private ClinicalAnalysis getClinicalAnalysis() throws CatalogException { assert(null != catalogManager); if (StringUtils.isNotEmpty(clinicalAnalysisId)) { final ClinicalAnalysisManager clinicalAnalysisManager = catalogManager.getClinicalAnalysisManager(); // have to convert session QueryResult<ClinicalAnalysis> clinicalAnalyses = clinicalAnalysisManager.get( studyStr, clinicalAnalysisId, QueryOptions.empty(), sessionId ); clinicalAnalysis = clinicalAnalyses.first(); return clinicalAnalysis; } return null; }
QueryResult<ClinicalAnalysis> clinicalAnalysisQueryResult = get(studyStr, query, new QueryOptions(), sessionId); ClinicalAnalysis clinicalAnalysis = clinicalAnalysisQueryResult.first();
private void checkInterpretationPermissions(String study, long interpretationId, String token) throws CatalogException, ClinicalVariantException { // Get user ID from token and study numeric ID String userId = catalogManager.getUserManager().getUserId(token); String studyId = catalogManager.getStudyManager().resolveId(study, userId).getFqn(); // This checks that the user has permission to this interpretation Query query = new Query(ClinicalAnalysisDBAdaptor.QueryParams.INTERPRETATIONS_ID.key(), interpretationId); QueryResult<ClinicalAnalysis> clinicalAnalysisQueryResult = catalogManager.getClinicalAnalysisManager() .get(studyId, query, QueryOptions.empty(), token); if (clinicalAnalysisQueryResult.getResult().isEmpty()) { throw new ClinicalVariantException("Either the interpretation ID (" + interpretationId + ") does not exist or the user does" + " not have access permissions"); } }
.get(studyIds.get(0), query, QueryOptions.empty(), token);
QueryResult<ClinicalAnalysis> clinicalAnalysisQueryResult = catalogManager.getClinicalAnalysisManager().get(studyStr, clinicalAnalysisId, QueryOptions.empty(), token); if (clinicalAnalysisQueryResult.getNumResults() == 0) {
QueryResult<ClinicalAnalysis> clinicalAnalysisQueryResult = catalogManager.getClinicalAnalysisManager().get(studyStr, clinicalAnalysisId, QueryOptions.empty(), token); if (clinicalAnalysisQueryResult.getNumResults() == 0) {