Django app to parse/load phenotype ontologies (OncoTree, HPO, MONDO, etc)
Project description
=============================
Django Phenotype Ontologies
=============================
.. image:: https://badge.fury.io/py/django-phenotype-ontologies.svg
:target: https://badge.fury.io/py/django-phenotype-ontologies
.. image:: https://travis-ci.org/chopdgd/django-phenotype-ontologies.svg?branch=develop
:target: https://travis-ci.org/chopdgd/django-phenotype-ontologies
.. image:: https://codecov.io/gh/chopdgd/django-phenotype-ontologies/branch/develop/graph/badge.svg
:target: https://codecov.io/gh/chopdgd/django-phenotype-ontologies
.. image:: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/shield.svg
:target: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/
:alt: Updates
.. image:: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/python-3-shield.svg
:target: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/
:alt: Python 3
Django app to parse/load phenotype ontologies (OncoTree, HPO, MONDO, etc)
Documentation
-------------
The full documentation is at https://django-phenotype-ontologies.readthedocs.io.
Quickstart
----------
Install Django Phenotype Ontologies::
pip install django-phenotype-ontologies
Add it to your `INSTALLED_APPS`:
.. code-block:: python
INSTALLED_APPS = (
...
'phenotype_ontologies',
...
)
Add Django Phenotype Ontologies's URL patterns:
.. code-block:: python
from phenotype_ontologies import urls as phenotype_ontologies_urls
urlpatterns = [
...
url(r'^', include(phenotype_ontologies_urls, namespace='phenotype_ontologies')),
...
]
Features
--------
* syncs OBO from MONDO, HPO, and NCIT (OncoTree)
* REST API to interact with models
* GraphQL Nodes to be incorporated to existing GraphQL setups with graphene_django
Running Tests
-------------
Does the code actually work?
::
source <YOURVIRTUALENV>/bin/activate
(myenv) $ pip install tox
(myenv) $ tox
Credits
-------
Tools used in rendering this package:
* Cookiecutter_
* `cookiecutter-djangopackage`_
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`cookiecutter-djangopackage`: https://github.com/pydanny/cookiecutter-djangopackage
History
-------
0.1.0 (2018-04-10)
++++++++++++++++++
* Models for Phenotype Ontologies
* REST API
* GraphQL Nodes
* Sync methods for PURL of MONDO, HPO, NCIT
0.1.1 (2018-04-10)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.0...v0.1.1>`_
* Updated sync to sync_ontology to make it more descriptive
0.1.2 (2018-04-10)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.1...v0.1.2>`_
* Added better support for MONDO. A few oddities were causing errors w/ pronto.
0.1.3 (2018-04-18)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.2...v0.1.3>`_
* Updated 3rd party libs
0.1.4 (2018-05-16)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.3...v0.1.4>`_
* Updated setup.py to read from requirements.txt
0.2.0 (2018-06-01)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.4...v0.2.0>`_
* Removed support for GraphQL
0.2.1 (2018-07-27)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.0...v0.2.1>`_
* Updated NCIT to be OncoTree - since we are using the onco tree specific ontology
0.2.2 (2018-08-13)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.1...v0.2.2>`_
* Updated 3rd party requirements. Some requirements had changed so it was causing failures
0.2.3 (2018-10-29)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.2...v0.2.3>`_
* Updated 3rd party requirements.
0.2.4 (2018-11-27)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.3...v0.2.4>`_
* Updated 3rd party requirements.
0.2.5 (2019-02-08)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.4...v0.2.5>`_
* Updated 3rd party requirements.
* Updated tests to use py.test fixtures
0.2.6 (2019-04-10)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.5...v0.2.6>`_
* Updated 3rd party requirements.
