List of usage examples for java.util Arrays stream
public static DoubleStream stream(double[] array)
From source file:com.yahoo.bard.webservice.config.ConfigResourceLoader.java
/** * Use a string to load a stream of all resources from the class path which match a given name. * * @param name The class path address of a resource ('/foo' means a resource named foo in the default package) * * @return A stream of all class path resources corresponding to a particular name * * @throws IOException if any resources cannot be read from the class path successfully. *///from w w w . ja v a 2 s . co m public Stream<Resource> loadResourcesWithName(String name) throws IOException { String resourceName = RESOURCE_LOADER_PREFIX + name; LOG.debug("Attempting to load resources named {}", resourceName); return Arrays.stream(resolver.getResources(resourceName)) .peek(it -> LOG.debug(RESOURCE_LOAD_MESSAGE.logFormat(name, it))); }
From source file:io.wcm.devops.conga.tooling.maven.plugin.PackageMojo.java
@Override public void execute() throws MojoExecutionException, MojoFailureException { resourceLoader = new ResourceLoader(); Set<String> selectedEnvironments; if (environments != null && environments.length > 0) { selectedEnvironments = ImmutableSet.copyOf(environments); } else {/*w ww .j a va 2s . c o m*/ selectedEnvironments = null; } // collect configuration environment directories File configRootDir = getTargetDir(); List<File> environmentDirs = Arrays.stream(configRootDir.listFiles()).filter(file -> file.isDirectory()) .filter(dir -> selectedEnvironments == null || selectedEnvironments.contains(dir.getName())) .collect(Collectors.toList()); if (artifactPerEnvironment) { // generate an ZIP artifact with generated configurations for each environment for (File environmentDir : environmentDirs) { // classifier is environment name // if current project is not a config project, prefix the classifier String classifier = environmentDir.getName(); if (!StringUtils.equals(project.getPackaging(), PACKAGING_CONFIGURATION)) { classifier = CLASSIFIER_CONFIGURATION + "-" + classifier; } validateClassifier(classifier); // build ZIP artifact File outputFile = buildZipFile(environmentDir, classifier); // attach ZIP artifact projectHelper.attachArtifact(project, outputFile, classifier); } } else { // generate an ZIP artifact containing all environments String classifier = null; if (!StringUtils.equals(project.getPackaging(), PACKAGING_CONFIGURATION)) { classifier = CLASSIFIER_CONFIGURATION; } validateClassifier(classifier); File outputFile = buildZipFile(configRootDir, classifier); // set or attach ZIP artifact if (StringUtils.equals(project.getPackaging(), PACKAGING_CONFIGURATION)) { project.getArtifact().setFile(outputFile); } else { projectHelper.attachArtifact(project, outputFile, CLASSIFIER_CONFIGURATION); } } }
From source file:org.createnet.raptor.auth.service.services.AclTokenService.java
@Retryable(maxAttempts = 3, value = AclManagerService.AclManagerException.class, backoff = @Backoff(delay = 500, multiplier = 3)) public void register(Token token) { User owner = token.getUser();/*from ww w.j a v a 2 s . co m*/ List<Permission> permissions = list(token, owner); Sid sid = new UserSid(owner); logger.debug("Found {} permissions for {}", permissions.size(), owner.getUuid()); if (permissions.isEmpty()) { logger.debug("Set default permission"); List<Permission> newPerms = Arrays.stream(defaultPermissions).collect(Collectors.toList()); if (owner.getId().equals(token.getUser().getId())) { newPerms.add(RaptorPermission.ADMINISTRATION); } try { aclManagerService.addPermissions(Token.class, token.getId(), sid, newPerms); } catch (AclManagerService.AclManagerException ex) { logger.warn("Failed to store default permission for {} ({}): {}", token.getId(), sid, ex.getMessage()); throw ex; } permissions.addAll(newPerms); } String perms = String.join(", ", RaptorPermission.toLabel(permissions)); logger.debug("Permission set for device {} to {} - {}", token.getName(), token.getUser().getUuid(), perms); }
From source file:eu.itesla_project.online.tools.PrintOnlineWorkflowSimulationResultsTool.java
