genewiki

The GeneWiki Project

Overview

The code in this repo handles the automated updates of gene templates, and as well as the on-request article creation requests from the BioGPS plugin (http://biogps.org/genewikigenerator/). Both types of edits are made under the ProteinBoxBot Wikipedia account.

Project Setup

Server Dependencies

• sudo apt-get update

• sudo apt-get upgrade

• sudo apt-get install build-essential python python-dev python-pip python-virtualenv libmysqlclient-dev git-core nginx supervisor rabbitmq-server graphviz libgraphviz-dev pkg-config libncurses5-dev

• mkdir webapps

• cd webapps

• git clone https://github.com/SuLab/genewiki.git

• cd genewiki

• git fetch --all

• git reset --hard origin/master

virtualenv

A Python Virtual Environment is used to ensure that the application runs in an isolated and protected environment

• Create a new virtual environment: sudo virtualenv /opt/genewiki-venv
• Activate the environment source /opt/genewiki-venv/bin/activate

If you see (genewiki-venv) in front of your shell, this worked.

• sudo /opt/genewiki-venv/bin/pip install -r requirements.txt

Setup

The config directory in this project hosts template files and their location for nginx, gunicorn and supervisor

• Supervisor : Copy config/*.conf into /etc/supervisor/conf.d (must update permissions on conf.d)
• nginx : Copy config/default into /etc/nginx/conf.d (upd perm on conf.d to allow copy)
• copy config/gunicorn_start into /bin

Configuration

The settings files are not included in the repo for security reasons and must be uploaded to the server.

• sudo adduser deploy

• sudo /etc/init.d/nginx restart

• cd /home/ubuntu/webapps/genewiki/ & mkdir logs

• sudo supervisorctl reread

• sudo supervisorctl add genewiki

• sudo supervisorctl add genewiki_celery

• touch debug.log

• chmod 777 debug.log

• sudo chown deploy:deploy /bin/gunicorn_start

• sudo chmod a+x /bin/gunicorn_start

• sudo chmod 777 webapps/genewiki/logs/

• import os os.environ['DJANGO_SETTINGS_MODULE'] = 'genewiki.settings'

• 'python manage.py syncdb'

Application

• sudo supervisorctl restart genewiki_celery
• sudo supervisorctl restart genewiki

Utils

• Flow diagram of the database relationships
• python manage.py graph_models -a -o myapp_models.png
• celery --app=genewiki.common worker -B -E -l INFO
• ssh -i .ssh/path/to/key ubuntu@suv05.scripps.edu

Notes

Known issues:

Definitions: