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data_extraction_protocol_charcoal

EHR Data Extraction protocol for Charcoal project.

Retrieves EHR JSON data and documents to dump to a location.

Classes​

DataExtractionProtocolCharcoal​

class DataExtractionProtocolCharcoal(    *,    patient_ids: Optional[list[str]] = None,    patient_ids_file: Optional[os.PathLike | str] = None,    algorithm: Sequence[NextGenPatientInfoDownloadAlgorithm],    trial_name: Optional[str] = None,    **kwargs: Any,):

Protocol for running EHR Data Extraction for Charcoal.

Data extraction protocol for Charcoal project.

Patient IDs can either be supplied as an explicit list of patient IDs or as a path to a file which contains one patient ID per line. These two options are mutually exclusive from each other.

Arguments

  • patient_ids: List of patient ID strings. Mutually exclusive with patient_ids_file.
  • patient_ids_file: Path to file containing patient ID strings, one per line. Mutually exclusive with patient_ids.
  • algorithm: The sequence of algorithms to be used. On the modeller side these will be noop algorithms.
  • trial_name: Name of the trial.
  • ****kwargs**: Additional keyword arguments.

Ancestors​

Variables​

  • algorithms : list - Returns the algorithms in the protocol.

Methods​

dump​

def dump(self) ‑> SerializedProtocol:

Inherited from:

BaseProtocolFactory.dump :

Returns the JSON-serializable representation of the protocol.

modeller​

def modeller(    self, mailbox: _ModellerMailbox, **kwargs: Any,) ‑> bitfount.federated.protocols.ehr.data_extraction_protocol_charcoal._ModellerSide:

Returns the Modeller side of the protocol.

run​

def run(    self,    pod_identifiers: Collection[str],    session: Optional[BitfountSession] = None,    username: Optional[str] = None,    hub: Optional[BitfountHub] = None,    ms_config: Optional[MessageServiceConfig] = None,    message_service: Optional[_MessageService] = None,    pod_public_key_paths: Optional[Mapping[str, Path]] = None,    identity_verification_method: IdentityVerificationMethod = IdentityVerificationMethod.OIDC_DEVICE_CODE,    private_key_or_file: Optional[Union[RSAPrivateKey, Path]] = None,    idp_url: Optional[str] = None,    require_all_pods: bool = False,    run_on_new_data_only: bool = False,    model_out: Optional[Union[Path, str]] = None,    project_id: Optional[str] = None,    batched_execution: Optional[bool] = None,) ‑> Optional[Any]:

Inherited from:

BaseProtocolFactory.run :

Sets up a local Modeller instance and runs the protocol.

Arguments

  • pod_identifiers: The BitfountHub pod identifiers to run against.
  • session: Optional. Session to use for authenticated requests. Created if needed.
  • username: Username to run as. Defaults to logged in user.
  • hub: BitfountHub instance. Default: hub.bitfount.com.
  • ms_config: Message service config. Default: messaging.bitfount.com.
  • message_service: Message service instance, created from ms_config if not provided. Defaults to "messaging.bitfount.com".
  • pod_public_key_paths: Public keys of pods to be checked against.
  • identity_verification_method: The identity verification method to use.
  • private_key_or_file: Private key (to be removed).
  • idp_url: The IDP URL.
  • require_all_pods: If true raise PodResponseError if at least one pod identifier specified rejects or fails to respond to a task request.
  • run_on_new_data_only: Whether to run the task on new datapoints only. Defaults to False.
  • model_out: The path to save the model to.
  • project_id: The project ID to run the task under.
  • batched_execution: Whether to run the task in batched mode. Defaults to False.

Returns Results of the protocol.

Raises

  • PodResponseError: If require_all_pods is true and at least one pod identifier specified rejects or fails to respond to a task request.
  • ValueError: If attempting to train on multiple pods, and the DataStructure table name is given as a string.

worker​

def worker(    self,    mailbox: _WorkerMailbox,    hub: BitfountHub,    context: Optional[ProtocolContext] = None,    **kwargs: Any,) ‑> _WorkerSide:

Returns worker side of the DataExtractionProtocolCharcoal protocol.

Arguments

  • mailbox: Worker mailbox instance to allow communication to the modeller.
  • hub: BitfountHub object to use for communication with the hub.
  • context: Optional. Run-time protocol context details for running.
  • ****kwargs**: Additional keyword arguments.