List of usage examples for org.apache.commons.lang ArrayUtils addAll
public static double[] addAll(double[] array1, double[] array2)
Adds all the elements of the given arrays into a new array.
From source file:gda.hrpd.pmac.EpicsCVScanController.java
private double[] getCount() { double[] y1 = ArrayUtils.EMPTY_DOUBLE_ARRAY; try {//from w ww. ja va 2 s. co m // logger.info("gets MAC1Y"); y1 = getMAC1Y(); // logger.info("gets MAC1Y DONE"); } catch (TimeoutException e) { logger.error("Timeout while gets MAC1Y", e); e.printStackTrace(); } catch (CAException e) { logger.error("CAException while gets MAC1Y", e); e.printStackTrace(); } catch (InterruptedException e) { logger.error("InterruptedException while gets MAC1Y", e); } double[] y2 = ArrayUtils.EMPTY_DOUBLE_ARRAY; try { // logger.info("gets MAC2Y"); y2 = getMAC2Y(); // logger.info("gets MAC2Y DONE"); } catch (TimeoutException e) { logger.error("Timeout while gets MAC2Y", e); e.printStackTrace(); } catch (CAException e) { logger.error("CAException while gets MAC2Y", e); e.printStackTrace(); } catch (InterruptedException e) { logger.error("InterruptedException while gets MAC2Y", e); } double[] y3 = ArrayUtils.EMPTY_DOUBLE_ARRAY; try { // logger.info("gets MAC3Y"); y3 = getMAC3Y(); // logger.info("gets MAC3Y DONE"); } catch (TimeoutException e) { logger.error("Timeout while gets MAC3Y", e); e.printStackTrace(); } catch (CAException e) { logger.error("CAException while gets MAC3Y", e); e.printStackTrace(); } catch (InterruptedException e) { logger.error("InterruptedException while gets MAC3Y", e); } double[] y4 = ArrayUtils.EMPTY_DOUBLE_ARRAY; try { // logger.info("gets MAC4Y"); y4 = getMAC4Y(); // logger.info("gets MAC4Y DONE"); } catch (TimeoutException e) { logger.error("Timeout while gets MAC4Y", e); e.printStackTrace(); } catch (CAException e) { logger.error("CAException while gets MAC4Y", e); e.printStackTrace(); } catch (InterruptedException e) { logger.error("InterruptedException while gets MAC4Y", e); } double[] y5 = ArrayUtils.EMPTY_DOUBLE_ARRAY; try { // logger.info("gets MAC5Y"); y5 = getMAC5Y(); // logger.info("gets MAC5Y DONE"); } catch (TimeoutException e) { logger.error("Timeout while gets MAC5Y", e); e.printStackTrace(); } catch (CAException e) { logger.error("CAException while gets MAC5Y", e); e.printStackTrace(); } catch (InterruptedException e) { logger.error("InterruptedException while gets MAC5Y", e); } return ArrayUtils.subarray( ArrayUtils.addAll(ArrayUtils.addAll(ArrayUtils.addAll(ArrayUtils.addAll(y1, y2), y3), y4), y5), 16500, 305000); }
From source file:com.linkedin.cubert.analyzer.physical.AggregateRewriter.java
private JsonNode createBlockgenForMV(ObjectNode programNode, ObjectNode cubeOperatorNode, Pair<ObjectNode, ObjectNode> bgInfo, String mvName, String mvPath, String[] mvColumns) throws AggregateRewriteException { String bgFactPath = null;/*from w w w . ja v a2 s . c om*/ String[] partitionKeys = null; String[] pivotKeys = null; String[] shufflePivotKeys = null; String mvInputPath = mvPath + "/avro"; if (lineage.isBlockgenByIndex(bgInfo.getSecond())) { partitionKeys = JsonUtils.asArray(bgInfo.getFirst().get("partitionKeys")); String indexName = bgInfo.getFirst().get("index").getTextValue(); ObjectNode jobNode = lineage.getOperatorJobNode(bgInfo.getSecond()); // This should include BLOCK_ID, else assert. shufflePivotKeys = JsonUtils.asArray(((ObjectNode) (jobNode.get("shuffle"))).get("pivotKeys")); String indexPath = lineage.traceIndexPath(jobNode, indexName); System.out.println("Traced blockgen index " + indexName + " path as" + indexPath); System.out.println("job node = " + jobNode.toString()); bgFactPath = indexPath; } else { bgFactPath = lineage.getDatedPathRoot((ArrayNode) (bgInfo.getSecond().get("path"))); partitionKeys = JsonUtils.asArray(bgInfo.getSecond().get("partitionKeys")); pivotKeys = JsonUtils.asArray(bgInfo.getSecond().get("pivotKeys")); shufflePivotKeys = (String[]) ArrayUtils.addAll(new String[] { "BLOCK_ID" }, pivotKeys); } ArrayNode cacheIndexNode = JsonUtils.createArrayNode(); cacheIndexNode.add(RewriteUtils.createObjectNode("name", mvName + "_fact_index", "path", bgFactPath)); JsonNode mapNode = JsonUtils.makeJson( String.format("[{'input' : {'name':'%s', 'type': 'AVRO', 'path':['%s']}}]", mvName, mvInputPath)); System.out.println("Blockgen partition keys = " + Arrays.toString(partitionKeys)); ObjectNode blockIndexJoin = RewriteUtils.createObjectNode("operator", "BLOCK_INDEX_JOIN", "input", mvName, "output", mvName, "index", mvName + "_fact_index", "partitionKeys", JsonUtils.createArrayNode(partitionKeys)); ObjectNode mapperNode = (ObjectNode) (((ArrayNode) mapNode).get(0)); mapperNode.put("operators", JsonUtils.createArrayNode()); ((ArrayNode) (mapperNode.get("operators"))).add(blockIndexJoin); JsonNode shuffleNode = RewriteUtils.createObjectNode("name", mvName, "type", "SHUFFLE", "partitionKeys", JsonUtils.createArrayNode(new String[] { "BLOCK_ID" }), "pivotKeys", JsonUtils.createArrayNode(shufflePivotKeys)); JsonNode reduceOpNode = RewriteUtils.createObjectNode("operator", "CREATE_BLOCK", "input", mvName, "output", mvName + "_blockgen", "blockgenType", "BY_INDEX", "index", mvName + "_fact_index", "indexPath", bgFactPath, "partitionKeys", JsonUtils.createArrayNode(new String[] { "BLOCK_ID" }), "pivotKeys", JsonUtils.createArrayNode(shufflePivotKeys), "originalPartitionKeys", JsonUtils.createArrayNode(partitionKeys)); ArrayNode reduceNode = JsonUtils.createArrayNode(); reduceNode.add(reduceOpNode); ObjectNode outputNode = RewriteUtils.createObjectNode("name", mvName + "_blockgen", "path", mvPath + "/blockgen", "type", "RUBIX", "params", RewriteUtils.createObjectNode("overwrite", "true")); ObjectNode jobNode = RewriteUtils.createObjectNode("name", "BLOCKGEN FOR MV", "map", mapNode, "shuffle", shuffleNode, "reduce", reduceNode, "output", outputNode); jobNode.put("cacheIndex", cacheIndexNode); jobNode.put("reducers", 100); System.out.println("JOB json = " + jobNode.toString()); return jobNode; }
From source file:com.oneops.inductor.WorkOrderExecutor.java
/** * Removes the remote work order after remote execution * * @param wo remote work order to be removed. * @param keyFile file to be used for executing the remote ssh * @param pr the process runner.//from www .ja va 2 s. c o m */ private void removeRemoteWorkOrder(CmsWorkOrderSimple wo, String keyFile, ProcessRunner pr) { String user = ONEOPS_USER; String comments = ""; if (!isDebugEnabled(wo)) { // clear the workorder files String logKey = getLogKey(wo); String host = getWorkOrderHost(wo, getLogKey(wo)); String port = "22"; if (host.contains(":")) { String[] parts = host.split(":"); host = parts[0]; port = parts[1]; logger.info("using port from " + config.getIpAttribute()); } String remoteCmd = "rm " + getRemoteFileName(wo); String[] cmd = (String[]) ArrayUtils.addAll(sshCmdLine, new String[] { keyFile, "-p " + port, user + "@" + host, remoteCmd }); logger.info(logKey + " ### EXEC: " + user + "@" + host + " " + remoteCmd); ProcessResult result = pr.executeProcessRetry( new ExecutionContext(wo, cmd, getLogKey(wo), getRetryCountForWorkOrder(wo))); if (result.getResultCode() != 0) { // Not throwing exceptions, Should be ok if we are not able to // remove remote wo. logger.error(logKey + comments); } else { logger.info("removed remote workorder"); } } else { logger.info("debug enabled, not removing remote workorders"); } }
From source file:au.org.ala.biocache.dao.SearchDAOImpl.java
