Metriport FHIR Server

This FHIR server is a fork of https://github.com/hapifhir/hapi-fhir-jpaserver-starter.

The main difference from the original repository is Authorization - this is based on Metriport's OAuth2:

• it assumes it's begin used behind API Gateway or similar, with that upstream service validating the JWT and passing it through;
• it only checks JWT claims (no token validation), to make sure the request has access to the requested operation and information;
• see SimplifiedOAuthAuthorizationInterceptor for implementation details.

Prerequisites

In order to use this server, you should have:

• This project checked out. You may wish to create a GitHub Fork of the project and check that out instead so that you can customize the project and save the results to GitHub.
• Docker, as the entire project can be built using multistage docker (with both JDK and maven wrapped in docker).

Running Locally with Docker

You can use the docker-compose to run the app and DB servers by executing the following command:

$ docker-compose up --build

To run the secondary app and Servers for testing run:

$ docker compose -p fhirconverter -f docker-compose-fhir-converter.yml up -d

⚠️ WARNING: This secondary instance is used for testing purposes only. Data within this instance is constantly deleted as part of the normal testing workflow. Do not use it for any purposes that require data to persist for more than a few minutes.

Run the server from the docker image, on a specific Spring profile (in this case, application-staging.yaml), with environment variables being passed to the docker container:

Update environment variables in the docker-compose.yml file accordingly.

Alternative: Running Locally with Jetty

Install the following:

• Oracle Java (JDK) installed: Minimum JDK8 or newer.
• Apache Maven build tool (newest version)

Run the following command:

SPRING_PROFILES_ACTIVE="local" DB_URL="jdbc:postgresql://localhost:5432/db" DB_USERNAME="admin" DB_PASSWORD="admin" mvn -Djetty.port=8888 jetty:run

Server will then be accessible at http://localhost:8888/ and eg.http://localhost:8888/fhir/metadata.

Configurations

Much of this server can be configured using the yaml file in src/main/resources/application<-env>.yaml. There's a default application.yaml file included for simplicity and reference, configured to use H2 as the database.

It does not support MySQL as it is deprecated. See more at https://hapifhir.io/hapi-fhir/docs/server_jpa/database_support.html

One can create multiple configuration files (e.g., one for each environment the server is deployed to). In order to do that:

• duplicate/rename the application.yaml to application-env.yaml, where env is the environment name (e.g., local)
• run the server with an environment variable defining the name of the environment (this also sets a different server port):

  $ SPRING_PROFILES_ACTIVE=local mvn -Djetty.port=8888 jetty:run

PostgreSQL configuration

To configure the starter app to use PostgreSQL, instead of the default H2, update the application.yaml file to have the following:

spring:
  datasource:
    url: "jdbc:postgresql://localhost:5432/hapi"
    username: admin
    password: admin
    driverClassName: org.postgresql.Driver
  jpa:
    properties:
      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
      hibernate.search.enabled: false

      # Then comment all hibernate.search.backend.*

Because the integration tests within the project rely on the default H2 database configuration, it is important to either explicity skip the integration tests during the build process, i.e., mvn install -DskipTests, or delete the tests altogether. Failure to skip or delete the tests once you've configured PostgreSQL for the datasource.driver, datasource.url, and hibernate.dialect as outlined above will result in build errors and compilation failure.

Microsoft SQL Server configuration

To configure the starter app to use MS SQL Server, instead of the default H2, update the application.yaml file to have the following:

spring:
  datasource:
    url: "jdbc:sqlserver://<server>:<port>;databaseName=<databasename>"
    username: admin
    password: admin
    driverClassName: com.microsoft.sqlserver.jdbc.SQLServerDriver

Also, make sure you are not setting the Hibernate dialect explicitly, in other words remove any lines similar to:

hibernate.dialect: {some none Microsoft SQL dialect}

Because the integration tests within the project rely on the default H2 database configuration, it is important to either explicity skip the integration tests during the build process, i.e., mvn install -DskipTests, or delete the tests altogether. Failure to skip or delete the tests once you've configured PostgreSQL for the datasource.driver, datasource.url, and hibernate.dialect as outlined above will result in build errors and compilation failure.

NOTE: MS SQL Server by default uses a case-insensitive codepage. This will cause errors with some operations - such as when expanding case-sensitive valuesets (UCUM) as there are unique indexes defined on the terminology tables for codes. It is recommended to deploy a case-sensitive database prior to running this server when using MS SQL Server to avoid these and potentially other issues.

