https://github.com/anergictcell/pyhpoapi

A REST-API wrapper around PyHPO to handle the Human Phenotype Ontology (HPO) through HTTP(S)
https://github.com/anergictcell/pyhpoapi

fastapi hpo hpo-explorer hpo-similarity python rest-api

Last synced: about 1 month ago
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A REST-API wrapper around PyHPO to handle the Human Phenotype Ontology (HPO) through HTTP(S)

• Host: GitHub
• URL: https://github.com/anergictcell/pyhpoapi
• Owner: anergictcell
• License: mit
• Created: 2021-02-15T12:55:07.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2023-07-28T19:55:25.000Z (over 1 year ago)
• Last Synced: 2024-04-24T04:47:25.506Z (7 months ago)
• Topics: fastapi, hpo, hpo-explorer, hpo-similarity, python, rest-api
• Language: Python
• Homepage: https://github.com/Centogene/pyhpoapi
• Size: 82 KB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.rst
  • Changelog: CHANGELOG.rst
  • License: LICENSE

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README

        
*********

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 `_ 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