/** * Note - this method extracts from CASSANDRA rather than the Index. *///from w ww . j ava 2s . c om public Map<String, Integer> writeResultsToStream(DownloadRequestParams downloadParams, OutputStream out, int i, boolean includeSensitive, DownloadDetailsDTO dd) throws Exception { int resultsCount = 0; Map<String, Integer> uidStats = new HashMap<String, Integer>(); //stores the remaining limit for data resources that have a download limit Map<String, Integer> downloadLimit = new HashMap<String, Integer>(); try { SolrQuery solrQuery = initSolrQuery(downloadParams, false, null); //ensure that the qa facet is being ordered alphabetically so that the order is consistent. boolean getAssertionsFromFacets = "all".equals(downloadParams.getQa()); if (getAssertionsFromFacets) { //set the order for the facet to be based on the index - this will force the assertions to be returned in the same order each time //based on alphabetical sort. The number of QA's may change between searches so we can't guarantee that the order won't change solrQuery.add("f.assertions.facet.sort", "index"); } formatSearchQuery(downloadParams); //add context information updateQueryContext(downloadParams); logger.info("search query: " + downloadParams.getFormattedQuery()); solrQuery.setQuery(buildSpatialQueryString(downloadParams)); //Only the fields specified below will be included in the results from the SOLR Query solrQuery.setFields("row_key", "institution_uid", "collection_uid", "data_resource_uid", "data_provider_uid"); String dFields = downloadParams.getFields(); if (includeSensitive) { //include raw latitude and longitudes dFields = dFields .replaceFirst("decimalLatitude.p", "decimalLatitude,decimalLongitude,decimalLatitude.p") .replaceFirst(",locality,", ",locality,sensitive_locality,"); } StringBuilder sb = new StringBuilder(dFields); if (downloadParams.getExtra().length() > 0) sb.append(",").append(downloadParams.getExtra()); StringBuilder qasb = new StringBuilder(); QueryResponse qr = runSolrQuery(solrQuery, downloadParams.getFq(), 0, 0, "_docid_", "asc"); dd.setTotalRecords(qr.getResults().getNumFound()); //get the assertion facets to add them to the download fields List<FacetField> facets = qr.getFacetFields(); for (FacetField facet : facets) { if (facet.getName().equals("assertions") && facet.getValueCount() > 0) { for (FacetField.Count facetEntry : facet.getValues()) { //System.out.println("facet: " + facetEntry.getName()); if (qasb.length() > 0) qasb.append(","); qasb.append(facetEntry.getName()); } } else if (facet.getName().equals("data_resource_uid") && checkDownloadLimits) { //populate the download limit initDownloadLimits(downloadLimit, facet); } } //Write the header line String qas = qasb.toString(); String[] fields = sb.toString().split(","); String[] qaFields = qas.equals("") ? new String[] {} : qas.split(","); String[] qaTitles = downloadFields.getHeader(qaFields, false); String[] titles = downloadFields.getHeader(fields, true); String[] header = org.apache.commons.lang3.ArrayUtils.addAll(titles, qaTitles); //Create the Writer that will be used to format the records //construct correct RecordWriter based on the supplied fileType final au.org.ala.biocache.RecordWriter rw = downloadParams.getFileType().equals("csv") ? new CSVRecordWriter(out, header, downloadParams.getSep(), downloadParams.getEsc()) : new ShapeFileRecordWriter(downloadParams.getFile(), out, (String[]) ArrayUtils.addAll(fields, qaFields)); if (rw instanceof ShapeFileRecordWriter) { dd.setHeaderMap(((ShapeFileRecordWriter) rw).getHeaderMappings()); } //download the records that have limits first... if (downloadLimit.size() > 0) { String[] originalFq = downloadParams.getFq(); StringBuilder fqBuilder = new StringBuilder("-("); for (String dr : downloadLimit.keySet()) { //add another fq to the search for data_resource_uid downloadParams.setFq((String[]) ArrayUtils.add(originalFq, "data_resource_uid:" + dr)); resultsCount = downloadRecords(downloadParams, rw, downloadLimit, uidStats, fields, qaFields, resultsCount, dr, includeSensitive, dd); if (fqBuilder.length() > 2) fqBuilder.append(" OR "); fqBuilder.append("data_resource_uid:").append(dr); } fqBuilder.append(")"); //now include the rest of the data resources //add extra fq for the remaining records downloadParams.setFq((String[]) ArrayUtils.add(originalFq, fqBuilder.toString())); resultsCount = downloadRecords(downloadParams, rw, downloadLimit, uidStats, fields, qaFields, resultsCount, null, includeSensitive, dd); } else { //download all at once downloadRecords(downloadParams, rw, downloadLimit, uidStats, fields, qaFields, resultsCount, null, includeSensitive, dd); } rw.finalise(); } catch (SolrServerException ex) { logger.error("Problem communicating with SOLR server. " + ex.getMessage(), ex); } return uidStats; }
From source file:com.datatorrent.stram.cli.DTCli.java
private List<Completer> defaultCompleters() { Map<String, CommandSpec> commands = new TreeMap<String, CommandSpec>(); commands.putAll(logicalPlanChangeCommands); commands.putAll(connectedCommands);/*w w w. j a v a 2 s . c o m*/ commands.putAll(globalCommands); List<Completer> completers = new LinkedList<Completer>(); for (Map.Entry<String, CommandSpec> entry : commands.entrySet()) { String command = entry.getKey(); CommandSpec cs = entry.getValue(); List<Completer> argCompleters = new LinkedList<Completer>(); argCompleters.add(new StringsCompleter(command)); Arg[] args = (Arg[]) ArrayUtils.addAll(cs.requiredArgs, cs.optionalArgs); if (args != null) { if (cs instanceof OptionsCommandSpec) { // ugly hack because jline cannot dynamically change completer while user types if (args[0] instanceof FileArg || args[0] instanceof VarArg) { for (int i = 0; i < 10; i++) { argCompleters.add(new MyFileNameCompleter()); } } } else { for (Arg arg : args) { if (arg instanceof FileArg || arg instanceof VarArg) { argCompleters.add(new MyFileNameCompleter()); } else if (arg instanceof CommandArg) { argCompleters.add(new StringsCompleter(commands.keySet().toArray(new String[] {}))); } else { argCompleters.add(MyNullCompleter.INSTANCE); } } } } completers.add(new ArgumentCompleter(argCompleters)); } List<Completer> argCompleters = new LinkedList<Completer>(); Set<String> set = new TreeSet<String>(); set.addAll(aliases.keySet()); set.addAll(macros.keySet()); argCompleters.add(new StringsCompleter(set.toArray(new String[] {}))); for (int i = 0; i < 10; i++) { argCompleters.add(new MyFileNameCompleter()); } completers.add(new ArgumentCompleter(argCompleters)); return completers; }
From source file:com.novartis.opensource.yada.util.QueryUtils.java
/** * This method uses a variety of variables from {@code yq} to determine the * number of jdbc positional parameters which must be included in the SQL * {@code in} clause in the stored query. Once the parameter count is * determined, the original SQL is amended with additional jdbc parameter * placeholders (i.e., {@code ?}), and the amended SQL is stored in the * {@code yq}./*w ww. j av a 2 s .c om*/ * * @param yq * the query being processed * @param row * the index of the list of value lists in the query containing the * data to evaluate * @return modified SQL code * @deprecated as of 7.1.0 */ @Deprecated public String processInColumns(YADAQuery yq, int row) { String[] inColumns = yq.getIns(); String coreSql = yq.getYADACode(); LinkedHashMap<String, String[]> newData = new LinkedHashMap<>(); // to be i.e., YADA_1:[],YADA_2:[] if (inColumns.length > 0) { String[] columns = yq.getParameterizedColumns(); Map<String, String[]> data = yq.getDataRow(row); char[] dataTypes = yq.getDataTypes(row); Matcher matcher; l.debug("Processing inColumns [" + StringUtils.join(inColumns, ",") + "]"); for (String in : inColumns) { int colIndex = -1, j = 0; String inCol = in.toUpperCase(); // TODO case sensitivity // get the index of the 'incolumn' in the 'JDBCcolumns' array l.debug("Looking for column [" + inCol + "] in columns array " + ArrayUtils.toString(columns)); while (j < columns.length && colIndex != j) { if (inCol.contains(columns[j])) { colIndex = j; l.debug("Found column [" + inCol + "] at index [" + String.valueOf(colIndex) + "] of columns array."); break; } j++; } // get the value list associated to the column in the data hash String colName = ""; String[] inData = null; int inLen = 0; if (data.containsKey(columns[colIndex])) // JSONParams { colName = columns[colIndex]; if (data.get(colName).length == 1) { inData = data.get(colName)[0].split(","); for (int m = 0; m < columns.length; m++) { if (columns[m].equals(colName)) { // add the new data for the column newData.put(colName, inData); } else { // add the existing data for the column newData.put(columns[m], data.get(columns[m])); } // add data row yq.getData().set(row, newData); } yq.getData().set(row, newData); } else inData = data.get(colName); l.debug("Splitting in args [" + data.get(colName) + "]"); } else // Standard Params { // Get an array of keys to compare and potentially manipulate String[] colNames = new String[data.size()]; int k = 0; for (String col : data.keySet()) { colNames[k] = col; k++; } // if colNames and columns array are of equal size, // then there is no param value manipulation required if (colNames.length == columns.length) { colName = QueryUtils.YADA_COLUMN + (colIndex + 1); inData = data.get(colName); } else // there is a length discrepancy { for (int m = colIndex; m < colNames.length; m++) { if (m == colIndex) // it's the first index inData = data.get(colNames[m]); else // further indexes must build aggregate array inData = (String[]) ArrayUtils.addAll(inData, data.get(colNames[m])); } for (int m = 0; m < columns.length; m++) { if (m == columns.length - 1) { // it's the last index, so add the aggregrate inData array newData.put(colNames[m], inData); } else { // not the last index, add the existing array newData.put(colNames[m], data.get(colNames[m])); } // add data row yq.getData().set(row, newData); } } l.debug("Setting IN args [" + ArrayUtils.toString(inData) + "]"); } if (inData != null) { inLen = inData.length; } if (inLen > 1) // there's an aggregate of multiple values { l.debug("Length of value list [" + String.valueOf(inLen) + "]"); l.debug("Getting data type of [" + columns[colIndex] + "]"); char dt = dataTypes[colIndex]; String dtStr = "?" + String.valueOf(dt); // generate the new parameter string with data type markers String[] pList = new String[inLen]; for (int k = 0; k < inLen; k++) { pList[k] = dtStr; } String pListStr = StringUtils.join(pList, ","); l.debug("New parameter list [" + pListStr + "]"); // add additional parameters to coreSql String rx = "(.+)(" + inCol + "\\s+in\\s+\\(\\" + dtStr + "\\))(.*)"; String repl = inCol + " IN (" + pListStr + ")"; String sql = coreSql.replaceAll(NEWLINE, " "); l.debug("Attempting to replace part of [" + sql + "] with [" + repl + "]"); matcher = Pattern.compile(rx, Pattern.CASE_INSENSITIVE).matcher(sql); if (matcher.matches()) { coreSql = matcher.group(1) + repl + matcher.group(3); } l.debug("Matched clause in coreSql [" + matcher.toString() + "]"); } // end current incolumn processing } // end all incolumn processing } // reset datatype and param count with new coreSql yq.addDataTypes(row, this.getDataTypes(coreSql)); yq.addParamCount(row, yq.getDataTypes(row).length); return coreSql; }
From source file:com.abssh.util.GenericDao.java
/** * // w w w .j av a2s. co m * * @date 2012-04-06 * @param page * @param filters * @param criterions * @return */ @SuppressWarnings("unchecked") public Page<T> findPage(final Page<T> page, final List<PropertyFilter> filters, final Criterion... criterions) { Assert.notNull(page, "page should not be null!"); Criterion[] cs = (Criterion[]) ArrayUtils.addAll(buildPropertyFilterCriterions(filters), criterions); Criteria c = createCriteria(cs); if (page.isAutoCount()) { int totalCount = countCriteriaResult(c); page.setTotalCount(totalCount); } if (page != null && page.getPageSize() > 0 && page.getTotalPages() < page.getPageNo()) { page.setPageNo(1L); } setPageParameter(c, page); List<T> result = c.list(); page.setResult(result); return page; }