Adding custom interceptors

Custom interceptors can be registered with the server by including the property hapi.fhir.custom-interceptor-classes. This will take a comma separated list of fully-qualified class names which will be registered with the server. Interceptors will be discovered in one of two ways:

1. discovered from the Spring application context as existing Beans (can be used in conjunction with hapi.fhir.custom-bean-packages) or registered with Spring via other methods

or

2. classes will be instantiated via reflection if no matching Bean is found

Customizing The Web Testpage UI

The UI that comes with this server is an exact clone of the server available at http://hapi.fhir.org. You may skin this UI if you'd like. For example, you might change the introductory text or replace the logo with your own.

The UI is customized using Thymeleaf template files. You might want to learn more about Thymeleaf, but you don't necessarily need to: they are quite easy to figure out.

Several template files that can be customized are found in the following directory: https://github.com/hapifhir/hapi-fhir-jpaserver-starter/tree/master/src/main/webapp/WEB-INF/templates

Deploying to an Application Server

Using the Maven-Embedded Jetty method above is convenient, but it is not a good solution if you want to leave the server running in the background.

Most people who are using this as a server that is accessible to other people (whether internally on your network or publically hosted) will do so using an Application Server, such as Apache Tomcat or Jetty. Note that any Servlet 3.0+ compatible Web Container will work (e.g Wildfly, Websphere, etc.).

Tomcat is very popular, so it is a good choice simply because you will be able to find many tutorials online. Jetty is a great alternative due to its fast startup time and good overall performance.

To deploy to a container, you should first build the project:

mvn clean install

This will create a file called ROOT.war in your target directory. This should be installed in your Web Container according to the instructions for your particular container. For example, if you are using Tomcat, you will want to copy this file to the webapps/ directory.

Again, browse to the following link to use the server (note that the port 8080 may not be correct depending on how your server is configured).

http://localhost:8080/

You will then be able access the JPA server e.g. using http://localhost:8080/fhir/metadata.

If you would like it to be hosted at eg. hapi-fhir-jpaserver, eg. http://localhost:8080/hapi-fhir-jpaserver/ or http://localhost:8080/hapi-fhir-jpaserver/fhir/metadata - then rename the WAR file to hapi-fhir-jpaserver.war and adjust the overlay configuration accordingly e.g.

tester:
  - id: home
    name: Local Tester
    server_address: "http://localhost:8080/hapi-fhir-jpaserver/fhir"
    refuse_to_fetch_third_party_urls: false
    fhir_version: R4

Deploy with Docker on AWS

Follow the README on ./infra/

Deploy with docker compose

Docker compose is a simple option to build and deploy container. To deploy with docker compose, you should build the project with mvn clean install and then bring up the containers with docker-compose up -d --build. The server can be reached at http://localhost:8080/.

In order to use another port, change the ports parameter inside docker-compose.yml to 8888:8080, where 8888 is a port of your choice.

The docker compose set also includes PostgreSQL database, if you choose to use PostgreSQL instead of H2, change the following properties in src/main/resources/application.yaml:

spring:
  datasource:
    url: "jdbc:postgresql://hapi-fhir-postgres:5432/hapi"
    username: admin
    password: admin
    driverClassName: org.postgresql.Driver
jpa:
  properties:
    hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
    hibernate.search.enabled: false

    # Then comment all hibernate.search.backend.*

Running directly from IntelliJ as Spring Boot

Make sure you run with the maven profile called boot and NOT also jetty. Then you are ready to press debug the project directly without any extra Application Servers.

Running in Tomcat from IntelliJ

Install Tomcat.

Make sure you have Tomcat set up in IntelliJ.

• File->Settings->Build, Execution, Deployment->Application Servers
• Click +
• Select "Tomcat Server"
• Enter the path to your tomcat deployment for both Tomcat Home (IntelliJ will fill in base directory for you)

Add a Run Configuration for running this server under Tomcat

• Run->Edit Configurations
• Click the green +
• Select Tomcat Server, Local
• Change the name to whatever you wish
• Uncheck the "After launch" checkbox
• On the "Deployment" tab, click the green +
• Select "Artifact"
• Select "hapi-fhir-jpaserver-example:war"
• In "Application context" type /hapi

Run the configuration.

