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Python scripts used in the FHIR integration pipeline to clean input data for different external sources.

Project description

cleaning-scripts

Arkhn GitHub license

This is a repository of Python scripts used in the FHIR integration pipeline to clean input data for different external sources.

Scripts

There are 4 types of scripts:

  • scripts/custom User defined scripts to perform specific tasks like cleaning a Patient phone number for example
  • scripts/utils Basic scripts (like capitalize, test if empty, etc.)
  • scripts/logic (Beta) Scripts that operate like logic statement and take other scripts as argument

scripts/custom can be extended by users, either by completing new scripts or by adding new ones when no one is addressing their needs. This is done using the API.

API

The API can be used either as a small web service, or directly accessed through the Pyrog interface.

Manual install

To set up the API:

set GITHUB_TOKEN=<your_github_token>
flask run

Check `http://localhost:5000

Docker

docker-compose up --build

Or

docker build -t cleaning-scripts:latest .
docker run -p 5000:5000 --env-file=app/.env cleaning-scripts

Start contributing

We have reported several issues with the label Good first issue which can be a good way to start! You can also join our Slack to contact us if you have trouble or questions :)

If you're enthusiastic about our project, :star: it to show your support! :heart:

Project details


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