Starting a FHIR export job - AWS HealthLake

Starting a FHIR export job

Use StartFHIRExportJob to start a FHIR export job from a HealthLake data store. The following menus provide a procedure for the AWS Management Console and code examples for the AWS CLI and AWS SDKs. For more information, see StartFHIRExportJob in the AWS HealthLake API Reference.

Note

HealthLake supports the FHIR R4 specification for health care data exchange. Therefore, all health data is exported in FHIR R4 format.

To start a FHIR export job

Choose a menu based on your access preference to AWS HealthLake.

CLI
AWS CLI

To start a FHIR export job

The following start-fhir-export-job example shows how to start a FHIR export job using AWS HealthLake.

aws healthlake start-fhir-export-job \
    --output-data-config '{"S3Configuration": {"S3Uri":"s3://(Bucket Name)/(Prefix Name)/","KmsKeyId":"arn:aws:kms:us-east-1:012345678910:key/d330e7fc-b56c-4216-a250-f4c43ef46e83"}}' \
    --datastore-id (Data store ID) \
    --data-access-role-arn arn:aws:iam::(AWS Account ID):role/(Role Name)

Output:

{
    "DatastoreId": "(Data store ID)",
    "JobStatus": "SUBMITTED",
    "JobId": "9b9a51943afaedd0a8c0c26c49135a31"
}

Python
SDK for Python (Boto3)
    @classmethod
    def from_client(cls) -> "HealthLakeWrapper":
        """
        Creates a HealthLakeWrapper instance with a default AWS HealthLake client.

        :return: An instance of HealthLakeWrapper initialized with the default HealthLake client.
        """
        health_lake_client = boto3.client("healthlake")
        return cls(health_lake_client)


    def start_fhir_export_job(
        self,
        job_name: str,
        datastore_id: str,
        output_s3_uri: str,
        kms_key_id: str,
        data_access_role_arn: str,
    ) -> dict[str, str]:
        """
        Starts a HealthLake export job.
        :param job_name: The export job name.
        :param datastore_id: The data store ID.
        :param output_s3_uri: The output S3 URI.
        :param kms_key_id: The KMS key ID associated with the output S3 bucket.
        :param data_access_role_arn: The data access role ARN.
        :return: The export job.
        """
        try:
            response = self.health_lake_client.start_fhir_export_job(
                OutputDataConfig={
                    "S3Configuration": {"S3Uri": output_s3_uri, "KmsKeyId": kms_key_id}
                },
                DataAccessRoleArn=data_access_role_arn,
                DatastoreId=datastore_id,
                JobName=job_name,
            )

            return response
        except ClientError as err:
            logger.exception(
                "Couldn't start export job. Here's why %s",
                err.response["Error"]["Message"],
            )
            raise
Note

There's more on GitHub. Find the complete example and learn how to set up and run in the AWS Code Examples Repository.

Example availability

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  1. Sign in to the Data stores page on the HealthLake Console.

  2. Choose a data store.

  3. Choose Export.

    The Export page opens.

  4. Under the Output data section, enter the following information:

    • Output data location in Amazon S3

    • Output encyryption

  5. Under the Access permissions section, choose Use an existing IAM service role and select the role from the Role name menu or choose Create an IAM role.

  6. Choose Export data.

    Note

    During export, choose Copy job ID on the banner at the top of the page. You can use the JobID to request export job properties using the AWS CLI. For more information, see Getting FHIR export job properties.