public File setAnnotationSets(List<AnnotationSet> annotationSets) { super.setAnnotationSets(annotationSets); return this; }
@Override public Sample setStudyUid(long studyUid) { super.setStudyUid(studyUid); return this; }
@Override public Cohort setUid(long uid) { super.setUid(uid); return this; }
public Document convertToStorageType(T object, List<VariableSet> variableSetList) { List<Document> documentList = new ArrayList<>(); Document privateVariableSetMap = new Document(); if (variableSetList != null && !variableSetList.isEmpty() && object.getAnnotationSets() != null && !object.getAnnotationSets().isEmpty()) { Map<String, VariableSet> variableSetMap = new HashMap<>(); for (VariableSet variableSet : variableSetList) { variableSetMap.put(variableSet.getId(), variableSet); } for (AnnotationSet annotationSet : object.getAnnotationSets()) { VariableSet variableSet = variableSetMap.get(annotationSet.getVariableSetId()); if (variableSet != null) { documentList.addAll(annotationConverter.annotationToDB(variableSet, annotationSet)); privateVariableSetMap.put(String.valueOf(variableSet.getUid()), variableSet.getId()); } } } object.setAnnotationSets(null); Document document = super.convertToStorageType(object); document.put(ANNOTATION_SETS, documentList); document.put(PRIVATE_VS_MAP, privateVariableSetMap); return document; }
return new QueryResult<>("Update annotation set", update.getDbTime(), queryResult.first().getAnnotationSets().size(), queryResult.first().getAnnotationSets().size(), queryResult.getWarningMsg(), queryResult.getErrorMsg(), queryResult.first().getAnnotationSets());
public T convertToDataModelType(Document document, QueryOptions queryOptions) { List<AnnotationSet> annotationSets = annotationConverter.fromDBToAnnotation((List<Document>) document.get(ANNOTATION_SETS), (Document) document.get(AnnotationMongoDBAdaptor.AnnotationSetParams.PRIVATE_VARIABLE_SET_MAP.key()), queryOptions); T t = super.convertToDataModelType(document); t.setAnnotationSets(annotationSets); return t; } }
@Override public File setUid(long uid) { super.setUid(uid); return this; }
@Override public Cohort setStudyUid(long studyUid) { super.setStudyUid(studyUid); return this; }
@Override public Family setUid(long uid) { super.setUid(uid); return this; }
@Override public File setStudyUid(long studyUid) { super.setStudyUid(studyUid); return this; }
@Override public Sample setUid(long uid) { super.setUid(uid); return this; }
@Override public Family setStudyUid(long studyUid) { super.setStudyUid(studyUid); return this; }
@Override public Individual setUid(long uid) { super.setUid(uid); return this; }
@Override public Individual setStudyUid(long studyUid) { super.setStudyUid(studyUid); return this; }