream outputStream; if (cli.hasOption("file")) { outputStream = new FileOutputStream(cli.getOptionValue("file")); } else { outputStream = System.out; } // Separator String separator = cli.getOptionValue("separator", "\n"); if (separator.length() != 1) { throw new IllegalArgumentException("Separator must only be 1 character"); } final FileLogAggregator fileLogAggregator = new FileLogAggregator(sources, separator.charAt(0), outputStream); Runtime.getRuntime().addShutdownHook(new Thread() { @Override public void run() { try { fileLogAggregator.stop(); } catch (Exception e) { LOG.error("Error when stopping log aggregator", e); } } }); fileLogAggregator.start(); }
From source file:com.datascience.gal.scripts.MainClient.java
public static void main(String[] args) throws ParseException { DawidSkeneClient dsclient = new DawidSkeneClient(); String categoriesfile = null; String inputfile = null;//from w w w . ja v a 2 s .c om String correctfile = null; String costfile = null; int iterations = 1; boolean incremental = false; CommandLineParser parser = new GnuParser(); CommandLine line = parser.parse(cli_options, args); if (!line.hasOption("c") || !line.hasOption("l") || !line.hasOption("g") || !line.hasOption("C")) { printHelp(); System.exit(1); } categoriesfile = line.getOptionValue("c"); inputfile = line.getOptionValue("l"); if (line.hasOption("g")) correctfile = line.getOptionValue("g"); if (line.hasOption("C")) costfile = line.getOptionValue("C"); if (line.hasOption("i")) iterations = Integer.parseInt(line.getOptionValue("i")); if (line.hasOption("I")) incremental = true; // see if the thing is awake System.out.println(dsclient.isAlive() ? "pinged alive" : "problem with dsclient"); // hard reset System.out.println(dsclient.deleteDS(0) ? "deleted ds 0" : "failed to delete ds 0"); Collection<Category> categories = loadCategoriesFromFile(categoriesfile); if (categories.size() < 2) { System.err.println("invalid category input"); System.exit(1); } System.out.println("sending to service: " + JSONUtils.toJson(categories)); System.out.println( "response: " + (dsclient.initializeDS(0, categories, incremental) ? "success" : "failure")); // check the serialization of the json ds object DawidSkene ds = dsclient.getDawidSkene(0); System.out.println(ds); Collection<MisclassificationCost> costs = loadMisclassificationCosts(costfile); System.out.println("response: " + (dsclient.addMisclassificationCosts(0, costs) ? "successfully added costs" : "unable to add costs") + " - " + JSONUtils.toJson(costs)); Collection<AssignedLabel> labels = loadAssignedLabels(inputfile); System.out.println("response: " + (dsclient.addAssignedLabels(0, labels) ? "successfully added labels" : "unable to add labels") + " - " + JSONUtils.toJson(labels)); Collection<CorrectLabel> gold = loadGoldLabels(correctfile); System.out.println("response: " + (dsclient.addCorrectLabels(0, gold) ? "successfully added labels" : "unable to add labels") + " - " + JSONUtils.toJson(gold)); Map<String, String> preVotes = dsclient.computeMajorityVotes(0); ds = dsclient.getDawidSkene(0); System.out.println(ds); if (!incremental) System.out.println( dsclient.iterateBlocking(0, iterations) ? "successfully iterated" : "failed ds iterations"); ds = dsclient.getDawidSkene(0); System.out.println(ds); System.out.println(ds.printAllWorkerScores(false)); System.out.println(ds.printObjectClassProbabilities(0)); System.out.println(ds.printPriors()); Map<String, String> postVotes = dsclient.computeMajorityVotes(0); System.out.println("note- diff doesnt work with incremental\n" + printDiffVote(preVotes, postVotes)); System.out.println(JSONUtils.toJson(ds.getMajorityVote())); System.out.println(JSONUtils.toJson(ds.getObjectProbs())); Collection<String> objectNames = new HashSet<String>(); String name = null; for (AssignedLabel label : labels) { objectNames.add(label.getObjectName()); name = label.getObjectName(); } System.out.println(JSONUtils.toJson(ds.getMajorityVote(objectNames))); System.out.println(JSONUtils.toJson(ds.getObjectProbs(objectNames))); System.out.println(JSONUtils.toJson(ds.getMajorityVote(name))); System.out.println(JSONUtils.toJson(ds.getObjectProbs(name))); boolean contains; contains = dsclient.hasDSObject(0); System.out.println(contains ? "has 0" : "dont have 0"); contains = dsclient.hasDSObject(1); System.out.println(contains ? "has 1" : "dont have 1"); System.out.println("deleting 0"); dsclient.deleteDS(0); contains = dsclient.hasDSObject(0); System.out.println(contains ? "has 0" : "dont have 0"); }
From source file:com.github.fritaly.graphml4j.samples.GradleDependenciesWithGroups.java
public static void main(String[] args) throws Exception { if (args.length != 1) { System.out/*w w w.j av a 2 s .com*/ .println(String.format("%s <output-file>", GradleDependenciesWithGroups.class.getSimpleName())); System.exit(1); } final File file = new File(args[0]); System.out.println("Writing GraphML file to " + file.getAbsolutePath() + " ..."); FileWriter fileWriter = null; GraphMLWriter graphWriter = null; Reader reader = null; LineNumberReader lineReader = null; try { fileWriter = new FileWriter(file); graphWriter = new GraphMLWriter(fileWriter); // Customize the rendering of nodes final NodeStyle nodeStyle = graphWriter.getNodeStyle(); nodeStyle.setWidth(250.0f); nodeStyle.setHeight(50.0f); graphWriter.setNodeStyle(nodeStyle); // The dependency graph has been generated by Gradle with the // command "gradle dependencies". The output of this command has // been saved to a text file which will be parsed to rebuild the // dependency graph reader = new InputStreamReader( GradleDependenciesWithGroups.class.getResourceAsStream("gradle-dependencies.txt")); lineReader = new LineNumberReader(reader); String line = null; // Stack containing the artifacts per depth inside the dependency // graph (the topmost dependency is the first one in the stack) final Stack<Artifact> stack = new Stack<Artifact>(); final Map<String, Set<Artifact>> artifactsByGroup = new HashMap<String, Set<Artifact>>(); // List of parent/child relationships between artifacts final List<Relationship> relationships = new ArrayList<Relationship>(); while ((line = lineReader.readLine()) != null) { // Determine the depth of the current dependency inside the // graph. The depth can be inferred from the indentation used by // Gradle. Each level of depth adds 5 more characters of // indentation final int initialLength = line.length(); // Remove the strings used by Gradle to indent dependencies line = StringUtils.replace(line, "+--- ", ""); line = StringUtils.replace(line, "| ", ""); line = StringUtils.replace(line, "\\--- ", ""); line = StringUtils.replace(line, " ", ""); // The depth can easily be inferred now final int depth = (initialLength - line.length()) / 5; // Remove unnecessary artifacts while (depth <= stack.size()) { stack.pop(); } // Create an artifact from the dependency (group, artifact, // version) tuple final Artifact artifact = createArtifact(line); stack.push(artifact); if (stack.size() > 1) { // Store the artifact and its parent relationships.add(new Relationship(stack.get(stack.size() - 2), artifact)); } if (!artifactsByGroup.containsKey(artifact.group)) { artifactsByGroup.put(artifact.group, new HashSet<Artifact>()); } artifactsByGroup.get(artifact.group).add(artifact); } // Open the graph graphWriter.graph(); final Map<Artifact, String> nodeIdsByArtifact = new HashMap<Artifact, String>(); // Loop over the groups and generate the associated nodes for (String group : artifactsByGroup.keySet()) { graphWriter.group(group, true); for (Artifact artifact : artifactsByGroup.get(group)) { final String nodeId = graphWriter.node(artifact.getLabel()); nodeIdsByArtifact.put(artifact, nodeId); } graphWriter.closeGroup(); } // Generate the edges for (Relationship relationship : relationships) { final String parentId = nodeIdsByArtifact.get(relationship.parent); final String childId = nodeIdsByArtifact.get(relationship.child); graphWriter.edge(parentId, childId); } // Close the graph graphWriter.closeGraph(); System.out.println("Done"); } finally { // Calling GraphMLWriter.close() is necessary to dispose the underlying resources graphWriter.close(); fileWriter.close(); lineReader.close(); reader.close(); } }
