Aquarium Sample Search and Data Browser Prototype

Flask-based prototype for searching samples and browsing data in Aquarium

Requirements

This app is designed to be run in Docker

• Install Docker

Setup

1. Clone

Clone using git with the command

git clone https://github.com/aquariumbio/aq-search-prototype.git

2. Get a production database

This app is designed to work with a full database, and has no provision for adding data. The first time this app is run, the database is initialized from the database dump data/mysql_init/dump.sql. Although this file exists in the cloned repo, you will need to replace it with a dump of a full database. You can get one here. (Ask for access if you don't have it already.) Copy this file to data/mysql_init and then remove any contents of the data/db directory with the following command:

rm -rf data/db/*

Note: If you are running a large database, such as the BIOFAB production database, the app will be very slow if the database is not indexed. Please ask for help if you notice page loads of more than a few seconds.

3. Start with Docker Compose

docker-compose build # if running for the first time
docker-compose up

4. Open in a browser

Point a browser to http://0.0.0.0:5000/. You should see a page titled Contents that has links to the sample search and data browser pages.