• You should now have an "Application Servers" in the list of windows at the bottom.
• Click it.
• Select your server, and click the green triangle (or the bug if you want to debug)
• Wait for the console output to stop

Point your browser (or fiddler, or what have you) to http://localhost:8080/hapi/baseDstu3/Patient

Enabling Subscriptions

The server may be configured with subscription support by enabling properties in the application.yaml file:

• hapi.fhir.subscription.resthook_enabled - Enables REST Hook subscriptions, where the server will make an outgoing connection to a remote REST server

• hapi.fhir.subscription.email.* - Enables email subscriptions. Note that you must also provide the connection details for a usable SMTP server.

• hapi.fhir.subscription.websocket_enabled - Enables websocket subscriptions. With this enabled, your server will accept incoming websocket connections on the following URL (this example uses the default context path and port, you may need to tweak depending on your deployment environment): ws://localhost:8080/websocket

Enabling Clinical Reasoning

Set hapi.fhir.cr_enabled=true in the application.yaml file to enable Clinical Quality Language on this server.

Enabling MDM (EMPI)

Set hapi.fhir.mdm_enabled=true in the application.yaml file to enable MDM on this server. The MDM matching rules are configured in mdm-rules.json. The rules in this example file should be replaced with actual matching rules appropriate to your data. Note that MDM relies on subscriptions, so for MDM to work, subscriptions must be enabled.

Using Elasticsearch

By default, the server will use embedded lucene indexes for terminology and fulltext indexing purposes. You can switch this to using lucene by editing the properties in application.yaml

For example:

elasticsearch.enabled=true
elasticsearch.rest_url=localhost:9200
elasticsearch.username=SomeUsername
elasticsearch.password=SomePassword
elasticsearch.protocol=http
elasticsearch.required_index_status=YELLOW
elasticsearch.schema_management_strategy=CREATE

Enabling LastN

Set hapi.fhir.lastn_enabled=true in the application.yaml file to enable the $lastn operation on this server. Note that the $lastn operation relies on Elasticsearch, so for $lastn to work, indexing must be enabled using Elasticsearch.

Enabling Resource to be stored in Lucene Index

Set hapi.fhir.store_resource_in_lucene_index_enabled in the application.yaml file to enable storing of resource json along with Lucene/Elasticsearch index mappings.

Changing cached search results time

It is possible to change the cached search results time. The option reuse_cached_search_results_millis in the application.yaml is 6000 miliseconds by default. Set reuse_cached_search_results_millis: -1 in the application.yaml file to ignore the cache time every search.

Build the distroless variant of the image (for lower footprint and improved security)

The default Dockerfile contains a release-distroless stage to build a variant of the image using the gcr.io/distroless/java-debian10:11 base image:

docker build --target=release-distroless -t hapi-fhir:distroless .

Note that distroless images are also automatically built and pushed to the container registry, see the -distroless suffix in the image tags.

Adding custom operations

To add a custom operation, refer to the documentation in the core hapi-fhir libraries here.

Within this server, create a generic class (that does not extend or implement any classes or interfaces), add the @Operation as a method within the generic class, and then register the class as a provider using RestfulServer.registerProvider().

Enable OpenTelemetry auto-instrumentation

The container image includes the OpenTelemetry Java auto-instrumentation Java agent JAR which can be used to export telemetry data for this server. You can enable it by specifying the -javaagent flag, for example by overriding the JAVA_TOOL_OPTIONS environment variable:

docker run --rm -it -p 8080:8080 \
  -e JAVA_TOOL_OPTIONS="-javaagent:/app/opentelemetry-javaagent.jar" \
  -e OTEL_TRACES_EXPORTER="jaeger" \
  -e OTEL_SERVICE_NAME="hapi-fhir-server" \
  -e OTEL_EXPORTER_JAEGER_ENDPOINT="http://jaeger:14250" \
  docker.io/hapiproject/hapi:latest

You can configure the agent using environment variables or Java system properties, see https://opentelemetry.io/docs/instrumentation/java/automatic/agent-config/ for details.

Development setup

Install Java

There are multiple ways to install Java, we recommend using Eclipse Foundation's https://adoptium.net - it has the latest versions available in addition to older ones.

We recommend to install the LTS (Long Term Support) version.

VSCode IDE

Install these extensions:

• Extension Pack for Java: it will install 6 other extensions to support Java development on VSCode
• EditorConfig for VS Code: apply formatting settings found on .editorconfig files