120 lines
4.4 KiB
Markdown
120 lines
4.4 KiB
Markdown
---
|
|
gitea: none
|
|
include_toc: true
|
|
---
|
|
|
|
# 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.
|
|
|
|
|
|
|
|
|
|
## 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](home/fhirvalidation.py):
|
|
|
|
- Loading FHIR resources to be validated by [FHIR search](https://www.hl7.org/fhir/search.html) (for documentation see section "Select resources to be validated by FHIR Search parameters" below)
|
|
|
|
- [FHIR validation](https://www.hl7.org/fhir/validation.html#op) by [HAPI FHIR Validator](https://hapifhir.io/hapi-fhir/docs/validation/introduction.html) configured by Docker environment variables
|
|
|
|
- Aggregation by [Python Pandas](https://pandas.pydata.org/docs/user_guide/index.html) dataframe
|
|
|
|
- Presentation of validation results in web UI by [Jupyter Lab](https://jupyterlab.readthedocs.io/en/latest/)
|
|
|
|
|
|
## Architecture
|
|
|
|
|
|
|
|
## Installation and Configuration
|
|
|
|
### Setup FHIR Packages
|
|
|
|
Download the FHIR NPM Packages of the [German MII Core Dataset modules](https://www.medizininformatik-initiative.de/de/uebersicht-ueber-versionen-der-kerndatensatz-module) (Kerndatensatz der Medizininformatik Initiative) to the directory `fhir-packages`.
|
|
|
|
E.g. by running [download-packages.sh](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](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml)
|
|
|
|
|
|
### Create config file
|
|
|
|
Copy .env.skeleton 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](.env.example) 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](https://jupyterlab.readthedocs.io/en/latest/) 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](home/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](https://www.hl7.org/fhir/search.html) parameters.
|
|
|
|
For filter options you can set `search_parameters`, see [FHIR search common parameters for all resource types](https://www.hl7.org/fhir/search.html#standard), as well as additional FHIR search parameters for certain resource types like [Patient](https://www.hl7.org/fhir/patient.html#search), [Condition](https://www.hl7.org/fhir/condition.html#search), [Observation](https://www.hl7.org/fhir/observation.html#search), ...
|
|
|
|
|
|
### 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](home/fhirvalidation.py) returning a [pandas](https://pandas.pydata.org/docs/user_guide/index.html) dataframe independent from Jupyter Lab.
|
|
|
|
In the Jupyter Notebook, you can find documentation on how to use the library, including example with code snippets. |