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FHIR Works on AWS Development Instructions

In this guide we will go over how to develop and run the code locally. We will also go over how to deploy your local code packages to your AWS account.

Prerequisites

  • Initial Install: Please complete this installation guide and get the initial fhir-works-on-aws code deployed to your AWS account.
  • Yalc: We'll be using this to manage local packages, so please have this package installed on your system.

Development

Please download all the fhir-works-on-aws package and place them inside one directory. Your parent directory should have these folders inside of them

./fhir-works-on-aws-deployment
./fhir-works-on-aws-interface
./fhir-works-on-aws-persistence-ddb
./fhir-works-on-aws-search-es
./fhir-works-on-aws-authz-rbac
./fhir-works-on-aws-routing

Copy these files to your parent directory

Run ./fhir-works-local-develop.sh from the parent directory. This script will use yarn to link your persistence, search, authz, and routing package to your interface package. It will then link all five of those packages to your deployment package.

Once the script has finished running, you can run yarn watch in the directory of each package that you're developing in. This will pick up live changes from the packages. Then you can run this command in the deployment package directory to spin up your local environment:

AWS_ACCESS_KEY_ID=<Access-Key> AWS_SECRET_ACCESS_KEY=<Secret-Key> OFFLINE_BINARY_BUCKET=<FHIRBinaryBucket> OFFLINE_ELASTICSEARCH_DOMAIN_ENDPOINT=<ElasticSearchDomainEndpoint> serverless offline start

Local Development with Implementation Guides

If you're using Implementation Guides, then follow these steps to run FHIR Works with IG locally. You'll need to provide the OFFLINE_LAMBDA_VALIDATOR_ALIAS.

Run this command in the deployment package directory to start your local environment:

AWS_ACCESS_KEY_ID=<Access-Key> AWS_SECRET_ACCESS_KEY=<Secret-Key> OFFLINE_BINARY_BUCKET=<FHIRBinaryBucket> OFFLINE_ELASTICSEARCH_DOMAIN_ENDPOINT=<ElasticSearchDomainEndpoint> OFFLINE_VALIDATOR_LAMBDA_ALIAS=<ValidatorLambdaAlias> serverless offline start

The command above runs the local FHIR server with the appropriate environment variables.

If you don't know the value for OFFLINE_BINARY_BUCKET,OFFLINE_ELASTICSEARCH_DOMAIN_ENDPOINT, and OFFLINE_VALIDATOR_LAMBDA_ALIAS value, run the following command in the deployment package directory: serverless info --verbose

Deploy Local Packages to AWS

If you have made changes to the fhir-works-on-aws packages, and you would like to deploy those changes to your AWS account, follow the instructions below.

Before continuing with the rest of this section, be sure that you have followed the steps in the Development section to set up your folder structure.

If this is your first time deploying your local changes to AWS, we will need to set up yalc to publish your packages to the local package registry. You can do that by running this command from the parent directory: ./fhir-works-deploy-one-time-setup.sh

Once your packages have been published to the local package registry, run this command to package your code for deployment: ./fhir-works-deploy.sh.

Note: Before running the deploy script, remember to add the latest version of the deployment package's package.json file into Git. The deploy script will make changes to the deployment package's package.json file.

The deploy script will push all of your packages, except for the deployment package to the local package registry. It will then go into your deployment folder, and add those local packages as dependencies. It then pulls those local packages into the deployment package so that you are ready to run serverless deploy

Run this command to deploy your code to AWS: serverless deploy --aws-profile <PROFILE> --stage <STAGE>

Troubleshooting

Runtime.ImportModuleError on other FWoA package

If you run into error type Runtime.ImportModuleError with error message stating the offending method comes from another FWoA package, check the versions of local FWoA packages match the versions specified in package.json. If you see a mismatch, update the version number in package.json to match your local packages and commit the change should fix the issue.

As an example, if your local packages have versions specified as:

[email protected]+97caac97
[email protected]+7f1d59ed
[email protected]+60259b47
[email protected]+75ad6c2c
[email protected]+ceec8029

Then package.json should have the same versions specified as well:

"dependencies": {
    "aws-sdk": "^2.785.0",
    "axios": "^0.21.1",
    "fhir-works-on-aws-authz-rbac": "4.1.0",
    "fhir-works-on-aws-interface": "7.0.0",
    "fhir-works-on-aws-persistence-ddb": "3.0.0",
    "fhir-works-on-aws-routing": "4.0.0",
    "fhir-works-on-aws-search-es": "2.0.0",
    "serverless-http": "^2.3.1"
  },

If you have a mismatch in package.json, say fhir-works-on-aws-routing was set to 4.1.0 instead of 4.0.0. An error message

Accessing Logs and Debugging on FWoA

Logs and Debugging are handled by CloudWatch. Detailed instructions on customizing CloudWatch to organize troubleshooting can be found here.

To access the logs generated by FWoA:

  1. Log on to the AWS Console.
  2. From the list of AWS services, select CloudWatch.
  3. From the tab on the left, select Log Groups
  4. From the list of log groups, select the Lambda Function or the APIGateway service that you would like to debug.
  • /aws/lambda/fhir-service-{STAGE}-fhirServer contains all the logs from the FWoA API server, including transactions and requests. This will be the log group to check when receiving errors from the FWoA server, in most cases.
  • /aws/api-gateway/fhir-service-{STAGE} contains all the logs related to the setup of the API Gateway for FWoA.
  • /aws/lambda/fhir-service-{STAGE}-ddbtoES contains all the logs from the process of writing DynamoDB resources to ElasticSearch.
  • /aws-glue/jobs/output contains all the logs related to the Bulk Export Glue Job execution.
  • /aws/lambda/fhir-service-{STAGE}-getJobStatus contains all the logs related to querying the status of a Bulk Export job.
  • /aws/lambda/fhir-service-{STAGE}-startExportJob contains all the logs related to starting a Bulk Export job.
  • /aws/lambda/fhir-service-{STAGE}-stopExportJob contains all the logs related to stopping a Bulk Export job.
  • /aws/lambda/fhir-service-{STAGE}-updateStatus contains all the logs related to updating a Bulk Export job.
  • /aws/lambda/fhir-service-validator-{STAGE}-validator contains all the logs pertaining to validation and implementation guides. These are useful in troubleshooting custom resources and implementation guides.
  1. Select a stream to view the output for the function. If applicable, the version of the Lambda function will be prefixed in square brackets ([]) to help identify which stream corresponds to which version.
  2. To further refine the output of the function, the events in a stream can be filtered using the options at the top of the list. In addition, you can perform broader searches through the Log Insights option on the tab on the left, underneath Log Groups.