Java tutorial
/* * Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. * * This library is distributed in the hope that it will be useful, but WITHOUT * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no * obligations to provide maintenance, support, updates, enhancements or * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be * liable to any party for direct, indirect, special, incidental or * consequential damages, including lost profits, arising out of the use of this * software and its documentation, even if Memorial Sloan-Kettering Cancer * Center has been advised of the possibility of such damage. */ /* * This file is part of cBioPortal. * * cBioPortal is free software: you can redistribute it and/or modify * it under the terms of the GNU Affero General Public License as * published by the Free Software Foundation, either version 3 of the * License. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Affero General Public License for more details. * * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package org.mskcc.cbio.portal.servlet; import org.mskcc.cbio.portal.dao.*; import org.mskcc.cbio.portal.model.*; import org.mskcc.cbio.portal.oncoPrintSpecLanguage.*; import org.mskcc.cbio.portal.web_api.*; import org.mskcc.cbio.portal.util.*; import org.apache.log4j.Logger; import org.json.simple.JSONValue; import org.apache.commons.lang.StringUtils; import javax.servlet.ServletException; import javax.servlet.http.*; import java.io.*; import java.util.*; public class CrossCancerJSON extends HttpServlet { private static Logger logger = Logger.getLogger(CrossCancerJSON.class); // class which process access control to cancer studies private AccessControl accessControl; /** * Initializes the servlet. * * @throws ServletException Serlvet Init Error. */ public void init() throws ServletException { super.init(); accessControl = SpringUtil.getAccessControl(); } protected void doPost(HttpServletRequest request, HttpServletResponse response) throws IOException, ServletException { doGet(request, response); } /** * Processes requests for both HTTP <code>GET</code> and <code>POST</code> methods. * @param request servlet request * @param response servlet response * @throws javax.servlet.ServletException if a servlet-specific error occurs * @throws java.io.IOException if an I/O error occurs */ protected void doGet(HttpServletRequest request, HttpServletResponse response) throws IOException, ServletException { XDebug xdebug = new XDebug(); xdebug.startTimer(); response.setContentType("application/json"); PrintWriter writer = response.getWriter(); try { List resultsList = new LinkedList(); // Get the gene list String geneList = request.getParameter(QueryBuilder.GENE_LIST); if (request instanceof XssRequestWrapper) { geneList = ((XssRequestWrapper) request).getRawParameter(QueryBuilder.GENE_LIST); } String cancerStudyIdListString = request.getParameter(QueryBuilder.CANCER_STUDY_LIST); String[] cancerStudyIdList = cancerStudyIdListString.split(","); // Get the priority Integer dataTypePriority; try { dataTypePriority = Integer.parseInt(request.getParameter(QueryBuilder.DATA_PRIORITY).trim()); } catch (NumberFormatException e) { dataTypePriority = 0; } // Cancer All Cancer Studies List<CancerStudy> cancerStudiesList = accessControl.getCancerStudies(); HashMap<String, Boolean> studyMap = new HashMap<>(); for (String studyId : cancerStudyIdList) { studyMap.put(studyId, Boolean.TRUE); } for (CancerStudy cancerStudy : cancerStudiesList) { String cancerStudyId = cancerStudy.getCancerStudyStableId(); if (!studyMap.containsKey(cancerStudyId)) { continue; } if (cancerStudyId.equalsIgnoreCase("all")) continue; Map cancerMap = new LinkedHashMap(); cancerMap.put("studyId", cancerStudyId); cancerMap.put("typeOfCancer", cancerStudy.getTypeOfCancerId()); // Get all Genetic Profiles Associated with this Cancer Study ID. ArrayList<GeneticProfile> geneticProfileList = GetGeneticProfiles.getGeneticProfiles(cancerStudyId); // Get all Patient Lists Associated with this Cancer Study ID. ArrayList<SampleList> sampleSetList = GetSampleLists.getSampleLists(cancerStudyId); // Get the default patient set AnnotatedSampleSets annotatedSampleSets = new AnnotatedSampleSets(sampleSetList, dataTypePriority); SampleList defaultSampleSet = annotatedSampleSets.getDefaultSampleList(); if (defaultSampleSet == null) { continue; } List<String> sampleIds = defaultSampleSet.getSampleList(); // Get the default genomic profiles CategorizedGeneticProfileSet categorizedGeneticProfileSet = new CategorizedGeneticProfileSet( geneticProfileList); HashMap<String, GeneticProfile> defaultGeneticProfileSet = null; switch (dataTypePriority) { case 2: defaultGeneticProfileSet = categorizedGeneticProfileSet.getDefaultCopyNumberMap(); break; case 1: defaultGeneticProfileSet = categorizedGeneticProfileSet.getDefaultMutationMap(); break; case 0: default: defaultGeneticProfileSet = categorizedGeneticProfileSet.getDefaultMutationAndCopyNumberMap(); } String