List of usage examples for org.apache.commons.collections.map MultiKeyMap get
public Object get(Object key1, Object key2)
From source file:com.navercorp.pinpoint.collector.dao.hbase.stat.HbaseDataSourceListDao.java
private List<DataSourceListBo> reorderDataSourceListBos(List<DataSourceListBo> dataSourceListBos) { // reorder dataSourceBo using id and timeSlot MultiKeyMap dataSourceListBoMap = new MultiKeyMap(); for (DataSourceListBo dataSourceListBo : dataSourceListBos) { for (DataSourceBo dataSourceBo : dataSourceListBo.getList()) { int id = dataSourceBo.getId(); long timestamp = dataSourceBo.getTimestamp(); long timeSlot = AgentStatUtils.getBaseTimestamp(timestamp); DataSourceListBo mappedDataSourceListBo = (DataSourceListBo) dataSourceListBoMap.get(id, timeSlot); if (mappedDataSourceListBo == null) { mappedDataSourceListBo = new DataSourceListBo(); mappedDataSourceListBo.setAgentId(dataSourceBo.getAgentId()); mappedDataSourceListBo.setStartTimestamp(dataSourceBo.getStartTimestamp()); mappedDataSourceListBo.setTimestamp(dataSourceBo.getTimestamp()); dataSourceListBoMap.put(id, timeSlot, mappedDataSourceListBo); }//ww w . j av a 2 s . c o m // set fastest timestamp if (mappedDataSourceListBo.getTimestamp() > dataSourceBo.getTimestamp()) { mappedDataSourceListBo.setTimestamp(dataSourceBo.getTimestamp()); } mappedDataSourceListBo.add(dataSourceBo); } } Collection values = dataSourceListBoMap.values(); return new ArrayList<DataSourceListBo>(values); }
From source file:com.gs.obevo.db.apps.reveng.DbFileMerger.java
public void generateDiffs(DbPlatform dialect, MutableCollection<DbMergeInfo> dbNameLocationPairs, File outputDir) {//from w w w . j a v a2 s.co m System.out.println("Generating diffs for " + dbNameLocationPairs); MultiKeyMap objectMap = new MultiKeyMap(); for (DbMergeInfo dbNameLocationPair : dbNameLocationPairs) { FileObject mainDir = FileRetrievalMode.FILE_SYSTEM .resolveSingleFileObject(dbNameLocationPair.getInputDir().getAbsolutePath()); for (FileObject schemaDir : mainDir.getChildren()) { if (schemaDir.getType() != FileType.FOLDER) { continue; } for (ChangeType changeType : dialect.getChangeTypes()) { FileObject changeTypeDir = schemaDir.getChild(changeType.getDirectoryName()); if (changeTypeDir != null && changeTypeDir.isReadable() && changeTypeDir.getType() == FileType.FOLDER) { FileObject[] childFiles = changeTypeDir.getChildren(); for (FileObject objectFile : childFiles) { if (objectFile.getType() == FileType.FILE) { FileComparison fileComparison = (FileComparison) objectMap.get(changeType, objectFile.getName().getBaseName()); if (fileComparison == null) { fileComparison = new FileComparison(schemaDir.getName().getBaseName(), changeType, objectFile.getName().getBaseName()); objectMap.put(changeType, objectFile.getName().getBaseName(), fileComparison); } fileComparison.addFilePair(Tuples.pair(dbNameLocationPair.getName(), objectFile)); String fileContent = objectFile.getStringContent(); String normalizedContent = DAStringUtil .normalizeWhiteSpaceFromStringOld(fileContent); // modify the content here if needed fileComparison.addContentValues(fileContent); fileComparison.addDistinctValue(normalizedContent); fileComparison.incrementCount(); } } } } } } for (FileComparison fileComparison : (Collection<FileComparison>) objectMap.values()) { File fileComparisonFileRoot = new File(new File(outputDir, fileComparison.getSchemaName()), fileComparison.getChangeType().getDirectoryName()); if (fileComparison.getDistinctValues().size() == 1) { File outputFile; if (fileComparison.getCount() == dbNameLocationPairs.size()) { outputFile = new File(fileComparisonFileRoot, fileComparison.getName()); } else { MutableList<String> dbNames = fileComparison.getFilePairs() .collect(Functions.