@Override public void run(CommandLine line) throws Exception { OnlineConfig config = OnlineConfig.load(); OnlineDb onlinedb = config.getOnlineDbFactoryClass().newInstance().create(); String workflowId = line.getOptionValue("workflow"); OnlineWorkflowResults wfResults = onlinedb.getResults(workflowId); if (wfResults != null) { if (!wfResults.getUnsafeContingencies().isEmpty()) { OnlineWorkflowParameters parameters = onlinedb.getWorkflowParameters(workflowId); SecurityIndexType[] securityIndexTypes = null; if (line.hasOption(SECURITY_INDEXES)) { Set<SecurityIndexType> securityIndexesTypeSet = Arrays .stream(line.getOptionValue(SECURITY_INDEXES).split(",")) .map(SecurityIndexType::valueOf).collect(Collectors.toSet()); securityIndexTypes = securityIndexesTypeSet .toArray(new SecurityIndexType[securityIndexesTypeSet.size()]); } else { securityIndexTypes = parameters.getSecurityIndexes() == null ? SecurityIndexType.values() : parameters.getSecurityIndexes() .toArray(new SecurityIndexType[parameters.getSecurityIndexes().size()]); }/*from w w w. j a v a 2 s . c o m*/ Table table = new Table(securityIndexTypes.length + 2, BorderStyle.CLASSIC_WIDE); StringWriter content = new StringWriter(); CsvWriter cvsWriter = new CsvWriter(content, ','); String[] headers = new String[securityIndexTypes.length + 2]; int i = 0; table.addCell("Contingency", new CellStyle(CellStyle.HorizontalAlign.center)); headers[i++] = "Contingency"; table.addCell("State", new CellStyle(CellStyle.HorizontalAlign.center)); headers[i++] = "State"; for (SecurityIndexType securityIndexType : securityIndexTypes) { table.addCell(securityIndexType.getLabel(), new CellStyle(CellStyle.HorizontalAlign.center)); headers[i++] = securityIndexType.getLabel(); } cvsWriter.writeRecord(headers); for (String contingencyId : wfResults.getUnsafeContingencies()) { for (Integer stateId : wfResults.getUnstableStates(contingencyId)) { String[] values = new String[securityIndexTypes.length + 2]; i = 0; table.addCell(contingencyId); values[i++] = contingencyId; table.addCell(stateId.toString(), new CellStyle(CellStyle.HorizontalAlign.right)); values[i++] = stateId.toString(); HashMap<String, String> indexesValues = getIndexesValues( wfResults.getIndexesData(contingencyId, stateId), securityIndexTypes); for (SecurityIndexType securityIndexType : securityIndexTypes) { table.addCell(indexesValues.get(securityIndexType.getLabel()), new CellStyle(CellStyle.HorizontalAlign.center)); values[i++] = indexesValues.get(securityIndexType.getLabel()); } cvsWriter.writeRecord(values); } } cvsWriter.flush(); if (line.hasOption("csv")) System.out.println(content.toString()); else System.out.println(table.render()); cvsWriter.close(); } else System.out.println("\nNo contingencies requiring T-D simulation"); } else System.out.println("No results for this workflow"); onlinedb.close(); }
From source file:com.ikanow.aleph2.v1.document_db.utils.V1DocumentDbHadoopUtils.java
/** * @param input_config - the input settings * @return//from w w w. j a va2 s . c o m */ @SuppressWarnings({ "rawtypes", "unchecked" }) public static IAnalyticsAccessContext<InputFormat> getInputFormat(final String user_id, final AnalyticThreadJobBean.AnalyticThreadJobInputBean job_input, final Optional<ISecurityService> maybe_security, final V1DocDbConfigBean config) { //TODO (ALEPH-20): need to perform security in here return new IAnalyticsAccessContext<InputFormat>() { private LinkedHashMap<String, Object> _mutable_output = null; @Override public String describe() { //(return the entire thing) return ErrorUtils.get("service_name={0} options={1}", this.getAccessService().right().value().getSimpleName(), this.getAccessConfig().get().entrySet().stream() .filter(kv -> !DESCRIBE_FILTER.contains(kv.getKey())) .collect(Collectors.toMap(kv -> kv.getKey(), kv -> kv.getValue()))); } /* (non-Javadoc) * @see com.ikanow.aleph2.data_model.interfaces.data_analytics.IAnalyticsAccessContext#getAccessService() */ @Override public Either<InputFormat, Class<InputFormat>> getAccessService() { return Either.right((Class<InputFormat>) (Class<?