Name: magi-annotations
Owner: raphael-group
Description: null
Created: 2016-07-08 19:32:55.0
Updated: 2017-02-06 23:22:40.0
Pushed: 2017-02-06 23:22:39.0
Homepage: http://annotations.cs.brown.edu
Size: 106
Language: Python
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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.
Set your environment variables (see below). We suggest making a file ENVIRONMENT and then loading the variables into your shell with source ENVIRONMENT.
Install dependencies (see below).
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
Run the migrations. This will setup the tables in your Postgres database.
python manage.py migrate
Create a superuser.
python manage.py createsuperuser
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.
Latest tested version in parentheses.
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
Postgres (9.5.3).
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.
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.
Run the server:
python manage.py runserver $MAGIPY_PORT