<String>firstOfPair()); String dbNameString = "only-" + dbNames.sortThis().makeString("-"); File dbDir = new File(fileComparisonFileRoot, dbNameString); outputFile = new File(dbDir, fileComparison.getName()); File packageInfoFile = new File(dbDir, "package-info.txt"); FileUtilsCobra.writeStringToFile(packageInfoFile, "//// METADATA includeEnvs=\"" + dbNames.sortThis().collect(StringFunctions.append("*")).makeString(",") + "\""); } FileUtilsCobra.writeStringToFile(outputFile, fileComparison.getContentValues().getFirst()); } else { for (Pair<String, FileObject> dbNameFileObjectPair : fileComparison.getFilePairs()) { String dbName = dbNameFileObjectPair.getOne(); File outputFile = new File(new File(fileComparisonFileRoot, dbName), fileComparison.getName()); File packageInfoFile = new File(new File(fileComparisonFileRoot, dbName), "package-info.txt"); String fileContent = dbNameFileObjectPair.getTwo().getStringContent(); FileUtilsCobra.writeStringToFile(outputFile, fileContent); FileUtilsCobra.writeStringToFile(packageInfoFile, "//// METADATA includeEnvs=\"" + StringFunctions.append("*").valueOf(dbName) + "\""); } } } }
From source file:edu.cmu.tetrad.search.SearchGraphUtils.java
/** * Returns the set of nodes reachable from the given set of initial nodes in the given graph according to the * criteria in the given legal pairs object. * <p/>//from www . j av a2 s .c om * A variable V is reachable from initialNodes iff for some variable X in initialNodes thers is a path U [X, Y1, * ..., V] such that legalPairs.isLegalFirstNode(X, Y1) and for each [H1, H2, H3] as subpaths of U, * legalPairs.isLegalPairs(H1, H2, H3). * <p/> * The algorithm used is a variant of Algorithm 1 from Geiger, Verma, & Pearl (1990). * * @param initialNodes The nodes that reachability paths start from. * @param legalPairs Specifies initial edges (given initial nodes) and legal edge pairs. * @param c a set of vertices (intuitively, the set of variables to be conditioned on. * @param d a set of vertices (intuitively to be used in tests of legality, for example, the set of * ancestors of c). * @param graph the graph with respect to which reachability is * @param maxPathLength */ public static Set<Node> getReachableNodes(List<Node> initialNodes, LegalPairs legalPairs, List<Node> c, List<Node> d, Graph graph, int maxPathLength) { HashSet<Node> reachable = new HashSet<Node>(); MultiKeyMap visited = new MultiKeyMap(); List<ReachabilityEdge> nextEdges = new LinkedList<ReachabilityEdge>(); for (Node x : initialNodes) { List<Node> adjX = graph.getAdjacentNodes(x); for (Node y : adjX) { if (legalPairs.isLegalFirstEdge(x, y)) { reachable.add(y); nextEdges.add(new ReachabilityEdge(x, y)); visited.put(x, y, Boolean.TRUE); } } } int pathLength = 1; while (nextEdges.size() > 0) { // System.out.println("Path length = " + pathLength); if (++pathLength > maxPathLength) return reachable; List<ReachabilityEdge> currEdges = nextEdges; nextEdges = new LinkedList<ReachabilityEdge>(); for (ReachabilityEdge edge : currEdges) { Node x = edge.getFrom(); Node y = edge.getTo(); List<Node> adjY = graph.getAdjacentNodes(y); for (Node z : adjY) { if ((visited.get(y, z)) == Boolean.TRUE) { continue; } if (legalPairs.isLegalPair(x, y, z, c, d)) { reachable.add(z); nextEdges.add(new ReachabilityEdge(y, z)); visited.put(y, z, Boolean.TRUE); } } } } return reachable; }
From source file:org.cbio.portal.pipelines.foundation.CnaDataReader.java
