*********
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
.. code:: bash
pip install pyhpoapi
.. note::
**PyHPO-API** ships with ``pyhpo`` as the underlying Ontology by default. it is also possible to use `hpo3 <https://pypi.org/project/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
.. code:: bash
pip uninstall -y pyhpo
pip install hpo3
Usage
=====
Getting started
---------------
The easiest way to get started is to run the API via
.. code:: bash
uvicorn pyhpoapi.main:app
Parallel processing
-------------------
If you want better performance for parallel request handling,
you can run PyHPO-API with multiple workers
.. code:: bash
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
.. code:: bash
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
.. code:: bash
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
.. code:: bash
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
.. _PyHPO: https://github.com/Centogene/pyhpo
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