Setting up AWS HealthLake - AWS HealthLake

Setting up AWS HealthLake

In this chapter, you use the AWS Management Console to set up the required permissions to start using AWS HealthLake and create a data store. To set up permissions to create a data store, you create an IAM user or role that is a data lake administrator and HealthLake administrator. You make this user a data lake administrator in AWS Lake Formation. The data lake administrator grants Lake Formation access to resources needed to use Amazon Athena to query a data store. After you create a HealthLake data store, you can set up permissions for importing and exporting files.

Sign up for an AWS account

If you do not have an AWS account, complete the following steps to create one.

To sign up for an AWS account
  1. Open https://portal.aws.amazon.com/billing/signup.

  2. Follow the online instructions.

    Part of the sign-up procedure involves receiving a phone call and entering a verification code on the phone keypad.

    When you sign up for an AWS account, an AWS account root user is created. The root user has access to all AWS services and resources in the account. As a security best practice, assign administrative access to a user, and use only the root user to perform tasks that require root user access.

AWS sends you a confirmation email after the sign-up process is complete. At any time, you can view your current account activity and manage your account by going to https://aws.amazon.com/ and choosing My Account.

Create a user with administrative access

After you sign up for an AWS account, secure your AWS account root user, enable AWS IAM Identity Center, and create an administrative user so that you don't use the root user for everyday tasks.

Secure your AWS account root user
  1. Sign in to the AWS Management Console as the account owner by choosing Root user and entering your AWS account email address. On the next page, enter your password.

    For help signing in by using root user, see Signing in as the root user in the AWS Sign-In User Guide.

  2. Turn on multi-factor authentication (MFA) for your root user.

    For instructions, see Enable a virtual MFA device for your AWS account root user (console) in the IAM User Guide.

Create a user with administrative access
  1. Enable IAM Identity Center.

    For instructions, see Enabling AWS IAM Identity Center in the AWS IAM Identity Center User Guide.

  2. In IAM Identity Center, grant administrative access to a user.

    For a tutorial about using the IAM Identity Center directory as your identity source, see Configure user access with the default IAM Identity Center directory in the AWS IAM Identity Center User Guide.

Sign in as the user with administrative access
  • To sign in with your IAM Identity Center user, use the sign-in URL that was sent to your email address when you created the IAM Identity Center user.

    For help signing in using an IAM Identity Center user, see Signing in to the AWS access portal in the AWS Sign-In User Guide.

Assign access to additional users
  1. In IAM Identity Center, create a permission set that follows the best practice of applying least-privilege permissions.

    For instructions, see Create a permission set in the AWS IAM Identity Center User Guide.

  2. Assign users to a group, and then assign single sign-on access to the group.

    For instructions, see Add groups in the AWS IAM Identity Center User Guide.

Configure an IAM user or role to use HealthLake (IAM Administrator)

Persona: IAM Administrator

A user who can create IAM users and roles, and can add data lake administrators.

These steps in this topic must be carried out by an IAM administrator.

To connect your HealthLake data store to Athena, you need create an IAM user or role that is a data lake administrator and a HealthLake administrator. This new user or role grants access to resources found in a data store via AWS Lake Formation, and has the AmazonHealthLakeFullAccess AWS managed policy added to their user or role.

Important

An IAM user or role that is a data lake administrator cannot create new data lake administrators. To add additional data lake administrator you must use a IAM user or role which has been granted AdministratorAccess access.

To create an administrator
  1. Add the AmazonHealthlakeFullAccess IAM AWS managed policy to a user or role in your organization.

    If you're unfamiliar with creating an IAM user, see Creating an IAM User and Overview of AWS IAM Policies in the IAM User Guide.

  2. Grant the IAM user or role access to AWS Lake Formation.

    • Add the following IAM AWS managed policy to a user or role in your organization: AWSLakeFormationDataAdmin

      Note

      The AWSLakeFormationDataAdmin policy grants access to all AWS Lake Formation resources. We recommend that you always use the minimum permissions required to accomplish your task. For more information, see IAM Best Practices in the IAM User Guide.

  3. Add the following inline policy to the user or role. For more information, see Inline policies in the IAM User Guide.

    { "Version": "2012-10-17", "Statement": [ { "Effect": "Allow", "Action": [ "s3:GetObject", "s3:PutObject" ], "Resource": [ "arn:aws:s3:::amzn-s3-demo-source-bucket/*", "arn:aws:s3:::amzn-s3-demo-logging-bucket/*" ] }, { "Effect": "Allow", "Action": [ "ram:GetResourceShareInvitations", "ram:AcceptResourceShareInvitation", "glue:CreateDatabase", "glue:DeleteDatabase" ], "Resource": "*" } ] }

For more information on the AWSLakeFormationDataAdmin policy, see Lake Formation Personas and IAM Permissions Reference in the AWS Lake Formation Developer Guide.

