ecr-cda-to-fhir-lambda

S3 Trigger to convert FHIR to CDA format

Prerequisites:

1. Java 17
2. AWS SDK - STS or Eclipse
3. AWS Account
4. Maven 3.3.x
5. GIT

Clone the Repository

Clone the repository using the below command in command prompt

git clone https://github.com/drajer-health/ecr-cda-to-fhir-lambda.git

Create Build:

Import Project as Maven Project Build:

Navigate to ecr-cda-to-fhir-lambda directory ..../ and run Maven build to build lambda jar file.

$ mvn clean

$ mvn clean install

This will generate a war file under target/ecr-cda-to-fhir-lambda-1.0.0.jar.

AWS Lambda

Deploy eCR FHIR to CDA Lambda:

Login to your AWS Account

1. Click on Services then select Lambda

2. Click on Create Function

3. Select "Author from Scratch" option

4. Enter:

Function Name: ecrCDA-to-FHIR-lambda
Runtime: Java 17
Permissions: Create a new role with basic Lambda permissions or select your organization specific security

5. Click on "Create Function"

At this point Lambda function would be created, navigate to the newly created function and configure the lambda function and environment variable.

1. Go to the newly created Role.

2. Under Permissions tab click on Create inline Policy

3. Click on { } JSON tab and ad the following security policy.

   Replace the SQS-NAME with your SQS name.

   Replace the S3-BUCKET-NAME with your S3 bucket name.

   Replace the S3-LIC_BUCKET-NAME with your S3 bucket name for saxon license.

{
    "Version": "2012-10-17",
    "Statement": [
        {
            "Sid": "Statement1",
            "Effect": "Allow",
            "Action": "sqs:ReceiveMessage",
            "Resource": "arn:aws:sqs:SQS-NAME"
        },
        {
            "Sid": "Statement2",
            "Effect": "Allow",
            "Action": "sqs:DeleteMessage",
            "Resource": "arn:aws:sqs:SQS-NAME"
        },
        {
            "Sid": "Statement3",
            "Effect": "Allow",
            "Action": "sqs:GetQueueAttributes",
            "Resource": "arn:aws:sqs:SQS-NAME"
        },
        {
            "Sid": "ListObjectsInBucket",
            "Effect": "Allow",
            "Action": [
                "s3:GetObjectVersion",
                "s3:GetBucketLocation",
                "s3:GetObject",
                "s3:PutObject",
                "s3:PutObjectAcl"
            ],
            "Resource": "arn:aws:s3:::S3-LIC_BUCKET-NAME/*"
        },
        {
            "Sid": "ListObjectsInBucketS3",
            "Effect": "Allow",
            "Action": [
                "s3:GetObjectVersion",
                "s3:GetBucketLocation",
                "s3:GetObject",
                "s3:PutObject",
                "s3:PutObjectAcl"
            ],
            "Resource": "arn:aws:s3:::S3-BUCKET-NAME/*"
        }
    ]
}

4. Click on button Next

5. Enter policy name ecrCdaToFhirLamdaPolcy

6. Click on Create policy

7. Come back to your AWS Lambda Function and navigate to Configuration tab.

8. Go to the General Configuration and click on Edit button. Increase the Timeout to minimum 10 minute.

9. Under the "Code" tab select "Upload from"

10. Select .zip or .jar file option.

11. Click upload and navigate to your local workspace target folder and select ecr-cda-to-fhir-lambda-1.0.1.jar and click "Save".

12. Click on "Edit" on "Runtime Settings".

13. Enter below value for Handler

com.drajer.ecr.cda2fhir.converter.CDA2FHIRConverterLambdaFunctionHandler::handleRequest

12. Click "Save"

Lambda Configuration

To process the file from the S3 bucket, lambda function needs to be configured to process from the specified folder. Add the Environment Variable to the lambda function specifying the S3 bucket folder name.

1. Click on "Configuration" tab and then "Environment Variables"

2. Click on "Edit" to add new environment variable

3. Click on "Add new environment variable"

4. Enter

Environment Variable	Value
BUCKET_NAME	<- S3-FolderName ->
LICENSE_BUCKET_NAME	<- S3-FolderName ->

SQS Queue

Choose the SQS queue and click Create Queue

1. Select Standard and Enter the Name for the Queue as eg: fhir-ecr1-cda-fhir-sqs-queue

2. Enter 10 minutes as Visibility timeout

3. Server-Side encryption as disabled

4. Access Policy Advanced

5. Make neccessary changes to below and copy as in-line policy

{
  "Version": "2012-10-17",
  "Id": "__default_policy_ID",
  "Statement": [
    {
      "Sid": "__owner_statement",
      "Effect": "Allow",
      "Principal": {
        "Service": "s3.amazonaws.com"
      },
      "Action": "SQS:SendMessage",
      "Resource": "arn:aws:sqs:us-east-1:<<AWS_ACCOUNT_INFO>>:<<QUEUE_NAME (from the SQS Queue Step 1)>>",
      "Condition": {
        "StringEquals": {
          "aws:SourceAccount": "<<AWS ACCOUNT INFO>>"
        },
        "ArnLike": {
          "aws:SourceArn": "arn:aws:s3:::<<S3 BUCKET NAME>>"
        }
      }
    }
  ]
}

6. Click Save

Lambda Trigger

Lambda function needs to be triggered, for this we need to add and configure the trigger. Follow the following steps to add the trigger to your lambda function.

1. Go to you Lambda function

2. Click on Add trigger

3. From the Trigger configuration drop down select SQS option

4. From the SQS queque drop down select your SQS that this lambda function will listen.

5. Click Add.

At this point the Lambda function is created and configured to listen to the S3 Bucket.

S3 Event Notification

1. Go to S3 bucket and to Properties Tab

2. Scroll down to Event Notification and Click Create event Notification

3. Enter Name eg: cda-fhir-event

4. Enter Suffix as RR_CDA.xml

5. Event Types as All object create events

6. Destination as SQS queue

7. Specify SQS queue Enter SQS queque

   arn:aws:<<SQS Name (from the SQS Queue Step 1) >>

8. Click Save Changes

S3 Saxon License

Here are the steps to store the Saxon license in an S3 bucket and configure your AWS Lambda function to use the bucket name as an environment variable:

1. Create an S3 Bucket (if you don't already have one): Go to the AWS Management Console. Navigate to S3. Click on "Create bucket." Choose a unique name for your bucket and select your preferred region. Click "Create bucket."

2. Upload the Saxon License File: In the S3 console, click on your bucket name to open it and create & open license folder if it doesn’t exis Click the "Upload" button. Select the Saxon license file (e.g., saxon-license.lic) from your local file system. Optionally, set the permissions for the file based on your access requirements. Click "Upload."

3. Set Up Environment Variable in Lambda Go to the AWS Management Console. Navigate to the Lambda service. Find and select the Lambda function that you want to configure. Scroll down to the "Environment variables" section. Click on "Edit." Add a new key-value pair: Key: BUCKET_NAME Value: (replace this with the name of your S3 bucket)

4. Test Your Lambda Function In the AWS Lambda console, you can create a test event based on the input your Lambda function expects. Click on "Test" to execute the function and check the logs to verify that it retrieves the license file from S3.

5. Check CloudWatch Logs If there are any issues, check the CloudWatch logs for your Lambda function to debug the problem.

By following these steps, you'll be able to store the Saxon license in an S3 bucket and configure your Lambda function to use the bucket name as an environment variable. If you have any further questions or need assistance with anything else, feel free to ask!