From source file:edu.msu.cme.rdp.probematch.cli.SliceToPrimer.java
public static void main(String[] args) throws Exception { //args = "--fedit-dist 4 --redit-dist=4 -k --max-length=400 --min-length=280 -o java_sliced_edit4.fasta TGCGAYCCSAARGCBGACTC ATSGCCATCATYTCRCCGGA /scratch/fishjord/tae_kwon_primer_match/all_genomes.fasta".split(" "); PatternBitMask64[] fprimers;/*from w ww . j a va 2 s . c o m*/ String[] fprimerStrs, rprimerStrs; PatternBitMask64[] rprimers; FastaWriter seqOut; PrintStream statsOut; int fEdit = 3; int rEdit = 3; int minLength = Integer.MIN_VALUE; int maxLength = Integer.MAX_VALUE; boolean allowAmbiguities = true; boolean keepPrimers = false; SequenceReader inSeqs; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("edit-dist")) { fEdit = rEdit = Integer.parseInt(line.getOptionValue("edit-dist")); if (line.hasOption("redit-dist") || line.hasOption("fedit-dist")) { throw new Exception("edit-dist, [fedit-dist, redit-dist] are mutually exclusive"); } } if (line.hasOption("fedit-dist")) { fEdit = Integer.parseInt(line.getOptionValue("fedit-dist")); } if (line.hasOption("no-ambiguities")) { allowAmbiguities = false; } if (line.hasOption("keep-primers")) { keepPrimers = true; } if (line.hasOption("redit-dist")) { rEdit = Integer.parseInt(line.getOptionValue("redit-dist")); } if (line.hasOption("seq-out")) { seqOut = new FastaWriter(new File(line.getOptionValue("seq-out"))); } else { throw new Exception("Must specify seq-out"); } if (line.hasOption("stats-out")) { statsOut = new PrintStream(new File(line.getOptionValue("stats-out"))); } else { statsOut = System.out; } if (line.hasOption("min-length")) { minLength = Integer.parseInt(line.getOptionValue("min-length")); } if (line.hasOption("max-length")) { maxLength = Integer.parseInt(line.getOptionValue("max-length")); } args = line.getArgs(); if (args.length != 3) { throw new Exception("Unexpected number of command line arguments"); } fprimers = translateStringPrimers(args[0].split(","), allowAmbiguities, false); fprimerStrs = args[0].split(","); rprimers = translateStringPrimers(args[1].split(","), allowAmbiguities, true); rprimerStrs = args[1].split(","); inSeqs = new SequenceReader(new File(args[2])); } catch (Exception e) { new HelpFormatter().printHelp("SliceToPrimer [options] <f,p,r,i,m,e,r> <r,p,r,i,m,e,r> <in_seq_file>", options); System.err.println("ERROR: " + e.getMessage()); return; } Sequence seq; statsOut.println( "orig_seqid\tsliced_seqid\tfprimer\tstart\tend\tscore\trprimer\tstart\tend\tscore\tlength"); ScoringMatrix sccoringMatrix = ScoringMatrix.getDefaultNuclMatrix(); DPMAligner[] faligners = new DPMAligner[fprimers.length]; for (int index = 0; index < faligners.length; index++) { faligners[index] = new DPMAligner(fprimerStrs[index], Integer.MAX_VALUE); } try { while ((seq = inSeqs.readNextSequence()) != null) { Set<PrimerMatch> fprimerMatches = new HashSet(); Set<PrimerMatch> rprimerMatches = new HashSet(); for (int index = 0; index < fprimers.length; index++) { PatternBitMask64 primer = fprimers[index]; for (BitVector64Match r : BitVector64.process(seq.getSeqString().toCharArray(), primer, fEdit) .getResults()) { PrimerMatch match = new PrimerMatch(); match.start = r.getPosition() - (primer.getPatternLength() + r.getScore()); match.end = r.getPosition(); match.score = r.getScore(); match.primerIndex = index; fprimerMatches.add(match); } } for (int index = 0; index < rprimers.length; index++) { PatternBitMask64 primer = rprimers[index]; for (BitVector64Match r : BitVector64.process(seq.getSeqString().toCharArray(), primer, rEdit) .getResults()) { PrimerMatch match = new PrimerMatch(); match.start = r.getPosition() - (primer.getPatternLength() + r.getScore()); match.end = r.getPosition(); match.score = r.getScore(); match.primerIndex = index; rprimerMatches.add(match); } } if (fprimerMatches.isEmpty() || rprimerMatches.isEmpty()) { statsOut.println(seq.getSeqName() + "\tEither/or no forward/reverse primer hits"); continue; } for (PrimerMatch fmatch : fprimerMatches) { PrimerMatch bestReverse = null; int bestScore = Integer.MAX_VALUE; for (PrimerMatch rmatch : rprimerMatches) { if (rmatch.start > fmatch.end && rmatch.start - fmatch.end < bestScore) { bestReverse = rmatch; bestScore = rmatch.start - fmatch.end; } } if (bestReverse == null) { statsOut.println(seq.getSeqName() + "\tNo reverse primer before " + fmatch.end); continue; } String slicedSeq = null; if (keepPrimers) { slicedSeq = seq.getSeqString().substring(fmatch.start, bestReverse.end); } else { slicedSeq = seq.getSeqString().substring(fmatch.end, bestReverse.start); } String seqid = seq.getSeqName() + "_" + fmatch.primerIndex + "_" + fmatch.start; if (slicedSeq.length() > minLength && slicedSeq.length() < maxLength) { seqOut.writeSeq(seqid, "", slicedSeq); } DPMAlignment seqs = faligners[fmatch.primerIndex] .align(seq.getSeqString().substring(fmatch.start, fmatch.end)); System.err.println(">" + seqid); System.err.println(fprimerStrs[fmatch.primerIndex]); System.err.println(seq.getSeqString().substring(fmatch.start, fmatch.end)); System.err.println(); System.err.println(seqs.getAlignedMatchFragment()); System.err.println(seqs.getAlignedProbe()); System.err.println(); statsOut.println(seq.getSeqName() + "\t" + seqid + "\t" + fmatch.primerIndex + "\t" + fmatch.start + "\t" + fmatch.end + "\t" + fmatch.score + "\t" + bestReverse.primerIndex + "\t" + bestReverse.start + "\t" + bestReverse.end + "\t" + bestReverse.score + "\t" + slicedSeq.length()); } } } catch (Exception e) { e.printStackTrace(); } finally { statsOut.close(); seqOut.close(); } }
From source file:org.biopax.validator.BiopaxValidatorClient.java
/** * Checks BioPAX files using the online BioPAX Validator. * // w ww . j ava 2 s . c o m * @see <a href="http://www.biopax.org/validator">BioPAX Validator Webservice</a> * * @param argv * @throws IOException */ public static void main(String[] argv) throws IOException { if (argv.length == 0) { System.err.println("Available parameters: \n" + "<path> <output> [xml|html|biopax] [auto-fix] [only-errors] [maxerrors=n] [notstrict]\n" + "\t- validate a BioPAX file/directory (up to ~25MB in total size, -\n" + "\totherwise, please use the biopax-validator.jar instead)\n" + "\tin the directory using the online BioPAX Validator service\n" + "\t(generates html or xml report, or gets the processed biopax\n" + "\t(cannot fix all errros though) see http://www.biopax.org/validator)"); System.exit(-1); } final String input = argv[0]; final String output = argv[1]; File fileOrDir = new File(input); if (!fileOrDir.canRead()) { System.err.println("Cannot read from " + input); System.exit(-1); } if (output == null || output.isEmpty()) { System.err.println("No output file specified (for the validation report)."); System.exit(-1); } // default options RetFormat outf = RetFormat.HTML; boolean fix = false; Integer maxErrs = null; Behavior level = null; //will report both errors and warnings String profile = null; // match optional arguments for (int i = 2; i < argv.length; i++) { if ("html".equalsIgnoreCase(argv[i])) { outf = RetFormat.HTML; } else if ("xml".equalsIgnoreCase(argv[i])) { outf = RetFormat.XML; } else if ("biopax".equalsIgnoreCase(argv[i])) { outf = RetFormat.OWL; } else if ("auto-fix".equalsIgnoreCase(argv[i])) { fix = true; } else if ("only-errors".equalsIgnoreCase(argv[i])) { level = Behavior.ERROR; } else if ((argv[i]).toLowerCase().startsWith("maxerrors=")) { String num = argv[i].substring(10); maxErrs = Integer.valueOf(num); } else if ("notstrict".equalsIgnoreCase(argv[i])) { profile = "notstrict"; } } // collect files Collection<File> files = new HashSet<File>(); if (fileOrDir.isDirectory()) { // validate all the OWL files in the folder FilenameFilter filter = new FilenameFilter() { public boolean accept(File dir, String name) { return (name.endsWith(".owl")); } }; for (String s : fileOrDir.list(filter)) { files.add(new File(fileOrDir.getCanonicalPath() + File.separator + s)); } } else { files.add(fileOrDir); } // upload and validate using the default URL: http://www.biopax.org/biopax-validator/check.html if (!files.isEmpty()) { BiopaxValidatorClient val = new BiopaxValidatorClient(); val.validate(fix, profile, outf, level, maxErrs, null, files.toArray(new File[] {}), new FileOutputStream(output)); } }
From source file:io.cloudslang.lang.tools.build.SlangBuildMain.java
public static void main(String[] args) { loadUserProperties();/* www .ja v a2s . co m*/ configureLog4j(); ApplicationArgs appArgs = new ApplicationArgs(); parseArgs(args, appArgs); String projectPath = parseProjectPathArg(appArgs); final String contentPath = defaultIfEmpty(appArgs.getContentRoot(), projectPath + CONTENT_DIR); final String testsPath = defaultIfEmpty(appArgs.getTestRoot(), projectPath + TEST_DIR); List<String> testSuites = parseTestSuites(appArgs); boolean shouldPrintCoverageData = appArgs.shouldOutputCoverage(); boolean runTestsInParallel = appArgs.isParallel(); int threadCount = parseThreadCountArg(appArgs, runTestsInParallel); String testCaseTimeout = parseTestTimeout(appArgs); setProperty(TEST_CASE_TIMEOUT_IN_MINUTES_KEY, valueOf(testCaseTimeout)); final boolean shouldValidateDescription = appArgs.shouldValidateDescription(); final boolean shouldValidateCheckstyle = appArgs.shouldValidateCheckstyle(); String runConfigPath = FilenameUtils.normalize(appArgs.getRunConfigPath()); BuildMode buildMode = null; Set<String> changedFiles = null; try { String smartModePath = appArgs.getChangesOnlyConfigPath(); if (StringUtils.isEmpty(smartModePath)) { buildMode = BuildMode.BASIC; changedFiles = new HashSet<>(); printBuildModeInfo(buildMode); } else { buildMode = BuildMode.CHANGED; changedFiles = readChangedFilesFromSource(smartModePath); printBuildModeInfo(buildMode); } } catch (Exception ex) { log.error("Exception: " + ex.getMessage()); System.exit(1); } // Override with the values from the file if configured List<String> testSuitesParallel = new ArrayList<>(); List<String> testSuitesSequential = new ArrayList<>(); BulkRunMode bulkRunMode = runTestsInParallel ? ALL_PARALLEL : ALL_SEQUENTIAL; TestCaseRunMode unspecifiedTestSuiteRunMode = runTestsInParallel ? TestCaseRunMode.PARALLEL : TestCaseRunMode.SEQUENTIAL; if (get(runConfigPath).isAbsolute() && isRegularFile(get(runConfigPath), NOFOLLOW_LINKS) && equalsIgnoreCase(PROPERTIES_FILE_EXTENSION, FilenameUtils.getExtension(runConfigPath))) { Properties runConfigurationProperties = ArgumentProcessorUtils.getPropertiesFromFile(runConfigPath); shouldPrintCoverageData = getBooleanFromPropertiesWithDefault(TEST_COVERAGE, shouldPrintCoverageData, runConfigurationProperties); threadCount = getIntFromPropertiesWithDefaultAndRange(TEST_PARALLEL_THREAD_COUNT, Runtime.getRuntime().availableProcessors(), runConfigurationProperties, 1, MAX_THREADS_TEST_RUNNER + 1); testSuites = getTestSuitesForKey(runConfigurationProperties, TEST_SUITES_TO_RUN); testSuitesParallel = getTestSuitesForKey(runConfigurationProperties, TEST_SUITES_PARALLEL); testSuitesSequential = getTestSuitesForKey(runConfigurationProperties, TEST_SUITES_SEQUENTIAL); addErrorIfSameTestSuiteIsInBothParallelOrSequential(testSuitesParallel, testSuitesSequential); unspecifiedTestSuiteRunMode = getEnumInstanceFromPropertiesWithDefault(TEST_SUITES_RUN_UNSPECIFIED, unspecifiedTestSuiteRunMode, runConfigurationProperties); addWarningsForMisconfiguredTestSuites(unspecifiedTestSuiteRunMode, testSuites, testSuitesSequential, testSuitesParallel); bulkRunMode = POSSIBLY_MIXED; } else { // Warn when file is misconfigured, relative path, file does not exist or is not a properties file log.info(format(DID_NOT_DETECT_RUN_CONFIGURATION_PROPERTIES_FILE, runConfigPath)); } String testCaseReportLocation = getProperty(TEST_CASE_REPORT_LOCATION); if (StringUtils.isBlank(testCaseReportLocation)) { log.info("Test case report location property [" + TEST_CASE_REPORT_LOCATION + "] is not defined. Report will be skipped."); } // Setting thread count for visibility in ParallelTestCaseExecutorService setProperty(SLANG_TEST_RUNNER_THREAD_COUNT, valueOf(threadCount)); log.info(NEW_LINE + "------------------------------------------------------------"); log.info("Building project: " + projectPath); log.info("Content root is at: " + contentPath); log.info("Test root is at: " + testsPath); log.info("Active test suites are: " + getListForPrint(testSuites)); log.info("Parallel run mode is configured for test suites: " + getListForPrint(testSuitesParallel)); log.info("Sequential run mode is configured for test suites: " + getListForPrint(testSuitesSequential)); log.info("Default run mode '" + unspecifiedTestSuiteRunMode.name().toLowerCase() + "' is configured for test suites: " + getListForPrint( getDefaultRunModeTestSuites(testSuites, testSuitesParallel, testSuitesSequential))); log.info("Bulk run mode for tests: " + getBulkModeForPrint(bulkRunMode)); log.info("Print coverage data: " + valueOf(shouldPrintCoverageData)); log.info("Validate description: " + valueOf(shouldValidateDescription)); log.info("Validate checkstyle: " + valueOf(shouldValidateCheckstyle)); log.info("Thread count: " + threadCount); log.info("Test case timeout in minutes: " + (isEmpty(testCaseTimeout) ? valueOf(MAX_TIME_PER_TESTCASE_IN_MINUTES) : testCaseTimeout)); log.info(NEW_LINE + "Loading..."); ClassPathXmlApplicationContext context = new ClassPathXmlApplicationContext("spring/testRunnerContext.xml"); context.registerShutdownHook(); SlangBuilder slangBuilder = context.getBean(SlangBuilder.class); LoggingService loggingService = context.getBean(LoggingServiceImpl.class); Slang slang = context.getBean(Slang.class); try { updateTestSuiteMappings(context.getBean(TestRunInfoService.class), testSuitesParallel, testSuitesSequential, testSuites, unspecifiedTestSuiteRunMode); registerEventHandlers(slang); List<RuntimeException> exceptions = new ArrayList<>(); SlangBuildResults buildResults = slangBuilder.buildSlangContent(projectPath, contentPath, testsPath, testSuites, shouldValidateDescription, shouldValidateCheckstyle, bulkRunMode, buildMode, changedFiles); exceptions.addAll(buildResults.getCompilationExceptions()); if (exceptions.size() > 0) { logErrors(exceptions, projectPath, loggingService); } IRunTestResults runTestsResults = buildResults.getRunTestsResults(); Map<String, TestRun> skippedTests = runTestsResults.getSkippedTests(); if (isNotEmpty(skippedTests)) { printSkippedTestsSummary(skippedTests, loggingService); } printPassedTests(runTestsResults, loggingService); if (shouldPrintCoverageData) { printTestCoverageData(runTestsResults, loggingService); } if (isNotEmpty(runTestsResults.getFailedTests())) { printBuildFailureSummary(projectPath, runTestsResults, loggingService); } else { printBuildSuccessSummary(contentPath, buildResults, runTestsResults, loggingService); } loggingService.waitForAllLogTasksToFinish(); generateTestCaseReport(context.getBean(SlangTestCaseRunReportGeneratorService.class), runTestsResults, testCaseReportLocation); System.exit(isNotEmpty(runTestsResults.getFailedTests()) ? 1 : 0); } catch (Throwable e) { logErrorsPrefix(loggingService); loggingService.logEvent(Level.ERROR, "Exception: " + e.getMessage()); logErrorsSuffix(projectPath, loggingService); loggingService.waitForAllLogTasksToFinish(); System.exit(1); } }
