public FamilyAclEntry(String member, ObjectMap permissions) { super(member, EnumSet.noneOf(FamilyPermissions.class)); EnumSet<FamilyPermissions> aux = EnumSet.allOf(FamilyPermissions.class); for (FamilyPermissions permission : aux) { if (permissions.containsKey(permission.name()) && permissions.getBoolean(permission.name())) { this.permissions.add(permission); } } }
.map(PanelAclEntry.PanelPermissions::toString) .collect(Collectors.toList())); this.fullPermissionsMap.put(Entity.FAMILY, Arrays.stream(FamilyAclEntry.FamilyPermissions.values()) .map(FamilyAclEntry.FamilyPermissions::toString) .collect(Collectors.toList()));
@Override public QueryResult<Long> count(final Query query, final String user, final StudyAclEntry.StudyPermissions studyPermissions) throws CatalogDBException, CatalogAuthorizationException { filterOutDeleted(query); StudyAclEntry.StudyPermissions studyPermission = (studyPermissions == null ? StudyAclEntry.StudyPermissions.VIEW_FAMILIES : studyPermissions); // Get the study document Query studyQuery = new Query(StudyDBAdaptor.QueryParams.UID.key(), query.getLong(QueryParams.STUDY_UID.key())); QueryResult queryResult = dbAdaptorFactory.getCatalogStudyDBAdaptor().nativeGet(studyQuery, QueryOptions.empty()); if (queryResult.getNumResults() == 0) { throw new CatalogDBException("Study " + query.getLong(QueryParams.STUDY_UID.key()) + " not found"); } // Get the document query needed to check the permissions as well Document queryForAuthorisedEntries = getQueryForAuthorisedEntries((Document) queryResult.first(), user, studyPermission.name(), studyPermission.getFamilyPermission().name(), Entity.FAMILY.name()); Bson bson = parseQuery(query, false, queryForAuthorisedEntries); logger.debug("Family count: query : {}, dbTime: {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry())); return familyCollection.count(bson); }
private MongoCursor<Document> getMongoCursor(Query query, QueryOptions options, Document studyDocument, String user) throws CatalogDBException, CatalogAuthorizationException { Document queryForAuthorisedEntries = null; if (studyDocument != null && user != null) { // Get the document query needed to check the permissions as well queryForAuthorisedEntries = getQueryForAuthorisedEntries(studyDocument, user, StudyAclEntry.StudyPermissions.VIEW_FAMILIES.name(), FamilyAclEntry.FamilyPermissions.VIEW.name(), Entity.FAMILY.name()); } filterOutDeleted(query); Bson bson = parseQuery(query, false, queryForAuthorisedEntries); QueryOptions qOptions; if (options != null) { qOptions = new QueryOptions(options); } else { qOptions = new QueryOptions(); } qOptions = removeInnerProjections(qOptions, QueryParams.MEMBERS.key()); qOptions = removeAnnotationProjectionOptions(qOptions); logger.debug("Family query : {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry())); return familyCollection.nativeQuery().find(bson, qOptions).iterator(); }
@Override public QueryResult groupBy(Query query, List<String> fields, QueryOptions options, String user) throws CatalogDBException, CatalogAuthorizationException { Document studyDocument = getStudyDocument(query); Document queryForAuthorisedEntries; if (containsAnnotationQuery(query)) { queryForAuthorisedEntries = getQueryForAuthorisedEntries(studyDocument, user, StudyAclEntry.StudyPermissions.VIEW_FAMILY_ANNOTATIONS.name(), FamilyAclEntry.FamilyPermissions.VIEW_ANNOTATIONS.name(), Entity.FAMILY.name()); } else { queryForAuthorisedEntries = getQueryForAuthorisedEntries(studyDocument, user, StudyAclEntry.StudyPermissions.VIEW_FAMILIES.name(), FamilyAclEntry.FamilyPermissions.VIEW.name(), Entity.FAMILY.name()); } filterOutDeleted(query); Bson bsonQuery = parseQuery(query, false, queryForAuthorisedEntries); return groupBy(familyCollection, bsonQuery, fields, QueryParams.ID.key(), options); }
@Override public QueryResult groupBy(Query query, String field, QueryOptions options, String user) throws CatalogDBException, CatalogAuthorizationException { Document studyDocument = getStudyDocument(query); Document queryForAuthorisedEntries; if (containsAnnotationQuery(query)) { queryForAuthorisedEntries = getQueryForAuthorisedEntries(studyDocument, user, StudyAclEntry.StudyPermissions.VIEW_FAMILY_ANNOTATIONS.name(), FamilyAclEntry.FamilyPermissions.VIEW_ANNOTATIONS.name(), Entity.FAMILY.name()); } else { queryForAuthorisedEntries = getQueryForAuthorisedEntries(studyDocument, user, StudyAclEntry.StudyPermissions.VIEW_FAMILIES.name(), FamilyAclEntry.FamilyPermissions.VIEW.name(), Entity.FAMILY.name()); } filterOutDeleted(query); Bson bsonQuery = parseQuery(query, false, queryForAuthorisedEntries); return groupBy(familyCollection, bsonQuery, field, QueryParams.ID.key(), options); }
public FamilyAclEntry.FamilyPermissions getFamilyPermission() { if (this.type == FAMILY) { return FamilyAclEntry.FamilyPermissions.valueOf(this.permission); } return null; }
@Override public DBIterator<Family> iterator(Query query, QueryOptions options, String user) throws CatalogDBException, CatalogAuthorizationException { Document studyDocument = getStudyDocument(query); MongoCursor<Document> mongoCursor = getMongoCursor(query, options, studyDocument, user); Function<Document, Document> iteratorFilter = (d) -> filterAnnotationSets(studyDocument, d, user, StudyAclEntry.StudyPermissions.VIEW_FAMILY_ANNOTATIONS.name(), FamilyAclEntry.FamilyPermissions.VIEW_ANNOTATIONS.name()); return new FamilyMongoDBIterator<>(mongoCursor, familyConverter, iteratorFilter, dbAdaptorFactory.getCatalogIndividualDBAdaptor(), query.getLong(PRIVATE_STUDY_ID), user, options); }
@Override public DBIterator nativeIterator(Query query, QueryOptions options, String user) throws CatalogDBException, CatalogAuthorizationException { QueryOptions queryOptions = options != null ? new QueryOptions(options) : new QueryOptions(); queryOptions.put(NATIVE_QUERY, true); Document studyDocument = getStudyDocument(query); MongoCursor<Document> mongoCursor = getMongoCursor(query, queryOptions, studyDocument, user); Function<Document, Document> iteratorFilter = (d) -> filterAnnotationSets(studyDocument, d, user, StudyAclEntry.StudyPermissions.VIEW_FAMILY_ANNOTATIONS.name(), FamilyAclEntry.FamilyPermissions.VIEW_ANNOTATIONS.name()); return new FamilyMongoDBIterator(mongoCursor, null, iteratorFilter, dbAdaptorFactory.getCatalogIndividualDBAdaptor(), query.getLong(PRIVATE_STUDY_ID), user, options); }