greenelab / django-organisms

A Django package to represent organisms

Organisms

Organisms is a simple Django app to represent organisms.

Download and Install

This package is registered as "django-organisms" in PyPI and is pip installable:

pip install django-organisms

If django is not found on your system, pip will install it too.

Quick Start

1. Add 'organisms' to your INSTALLED_APPS setting like this:

   INSTALLED_APPS = (
       ...
       'organisms',
   )
   

2. Run python manage.py migrate command to create organisms model.

3. (Optional) The following step is only needed if you have django-tastypie installed to create a REST API for your project and would like to have API endpoints for django-organisms.

   Add the following to your project's urls.py file:

   # There are probably already other imports here, such as:
   # from django.conf.urls import url, patterns, include
   
   # If you have not already done so, import the tastypie API:
   from tastypie.api import Api
   
   # Import the OrganismResource:
   from organisms.api import OrganismResource
   
   # If you have not already done so, initialize your API and
   # add the OrganismResource to it
   v0_api = Api()
   v0_api.register(OrganismResource())
   
   # In the urlpatterns, include the urls for this api:
   urlpatterns = patterns('',
       ...
       (r'^api/', include(v0_api.urls))
   )
   

Usage of Management Command

This app includes a management command management/commands/organisms_create_or_update.py, which can be used to populate the organisms table in the database. It takes 3 arguments:

• taxonomy_id
• scientific_name
• common_name

For example, to populate the Human object in the database, we would enter:

python manage.py organisms_create_or_update --taxonomy_id=9606 --scientific_name="Homo sapiens" --common_name="Human"

django-organisms's Issues

Open Issues in Bitbucket Repo

https://bitbucket.org/greenelab/django-organisms/issues?status=new&status=open

"BaseCommand.option_list" is deprecated

Since Django 1.8+, BaseCommand.option_list has been deprecated.
https://docs.djangoproject.com/en/1.8/howto/custom-management-commands/#django.core.management.BaseCommand.option_list

This affects the management command defined in organisms/management/commands/organisms_create_or_update.py.