meek0/clin-fhir

FHIR clinical data model and examples

CLIN Fhir

Installation

Prerequisite

Make sure you have Docker CE installed: https://docs.docker.com/install/

Docker is needed because it is used by both the fhirutil CLI and the integration tests.

1. Git clone this repository

   git clone [email protected]:Ferlab-Ste-Justine/clin-fhir.git
   cd clin-fhir

2. Install the necessary requirements

   scripts/build.sh

3. Setup the Python virtual environment

   source ./venv/bin/activate

4. Install Jekyll following these instructions

3. Validate the model

fhirutil validate ./site_root/ig.ini --publisher_opts='-tx n/a'

4. Validate and Generate the IG

In case you have new resources files :

fhirutil add ./site_root/input/resources

And then to generate the IG :

java -jar scripts/publisher.jar -ig site_root/ig.ini -tx n/a

5. Publishing the model

fhirutil publish --base_url <FHIR_API_BASE_URL> --username <USERNAME> --password <PWD>

Alternatively you can use docker image :

docker run -e OAUTH_CLIENT_ID=client_id \
 -e OAUTH_CLIENT_SECRET=client_secret clin-fhir \
 --base_url https://fhir-green.qa.clin.ferlab.bio/fhir \
 --oauth-url https://auth.qa.clin.ferlab.bio/auth/realms/clin/protocol/openid-connect/token \
 --oauth-uma-audience clin-acl