Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/google/fhir-py
Python utilities for working with FHIR, including libraries to build simple, flat FHIR views in BigQuery.
https://github.com/google/fhir-py
bigquery fhir python
Last synced: 6 days ago
JSON representation
Python utilities for working with FHIR, including libraries to build simple, flat FHIR views in BigQuery.
- Host: GitHub
- URL: https://github.com/google/fhir-py
- Owner: google
- License: apache-2.0
- Created: 2022-08-30T17:10:28.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-12-03T16:41:52.000Z (2 months ago)
- Last Synced: 2025-01-22T10:05:02.852Z (13 days ago)
- Topics: bigquery, fhir, python
- Language: Python
- Homepage:
- Size: 2.15 MB
- Stars: 83
- Watchers: 6
- Forks: 14
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
Google's tools for working with FHIR data in Python. This includes:
* Support for converting FHIR data to and from an efficient Protocol Buffer-based format.
* Support for creating and analyzing views over large FHIR datasets. See the [Google FHIR Views](google-fhir-views/README.md) documentation and [notebook examples](examples) for details.
This is not an officially supported Google product.
# Installation
__Note: Requires Python >= `3.8`.__
These libraries are installed via pip.
## From PyPi
Users interested in FHIR Views and the underlying libraries can simply run the
following to install the views library, BigQuery, Spark and FHIR R4 dependencies:
```
pip install google-fhir-views[r4,bigquery,spark]
```
Users who only need the BigQuery or Spark runners can run:
```
pip install google-fhir-views[r4,bigquery]
```
or
```
pip install google-fhir-views[r4,spark]
```
respectively, to reduce the installation size.
Note: If installing for use in a Jupyter notebook, it's best `pip install ...` _before_ starting the notebook kernel to avoid dependency version issues.
Users looking for only the underlying FHIR Protocol Buffer support can
run `pip install google-fhir-r4` to retrieve only that and its dependencies.
## From source code
This can be installed locally, directly from source by running the following
commands in this directory. As always, doing so within a Python virtual
environment is recommended.
### protoc installation prerequisite
This library generates Protocol Buffers for FHIR resources, so the protoc
executable must be available. This can be done on Linux by running:
```
apt install protobuf-compiler
protoc --version # Ensure version 3+
```
Or on MacOS with Homebrew:
```
brew install protobuf
protoc --version # Ensure version 3+
```
Windows users can download protoc releases [here](https://github.com/protocolbuffers/protobuf/releases).
### pip installation
Once protoc is available, the fhir-py libraries can be installed from source by
running the following in the fhir-py directory:
```
pip install ./google-fhir-core[bigquery,spark]
pip install ./google-fhir-r4
pip install ./google-fhir-views[r4,bigquery,spark]
```
See the [Google FHIR Views](google-fhir-views/README.md) documentation for
details on use.
# Contributors
Due to the nature of the initial commit squashing internal contributor history,
we would like to recognize some of those who contributed to the initial
commit work:
Ryan Brush ([@rbrush](https://github.com/rbrush)),
Cameron Tew ([@cam2337](https://github.com/cam2337)),
Ose Umolu ([@luid101](https://github.com/luid101)),
Walt Askew ([@waltaskew](https://github.com/waltaskew)),
Nick George ([@nickgeorge](https://github.com/nickgeorge)),
Wilson Sun ([@wilsonssun](https://github.com/wilsonssun))
Lisa Yin ([@lisayin](https://github.com/lisayin)),
Suyash Kumar ([@suyashkumar](https://github.com/suyashkumar)), and other Googlers.
In addition, contributors who committed after the initial squash commit can be
found in the
[GitHub contributors tab](https://github.com/google/fhir-py/graphs/contributors).
Thank you to all contributors!
# Trademark
FHIR® is the registered trademark of HL7 and is used with the permission of HL7. Use of the FHIR trademark does not constitute endorsement of this product by HL7.