* Updated travis to use xenial distribution. Django 2.1 dropped support for SQLite < 3.8.3
Django Phenotype Ontologies
=============================
.. image:: https://badge.fury.io/py/django-phenotype-ontologies.svg
:target: https://badge.fury.io/py/django-phenotype-ontologies
.. image:: https://travis-ci.org/chopdgd/django-phenotype-ontologies.svg?branch=develop
:target: https://travis-ci.org/chopdgd/django-phenotype-ontologies
.. image:: https://codecov.io/gh/chopdgd/django-phenotype-ontologies/branch/develop/graph/badge.svg
:target: https://codecov.io/gh/chopdgd/django-phenotype-ontologies
.. image:: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/shield.svg
:target: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/
:alt: Updates
.. image:: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/python-3-shield.svg
:target: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/
:alt: Python 3
Django app to parse/load phenotype ontologies (OncoTree, HPO, MONDO, etc)
Documentation
-------------
The full documentation is at https://django-phenotype-ontologies.readthedocs.io.
Quickstart
----------
Install Django Phenotype Ontologies::
pip install django-phenotype-ontologies
Add it to your `INSTALLED_APPS`:
.. code-block:: python
INSTALLED_APPS = (
...
'phenotype_ontologies',
...
)
Add Django Phenotype Ontologies's URL patterns:
.. code-block:: python
from phenotype_ontologies import urls as phenotype_ontologies_urls
urlpatterns = [
...
url(r'^', include(phenotype_ontologies_urls, namespace='phenotype_ontologies')),
...
]
Features
--------
* syncs OBO from MONDO, HPO, and NCIT (OncoTree)
* REST API to interact with models
* GraphQL Nodes to be incorporated to existing GraphQL setups with graphene_django
Running Tests
-------------
Does the code actually work?
::
source <YOURVIRTUALENV>/bin/activate
(myenv) $ pip install tox
(myenv) $ tox
Credits
-------
Tools used in rendering this package:
* Cookiecutter_
* `cookiecutter-djangopackage`_
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`cookiecutter-djangopackage`: https://github.com/pydanny/cookiecutter-djangopackage
History
-------
0.1.0 (2018-04-10)
++++++++++++++++++
* Models for Phenotype Ontologies
* REST API
* GraphQL Nodes
* Sync methods for PURL of MONDO, HPO, NCIT
0.1.1 (2018-04-10)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.0...v0.1.1>`_
* Updated sync to sync_ontology to make it more descriptive
0.1.2 (2018-04-10)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.1...v0.1.2>`_
* Added better support for MONDO. A few oddities were causing errors w/ pronto.
0.1.3 (2018-04-18)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.2...v0.1.3>`_
* Updated 3rd party libs
0.1.4 (2018-05-16)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.3...v0.1.4>`_
* Updated setup.py to read from requirements.txt
0.2.0 (2018-06-01)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.4...v0.2.0>`_
* Removed support for GraphQL
0.2.1 (2018-07-27)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.0...v0.2.1>`_
* Updated NCIT to be OncoTree - since we are using the onco tree specific ontology
0.2.2 (2018-08-13)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.1...v0.2.2>`_
* Updated 3rd party requirements. Some requirements had changed so it was causing failures
0.2.3 (2018-10-29)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.2...v0.2.3>`_
* Updated 3rd party requirements.
0.2.4 (2018-11-27)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.3...v0.2.4>`_
* Updated 3rd party requirements.
0.2.5 (2019-02-08)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.4...v0.2.5>`_
* Updated 3rd party requirements.
* Updated tests to use py.test fixtures
0.2.6 (2019-04-10)
++++++++++++++++++
`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.5...v0.2.6>`_
* Updated 3rd party requirements.
* Updated travis to use xenial distribution. Django 2.1 dropped support for SQLite < 3.8.3
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Close
Hashes for django-phenotype-ontologies-0.2.6.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 954d6510decefccc27c0d15b35bf2f249f3d3c0720232edf21d2a4b7acea9ece |
|
MD5 | f4e41f618666bf8d49ded5ab76ae1366 |
|
BLAKE2b-256 | 355c2056293553ad4e1ed75bf7227f47fc42f67ee60bf5520ae9b6426dc9b2dd |
Close
Hashes for django_phenotype_ontologies-0.2.6-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ebfdc3d90bb10d8533b9b08e1ba37143b4db6107d45688af52ebe99fc364838b |
|
MD5 | 183244490b5e5afef183f575c92e8125 |
|
BLAKE2b-256 | 3f26de575a84574a7065a0ee9215987ddfa76f49f8bc581754c9997832b2d849 |