HealthLake examples using AWS CLI

The following code examples show you how to perform actions and implement common scenarios by using the AWS Command Line Interface with HealthLake.

Actions are code excerpts from larger programs and must be run in context. While actions show you how to call individual service functions, you can see actions in context in their related scenarios.

Each example includes a link to the complete source code, where you can find instructions on how to set up and run the code in context.

Topics

Actions

Actions

The following code example shows how to use create-fhir-datastore.

AWS CLI

Example 1: Create a SigV4-enabled HealthLake data store

The following create-fhir-datastore example demonstrates how to create a new data store in AWS HealthLake.


aws healthlake create-fhir-datastore \
    --datastore-type-version R4 \
    --datastore-name "FhirTestDatastore"

Output:


{
    "DatastoreEndpoint": "https://healthlake.us-east-1.amazonaws.com/datastore/(Data store ID)/r4/",
    "DatastoreArn": "arn:aws:healthlake:us-east-1:(AWS Account ID):datastore/(Data store ID)",
    "DatastoreStatus": "CREATING",
    "DatastoreId": "(Data store ID)"
}

Example 2: Create a SMART on FHIR-enabled HealthLake data store

The following create-fhir-datastore example demonstrates how to create a new SMART on FHIR-enabled data store in AWS HealthLake.


aws healthlake create-fhir-datastore \
    --datastore-name "your-data-store-name" \
    --datastore-type-version R4 \
    --preload-data-config PreloadDataType="SYNTHEA" \
    --sse-configuration '{ "KmsEncryptionConfig": {  "CmkType": "CUSTOMER_MANAGED_KMS_KEY", "KmsKeyId": "arn:aws:kms:us-east-1:your-account-id:key/your-key-id" } }' \
    --identity-provider-configuration  file://identity_provider_configuration.json

Contents of identity_provider_configuration.json:


{
    "AuthorizationStrategy": "SMART_ON_FHIR_V1",
    "FineGrainedAuthorizationEnabled": true,
    "IdpLambdaArn": "arn:aws:lambda:your-region:your-account-id:function:your-lambda-name",
    "Metadata": "{\"issuer\":\"https://ehr.example.com\", \"jwks_uri\":\"https://ehr.example.com/.well-known/jwks.json\",\"authorization_endpoint\":\"https://ehr.example.com/auth/authorize\",\"token_endpoint\":\"https://ehr.token.com/auth/token\",\"token_endpoint_auth_methods_supported\":[\"client_secret_basic\",\"foo\"],\"grant_types_supported\":[\"client_credential\",\"foo\"],\"registration_endpoint\":\"https://ehr.example.com/auth/register\",\"scopes_supported\":[\"openId\",\"profile\",\"launch\"],\"response_types_supported\":[\"code\"],\"management_endpoint\":\"https://ehr.example.com/user/manage\",\"introspection_endpoint\":\"https://ehr.example.com/user/introspect\",\"revocation_endpoint\":\"https://ehr.example.com/user/revoke\",\"code_challenge_methods_supported\":[\"S256\"],\"capabilities\":[\"launch-ehr\",\"sso-openid-connect\",\"client-public\"]}"
}

Output:


{
    "DatastoreEndpoint": "https://healthlake.us-east-1.amazonaws.com/datastore/(Data store ID)/r4/",
    "DatastoreArn": "arn:aws:healthlake:us-east-1:(AWS Account ID):datastore/(Data store ID)",
    "DatastoreStatus": "CREATING",
    "DatastoreId": "(Data store ID)"
}

For more information, see Creating and monitoring a FHIR data store in the AWS HealthLake Developer Guide.

For API details, see CreateFHIRDatastore in AWS CLI Command Reference.

The following code example shows how to use delete-fhir-datastore.

AWS CLI

To delete a FHIR data store

The following delete-fhir-datastore example demonstrates how to delete a data store and all of its contents in AWS HealthLake.


aws healthlake delete-fhir-datastore \
    --datastore-id (Data store ID)

Output:


{
    "DatastoreEndpoint": "https://healthlake.us-east-1.amazonaws.com/datastore/(Data store ID)/r4/",
    "DatastoreArn": "arn:aws:healthlake:us-east-1:(AWS Account ID):datastore/(Data store ID)",
    "DatastoreStatus": "DELETING",
    "DatastoreId": "(Data store ID)"
}

For more information, see Creating and monitoring a FHIR data store <https://docs.aws.amazon.com/healthlake/latest/devguide/working-with-FHIR-healthlake.html> in the AWS HealthLake Developer Guide.

