🔥 NCPI FHIR Utility

A small Python library and CLI that aids in FHIR model development.

Some features are:

1. Validation - Provides a more user-friendly interface to the Java-based HL7 FHIR IG Publisher. It also adds additional validation to ensure consistency among FHIR resource file names and payloads.
2. Model publication - Submits a directory of FHIR resources to a FHIR server.
3. JSON/XML conversion - Converts FHIR resource payloads between JSON and XML.

Installation

Prerequisite

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

Docker is needed because the fhirutil CLI executes the model validation inside a Docker container which runs the HL7 FHIR IG Publisher.

1. Setup a Python virtual environment (optional but recommended)

   python3 -m venv venv
   source ./venv/bin/activate

2. Install the library with pip

   pip install git+https://github.com/ncpi-fhir/ncpi-fhir-utility.git

   Test the installation by running the CLI: fhirutil -h. You should see something that contains:

   Usage: fhirutil [OPTIONS] COMMAND [ARGS]...
   
     A CLI utility for validating FHIR Profiles and Resources

Model Validation

The fhirutil validation feature is meant to be used on a folder which follows the required structure and content of a FHIR ImplementationGuide. The phrase "FHIR model" refers to the conformance resources in the ImplementationGuide.

Setup

Copy a FHIR resource into the test IG

cp tests/data/profiles/valid/StructureDefinition-participant.json tests/data/site_root/input/resources/profiles

Validate

You can use the CLI in two different ways to aid in validating your model:

1. Use the CLI to do all steps of validation:

   • Add necessary configuration for the FHIR resources in your model to the ImplementationGuide FHIR resource
   • Validate file names and FHIR resource IDs according to naming standards
   • Invoke the Dockerized version of the IG Publisher to validate the model

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

2. Use the CLI along with the native IG Publisher:

   • Add necessary configuration for the FHIR resources in your model to the ImplementationGuide FHIR resource
   • Validate file names and FHIR resource IDs according to naming standards
   • Run the IG Publisher Java jar natively on your machine to validate the model

   fhirutil add ./tests/data/site_root/input/resources
   java -jar org.hl7.fhir.publisher.jar -ig site_root/ig.ini -tx n/a

This method is a bit faster since it's running the IG Publisher directly and does not need to spin up a Docker container, but it means that you must first install the IG Publisher yourself (IG Publisher installation instructions).

Results

The CLI will log output to the screen and tell you whether validation succeeded or failed. You can view detailed validation results from the IG Publisher at ./tests/data/site_root/output/qa.html