Data Model Cafe Variome V3 uses MongoDB for primary data storage. All operational data, including the user information, networks, sources, etc. are all stored in it. Additionally, the data loaded for discovery (subject data and metadata) is also stored in MongoDB, unless Molgenis is being used as a storage backend.
Class Diagram BeaconAuthMethod NO_AUTH AUTH_KEY TOKEN UserMappingType NO_MAPPING STATIC DYNAMIC DatabaseCollection mongo_client : AsyncIOMotorClient db : AsyncIOMotorDatabase sem : asyncio.Semaphore init_driver(database_client: AsyncIOMotorClient) counter() : AsyncIOMotorCollection datafiles() : AsyncIOMotorCollection config() : AsyncIOMotorCollection logs() : AsyncIOMotorCollection beacon_endpoints() : AsyncIOMotorCollection discovery_groups() : AsyncIOMotorCollection nodes() : AsyncIOMotorCollection pending_nodes() : AsyncIOMotorCollection networks() : AsyncIOMotorCollection network_messages() : AsyncIOMotorCollection nexus_credentials() : AsyncIOMotorCollection nexus_installations() : AsyncIOMotorCollection nexus_networks() : AsyncIOMotorCollection nexus_requests() : AsyncIOMotorCollection pipelines() : AsyncIOMotorCollection queries() : AsyncIOMotorCollection responses() : AsyncIOMotorCollection sources() : AsyncIOMotorCollection source_index() : AsyncIOMotorCollection meta_sources() : AsyncIOMotorCollection users() : AsyncIOMotorCollection access_requests() : AsyncIOMotorCollection getters DataModel db : DatabaseCollection Schema : marshmallow.Schema init_driver() load() : DataModel load_all() : list[DataModel] store() update(payload: dict) delete() to_dict(self) : dict from_dict(payload: dict) : DataModel validate_json(json_data: dict) : bool AccessRequest request_id : str first_name : str last_name : str email : str affiliation : str justification : str BeaconEndpoint endpoint_id : str endpoint_path : str network_id : str mapping : UserMapping beacon_auth_method : BeaconAuthMethod beacon_auth_key : str load_by_path(beacon_path: str) : BeaconEndpoint generate_auth_key() : str UserMapping mapping_type : UserMappingType mapping_user : str mapping : dict[str, str] to_storage() : str | dict[str, str] from_storage(payload: str | dict[str, str]) : UserMapping remap(user_id: str) : str Class diagram is under development. The diagram you see here may not be complete or accurate. This warning will be removed when the diagram is ready.
Last modified: 09 September 2024