/** * Generate map of gene to CNA data /*w ww . jav a2 s .c o m*/ * @param fmiCaseMap * @return */ private List<String> generateCnaRowData(Map<String, CaseType> fmiCaseTypeMap) { Set<String> geneList = new HashSet<>(); MultiKeyMap cnaMap = new MultiKeyMap(); int noCnaCount = 0; // keep track of how many cases don't have copy number data for (CaseType ct : fmiCaseTypeMap.values()) { List<CopyNumberAlterationType> cnaTypeList = ct.getVariantReport().getCopyNumberAlterations() .getCopyNumberAlteration(); if (cnaTypeList != null) { for (CopyNumberAlterationType cnaType : cnaTypeList) { cnaMap.put(cnaType.getGene(), ct.getCase(), FoundationUtils.resolveCnaType(cnaType)); geneList.add(cnaType.getGene()); } } else { noCnaCount++; } } if (noCnaCount > 0) { LOG.info("Number of cases without CNA data: " + noCnaCount); } // format row data for CNA file List<String> cnaRowData = new ArrayList(); for (String gene : geneList) { List<String> geneCnaData = new ArrayList(); geneCnaData.add(gene); for (String caseId : fmiCaseTypeMap.keySet()) { if (cnaMap.containsKey(gene, caseId)) { geneCnaData.add((String) cnaMap.get(gene, caseId)); } else { geneCnaData.add("0"); } } cnaRowData.add(StringUtils.join(geneCnaData, "\t")); } return cnaRowData; }
From source file:org.mskcc.cbio.portal.scripts.ImportClinicalData.java
private boolean addDatum(String[] fields, List<ClinicalAttribute> columnAttrs, MultiKeyMap attributeMap) throws Exception { int sampleIdIndex = findSampleIdColumn(columnAttrs); String stableSampleId = (sampleIdIndex >= 0) ? fields[sampleIdIndex] : ""; stableSampleId = StableIdUtil.getSampleId(stableSampleId); int patientIdIndex = findPatientIdColumn(columnAttrs); String stablePatientId = (patientIdIndex >= 0) ? fields[patientIdIndex] : ""; stablePatientId = StableIdUtil.getPatientId(stablePatientId); int internalSampleId = -1; int internalPatientId = -1; //check if sample is not already added: Sample sample = DaoSample.getSampleByCancerStudyAndSampleId(cancerStudy.getInternalId(), stableSampleId, false);/*from ww w .j av a2 s .c o m*/ if (sample != null) { //this should be a WARNING in case of TCGA studies (see https://github.com/cBioPortal/cbioportal/issues/839#issuecomment-203452415) //and an ERROR in other studies. I.e. a sample should occur only once in clinical file! if (stableSampleId.startsWith("TCGA-")) { ProgressMonitor.logWarning("Sample " + stableSampleId + " found to be duplicated in your file. Only data of the first sample will be processed."); return false; } //give error or warning if sample is already in DB and this is NOT expected (i.e. not supplemental data): if (!this.isSupplementalData()) { throw new RuntimeException( "Error: Sample " + stableSampleId + " found to be duplicated in your file."); } else { internalSampleId = sample.getInternalId(); } } else { Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudy.getInternalId(), stablePatientId); if (patient != null) { //patient exists, get internal id: internalPatientId = patient.getInternalId(); } else { //add patient: internalPatientId = (patientIdIndex >= 0) ? addPatientToDatabase(fields[patientIdIndex]) : -1; } // sample is new, so attempt to add to DB internalSampleId = (stableSampleId.length() > 0) ? addSampleToDatabase(stableSampleId, fields, columnAttrs) : -1; } //validate and count: if (internalSampleId != -1) { //some minimal validation/fail safe for now: only continue if patientId is same as patient id in //existing sample (can occur in case of this.isSupplementalData or in case of parsing bug in addSampleToDatabase): internalPatientId = DaoPatient .getPatientByCancerStudyAndPatientId(cancerStudy.getInternalId(), stablePatientId) .getInternalId(); if (internalPatientId != DaoSample.getSampleById(internalSampleId).getInternalPatientId()) { throw new