MAGI Annotations

MAGI Annotations is a Django web server that allows users to view and edit annotations of mutation and protein-protein interactions. It is complementary to MAGI. MAGI Annotations was built and is maintained by the Raphael group at Brown University.

Setup

1. Set your environment variables (see below). We suggest making a file ENVIRONMENT and then loading the variables into your shell with source ENVIRONMENT.

2. Install dependencies (see below).

3. Setup your Postgres user and database. Then set up your Postgres user and database. For example (depending on your set up, these commands may differ slightly):

    createuser $POSTGRES_DJANGO_USER
    createdb $POSTGRES_DJANGO_DBNAME
   

4. Run the migrations. This will setup the tables in your Postgres database.

    python manage.py migrate
   

5. Create a superuser.

    python manage.py createsuperuser
   

6. Initialize the database. We provide a tarball of the data used to initialize MAGI Annotations on our group website. We provide the setup.sh script for convenience which includes the contains the commands for initializing the database.

Dependencies

Latest tested version in parentheses.

1. Python (2.7.11). We suggest managing Python requirements using virtualenv and pip. Execute the following commands on the command-line:

    virtualenv venv
    source venv/bin/activate
    pip install -r requirements.txt
   

2. Postgres (9.5.3).

3. Bower. Bower is required for managing Javascript dependencies. First, you will need to install Node.js and NPM. Then, install Bower, and use it to install the Javascript dependencies:

    npm install -g bower
    bower install
   

See our wiki page Getting set up with MAGI Annotations for additional instructions.

Environment variables

Many of the settings of MAGI Annotations are configurable with the following environment variables. Note that some of these environment variables overlap with MAGI (see MAGI: Environment), so be sure to set these appropriately.

Name	Default	Description
MAGIPY_PORT	'8080'	Port from which you are serving MAGI
MAGIPY_ENV	'development'	"production" for publicly available on the web, or "development" for local/testing
MAGIPY_SITE_URL	''	URL for MAGI Annotations server (required in production only)
MAGI_SECRET_KEY	'MAGI_FOR_PRESIDENT'	Secret key (required in production only)
POSTGRES_DJANGO_DBNAME	'magipy'	Name of Postgres database
POSTGRES_DJANGO_HOST	None	Name of Postgres host
POSTGRES_DJANGO_PORT	'5432'	Name of Postgres port
POSTGRES_DJANGO_USER	'postgres'	Name of Postgres user
POSTGRES_DJANGO_PASSWORD	None	Name of Postgres host
MAGI_STATIC_ROOT	'/var/www/magipy/static/'	Path for static files
MAGIPY_GOOGLE_CLIENT_ID	None	Google OAuth2 client ID
MAGIPY_GOOGLE_CLIENT_SECRET	None	Google OAuth2 client secret
NODE_MAGI_URL	'http://localhost:8000'	URL for MAGI server

We suggest creating a file ENVIRONMENT and exporting each variable (e.g. export MAGI_SITE_URL="http://localhost:8000"), and then loading these into your shell with source ENVIRONMENT.

Usage

Run the server:

python manage.py runserver $MAGIPY_PORT