fhirsnake: turn static files to a FHIR server

What is it?

fhirsnake is a minimalistic FHIR server that serve yaml and json files as FHIR resources

How it works?

The server reads all yaml and json files from resources directory. Resources directory should have subdirectories with names equal resource types:

resources/
├── Patient/
│   ├── example.yaml
│   ├── john-doe.json
│   └── patient3.yaml
├── Questionnaire/
│   ├── questionnaire1.yaml
│   ├── questionnaire2.yaml
│   └── sudbir/
│       └── questionnaire3.yaml

Environment variable substitution

To use environment variables in resources, you can use the syntax ${VAR_NAME}. In the case of missing environment variable, the exception will be raised.

NOTE: The syntax $VAR without braces is not supported because it might be used in resources.

Supported operations

Important

All created and updated resources persist in runtime only. All changes are vanished after service restart

• read, create and update operations are supported
• search - limied support without any search params
• GET /$index operation returns a map of all resources in format <resource_type>:<id>

Usage

1. Organize resources in a directory

Server

1. Option A: Run a container

   docker run -p 8002:8000 -v ./resources:/app/resources bedasoftware/fhirsnake

2. Option B: Adjust source destination in Dockerfile.resources if required 2.1. Build an image using the base image

   docker build -t fhirsnake-resources:latest -f Dockerfile.resources .
   docker run -p 8000:8000 fhirsnake-resources 

Export

1. Export resources as .json (Bundle) or .ndjson or ndjson.gz

   docker run -v ./resources:/app/resources -v ./output:/output bedasoftware/fhirsnake export --external-questionnaire-fce-fhir-converter-url=http://host.docker.internal:3000/to-fhir --output /output/seeds.ndjson.gz

Watch

1. Watch resources for changes and send as PUT requests to external fhir server

   docker run -v ./resources:/app/resources -v ./output:/output bedasoftware/fhirsnake watch --external-fhir-server-url http://host.docker.internal:8080 --external-fhir-server-header "Authorization: Token token" --external-questionnaire-fce-fhir-converter-url=http://host.docker.internal:3000/to-fhir

Using external questionnaire FCE->FHIR converter

There's an image bedasoftware/questionnaire-fce-fhir-converter:latest available that provides /to-fhir endpoint that can be used along with --external-questionnaire-fce-fhir-converter-url args for watch and export commands.

Contribution and feedback

Please, use Issues

Development

Format and fix with ruff

ruff format
ruff check . --fix

Issue new version - run semantic release locally

npx semantic-release --no-ci

Publish to pypi

poetry build
poetry publish