Awesome-Technologies / hapi-fhir-jpaserver-starter

HAPI-FHIR Starter Project

This project is a complete starter project you can use to deploy a FHIR server using HAPI FHIR JPA.

Note that this project is specifically intended for end users of the HAPI FHIR JPA server module (in other words, it helps you implement HAPI FHIR, it is not the source of the library itself). If you are looking for the main HAPI FHIR project, see here: https://github.com/jamesagnew/hapi-fhir

Prerequisites

In order to use this sample, 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.
• Oracle Java (JDK) installed: Minimum JDK8 or newer.
• Apache Maven build tool (newest version)

Running via Docker Hub

Each tagged/released version of hapi-fhir-jpaserver is built as a Docker image and published to Docker hub. To run the published Docker image from DockerHub:

docker pull hapiproject/hapi:latest
docker run -p 8080:8080 hapiproject/hapi:tagname

This will run the docker image with the default configuration, mapping port 8080 from the container to port 8080 in the host. Once running, you can access http://localhost:8080/hapi-fhir-jpaserver/fhir in the browser to access the HAPI FHIR server's UI.

If you change the mapped port, you need to change the configuration used by HAPI to have the correct server_address property/value.

Configuration via environment variables

You can customize HAPI directly from the run command using environment variables. For example:

docker run -p 8090:8080 -e server_address=http://localhost:8090/hapi-fhir-jpaserver/fhir hapiproject/hapi:tagname

HAPI looks in the environment variables for properties in the hapi.properties file.

Configuration via overridden hapi.properties file

You can customize HAPI by telling HAPI to look for the hapi.properties file in a different location:

docker run -p 8090:8080 -e hapi.properties=/some/directory/with/hapi.properties hapiproject/hapi:tagname

Example docker-compose.yml

version: '3.7'
services:
  web:
    image: "hapiproject/hapi:tagname"
    ports:
      - "8090:8080"
    configs:
      - source: hapi
        target: /data/hapi/hapi.properties
    volumes:
      - hapi-data:/data/hapi
    environment:
      JAVA_OPTS: '-Dhapi.properties=/data/hapi/hapi.properties'
configs:
  hapi:
     external: true
volumes:
    hapi-data:
        external: true

Running locally

The easiest way to run this server is to run it directly in Maven using a built-in Jetty server. To do this, change src/main/resources/hapi.properties server_address and server.base with the values commented out as For Jetty, use this and then execute the following command:

mvn jetty:run

Then, browse to the following link to use the server:

http://localhost:8080/hapi-fhir-jpaserver/

If you need to run this server on a different port (using Maven), you can change the port in the run command as follows:

mvn -Djetty.port=8888 jetty:run

And replacing 8888 with the port of your choice.

Configurations

Much of this HAPI starter project can be configured using the properties file in src/main/resources/hapi.properties. By default, this starter project is configured to use Derby as the database.

MySql configuration

To configure the starter app to use MySQL, instead of the default Derby, update the hapi.properties file to have the following:

• datasource.driver=com.mysql.jdbc.Driver
• datasource.url=jdbc:mysql://localhost:3306/hapi_dstu3
• hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect
• datasource.username=admin
• datasource.password=admin

PostgreSQL configuration

To configure the starter app to use PostgreSQL, instead of the default Derby, update the hapi.properties file to have the following:

• datasource.driver=org.postgresql.Driver
• datasource.url=jdbc:postgresql://localhost:5432/hapi_dstu3
• hibernate.dialect=org.hibernate.dialect.PostgreSQL95Dialect
• datasource.username=admin
• datasource.password=admin

Because the integration tests within the project rely on the default Derby 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.

It is important to use PostgreSQL95Dialect when using PostgreSQL version 10+.

Overriding application properties

You can override the properties that are loaded into the compiled web app (.war file) making a copy of the hapi.properties file on the file system, making changes to it, and then setting the JAVA_OPTS environment variable on the tomcat server to tell hapi-jpaserver-starter where the overriding properties file is. For example:

-Dhapi.properties=/some/custom/directory/hapi.properties

Note: This property name and the path is case-sensitive. "-DHAPI.PROPERTIES=XXX" will not work.

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 a Container

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 HAPI FHIR JPA 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 hapi-fhir-jpaserver.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/hapi-fhir-jpaserver/

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/hapi-fhir-jpaserver/.

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 my MySQL database, if you choose to use MySQL instead of derby, change the following properties in hapi.properties:

• datasource.driver=com.mysql.jdbc.Driver
• datasource.url=jdbc:mysql://hapi-fhir-mysql:3306/hapi
• hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect
• datasource.username=admin
• datasource.password=admin

Running hapi-fhir-jpaserver-example 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 hapi-fhir-jpaserver-example 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

It is important to use MySQL5Dialect when using MySQL version 5+.

Enabling Subscriptions

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

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

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

• 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/hapi-fhir-jpaserver/websocket

Enabling EMPI

Set empi.enabled=true in the hapi.properties file to enable EMPI on this server. The EMPI matching rules are configured in empi-rules.json. The rules in this example file should be replaced with actual matching rules appropriate to your data. Note that EMPI relies on subscriptions, so for EMPI 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 hapi.properties

For example:

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