CURDM/Bulk-FHIR-Validation
0
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
This bulk FHIR validation environment aggregates/groups and presents validation results of bulk FHIR validation of FHIR Search results
5 Commits 1 Branch 0 Tags 196 KiB
Jupyter Notebook 49.3%
Python 45.9%
Shell 4.8%
8cc27759b7
Go to file
mandalkam 8cc27759b7 Changed file name
2024-09-11 12:31:17 +02:00
home Initial commit 2024-09-08 23:35:23 +02:00
.env.example Initial commit 2024-09-08 23:35:23 +02:00
.gitignore Initial commit 2024-09-08 23:35:23 +02:00
bulk-fhir-validation.png Initial commit 2024-09-08 23:35:23 +02:00
bulk-fhir-validator.drawio.png Initial commit 2024-09-08 23:35:23 +02:00
docker-compose.yml No need to expose HAPI port to outside, since in same docker compose environment/internal network 2024-09-11 12:19:37 +02:00
download-packages.sh Initial commit 2024-09-08 23:35:23 +02:00
LICENSE Initial commit 2024-09-06 11:39:41 +02:00
README.md Changed file name 2024-09-11 12:31:17 +02:00

README.md

Table of Contents

Bulk FHIR validation

Dockerized Open Source environment for bulk FHIR validation of FHIR resources.

Aggregation and presentation of bulk validation results

This bulk FHIR validation environment aggregates/groups and presents validation results of bulk FHIR validation of FHIR Search results.

Bulk FHIR validation

Based on open standards and powerfull and flexible Open Source Software

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

Architecture

Software architecture

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 fhir-packages.

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

bash download-packages.sh

If you want to use other FHIR packages, download the NPM packages to the fhir-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

Usage

Web UI

Access the web user interface of Jupyter Lab on the configured (default: 80) port: http://yourserver/

Login

Login with the initial password / token you configured in .env

Start validation

Now you can start the validation and aggregation of validation results.

Therefore run the Jupyter Notebook fhir-validation.ipynb.

Navigate validation results

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 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, ...

Python library

If you dont 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.