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README.rst

annotation_tool

Bioinformatics annotation tool.

LICENSE: BSD

Settings

Moved to settings.

Basic Commands

Setting Up Your Users

To create a normal user account, just go to Sign Up and fill out the form. Once you submit it, you'll see a "Verify Your E-mail Address" page. Go to your console to see a simulated email verification message. Copy the link into your browser. Now the user's email should be verified and ready to go.

To create an superuser account, use this command:

$ python manage.py createsuperuser

For convenience, you can keep your normal user logged in on Chrome and your superuser logged in on Firefox (or similar), so that you can see how the site behaves for both kinds of users.

Test coverage

To run the tests, check your test coverage, and generate an HTML coverage report:

$ coverage run manage.py test
$ coverage html
$ open htmlcov/index.html

Live reloading and Sass CSS compilation

Moved to Live reloading and SASS compilation.

Sentry

Sentry is an error logging aggregator service. You can sign up for a free account at http://getsentry.com or download and host it yourself. The system is setup with reasonable defaults, including 404 logging and integration with the WSGI application.

You must set the DSN url in production.

It's time to write the code!!!

Running end to end integration tests

N.B. The integration tests will not run on Windows.

To install the test runner:

$ pip install hitch

To run the tests, enter the annotation_tool/tests directory and run the following commands:

$ hitch init

Then run the stub test:

$ hitch test stub.test

This will download and compile python, postgres and redis and install all python requirements so the first time it runs it may take a while.

Subsequent test runs will be much quicker.

The testing framework runs Django, Celery (if enabled), Postgres, HitchSMTP (a mock SMTP server), Firefox/Selenium and Redis.

Deployment

We providing tools and instructions for deploying using Docker and Heroku.

Heroku

https://www.herokucdn.com/deploy/button.png

See detailed cookiecutter-django Heroku documentation.

Docker

See detailed cookiecutter-django Docker documentation.