pyhpoapi 2.0.0

A REST API for the HPO ontology using PyHPO

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 pyhpoapi

Note

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 hpo3

Usage

Getting started

The easiest way to get started is to run the API via

uvicorn pyhpoapi.main:app

Parallel processing

If you want better performance for parallel request handling, you can run PyHPO-API with multiple workers

uvicorn pyhpoapi.main:app --workers 15

Note

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 pyhpoapi

Use 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:app

Or 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