You can navigate the validation results by "Table of Content" of Jupyter Lab. Therefore switch the left navigation bar from "File browser" to "Table of Contents".

User documentation

The further user documentation is embedded in the Jupyter Notebook:

The different outputs are described in markdown cells and used parameters are described in the code cells.

Select resources to be validated by FHIR Search parameters

You can select/filter the resources to be validated by additional FHIR search parameters.

For filter options you can set search_parameters, see FHIR search common parameters for all resource types, as well as additional FHIR search parameters for certain resource types like Patient, Condition, Observation, ...

Installation and configuration

Setup FHIR Packages

Download the FHIR NPM Packages of the German MII Core Dataset modules (Kerndatensatz der Medizininformatik Initiative) to the directory packages.

E.g. by running download-packages.sh:

bash download-packages.sh

If you want to use other FHIR packages, download the FHIR NPM packages to the packages directory and set them up by the environment variables of the HAPI validation service.

The environment variable names is derived from config section implementationguides in HAPIs application.yaml

Create config file

Copy .env.example to .env (so .env which will contain your credentials will be excluded from the git repo by .gitignore):

cp .env.example .env

Setup your FHIR server parameters

Edit .env and set up custom parameters like the URL for your FHIR Server.

Setup initial password for Jupyter Lab UI

Set a custom initial token in variable JUPYTER_TOKEN in .env

Start validation environment

Start the validation environment by

docker compose up -d

Software architecture

Based on open standards and powerful and flexible Open Source Software

The FHIR validation environment uses following standards and Open Source Software by the Python Library fhirvalidation.py:

Loading FHIR resources to be validated by FHIR search (for documentation see section "Select resources to be validated by FHIR Search parameters" below)
FHIR validation by HAPI FHIR Validator configured by Docker environment variables
Aggregation by Python Pandas dataframe
Presentation of validation results in web UI by Jupyter Lab

Software architecture diagram

Visualization of the components and the deployment:

Python library

If you don't want to use Jupyter Lab as a user interface (e.g. if you want to generate markdown for CI/CD reports), you can use the Python library fhirvalidation.py returning a pandas dataframe independent from Jupyter Lab.

In the Jupyter Notebook, you can find documentation on how to use the library, including example with code snippets.

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Bulk FHIR validation

Aggregation and presentation of bulk validation results

Usage

Web UI

Login

Start validation

Navigate validation results