PyHPO-API
A HTTP REST-API wrapper for PyHPO
Main features
This package allows an easy setup of a REST API to interact with HPO Terms using the PyHPO package.
API Documentation
To see an interactive API documentation, install PyHPO-API, run the app and visit http://127.0.0.1:8000/docs
Installation / Setup
The easiest way to install PyHPO-API is via pip
pip install pyhpoapiNote
PyHPO-API ships with pyhpo as the underlying Ontology by default. it is also possible to use hpo3 instead. hpo3 is a drop-in replacement of pyhpo written in Rust and is much faster. It is not 100% feature complete, so use it with caution. To switch to hpo3 unintstall pyhpo and then install hpo3
pip uninstall -y pyhpo
pip install hpo3Usage
Getting started
The easiest way to get started is to run the API via
uvicorn pyhpoapi.main:appParallel processing
If you want better performance for parallel request handling, you can run PyHPO-API with multiple workers
uvicorn pyhpoapi.main:app --workers 15Note
Don't use more workers than available CPUs as it will backfire and slow down processing due to constant context-switches
CORS
If you need to allow cross-origin requests, you specify CORS settings through environment variables:
export PYHPOAPI_CORS_ORIGINS="*" export PYHPOAPI_CORS_METHODS="GET,POST" export PYHPOAPI_CORS_HEADERS="*"
Dev
Getting started for development
Clone the repository
git clone https://github.com/anergictcell/pyhpoapi.git
cd pyhpoapiUse Docker for development
One way to do this is to run a docker container during development
docker run --rm -v $(pwd):/src -p 8000:8000 -it python:3.9-slim-buster bash
cd src
pip3 install -r requirements.txt
pip3 install -r requirements-dev.txt
python3 -m unittest discover tests
uvicorn --host 0.0.0.0 --reload pyhpoapi.main:appOr local development without Docker
Create a virtual environment and install requirements in the virtual environment
virtualenv venv_pyhpoapi
source venv_pyhpoapi/bin/activate
pip3 install -r requirements.txt
pip3 install -r requirements-dev.txt
python3 -m unittest discover tests
uvicorn --reload pyhpoapi.main:app
