private void setGeneticProfiles(HttpServletRequest request) throws DaoException { CancerStudy cancerStudy = (CancerStudy) request.getAttribute(CANCER_STUDY); GeneticProfile mutProfile = cancerStudy.getMutationProfile(); if (mutProfile != null) { request.setAttribute(MUTATION_PROFILE, mutProfile); } GeneticProfile cnaProfile = cancerStudy.getCopyNumberAlterationProfile(true); if (cnaProfile != null) { request.setAttribute(CNA_PROFILE, cnaProfile); } }
private boolean validate(HttpServletRequest request) throws DaoException { String cancerStudyID = request.getParameter(ID); if (cancerStudyID == null) { cancerStudyID = request.getParameter(QueryBuilder.CANCER_STUDY_ID); } CancerStudy cancerStudy = DaoCancerStudy.getCancerStudyByStableId(cancerStudyID); if (cancerStudy == null) { try { cancerStudy = DaoCancerStudy.getCancerStudyByInternalId(Integer.parseInt(cancerStudyID)); } catch (NumberFormatException ex) { } } if (cancerStudy == null) { request.setAttribute(ERROR, "No such cancer study"); return false; } String cancerStudyIdentifier = cancerStudy.getCancerStudyStableId(); if (accessControl.isAccessibleCancerStudy(cancerStudyIdentifier).size() != 1) { request.setAttribute( ERROR, "You are not authorized to view the cancer study with id: '" + cancerStudyIdentifier + "'. "); return false; } else { UserDetails ud = accessControl.getUserDetails(); if (ud != null) { logger.info("CancerStudyView.validate: Query initiated by user: "******"_all"; request.setAttribute(QueryBuilder.CASE_SET_ID, sampleListId); } SampleList sampleList = daoSampleList.getSampleListByStableId(sampleListId); if (sampleList == null) { request.setAttribute(ERROR, "Could not find sample list of '" + sampleListId + "'. "); return false; } request.setAttribute(QueryBuilder.CASE_IDS, sampleList.getSampleList()); request.setAttribute(CANCER_STUDY, cancerStudy); request.setAttribute(QueryBuilder.HTML_TITLE, cancerStudy.getName()); return true; }
private void processRequestStatistics( HttpServletRequest request, HttpServletResponse response, String type) throws ServletException, IOException { String cancerStudyIds = request.getParameter(QueryBuilder.CANCER_STUDY_ID); try { boolean includeMut = "mut".equalsIgnoreCase(type); boolean includeCna = "cna".equalsIgnoreCase(type); Map<String, Map<String, Object>> data = new HashMap<String, Map<String, Object>>(); // get list of cancer studies AccessControl accessControl = getaccessControl(); List<CancerStudy> cancerStudies; if (cancerStudyIds == null || cancerStudyIds.isEmpty()) { cancerStudies = accessControl.getCancerStudies(); } else { cancerStudies = new ArrayList<CancerStudy>(); for (String studyId : cancerStudyIds.split("[ ,]+")) { CancerStudy study = DaoCancerStudy.getCancerStudyByStableId(studyId); if (study != null && !accessControl.isAccessibleCancerStudy(studyId).isEmpty()) { cancerStudies.add(study); } } } for (CancerStudy cancerStudy : cancerStudies) { if (cancerStudy.getCancerStudyStableId().equalsIgnoreCase("all")) { continue; } Map<String, Object> row = new HashMap<String, Object>(); data.put(cancerStudy.getCancerStudyStableId(), row); if (!includeMut && !includeMut) { row.put("name", cancerStudy.getName()); String pmid = cancerStudy.getPmid(); if (pmid != null) { row.put("pmid", pmid); } String citation = cancerStudy.getCitation(); if (citation != null) { row.put("citation", citation); } row.put( "cases", DaoPatient.getPatientsByCancerStudyId(cancerStudy.getInternalId()).size()); } if (includeMut) { GeneticProfile mutProfile = cancerStudy.getMutationProfile(); if (mutProfile == null) { row.put("mut", 0); } else { int mutEvents = DaoMutation.countMutationEvents(mutProfile.getGeneticProfileId()); int samplesWithMut = DaoSampleProfile.countSamplesInProfile(mutProfile.getGeneticProfileId()); row.put("mut", 1.0 * mutEvents / samplesWithMut); } } if (includeCna) { GeneticProfile cnaProfile = cancerStudy.getCopyNumberAlterationProfile(false); if (cnaProfile == null) { row.put("cna", 0); } else { List<Integer> samples = DaoSampleProfile.getAllSampleIdsInProfile(cnaProfile.getGeneticProfileId()); Map<Integer, Double> fracs = DaoCopyNumberSegment.getCopyNumberActeredFraction( samples, cnaProfile.getCancerStudyId(), GlobalProperties.getPatientViewGenomicOverviewCnaCutoff()[0]); double aveFrac = 0; for (double frac : fracs.values()) { aveFrac += frac; } aveFrac /= samples.size(); row.put("cna", aveFrac); } } } response.setContentType("application/json"); PrintWriter out = response.getWriter(); try { JSONValue.writeJSONString(data, out); } finally { out.close(); } } catch (DaoException ex) { throw new ServletException(ex); } catch (ProtocolException ex) { throw new ServletException(ex); } }