From source file:com.abssh.util.GenericDao.java
/** * /* ww w.ja v a2s .co m*/ * * @date 2012-04-06 * @param page * @param filters * @param criterions * @return */ @SuppressWarnings("unchecked") public Page<T> findPage(final Page<T> page, final List<PropertyFilter> filters, String[] fetchObject, final Criterion... criterions) { Assert.notNull(page, "page should not be null!"); Criterion[] cs = (Criterion[]) ArrayUtils.addAll(buildPropertyFilterCriterions(filters), criterions); Criteria c = createCriteria(cs); if (page.isAutoCount()) { int totalCount = countCriteriaResult(c); page.setTotalCount(totalCount); } if (page != null && page.getPageSize() > 0 && page.getTotalPages() < page.getPageNo()) { page.setPageNo(1L); } setPageParameter(c, page); if (fetchObject != null) { for (int i = 0; i < fetchObject.length; i++) { c.setFetchMode(fetchObject[i], FetchMode.JOIN); } } List<T> result = c.list(); page.setResult(result); return page; }
From source file:com.datatorrent.stram.cli.ApexCli.java
private List<Completer> defaultCompleters() { Map<String, CommandSpec> commands = new TreeMap<>(); commands.putAll(logicalPlanChangeCommands); commands.putAll(connectedCommands);/* w ww. j a v a 2s.com*/ commands.putAll(globalCommands); List<Completer> completers = new LinkedList<>(); for (Map.Entry<String, CommandSpec> entry : commands.entrySet()) { String command = entry.getKey(); CommandSpec cs = entry.getValue(); List<Completer> argCompleters = new LinkedList<>(); argCompleters.add(new StringsCompleter(command)); Arg[] args = (Arg[]) ArrayUtils.addAll(cs.requiredArgs, cs.optionalArgs); if (args != null) { if (cs instanceof OptionsCommandSpec) { // ugly hack because jline cannot dynamically change completer while user types if (args[0] instanceof FileArg || args[0] instanceof VarArg) { for (int i = 0; i < 10; i++) { argCompleters.add(new MyFileNameCompleter()); } } } else { for (Arg arg : args) { if (arg instanceof FileArg || arg instanceof VarArg) { argCompleters.add(new MyFileNameCompleter()); } else if (arg instanceof CommandArg) { argCompleters.add(new StringsCompleter(commands.keySet().toArray(new String[] {}))); } else { argCompleters.add(MyNullCompleter.INSTANCE); } } } } completers.add(new ArgumentCompleter(argCompleters)); } List<Completer> argCompleters = new LinkedList<>(); Set<String> set = new TreeSet<>(); set.addAll(aliases.keySet()); set.addAll(macros.keySet()); argCompleters.add(new StringsCompleter(set.toArray(new String[] {}))); for (int i = 0; i < 10; i++) { argCompleters.add(new MyFileNameCompleter()); } completers.add(new ArgumentCompleter(argCompleters)); return completers; }
From source file:de.tudarmstadt.ukp.dkpro.core.corenlp.CoreNlpParserTest.java
private JCas runTestWithPosTagger(String aLanguage, String aVariant, String aText, Object... aExtraParams) throws Exception { AssumeResource.assumeResource(CoreNlpParser.class, "de/tudarmstadt/ukp/dkpro/core/stanfordnlp", "parser", aLanguage, aVariant);// www . j av a2 s.c o m AggregateBuilder aggregate = new AggregateBuilder(); aggregate.add(createEngineDescription(CoreNlpPosTagger.class)); Object[] params = new Object[] { CoreNlpParser.PARAM_VARIANT, aVariant, CoreNlpParser.PARAM_PRINT_TAGSET, true, CoreNlpParser.PARAM_WRITE_CONSTITUENT, true, CoreNlpParser.PARAM_WRITE_DEPENDENCY, true, CoreNlpParser.PARAM_WRITE_PENN_TREE, true, CoreNlpParser.PARAM_WRITE_POS, false }; params = ArrayUtils.addAll(params, aExtraParams); aggregate.add(createEngineDescription(CoreNlpParser.class, params)); return TestRunner.runTest(aggregate.createAggregateDescription(), aLanguage, aText); }