For API details, see DeleteFHIRDatastore in AWS CLI Command Reference.

The following code example shows how to use describe-fhir-datastore.

AWS CLI

To describe a FHIR data store

The following describe-fhir-datastore example demonstrates how to find the properties of a data store in AWS HealthLake.


aws healthlake describe-fhir-datastore \
    --datastore-id "1f2f459836ac6c513ce899f9e4f66a59"

Output:


{
    "DatastoreProperties": {
        "PreloadDataConfig": {
            "PreloadDataType": "SYNTHEA"
        },
        "SseConfiguration": {
            "KmsEncryptionConfig": {
                "CmkType": "CUSTOMER_MANAGED_KMS_KEY",
                "KmsKeyId": "arn:aws:kms:us-east-1:123456789012:key/a1b2c3d4-5678-90ab-cdef-EXAMPLE11111"
            }
        },
        "DatastoreName": "Demo",
        "DatastoreArn": "arn:aws:healthlake:us-east-1:<AWS Account ID>:datastore/<Data store ID>",
        "DatastoreEndpoint": "https://healthlake.us-east-1.amazonaws.com/datastore/<Data store ID>/r4/",
        "DatastoreStatus": "ACTIVE",
        "DatastoreTypeVersion": "R4",
        "CreatedAt": 1603761064.881,
        "DatastoreId": "<Data store ID>",
        "IdentityProviderConfiguration": {
            "AuthorizationStrategy": "AWS_AUTH",
            "FineGrainedAuthorizationEnabled": false
        }
    }
}

For more information, see Creating and monitoring a FHIR data stores in the AWS HealthLake Developer Guide.

For API details, see DescribeFHIRDatastore in AWS CLI Command Reference.

The following code example shows how to use describe-fhir-export-job.

AWS CLI

To describe a FHIR export job

The following describe-fhir-export-job example shows how to find the properties of a FHIR export job in AWS HealthLake.


aws healthlake describe-fhir-export-job \
    --datastore-id (Data store ID) \
    --job-id 9b9a51943afaedd0a8c0c26c49135a31

Output:


{
    "ExportJobProperties": {
        "DataAccessRoleArn": "arn:aws:iam::(AWS Account ID):role/(Role Name)",
        "JobStatus": "IN_PROGRESS",
        "JobId": "9009813e9d69ba7cf79bcb3468780f16",
        "SubmitTime": "2024-11-20T11:31:46.672000-05:00",
        "EndTime": "2024-11-20T11:34:01.636000-05:00",
        "OutputDataConfig": {
            "S3Configuration": {
            "S3Uri": "s3://(Bucket Name)/(Prefix Name)/",
            "KmsKeyId": "arn:aws:kms:us-east-1:012345678910:key/d330e7fc-b56c-4216-a250-f4c43ef46e83"
        }

        },
        "DatastoreId": "(Data store ID)"
    }
}

For more information, see Exporting files from a FHIR data store in the AWS HealthLake Developer Guide.

For API details, see DescribeFHIRExportJob in AWS CLI Command Reference.

The following code example shows how to use describe-fhir-import-job.

AWS CLI

To describe a FHIR import job

The following describe-fhir-import-job example shows how to learn the properties of a FHIR import job using AWS HealthLake.


aws healthlake describe-fhir-import-job \
    --datastore-id (Data store ID) \
    --job-id c145fbb27b192af392f8ce6e7838e34f

Output:


{
    "ImportJobProperties": {
    "InputDataConfig": {
        "S3Uri": "s3://(Bucket Name)/(Prefix Name)/"
        { "arrayitem2": 2 }
    },
    "DataAccessRoleArn": "arn:aws:iam::(AWS Account ID):role/(Role Name)",
    "JobStatus": "COMPLETED",
    "JobId": "c145fbb27b192af392f8ce6e7838e34f",
    "SubmitTime": 1606272542.161,
    "EndTime": 1606272609.497,
    "DatastoreId": "(Data store ID)"
    }
}

For more information, see Importing files to a FHIR data store in the AWS HealthLake Developer Guide.