RuntimeException("Error: Sample " + stableSampleId + " was previously linked to another patient, and not to " + stablePatientId); } numSamplesProcessed++; } // this will happen when clinical file contains sample id, but not patient id //TODO - this part, and the dummy patient added in addSampleToDatabase, can be removed as the field PATIENT_ID is now //always required (as validated at start of importData() ). Probably kept here for "old" studies, but Ben's tests did not find anything... // --> alternative would be to be less strict in validation at importData() and allow for missing PATIENT_ID when type is MIXED... if (internalPatientId == -1 && internalSampleId != -1) { sample = DaoSample.getSampleById(internalSampleId); internalPatientId = sample.getInternalPatientId(); } for (int lc = 0; lc < fields.length; lc++) { //if lc is sampleIdIndex or patientIdIndex, skip as well since these are the relational fields: if (lc == sampleIdIndex || lc == patientIdIndex) { continue; } //if the value matches one of the missing values, skip this attribute: if (MissingAttributeValues.has(fields[lc])) { numEmptyClinicalAttributesSkipped++; continue; } boolean isPatientAttribute = columnAttrs.get(lc).isPatientAttribute(); if (isPatientAttribute && internalPatientId != -1) { // The attributeMap keeps track what patient/attribute to value pairs are being added to the DB. If there are duplicates, // (which can happen in a MIXED_ATTRIBUTES type clinical file), we need to make sure that the value for the same // attributes are consistent. This prevents duplicate entries in the temp file that the MySqlBulkLoader uses. if (!attributeMap.containsKey(internalPatientId, columnAttrs.get(lc).getAttrId())) { addDatum(internalPatientId, columnAttrs.get(lc).getAttrId(), fields[lc], ClinicalAttribute.PATIENT_ATTRIBUTE); attributeMap.put(internalPatientId, columnAttrs.get(lc).getAttrId(), fields[lc]); } else if (!relaxed) { throw new RuntimeException("Error: Duplicated patient in file"); } else if (!attributeMap.get(internalPatientId, columnAttrs.get(lc).getAttrId()) .equals(fields[lc])) { ProgressMonitor.logWarning("Error: Duplicated patient " + stablePatientId + " with different values for patient attribute " + columnAttrs.get(lc).getAttrId() + "\n\tValues: " + attributeMap.get(internalPatientId, columnAttrs.get(lc).getAttrId()) + " " + fields[lc]); } } else if (internalSampleId != -1) { if (!attributeMap.containsKey(internalSampleId, columnAttrs.get(lc).getAttrId())) { addDatum(internalSampleId, columnAttrs.get(lc).getAttrId(), fields[lc], ClinicalAttribute.SAMPLE_ATTRIBUTE); attributeMap.put(internalSampleId, columnAttrs.get(lc).getAttrId(), fields[lc]); } else if (!relaxed) { throw new RuntimeException("Error: Duplicated sample in file"); } else if (!attributeMap.get(internalSampleId, columnAttrs.get(lc).getAttrId()) .equals(fields[lc])) { ProgressMonitor.logWarning("Error: Duplicated sample " + stableSampleId + " with different values for sample attribute " + columnAttrs.get(lc).getAttrId() + "\n\tValues: " + attributeMap.get(internalSampleId, columnAttrs.get(lc).getAttrId()) + " " + fields[lc]); } } } return true; }
From source file:org.talend.repository.ui.wizards.exportjob.scriptsmanager.JobJavaScriptsManager.java
protected void addModuleNeededsInMap(MultiKeyMap modulesMap, String processId, String processVersion, ModuleNeeded module) {/* www. j av a 2s . c o m*/ if (modulesMap != null && module != null) { Set<ModuleNeeded> modulesSet = (Set<ModuleNeeded>) modulesMap.get(processId, processVersion); if (modulesSet == null) { modulesSet = new LinkedHashSet<ModuleNeeded>(50); modulesMap.put(processId, processVersion, modulesSet); } modulesSet.add(module); } }
