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insite_insights_protocol

In-site insights protocol.

This protocol is used to generate aggregated patient insights for clinics. First, the fovea model is run, then the GA model, then the GA calculation algorithm, and finally CSV generation. Each task run produces a CSV file as normal but no PDF files.

Classes​

InSiteInsightsProtocol​

class InSiteInsightsProtocol(    *,    algorithm: Sequence[Union[RecordFilterAlgorithm, ModelInference, GATrialCalculationAlgorithmBronze, CSVReportGeneratorOphthalmologyAlgorithm]],    results_notification_email: Optional[bool] = False,    **kwargs: Any,):

Protocol for generating aggregated patient insights for clinics.

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,    context: Optional[ProtocolContext] = None,    **kwargs: Any,) ‑> GenericOphthalmologyModellerSide:

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,    project_id: Optional[str] = None,    batched_execution: Optional[bool] = None,    test_run: bool = False,    force_rerun_failed_files: bool = True,) ‑> 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.
  • project_id: The project ID to run the task under.
  • batched_execution: Whether to run the task in batched mode. Defaults to False.
  • test_run: If True, runs the task in test mode, on a limited number of datapoints. Defaults to False.
  • force_rerun_failed_files: If True, forces a rerun on files that the task previously failed on. If False, the task will skip files that have previously failed. Note: This option can only be enabled if both enable_batch_resilience and individual_file_retry_enabled are True. Defaults to True.

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 InSiteInsightsProtocol 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.