For API details, see DescribeFHIRImportJob in AWS CLI Command Reference.

The following code example shows how to use list-fhir-datastores.

AWS CLI

To list FHIR data stores

The following list-fhir-datastores example shows to how to use the command and how users can filter results based on data store status in AWS HealthLake.


aws healthlake list-fhir-datastores \
    --filter DatastoreStatus=ACTIVE

Output:


{
    "DatastorePropertiesList": [
    {
        "PreloadDataConfig": {
            "PreloadDataType": "SYNTHEA"
        },
        "SseConfiguration": {
            "KmsEncryptionConfig": {
                "CmkType": "CUSTOMER_MANAGED_KMS_KEY",
                "KmsKeyId": "arn:aws:kms:us-east-1:123456789012:key/a1b2c3d4-5678-90ab-cdef-EXAMPLE11111"
            }
        },
        "DatastoreName": "Demo",
        "DatastoreArn": "arn:aws:healthlake:us-east-1:<AWS Account ID>:datastore/<Data store ID>",
        "DatastoreEndpoint": "https://healthlake.us-east-1.amazonaws.com/datastore/<Data store ID>/r4/",
        "DatastoreStatus": "ACTIVE",
        "DatastoreTypeVersion": "R4",
        "CreatedAt": 1603761064.881,
        "DatastoreId": "<Data store ID>",
        "IdentityProviderConfiguration": {
            "AuthorizationStrategy": "AWS_AUTH",
            "FineGrainedAuthorizationEnabled": false
        }
    }
    ]
}

For more information, see Creating and monitoring a FHIR data store in the AWS HealthLake Developer Guide.

For API details, see ListFHIRDatastores in AWS CLI Command Reference.

The following code example shows how to use list-fhir-export-jobs.

AWS CLI

To list all FHIR export jobs

The following list-fhir-export-jobs example shows how to use the command to view a list of export jobs associated with an account.


aws healthlake list-fhir-export-jobs \
    --datastore-id (Data store ID) \
    --submitted-before (DATE like 2024-10-13T19:00:00Z)\
    --submitted-after (DATE like 2020-10-13T19:00:00Z )\
    --job-name "FHIR-EXPORT" \
    --job-status SUBMITTED  \
    --max-results (Integer between 1 and 500)

Output:


{
    "ExportJobPropertiesList": [
        {
            "ExportJobProperties": {
                "OutputDataConfig": {
                    "S3Uri": "s3://(Bucket Name)/(Prefix Name)/",
                    "S3Configuration": {
                        "S3Uri": "s3://(Bucket Name)/(Prefix Name)/",
                        "KmsKeyId": "(KmsKey Id)"
                    }
                },
                "DataAccessRoleArn": "arn:aws:iam::(AWS Account ID):role/(Role Name)",
                "JobStatus": "COMPLETED",
                "JobId": "c145fbb27b192af392f8ce6e7838e34f",
                "JobName": "FHIR-EXPORT",
                "SubmitTime": "2024-11-20T11:31:46.672000-05:00",
                "EndTime": "2024-11-20T11:34:01.636000-05:00",
                "DatastoreId": "(Data store ID)"
            }
        }
    ]
}

For more information, see Exporting files from a FHIR data store in the AWS HealthLake Developer Guide.

For API details, see ListFHIRExportJobs in AWS CLI Command Reference.

The following code example shows how to use list-fhir-import-jobs.

AWS CLI

To list all FHIR import jobs

The following list-fhir-import-jobs example shows how to use the command to view a list of all import jobs associated with an account.


aws healthlake list-fhir-import-jobs \
    --datastore-id (Data store ID) \
    --submitted-before (DATE like 2024-10-13T19:00:00Z) \
    --submitted-after (DATE like 2020-10-13T19:00:00Z ) \
    --job-name "FHIR-IMPORT" \
    --job-status SUBMITTED  \
    -max-results (Integer between 1 and 500)

Output:


