RNAcentral Website

About

RNAcentral is an open public resource that offers integrated access to a comprehensive and up-to-date set of ncRNA sequences. For more information, please visit http://rnacentral.org/about-us.

The development of RNAcentral is coordinated by the European Bioinformatics Institute and is funded by the BBSRC.

Installation

Clone Git repository:

git clone --recursive https://github.com/RNAcentral/rnacentral-webcode.git

Edit database connection parameters in rnacentral/local_settings.py
Run the app using Docker:

export RNACENTRAL_HOME=/path/to/rnacentral/code
cd $RNACENTRAL_HOME
docker-compose up --build

Docker Cheat Sheet

# connect to a running container
docker ps
docker exec -it <container_id> bash

Testing

Selenium tests

Install selenium and requests using virtualenv:

virtualenv /path/to/testing/virtualenv
source /path/to/testing/virtualenv/bin/activate
pip install requests selenium

Install Gecko Driver and add it to the PATH:

export PATH=$PATH:/path/to/geckodriver

Start the website locally using Docker (see above).
Launch tests against the local RNAcentral website:

cd $RNACENTRAL_HOME
python rnacentral/portal/tests/selenium_tests.py

These tests run automatically using Travis.

API tests

Login to the running Docker container (see above).
Launch tests:

cd $RNACENTRAL_HOME
python rnacentral/apiv1/tests.py

Application-specific tests

Using Django test runner:

cd $RNACENTRAL_HOME
python manage.py test portal.tests.description_tests

Using py.test requires creating a file rnacentral/conftest.py:

import django
import pytest

django.setup()


@pytest.fixture(scope='session')
def django_db_setup():
    """Avoid creating/setting up the test database"""
    pass


@pytest.fixture
def db_access_without_rollback_and_truncate(request, django_db_setup,
                                            django_db_blocker):
    django_db_blocker.unblock()
    request.addfinalizer(django_db_blocker.restore)

The following file is also required:

$ cat pytest.ini
[pytest]
DJANGO_SETTINGS_MODULE = rnacentral.settings

Tests can then be run with:

cd $RNACENTRAL_HOME
py.test portal/tests/description_tests.py

Feedback

Feel free to give feedback using GitHub issues or get in touch using the Contact form on our website.

Technology overview

Python

Javascript

CSS

Testing

Other

About

RNAcentral website source code

http://rnacentral.org

Apache License 2.0

Languages

Language:Python 57.8%Language:HTML 19.0%Language:JavaScript 18.0%Language:CSS 4.9%Language:Shell 0.3%