hl7-be / matchbox

matchbox

matchbox is a FHIR server based on the hapifhir/hapi-fhir-jpaserver-starter

• (pre-)load FHIR implementation guides from the package server for conformance resources (StructureMap, Questionnaire, CodeSystem, ValueSet, ConceptMap, NamingSystem, StructureDefinition). The "with-preload" subfolder contains an example with the implementation guides provided for the public test server.
• validation support: [server]/$validate for checking FHIR resources conforming to the loaded implementation guides
• FHIR Mapping Language endpoints for creation of StructureMaps and support for the StructureMap/$transform operation
• SDC (Structured Data Capture) extraction support based on the FHIR Mapping language and Questionnaire/$extract

a public test server is hosted at https://test.ahdis.ch/matchbox/fhir with a corresponding gui https://test.ahdis.ch/matchbox/

containers

The docker file will create a docker image with no preloaded implementation guides. A list of implementation guides to load can be passed as config-map.

Prerequisites

• 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. Check out the main branch (master is kept in sync with hapi-fhir-jpaserver-starter
• Oracle Java (JDK) installed: Minimum JDK11 or newer.
• Apache Maven build tool (newest version)

Running locally

The easiest way to run this server entirely depends on your environment requirements. At least, the following 4 ways are supported:

Using spring-boot

With no implementation guide:

mvn clean install -DskipTests spring-boot:run

Load example implementation guides (needs postgres):

mvn clean install -DskipTests spring-boot:run -Dspring-boot.run.arguments=--spring.config.additional-location=file:with-preload/application.yaml

or

java -Dspring.config.additional-location=file:with-preload/application.yaml -jar target/matchbox.jar

mvn clean install -DskipTests spring-boot:run -Dspring-boot.run.jvmArguments="-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"

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

http://localhost:8080/matchbox/fhir or http://localhost:8080/matchbox/#/

Using docker-compose with a persistent postgreSQL database

The database will be stored in the "data" directory. The configuration can be found in the "with-postgres" directory or in the "with-preload" directory.

Change to either with-posgres directory or the with-preload directory (contains a list of swiss ig's).

For the first time, you might need to do

docker-compose up matchbox-db

that the database gets initialized before matchbox is starting up (needs a fix)

mkdir data
mvn clean package -DskipTests
docker build -t matchbox .
docker-compose up

matchbox will be available at http://localhost:8080/matchbox/fhir matchbox-gui will be available at http://localhost:8080/matchbox/#/

Export the DB data:

docker-compose exec -T matchbox-test-db pg_dump -Fc -U matchbox matchbox > mydump

Reimport the DB data:

docker-compose exec -T matchbox-test-db pg_restore -c -U matchbox -d matchbox < mydump

building with Docker

Configurable base image:

mvn package -DskipTests
docker build -t matchbox .
docker run -d --name matchbox -p 8080:8080 matchbox

Server will then be accessible at http://localhost:8080/matchbox/fhir/metadata.

To dynamically configure run in a kubernetes environment and add a kubernetes config map that provides /config/application.yaml file with implementation guide list like in "with-preload/application.yaml"

making container available

docker tag matchbox eu.gcr.io/fhir-ch/matchbox:v200

docker push eu.gcr.io/fhir-ch/matchbox:v200

API

Use VSCode, REST Client to work with the API:

• FHIR Mapping language
• Load Implementation Guide onto server
• Validation examples
• SDC examples

Kubernetes

kubectl cp matchbox-test-0:fhir.logdir_IS_UNDEFINED ./fhir.logdir/

kubectl cp matchbox-test-app-d684cf865 ./fhir.logdir/

matchbox's Issues

Add $extract mapping to the web page

Add dropdown to list and get Questionnaires from server

Add BE FINDRISC Questionnaire and mapping

Fix mapping diagram for FINDRISC

Add sample page