From source file:piecework.engine.concrete.ProcessEngineConcreteFacade.java
@Override public TaskResults findTasks(TaskCriteria... criterias) throws ProcessEngineException { String keyword = null;//from w ww .j av a 2s .c o m TaskResults.Builder builder = null; Set<String> allowedProcessDefinitionKeys = new HashSet<String>(); Set<String> engineProcessInstanceIds = new HashSet<String>(); if (criterias != null && criterias.length > 0) { for (TaskCriteria criteria : criterias) { if (StringUtils.isNotEmpty(criteria.getKeyword())) keyword = criteria.getKeyword(); if (criteria.getProcesses() != null && !criteria.getProcesses().isEmpty()) { Set<String> engineSet = new HashSet<String>(); for (Process process : criteria.getProcesses()) { ProcessDeployment deployment = processDeployment(process); allowedProcessDefinitionKeys.add(process.getProcessDefinitionKey()); if (deployment.getEngine() == null || engineSet.contains(deployment.getEngine())) continue; engineSet.add(deployment.getEngine()); ProcessEngineProxy proxy = registry.retrieve(ProcessEngineProxy.class, deployment.getEngine()); TaskResults localResults = proxy.findTasks(criteria); if (localResults == null) continue; engineProcessInstanceIds.addAll(localResults.getEngineProcessInstanceIds()); if (builder == null) builder = new TaskResults.Builder(localResults); else { builder.tasks(localResults.getTasks()); builder.addToTotal(localResults.getTotal()); } } } } } else { builder = new TaskResults.Builder(); } long time = 0; if (LOG.isDebugEnabled()) time = System.currentTimeMillis(); TaskResults.Builder resultsBuilder = new TaskResults.Builder(); List<Task> taskInstances = builder != null ? builder.build().getTasks() : null; List<Task> tasks; int count = 0; if (taskInstances != null && !taskInstances.isEmpty()) { tasks = new ArrayList<Task>(taskInstances.size()); List<ProcessInstance> processInstances; if (StringUtils.isNotEmpty(keyword)) processInstances = processInstanceRepository .findByProcessDefinitionKeyInAndEngineProcessInstanceIdInAndKeyword( allowedProcessDefinitionKeys, engineProcessInstanceIds, keyword); else processInstances = processInstanceRepository .findByProcessDefinitionKeyInAndEngineProcessInstanceIdIn(allowedProcessDefinitionKeys, engineProcessInstanceIds); if (processInstances != null && !processInstances.isEmpty()) { MultiKeyMap processInstanceMap = new MultiKeyMap(); for (ProcessInstance processInstance : processInstances) { if (processInstance == null) continue; if (org.apache.cxf.common.util.StringUtils.isEmpty(processInstance.getProcessDefinitionKey())) continue; if (org.apache.cxf.common.util.StringUtils .isEmpty(processInstance.getEngineProcessInstanceId())) continue; processInstanceMap.put(processInstance.getProcessDefinitionKey(), processInstance.getEngineProcessInstanceId(), processInstance); } for (Task taskInstance : taskInstances) { ProcessInstance instance = ProcessInstance.class.cast(processInstanceMap.get( taskInstance.getProcessDefinitionKey(), taskInstance.getEngineProcessInstanceId())); if (instance == null) continue; tasks.add(new Task.Builder(taskInstance, new PassthroughSanitizer()) .processInstanceId(instance.getProcessInstanceId()) .processInstanceAlias(instance.getAlias()) .processInstanceLabel(instance.getProcessInstanceLabel()).build()); count++; } } } else { tasks = Collections.emptyList(); } if (LOG.isDebugEnabled()) { LOG.debug("Searching for process instances took " + (System.currentTimeMillis() - time) + " ms"); } resultsBuilder.firstResult(1); resultsBuilder.maxResults(count); resultsBuilder.total(count); resultsBuilder.tasks(tasks); return resultsBuilder.build(); }