semvec/pypi-packages huggingface dataset:
pyhpoapi 2.0.0
A REST API for the HPO ontology using PyHPO
License: MIT License
Requires Python: >=3.7
Keywords: HPO,REST-API,Bioinformatics,Ontology,Phenotype

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PyHPO-API
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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