DEPRECATED client-apis

This repo was deprecated:

• gen3 no longer part of the anvil stack
• the Broad TDR project addresses data harmonization
• the Broad FHIR initiative addresses hosting FHIR data

About

• Provides a single auth layer from terra to gen3
• Wrangles diverse data from terra submissions, ingestion tracker, google buckets and gen3 into a single unified model (FHIR)

Built With

• Python 3
• Terra - firecloud
• Gen3 - gen3
• fhirclient
• google-cloud-storage

Getting Started

pip install pyAnVIL

If you are running in a Terra VM

unset PIP_TARGET
# Install our package, includes dependencies drsclient and gen3
pip install pyAnVIL==0.0.13rc13 --user
# Install other dependencies
pip install fhirclient@git+https://github.com/smart-on-fhir/client-py#egg=fhirclient  --user
# Restore original setting
set PIP_TARGET=/home/jupyter/notebooks/packages 
echo Please re-start jupyter kernel

Usage

See pyAnVIL's readme.

Roadmap

See pyAnVIL's readme.

Contact

Brian Walsh walsbr at ohsu dot edu

Contributing

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

Next steps

• FHIR->PFB
• Informatics Paper
• Investigate a terra/leo verified third party app facade to access FHIR service
• Galaxy client

License

Apache