>) Aleph2V1InputFormat.class); } /* (non-Javadoc) * @see com.ikanow.aleph2.data_model.interfaces.data_analytics.IAnalyticsAccessContext#getAccessConfig() */ @Override public Optional<Map<String, Object>> getAccessConfig() { if (null != _mutable_output) { return Optional.of(_mutable_output); } _mutable_output = new LinkedHashMap<>(); // Parse various inputs: final List<String> communities = Arrays .stream(job_input.resource_name_or_id() .substring(BucketUtils.EXTERNAL_BUCKET_PREFIX.length()).split("_")) .collect(Collectors.toList()); // Validate communities: maybe_security.ifPresent(sec -> { communities.stream().filter(cid -> !sec.isUserPermitted(user_id, Tuples._2T("community", cid), Optional.of(ISecurityService.ACTION_READ))).findAny().ifPresent(cid -> { throw new RuntimeException(ErrorUtils .get(V1DocumentDbErrorUtils.V1_DOCUMENT_USER_PERMISSIONS, user_id, cid)); }); }); final String query = _mapper .convertValue(Optional.ofNullable(job_input.filter()).orElse(Collections.emptyMap()), JsonNode.class) .toString(); final Tuple4<String, Tuple2<Integer, Integer>, BasicDBObject, DBObject> horrible_object = LegacyV1HadoopUtils .parseQueryObject(query, communities); final String db_server = config.mongodb_connection(); // Here's all the fields to fill in // 1) Generic MongoDB fields: //name of job shown in jobtracker --><name>mongo.job.name</name><value>title //run the job verbosely ? --><name>mongo.job.verbose</name><value>true //Run the job in the foreground and wait for response, or background it? --><name>mongo.job.background</name><value>false //If you are reading from mongo, the URI --><name>mongo.input.uri</name><value>mongodb://"+dbserver+"/"+input //The number of documents to limit to for read [OPTIONAL] --><name>mongo.input.limit</name><value>" + nLimit //The query, in JSON, to execute [OPTIONAL] --><name>mongo.input.query</name><value>" + StringEscapeUtils.escapeXml(query) //The fields, in JSON, to read [OPTIONAL] --><name>mongo.input.fields</name><value>"+( (fields==null) ? ("") : fields ) //InputFormat Class --><name>mongo.job.input.format</name><value>com.ikanow.infinit.e.data_model.custom.InfiniteMongoInputFormat _mutable_output.put("mongo.job.name", Optional.ofNullable(job_input.data_service()).orElse("unknown") + ":" + Optional.ofNullable(job_input.resource_name_or_id()).orElse("unknown")); // (i think this is ignored in fact) _mutable_output.put("mongo.job.verbose", "true"); _mutable_output.put("mongo.job.background", "false"); _mutable_output.put("mongo.input.uri", "mongodb://" + db_server + "/doc_metadata.metadata"); _mutable_output.put("mongo.input.query", horrible_object._1()); _mutable_output.put("mongo.input.fields", Optional.ofNullable(horrible_object._4()).map(o -> o.toString()).orElse("")); _mutable_output.put("mongo.input.limit", Optional.ofNullable(job_input.config()) .map(cfg -> cfg.test_record_limit_request()).map(o -> o.toString()).orElse("0")); // 2) Basic Infinit.e/MongoDB fields: //Maximum number of splits [optional] --><name>max.splits</name><value>"+nSplits //Maximum number of docs per split [optional] --><name>max.docs.per.split</name><value>"+nDocsPerSplit _mutable_output.put("max.splits", horrible_object._2()._1().toString()); _mutable_output.put("max.docs.per.split", horrible_object._2()._2().toString()); // 3) Advanced Infinit.e/MongoDB fields: //Infinit.e src tags filter [optional] --><name>infinit.e.source.tags.filter</name><value>"+srcTags.toString() if (null != horrible_object._3()) { _mutable_output.put("infinit.e.source.tags.filter", horrible_object._3().toString()); } return Optional.of(Collections.unmodifiableMap(_mutable_output)); } }; }
From source file:com.teradata.benchto.driver.graphite.GraphiteClient.java
@Retryable(value = { RestClientException.class,
IncompleteDataException.class }, backoff = @Backoff(delay = 5000, multiplier = 2), maxAttempts = 4)
public Map<String, double[]> loadMetrics(Map<String, String> metrics, long fromEpochSecond,
long toEpochSecond) {
URI uri = buildLoadMetricsURI(metrics, fromEpochSecond, toEpochSecond);
LOGGER.debug("Loading metrics: {}", uri);
ResponseEntity<GraphiteRenderResponseItem[]> response = restTemplate.getForEntity(uri,
GraphiteRenderResponseItem[].class);
if (response.getStatusCode() != OK) {
throw new BenchmarkExecutionException("Could not load metrics: " + metrics + " - error: " + response);
