gregfriedland/aml_browser

Use Django to provide a web app for browsing Cancer Genome Atlas AML data

AML data browser

This repo implements the project specified at https://gist.github.com/lawrlee/f5ce3d91e6b6e4c0878a09134206f4aa It uses Django, sqlite, Django REST framework, ReactJS, and Semantic UI to provide a web application that allows browsing the AML data from the Cancer Genome Atlas dataset. In addition to the base requirements, it contains a search box on the index page for searching for patients inside all fields (including hidden fields).

Setup the server

1. Setup your virtualenv and activate it
2. Install requirements: pip install -r requirements.txt
3. Load the data into the DB: rm -rf db.sqlite3 && python manage.py migrate && python manage.py shell -c "from aml_app.load_db_from_file import load_db; load_db('LAML.merged_only_clinical_clin_format.txt')"

Run the development server

1. python3 manage.py runserver
2. Go to: http://localhost:8000/aml/

Regenerate the ReactJS bundles

The ReactJS bundles are included in git. If you modify the code in assets/js/ they will need to be rebuilt:

1. Install webpack and dependencies: npm install
2. To regenerate the ReactJS webpack bundle: ./node_modules/.bin/webpack --config webpack.config.js

Rebuild semantic-ui

The Semantic UI files are also in git. To change the theme, etc.:

1. Install gulp: npm install -g gulp
2. Rebuild: (cd assets/semantic && gulp build)