mutationProfile = "", cnaProfile = ""; for (GeneticProfile geneticProfile : defaultGeneticProfileSet.values()) { GeneticAlterationType geneticAlterationType = geneticProfile.getGeneticAlterationType(); if (geneticAlterationType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION)) { cnaProfile = geneticProfile.getStableId(); } else if (geneticAlterationType.equals(GeneticAlterationType.MUTATION_EXTENDED)) { mutationProfile = geneticProfile.getStableId(); } } cancerMap.put("mutationProfile", mutationProfile); cancerMap.put("cnaProfile", cnaProfile); cancerMap.put("caseSetId", defaultSampleSet.getStableId()); cancerMap.put("caseSetLength", sampleIds.size()); ProfileDataSummary genomicData = getGenomicData(cancerStudyId, defaultGeneticProfileSet, defaultSampleSet, geneList, sampleSetList, request, response); ArrayList<GeneWithScore> geneFrequencyList = genomicData.getGeneFrequencyList(); ArrayList<String> genes = new ArrayList<String>(); for (GeneWithScore geneWithScore : geneFrequencyList) genes.add(geneWithScore.getGene()); int noOfMutated = 0, noOfCnaUp = 0, noOfCnaDown = 0, noOfCnaLoss = 0, noOfCnaGain = 0, noOfOther = 0, noOfAll = 0; boolean skipStudy = defaultGeneticProfileSet.isEmpty(); if (!skipStudy) { for (String sampleId : sampleIds) { if (sampleId == null) { continue; } if (!genomicData.isCaseAltered(sampleId)) continue; boolean isAnyMutated = false, isAnyCnaUp = false, isAnyCnaDown = false, isAnyCnaLoss = false, isAnyCnaGain = false; for (String gene : genes) { isAnyMutated |= genomicData.isGeneMutated(gene, sampleId); GeneticTypeLevel cnaLevel = genomicData.getCNALevel(gene, sampleId); boolean isCnaUp = cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.Amplified); isAnyCnaUp |= isCnaUp; boolean isCnaDown = cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.HomozygouslyDeleted); isAnyCnaDown |= isCnaDown; boolean isCnaLoss = cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.HemizygouslyDeleted); isAnyCnaLoss |= isCnaLoss; boolean isCnaGain = cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.Gained); isAnyCnaGain |= isCnaGain; } boolean isAnyCnaChanged = isAnyCnaUp || isAnyCnaDown; if (isAnyMutated && !isAnyCnaChanged) noOfMutated++; else if (isAnyMutated && isAnyCnaChanged) noOfOther++; else if (isAnyCnaUp) noOfCnaUp++; else if (isAnyCnaDown) noOfCnaDown++; else if (isAnyCnaGain) noOfCnaGain++; else if (isAnyCnaLoss) noOfCnaLoss++; noOfAll++; } } Map alterations = new LinkedHashMap(); cancerMap.put("alterations", alterations); alterations.put("all", noOfAll); alterations.put("mutation", noOfMutated); alterations.put("cnaUp", noOfCnaUp); alterations.put("cnaDown", noOfCnaDown); alterations.put("cnaLoss", noOfCnaLoss); alterations.put("cnaGain", noOfCnaGain); alterations.put("other", noOfOther); cancerMap.put("genes", genes); cancerMap.put("skipped", skipStudy); resultsList.add(cancerMap); } JSONValue.writeJSONString(resultsList, writer); } catch (DaoException e) { throw new ServletException(e); } catch (ProtocolException e) { throw new ServletException(e); } finally { writer.close(); } } /** * Gets all Genomic Data. */ private ProfileDataSummary getGenomicData(String cancerStudyId, HashMap<String, GeneticProfile> defaultGeneticProfileSet, SampleList defaultSampleSet, String geneListStr, ArrayList<SampleList> sampleList, HttpServletRequest request, HttpServletResponse response) throws IOException, ServletException, DaoException { // parse geneList, written in the OncoPrintSpec language (except for changes by XSS clean) double zScore = ZScoreUtil.getZScore(new HashSet<String>(defaultGeneticProfileSet.keySet()), new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()), request); double rppaScore = ZScoreUtil.getRPPAScore(request); ParserOutput theOncoPrintSpecParserOutput = OncoPrintSpecificationDriver.callOncoPrintSpecParserDriver( geneListStr, new HashSet<String>(defaultGeneticProfileSet.keySet()), new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()), zScore, rppaScore); ArrayList<String> geneList = new ArrayList<String>(); geneList.addAll(theOncoPrintSpecParserOutput.getTheOncoPrintSpecification().listOfGenes()); ArrayList<ProfileData> profileDataList = new ArrayList<ProfileData>(); Set<String> warningUnion = new HashSet<String>(); for (GeneticProfile profile : defaultGeneticProfileSet.values()) { try { GetProfileData remoteCall = new GetProfileData(profile, geneList, StringUtils.join(defaultSampleSet.getSampleList(), " ")); ProfileData pData = remoteCall.getProfileData(); warningUnion.addAll(remoteCall.getWarnings()); profileDataList.add(pData); } catch (IllegalArgumentException e) { e.getStackTrace(); } } ProfileMerger merger = new ProfileMerger(profileDataList); ProfileData mergedProfile = merger.getMergedProfile(); ProfileDataSummary dataSummary = new ProfileDataSummary(mergedProfile, theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(), zScore, rppaScore); return dataSummary; } }