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The ReproGenomics Viewer is a cross-species genomic resource for the reproductive science community. It aims to centralize and harmonize ultra-high-throughput sequencing data accumulated in the field of reproductive biology and to assist scientists in the exploration of these datasets.

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umr1085-irset/reproGenomicsViewer

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sdap

SciLicium Data Analytics Platform

Built with Cookiecutter Django Black code style

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.

Type checks

Running type checks with mypy:

$ mypy sdap

Test coverage

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

$ coverage run -m pytest
$ coverage html
$ open htmlcov/index.html

Running tests with py.test

$ pytest

Live reloading and Sass CSS compilation

Moved to Live reloading and SASS compilation.

Celery

This app comes with Celery.

To run a celery worker:

cd sdap
celery -A config.celery_app worker -l info

Please note: For Celery's import magic to work, it is important where the celery commands are run. If you are in the same folder with manage.py, you should be right.

Email Server

In development, it is often nice to be able to see emails that are being sent from your application. For that reason local SMTP server MailHog with a web interface is available as docker container.

Container mailhog will start automatically when you will run all docker containers. Please check cookiecutter-django Docker documentation for more details how to start all containers.

With MailHog running, to view messages that are sent by your application, open your browser and go to http://127.0.0.1:8025

Sentry

Sentry is an error logging aggregator service. You can sign up for a free account at https://sentry.io/signup/?code=cookiecutter 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.

Deployment

The following details how to deploy this application.

Heroku

See detailed cookiecutter-django Heroku documentation.

Docker

See detailed cookiecutter-django Docker documentation.

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The ReproGenomics Viewer is a cross-species genomic resource for the reproductive science community. It aims to centralize and harmonize ultra-high-throughput sequencing data accumulated in the field of reproductive biology and to assist scientists in the exploration of these datasets.

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