fhir2dataset 0.0.9

Transform FHIR to Dataset

FHIR2Dataset

Transform FHIR to dataset for ML applications

FHIR2Dataset in Detail

This project is still under development.

This repo is a POC allowing to make a query (close to SQL format) on a FHIR API and to retrieve tabular data.

The request that FHIR2Dataset performs on a FHIR API is specified in a configuration file of this form. The purpose of this file is to perform a query whose result will be identical to the next SQL query:

SELECT (alias n°1).a, (alias n°1).b, (alias n°1).c, (alias n°2).a FROM (Resource type 1) as (alias n°1)
INNER JOIN (Resource type 2) as (alias n°2)
ON (alias n°1).d = (alias n°2)
INNER JOIN (Resource type 3) as (alias n°3)
ON (alias n°2).b = (alias n°3) WHERE (alias n°2).c = "value 1"
AND (alias n°2).d = "value 2"
AND (alias n°3).a = "value 3"
AND (alias n°3).b = "value 4"

Installation

After cloning this repository, you can install the required dependencies

pip install -r requirements.txt
npm install --prefix ./fhir2dataset/metadata

For usage, refer to this turorial and then this Jupyer Notebook

Examples

Check out examples of queries and how they are transformed in call to the FHIR api!

• Select the gender and name for patients born after 2000
• Get the pressure measures of patients born after 1970, together with their gender and birthdate
• Get the number of patients currently in intensive care unit because of Coronavirus
• Get clinical information about patients that were in intensive care unit because of Coronavirus

Contributing

The following commands on a terminal and in your virtual environment allow you to do some minimal local testing before each commit:

pip install -r requirements-dev.txt
pre-commit install

If you ever want to delete them you just have to do:

pre-commit clean

Publish

First, you need to have twine installedd

pip install --user --upgrade twine

Make sure you have bumped the version number in setup.py, then run the following:

python setup.py sdist bdist_wheel
python -m twine upload dist/*