From source file:com.impetus.kundera.ycsb.benchmark.CouchDBNativeClient.java
public static void main(String[] args) { CouchDBNativeClient cli = new CouchDBNativeClient(); Properties props = new Properties(); props.setProperty("hosts", "localhost"); props.setProperty("port", "5984"); cli.setProperties(props);// w ww. ja va 2 s . co m try { cli.init(); } catch (Exception e) { e.printStackTrace(); System.exit(0); } HashMap<String, ByteIterator> vals = new HashMap<String, ByteIterator>(); vals.put("age", new StringByteIterator("57")); vals.put("middlename", new StringByteIterator("bradley")); vals.put("favoritecolor", new StringByteIterator("blue")); int res = cli.insert("usertable", "BrianFrankCooper", vals); System.out.println("Result of insert: " + res); HashMap<String, ByteIterator> result = new HashMap<String, ByteIterator>(); HashSet<String> fields = new HashSet<String>(); fields.add("middlename"); fields.add("age"); fields.add("favoritecolor"); res = cli.read("usertable", "BrianFrankCooper", null, result); System.out.println("Result of read: " + res); for (String s : result.keySet()) { System.out.println("[" + s + "]=[" + result.get(s) + "]"); } res = cli.delete("usertable", "BrianFrankCooper"); System.out.println("Result of delete: " + res); }
From source file:amie.keys.CSAKey.java
public static void main(String[] args) throws IOException, InterruptedException { final Triple<MiningAssistant, Float, String> parsedArgs = parseArguments(args); final Set<Rule> output = new LinkedHashSet<>(); // Helper object that contains the implementation for the calculation // of confidence and support // The file with the non-keys, one per line long timea = System.currentTimeMillis(); List<List<String>> inputNonKeys = Utilities.parseNonKeysFile(parsedArgs.third); System.out.println(inputNonKeys.size() + " input non-keys"); final List<List<String>> nonKeys = pruneBySupport(inputNonKeys, parsedArgs.second, parsedArgs.first.getKb());// ww w . ja v a 2 s . co m Collections.sort(nonKeys, new Comparator<List<String>>() { @Override public int compare(List<String> o1, List<String> o2) { int r = Integer.compare(o2.size(), o1.size()); if (r == 0) { return Integer.compare(o2.hashCode(), o1.hashCode()); } return r; } }); System.out.println(nonKeys.size() + " non-keys after pruning"); int totalLoad = computeLoad(nonKeys); System.out.println(totalLoad + " is the total load"); int nThreads = Runtime.getRuntime().availableProcessors(); //int batchSize = Math.max(Math.min(maxBatchSize, totalLoad / nThreads), minBatchSize); int batchSize = Math.max(Math.min(maxLoad, totalLoad / nThreads), minLoad); final Queue<int[]> chunks = new PriorityQueue(50, new Comparator<int[]>() { @Override public int compare(int[] o1, int[] o2) { return Integer.compare(o2[2], o1[2]); } }); final HashSet<HashSet<Integer>> nonKeysInt = new HashSet<>(); final HashMap<String, Integer> property2Id = new HashMap<>(); final HashMap<Integer, String> id2Property = new HashMap<>(); final List<Integer> propertiesList = new ArrayList<>(); int support = (int) parsedArgs.second.floatValue(); KB kb = parsedArgs.first.getKb(); buildDictionaries(nonKeys, nonKeysInt, property2Id, id2Property, propertiesList, support, kb); final List<HashSet<Integer>> nonKeysIntList = new ArrayList<>(nonKeysInt); int start = 0; int[] nextIdx = nextIndex(nonKeysIntList, 0, batchSize); int end = nextIdx[0]; int load = nextIdx[1]; while (start < nonKeysIntList.size()) { int[] chunk = new int[] { start, end, load }; chunks.add(chunk); start = end; nextIdx = nextIndex(nonKeysIntList, end, batchSize); end = nextIdx[0]; load = nextIdx[1]; } Thread[] threads = new Thread[Math.min(Runtime.getRuntime().availableProcessors(), chunks.size())]; for (int i = 0; i < threads.length; ++i) { threads[i] = new Thread(new Runnable() { @Override