}//w ww . ja v a 2 s.com
return Arrays.stream(response.getBody()).collect(toMap(GraphiteRenderResponseItem::getTarget,
responseItem -> parseDataPoints(responseItem.datapoints)));
}
From source file:eu.itesla_project.online.tools.PrintOnlineWorkflowPostContingencyViolationsTool.java
@Override public void run(CommandLine line) throws Exception { OnlineConfig config = OnlineConfig.load(); String workflowId = line.getOptionValue("workflow"); final LimitViolationFilter violationsFilter = (line.hasOption("type")) ? new LimitViolationFilter(Arrays.stream(line.getOptionValue("type").split(",")) .map(LimitViolationType::valueOf).collect(Collectors.toSet()), 0) : null;/*from w ww. ja va 2 s. c o m*/ TableFormatterConfig tableFormatterConfig = TableFormatterConfig.load(); Column[] tableColumns = { new Column("State"), new Column("Contingency"), new Column("Equipment"), new Column("Type"), new Column("Value"), new Column("Limit"), new Column("Limit reduction"), new Column("Voltage Level") }; Path cvsOutFile = (line.hasOption("csv")) ? Paths.get(line.getOptionValue("csv")) : null; try (OnlineDb onlinedb = config.getOnlineDbFactoryClass().newInstance().create()) { if (line.hasOption("state") && line.hasOption("contingency")) { Integer stateId = Integer.parseInt(line.getOptionValue("state")); String contingencyId = line.getOptionValue("contingency"); List<LimitViolation> violations = onlinedb.getPostContingencyViolations(workflowId, stateId, contingencyId); if (violations != null && !violations.isEmpty()) { try (TableFormatter formatter = PrintOnlineWorkflowUtils.createFormatter(tableFormatterConfig, cvsOutFile, TABLE_TITLE, tableColumns)) { printStateContingencyViolations(formatter, stateId, contingencyId, violations, violationsFilter); } } else { System.out.println("\nNo post contingency violations for workflow " + workflowId + ", contingency " + contingencyId + " and state " + stateId); } } else if (line.hasOption("state")) { Integer stateId = Integer.parseInt(line.getOptionValue("state")); Map<String, List<LimitViolation>> stateViolationsByStateId = onlinedb .getPostContingencyViolations(workflowId, stateId); if (stateViolationsByStateId != null && !stateViolationsByStateId.keySet().isEmpty()) { try (TableFormatter formatter = PrintOnlineWorkflowUtils.createFormatter(tableFormatterConfig, cvsOutFile, TABLE_TITLE, tableColumns)) { new TreeMap<>(stateViolationsByStateId) .forEach((contingencyId, violations) -> printStateContingencyViolations(formatter, stateId, contingencyId, violations, violationsFilter)); } } else { System.out.println("\nNo post contingency violations for workflow " + workflowId + " and state " + stateId); } } else { if (line.hasOption("contingency")) { String contingencyId = line.getOptionValue("contingency"); Map<Integer, List<LimitViolation>> contingencyViolationsByContingencyId = onlinedb .getPostContingencyViolations(workflowId, contingencyId); if (contingencyViolationsByContingencyId != null && !contingencyViolationsByContingencyId.keySet().isEmpty()) { try (TableFormatter formatter = PrintOnlineWorkflowUtils .createFormatter(tableFormatterConfig, cvsOutFile, TABLE_TITLE, tableColumns)) { new TreeMap<>(contingencyViolationsByContingencyId) .forEach((stateId, violations) -> printStateContingencyViolations(formatter, stateId, contingencyId, violations, violationsFilter)); } } else { System.out.println("\nNo post contingency violations for workflow " + workflowId + " and contingency " + contingencyId); } } else { Map<Integer, Map<String, List<LimitViolation>>> wfViolations = onlinedb .getPostContingencyViolations(workflowId); if (wfViolations != null && !wfViolations.keySet().isEmpty()) { try (TableFormatter formatter = PrintOnlineWorkflowUtils .createFormatter(tableFormatterConfig, cvsOutFile, TABLE_TITLE, tableColumns)) { new TreeMap<>(wfViolations).forEach((stateId, stateViolations) -> { if (stateViolations != null) { new TreeMap<>(stateViolations).forEach((contingencyId, violations) -> { printStateContingencyViolations(formatter, stateId, contingencyId, violations, violationsFilter); }); } }); } } else { System.out.println("\nNo post contingency violations for workflow " + workflowId); } } } } }