Add a user or role as the Data Lake Administrator in Lake Formation (IAM Administrator)

Note

This step is required if you are integrating SQL index and query.

Next, the IAM administrator must add the user or role created in the previous step as a data lake administrator in Lake Formation.

To add an IAM user or role as a data lake administrator
  1. Open the AWS Lake Formation console: https://console.aws.amazon.com/lakeformation/

    Note

    If this is your first time visiting Lake Formation, a Welcome to Lake Formation dialog box appears asking you to define a Lake Formation administrator.

    Image of a dialog box asking you to define a lake formation administrator
  2. Assign the new user or role to be a AWS Lake Formation data lake administrator.

    • Option 1: If you received the Welcome to Lake Formation dialog box.

      1. Choose Add other AWS users or roles.

      2. Choose the down arrow (▼).

      3. Choose the HealthLake administrator you would like to also be Lake Formation administrators.

      4. Choose Get started.

    • Option 2: Use the Navigation pane (☰).

      1. Choose the Navigation pane (☰).

      2. Under Permissions, choose Administrative roles and tasks.

      3. In the Data lake administrators section, select Choose administrators .

      4. In the Manage data lake administrators dialog box, choose the down arrow (▼).

      5. Next, select or search for the HealthLake administrators users or roles who you also want to be Lake Formation administrators.

      6. Choose Save.

  3. Change the default security settings to be managed by Lake Formation. The HealthLake data store resources need to be managed by Lake Formation not IAM. To update, see Change the default permission model in the AWS Lake Formation Developer Guide.

Create S3 buckets

To import FHIR R4 data into AWS HealthLake, two Amazon S3 buckets are recommended. The Amazon S3 input bucket holds the FHIR data to be imported and HealthLake reads from this bucket. The Amazon S3 output bucket stores the processing results of the import job and HealthLake writes (logs) to this bucket.

Note

Due to AWS Identity and Access Management (IAM) policy, your Amazon S3 bucket names must be unique. For more information, see Bucket naming rules in the Amazon Simple Storage Service User Guide.

For the purpose of this guide, we specify the following Amazon S3 input and output buckets when setting up import permissions later in this section.

  • Input bucket: arn:aws:s3:::amzn-s3-demo-source-bucket

  • Output bucket: arn:aws:s3:::amzn-s3-demo-logging-bucket

For additional information, see Creating a bucket in the Amazon S3 User Guide.

Create a data store

A HealthLake data store is a repository of FHIR R4 data that resides within a single AWS Region. An AWS account can have zero or many data stores. HealthLake supports two data store authorization strategies.

Important

Before you create a HealthLake data store, review the Service control policies (SCPs) in your AWS Organization that might restrict the creation or management of HealthLake resources. SCPs can prevent the successful creation of HealthLake data stores, even if your IAM permissions are set up correctly.

A datastoreID is generated when you create a HealthLake data store. You must use the datastoreID when setting up import permissions later in this section.

To create a HealthLake data store, see Creating a HealthLake data store.

Setting up permissions for import jobs

Before you import files into a data store, you must grant HealthLake permission to access your input and output buckets in Amazon S3. To grant HealthLake access, you create an IAM service role for HealthLake, add a trust policy to the role to grant HealthLake assume role permissions, and attach a permissions policy to role that grants it to access to your Amazon S3 buckets.

When you create an import job, you specify the Amazon Resource Name (ARN) of this role for the DataAccessRoleArn. For more information about IAM roles and trust policies, see IAM Roles.

After you set up permission, you are ready to import files into your data store with an import job. For more information, see Starting a FHIR import job.

To set up import permissions
  1. If haven't already, create a destination Amazon S3 bucket for output log files. The Amazon S3 bucket must be in the same AWS Region as the service, and Block Public Access must be turned on for all options. To learn more, see Using Amazon S3 block public access. An Amazon-owned or customer-owned KMS key must also be used for encryption. To learn more about using KMS keys, see Amazon Key Management Service.

  2. Create a data access service role for HealthLake and give the HealthLake service permission to assume it with the following trust policy. HealthLake uses this to write the output Amazon S3 bucket.

    { "Version": "2012-10-17", "Statement": [{ "Effect": "Allow", "Principal": { "Service": ["healthlake.amazonaws.com"] }, "Action": "sts:AssumeRole", "Condition": { "StringEquals": { "aws:SourceAccount": "accountID" }, "ArnEquals": { "aws:SourceArn": "arn:aws:healthlake:us-west-2:accountID:datastore/fhir/datastoreID" } } }] }
  3. Add a permissions policy to the data access role that allows it to access the Amazon S3 bucket. Replace amzn-s3-demo-bucket with your bucket's name.