public void run() { while (true) { int[] chunk = null; synchronized (chunks) { if (!chunks.isEmpty()) { chunk = chunks.poll(); } else { break; } } System.out.println("Processing chunk " + Arrays.toString(chunk)); mine(parsedArgs, nonKeysIntList, property2Id, id2Property, propertiesList, chunk[0], chunk[1], output); } } }); threads[i].start(); } for (int i = 0; i < threads.length; ++i) { threads[i].join(); } long timeb = System.currentTimeMillis(); System.out.println("==== Unique C-keys ====="); for (Rule r : output) { System.out.println(Utilities.formatKey(r)); } System.out.println( "VICKEY found " + output.size() + " unique conditional keys in " + (timeb - timea) + " ms"); }
From source file:com.act.biointerpretation.l2expansion.L2FilteringDriver.java
public static void main(String[] args) throws Exception { // Build command line parser. Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());/*ww w . j a v a 2 s . c o m*/ } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { LOGGER.error("Argument parsing failed: %s", e.getMessage()); HELP_FORMATTER.printHelp(L2FilteringDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } // Print help. if (cl.hasOption(OPTION_HELP)) { HELP_FORMATTER.printHelp(L2FilteringDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } checkFilterOptionIsValid(OPTION_CHEMICAL_FILTER, cl); checkFilterOptionIsValid(OPTION_REACTION_FILTER, cl); // Get corpus files. File corpusFile = new File(cl.getOptionValue(OPTION_INPUT_CORPUS)); if (!corpusFile.exists()) { LOGGER.error("Input corpus file does not exist."); return; } File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_PATH)); outputFile.createNewFile(); if (outputFile.isDirectory()) { LOGGER.error("Output file is directory."); System.exit(1); } LOGGER.info("Reading corpus from file."); L2PredictionCorpus predictionCorpus = L2PredictionCorpus.readPredictionsFromJsonFile(corpusFile); LOGGER.info("Read in corpus with %d predictions.", predictionCorpus.getCorpus().size()); LOGGER.info("Corpus has %d distinct substrates.", predictionCorpus.getUniqueSubstrateInchis().size()); if (cl.hasOption(OPTION_FILTER_SUBSTRATES)) { LOGGER.info("Filtering by substrates."); File substratesFile = new File(cl.getOptionValue(OPTION_FILTER_SUBSTRATES)); L2InchiCorpus inchis = new L2InchiCorpus(); inchis.loadCorpus(substratesFile); Set<String> inchiSet = new HashSet<String>(); inchiSet.addAll(inchis.getInchiList()); predictionCorpus = predictionCorpus .applyFilter(prediction -> inchiSet.containsAll(prediction.getSubstrateInchis())); predictionCorpus.writePredictionsToJsonFile(outputFile); LOGGER.info("Done writing filtered corpus to file."); return; } if (cl.hasOption(OPTION_SPLIT_BY_RO)) { LOGGER.info("Splitting corpus into distinct corpuses for each ro."); Map<String, L2PredictionCorpus> corpusMap = predictionCorpus .splitCorpus(prediction -> prediction.getProjectorName()); for (Map.Entry<String, L2PredictionCorpus> entry : corpusMap.entrySet()) { String fileName = cl.getOptionValue(OPTION_OUTPUT_PATH) + "." + entry.getKey(); File oneOutputFile = new File(fileName); entry.getValue().writePredictionsToJsonFile(oneOutputFile); } LOGGER.info("Done writing split corpuses to file."); return; } predictionCorpus = runDbLookups(cl, predictionCorpus, opts); LOGGER.info("Applying filters."); predictionCorpus = applyFilter(predictionCorpus, ALL_CHEMICALS_IN_DB, cl, OPTION_CHEMICAL_FILTER); predictionCorpus = applyFilter(predictionCorpus, REACTION_MATCHES_DB, cl, OPTION_REACTION_FILTER); LOGGER.info("Filtered corpus has %d predictions.", predictionCorpus.getCorpus().size()); LOGGER.info("Printing final corpus."); predictionCorpus.writePredictionsToJsonFile(outputFile); LOGGER.info("L2FilteringDriver complete!."); }
From source file:Main.java
public static <A> Set<A> set(A... a) { Set<A> set = new HashSet<A>(); Collections.addAll(set, a);/* w ww . j a v a 2 s. c o m*/ return set; }