From source file:gedi.atac.OnlinePeakFinder.java
@Override public IntervalTree<GenomicRegion, Double> map(ReferenceSequence reference, GenomicRegion region, PixelLocationMapping pixelMapping, MutablePair<PixelBlockToValuesMap, IntervalTree<GenomicRegion, AlignedReadsData>> data) { int bases = 0; int bins = data.Item1.size(); int[] c = new int[bins]; for (int b = 0; b < data.Item1.size(); b++) { PixelLocationMappingBlock bl = data.Item1.getBlock(b); bases += bl.getStopBp() + 1 - bl.getStartBp(); c[b] = (int) NumericArrayFunction.Sum.applyAsDouble(data.Item1.getValues(b)); }/*w w w. j av a 2 s . c o m*/ System.out.printf("Bases=%d\tBins=%d\tInsertions=%d\tSites=%d\n", bases, bins, ArrayUtils.sum(c), Arrays.stream(c).filter(v -> v > 0).count()); IntArrayList hist = new IntArrayList(); for (int i : c) hist.increment(i); try { r.eval("layout(t(1:2))"); r.set("h", hist.toIntArray()); r.eval("barplot(h,names.arg=1:length(h))"); } catch (RserveException e) { } hist.clear(); for (GenomicRegion d : data.Item2.keySet()) hist.increment(d.getTotalLength(), data.Item2.get(d).getTotalCountOverallFloor(ReadCountMode.Weight)); try { r.set("h", hist.toIntArray()); r.eval("barplot(h,names.arg=1:length(h))"); } catch (RserveException e) { } GenomicRegion re = new ArrayGenomicRegion(); double mean = ArrayUtils.sum(c) / c.length; // find consecutive ranges that are >=factor*mean int sizeBefore; do { sizeBefore = re.getTotalLength(); double min = mean * factor; int start = -1; double sum = 0; for (int i = 0; i < c.length; i++) { if (c[i] >= min) { // in range if (start == -1) start = i; } else { // not in range if (start > -1) { for (; start - 1 >= 0 && c[start - 1] > mean; start--) ; for (; i + 1 < c.length && c[i + 1] > mean; i++) ; re = re.union(new ArrayGenomicRegion(start, i)); start = -1; } sum += c[i]; } } if (start > -1) { for (; start - 1 >= 0 && c[start - 1] > mean; start--) ; re = re.union(new ArrayGenomicRegion(start, c.length)); } // compute new mean mean = sum / (c.length - re.getTotalLength()); } while (sizeBefore < re.getTotalLength()); IntervalTree<GenomicRegion, Double> re2 = new IntervalTree<GenomicRegion, Double>( data.Item2.getReference()); for (GenomicRegionPart p : re) re2.put(new ArrayGenomicRegion(data.Item1.getBlock(p.getStart()).getStartBp(), data.Item1.getBlock(p.getStop()).getStopBp() + 1), max(c, p.getStart(), p.getStop() + 1)); return re2; }
From source file:com.flipkart.flux.client.intercept.WorkflowInterceptor.java
private String checkForCorrelationId(Object[] arguments) throws IllegalAccessException { final String[] correlationId = { null }; /* Iterate over given arguments to find if there is any argument that has a field marked with <code>CorrelationId</code> */ for (Object anArgument : arguments) { final Field[] allFields = anArgument.getClass().getDeclaredFields(); /* Search for any field which is of type String and has a CorrelationId annotation */ final Optional<Field> possibleAnnotatedField = Arrays.stream(allFields) .filter(field -> String.class.isAssignableFrom(field.getType())) .filter(field -> field.getAnnotationsByType(CorrelationId.class).length > 0).findAny(); /* If we have a field that matches above criteria, we populate the correlationId variable and break */ if (possibleAnnotatedField.isPresent()) { final Field correlationIdAnnotatedField = possibleAnnotatedField.get(); final boolean originalAccessibility = correlationIdAnnotatedField.isAccessible(); if (!originalAccessibility) { correlationIdAnnotatedField.setAccessible(true); }/*ww w.j av a 2 s . com*/ try { correlationId[0] = (String) correlationIdAnnotatedField.get(anArgument); break; } finally { if (!originalAccessibility) { correlationIdAnnotatedField.setAccessible(false); } } } } return correlationId[0]; }
From source file:io.blobkeeper.file.service.FileListServiceImpl.java
@Override public List<Integer> getDisks() { java.io.File filePath = new java.io.File(configuration.getBasePath()); checkArgument(filePath.exists(), "Base path must be exists"); return Arrays.stream(filePath.list(DIRECTORY)).map(this::parseDisk).filter(disk -> disk != null) .collect(toImmutableList()); }