@Override public QueryResult<AnnotationSet> getAnnotationSet(long id, @Nullable String annotationSetName) throws CatalogDBException { QueryOptions queryOptions = new QueryOptions(); List<String> includeList = new ArrayList<>(); if (StringUtils.isNotEmpty(annotationSetName)) { includeList.add(Constants.ANNOTATION_SET_NAME + "." + annotationSetName); } else { includeList.add(QueryParams.ANNOTATION_SETS.key()); } queryOptions.put(QueryOptions.INCLUDE, includeList); QueryResult<Individual> individualQueryResult = get(id, queryOptions); if (individualQueryResult.first().getAnnotationSets().isEmpty()) { return new QueryResult<>("Get annotation set", individualQueryResult.getDbTime(), 0, 0, individualQueryResult.getWarningMsg(), individualQueryResult.getErrorMsg(), Collections.emptyList()); } else { List<AnnotationSet> annotationSets = individualQueryResult.first().getAnnotationSets(); int size = annotationSets.size(); return new QueryResult<>("Get annotation set", individualQueryResult.getDbTime(), size, size, individualQueryResult.getWarningMsg(), individualQueryResult.getErrorMsg(), annotationSets); } }
IndividualProperty.AffectationStatus.UNKNOWN)); individual.setPhenotypes(ParamUtils.defaultObject(individual.getPhenotypes(), Collections.emptyList())); individual.setAnnotationSets(ParamUtils.defaultObject(individual.getAnnotationSets(), Collections.emptyList())); individual.setAttributes(ParamUtils.defaultObject(individual.getAttributes(), Collections.emptyMap())); individual.setSamples(ParamUtils.defaultObject(individual.getSamples(), Collections.emptyList())); List<VariableSet> variableSetList = validateNewAnnotationSetsAndExtractVariableSets(studyUid, individual.getAnnotationSets());
individualSolrModel.setAnnotations(SolrConverterUtil.populateAnnotations(variableMap, individual.getAnnotationSets())); if (individual.getAnnotationSets() != null) { individualSolrModel.setAnnotationSets( individual.getAnnotationSets().stream().map(AnnotationSet::getId).collect(Collectors.toList())); } else { individualSolrModel.setAnnotationSets(Collections.emptyList());
QueryResult<Individual> individualQueryResult = catalogManager.getIndividualManager().get(studyFqn, individualId, new QueryOptions(QueryOptions.INCLUDE, SampleDBAdaptor.QueryParams.ANNOTATION_SETS.key()), sessionIdUser); assertEquals(1, individualQueryResult.first().getAnnotationSets().size());
ind = catalogManager.getIndividualManager().get(studyFqn, ind.getId(), null, sessionIdUser).first(); check.accept(sample.getAnnotationSets().get(0)); check.accept(ind.getAnnotationSets().get(0)); annotationSet.getAnnotations(), ParamUtils.CompleteUpdateAction.SET, new QueryOptions(Constants.INCREMENT_VERSION, true), sessionIdUser); check.accept(ind.getAnnotationSets().get(0)); ind = catalogManager.getIndividualManager().get(studyFqn, ind.getId(), null, sessionIdUser).first(); check.accept(sample.getAnnotationSets().get(0)); check.accept(ind.getAnnotationSets().get(0)); ind = catalogManager.getIndividualManager().get(studyFqn, ind.getId(), null, sessionIdUser).first(); check.accept(sample.getAnnotationSets().get(0)); check.accept(ind.getAnnotationSets().get(0)); ind = catalogManager.getIndividualManager().get(studyFqn, ind.getId(), null, sessionIdUser).first(); check.accept(sample.getAnnotationSets().get(0)); check.accept(ind.getAnnotationSets().get(0));