{
    "ImportJobPropertiesList": [
        {
            "JobId": "c0fddbf76f238297632d4aebdbfc9ddf",
            "JobStatus": "COMPLETED",
            "SubmitTime": "2024-11-20T10:08:46.813000-05:00",
            "EndTime": "2024-11-20T10:10:09.093000-05:00",
            "DatastoreId": "(Data store ID)",
            "InputDataConfig": {
                "S3Uri": "s3://(Bucket Name)/(Prefix Name)/"
            },
            "JobOutputDataConfig": {
                "S3Configuration": {
                    "S3Uri": "s3://(Bucket Name)/import/6407b9ae4c2def3cb6f1a46a0c599ec0-FHIR_IMPORT-c0fddbf76f238297632d4aebdbfc9ddf/",
                    "KmsKeyId": "arn:aws:kms:us-east-1:123456789012:key/b7f645cb-e564-4981-8672-9e012d1ff1a0"
                }
            },
            "JobProgressReport": {
                "TotalNumberOfScannedFiles": 1,
                "TotalSizeOfScannedFilesInMB": 0.001798,
                "TotalNumberOfImportedFiles": 1,
                "TotalNumberOfResourcesScanned": 1,
                "TotalNumberOfResourcesImported": 1,
                "TotalNumberOfResourcesWithCustomerError": 0,
                "TotalNumberOfFilesReadWithCustomerError": 0,
                "Throughput": 0.0
            },
            "DataAccessRoleArn": "arn:aws:iam::(AWS Account ID):role/(Role Name)"
        }
    ]
}

For more information, see Importing files to FHIR data store in the AWS HealthLake Developer Guide.

For API details, see ListFHIRImportJobs in AWS CLI Command Reference.

The following code example shows how to use list-tags-for-resource.

AWS CLI

To list tags for a data store

The following list-tags-for-resource example lists the tags associated with the specified data store.:


aws healthlake list-tags-for-resource \
    --resource-arn "arn:aws:healthlake:us-east-1:123456789012:datastore/fhir/0725c83f4307f263e16fd56b6d8ebdbe"

Output:


{
    "tags": {
        "key": "value",
        "key1": "value1"
    }
}

For more information, see Tagging resources in AWS HealthLake in the AWS HealthLake Developer Guide.

For API details, see ListTagsForResource in AWS CLI Command Reference.

The following code example shows how to use start-fhir-export-job.

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"
}

For more information, see Exporting files from a FHIR data store in the AWS HealthLake Developer Guide.

For API details, see StartFHIRExportJob in AWS CLI Command Reference.

The following code example shows how to use start-fhir-import-job.

AWS CLI

To start a FHIR import job

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


aws healthlake start-fhir-import-job \
    --input-data-config S3Uri="s3://(Bucket Name)/(Prefix Name)/" \
    --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": "c145fbb27b192af392f8ce6e7838e34f"
}

For more information, see Importing files to a FHIR data store in the AWS HealthLake Developer Guide.

For API details, see StartFHIRImportJob in AWS CLI Command Reference.

The following code example shows how to use tag-resource.

AWS CLI

To add a tag to data store

The following tag-resource example shows how to add a tag to a data store.


aws healthlake tag-resource \
    --resource-arn "arn:aws:healthlake:us-east-1:123456789012:datastore/fhir/0725c83f4307f263e16fd56b6d8ebdbe" \
    --tags '[{"Key": "key1", "Value": "value1"}]'

This command produces no output.

For more information, see Adding a tag to a data store in the AWS HealthLake Developer Guide..

For API details, see TagResource in AWS CLI Command Reference.

The following code example shows how to use untag-resource.

AWS CLI

To remove tags from a data store.

The following untag-resource example shows how to remove tags from a data store.


aws healthlake untag-resource \
    --resource-arn "arn:aws:healthlake:us-east-1:123456789012:datastore/fhir/b91723d65c6fdeb1d26543a49d2ed1fa" \
    --tag-keys '["key1"]'

This command produces no output.

For more information, see Removing tags from a data store in the AWS HealthLake Developer Guide.

For API details, see UntagResource in AWS CLI Command Reference.

Warning Javascript is disabled or is unavailable in your browser.

To use the Amazon Web Services Documentation, Javascript must be enabled. Please refer to your browser's Help pages for instructions.

Document Conventions

HealthImaging

HealthOmics