    { "Version": "2012-10-17", "Statement": [{ "Action": [ "s3:ListBucket", "s3:GetBucketPublicAccessBlock", "s3:GetEncryptionConfiguration" ], "Resource": [ "arn:aws:s3:::amzn-s3-demo-source-bucket" ], "Effect": "Allow" }, { "Action": [ "s3:PutObject" ], "Resource": [ "arn:aws:s3:::amzn-s3-demo-logging-bucket/*" ], "Effect": "Allow" }, { "Action": [ "kms:DescribeKey", "kms:GenerateDataKey*" ], "Resource": [ "arn:aws:kms:us-east-1:012345678910:key/d330e7fc-b56c-4216-a250-f4c43ef46e83" ], "Effect": "Allow" }] }

Setting up permissions for export jobs

Before you export files from a DynamoDB Streams, you must grant HealthLake permission to access your output bucket in Amazon S3. To grant HealthLake access, you create an IAM service role for HealthLake, add a trust policy to the role to grant HealthLake assume role permissions, and attach a permissions policy to role that grants it to access to your Amazon S3 bucket.

If you already created a role for HealthLake, you can reuse it and grant it the additional permissions for your export Amazon S3 bucket listed in this topic. To learn more about IAM roles and trust policies, see IAM Policies and Permissions.

Important

HealthLake SDK export requests using StartFHIRExportJob API operation and FHIR REST API export requests using StartFHIRExportJobWithPost API operation have separate IAM actions. Each IAM action, SDK export with StartFHIRExportJob and FHIR REST API export with StartFHIRExportJobWithPost, can have allow/deny permissions handled separately. If you want both SDK and FHIR REST API exports to be restricted, make sure to deny permissions for each IAM action. If you give users full access to HealthLake, no IAM user permissions changes are required.

The user or role that sets up permissions must have permission to create roles, create policies, and attach policies to roles. The following IAM policy grants these permissions.

{ "Version": "2012-10-17", "Statement": [{ "Action": ["iam:CreateRole", "iam:CreatePolicy", "iam:AttachRolePolicy"], "Effect": "Allow", "Resource": "*" }, { "Action": "iam:PassRole" "Effect": "Allow", "Resource": "*", "Condition": { "StringEquals": { "iam:PassedToService": "healthlake.amazonaws.com" } } }] }
To set up export permissions
  1. If haven't already, create a destination Amazon S3 bucket for the data you will export from your DynamoDB Streams. The Amazon S3 bucket must be in the same AWS Region as the service, and Block Public Access must be turned on for all options. To learn more, see Using Amazon S3 block public access. An Amazon-owned or customer-owned KMS key must also be used for encryption. To learn more about using KMS keys, see Amazon Key Management Service.

  2. If you haven't already, create a data access service role for HealthLake and give the HealthLake service permission to assume it with the following trust policy. HealthLake uses this to write the output Amazon S3 bucket. If you already created one in Setting up permissions for import jobs, you can reuse it and grant it permissions for your Amazon S3 bucket in the next step.

    { "Version": "2012-10-17", "Statement": [{ "Effect": "Allow", "Principal": { "Service": ["healthlake.amazonaws.com"] }, "Action": "sts:AssumeRole", "Condition": { "StringEquals": { "aws:SourceAccount": "accountID" }, "ArnEquals": { "aws:SourceArn": "arn:aws:healthlake:us-west-2:accountID:datastore/fhir/data store ID" } } }] }
  3. Add a permissions policy to the data access role that allows it to access your output Amazon S3 bucket. Replace amzn-s3-demo-bucket with your bucket's name.

    { "Version": "2012-10-17", "Statement": [{ "Action": [ "s3:ListBucket", "s3:GetBucketPublicAccessBlock", "s3:GetEncryptionConfiguration" ], "Resource": [ "arn:aws:s3:::amzn-s3-demo-source-bucket" ], "Effect": "Allow" }, { "Action": [ "s3:PutObject" ], "Resource": [ "arn:aws:s3:::amzn-s3-demo-logging-bucket/*" ], "Effect": "Allow" }, { "Action": [ "kms:DescribeKey", "kms:GenerateDataKey*" ], "Resource": [ "arn:aws:kms:us-east-1:012345678910:key/d330e7fc-b56c-4216-a250-f4c43ef46e83" ], "Effect": "Allow" }] }

Install the AWS CLI

The AWS CLI is required to describe and list HealthLake import and export job properties. You can also request this information using HealthLake SDKs.

To set up the AWS CLI
  1. Download and configure the AWS CLI. For instructions, see the following topics in the AWS Command Line Interface User Guide.

  2. In the AWS CLI config file, add a named profile for the administrator. You use this profile when running the AWS CLI commands. Under the security principle of least privilege, we recommend you create a separate IAM role with privileges specific to the tasks being performed. For more information about named profiles, see Configuration and credential file settings in the AWS Command Line Interface User Guide.

    [default] aws_access_key_id = default access key ID aws_secret_access_key = default secret access key region = region
  3. Verify the setup using the following help command.

    aws healthlake help

    If the AWS CLI is configured correctly, you see a brief description of AWS HealthLake and a list of available commands.