variant-search-app

Prerequisites

• npm or yarn
• docker-compose

Installation

Clone the repo

$ git clone [email protected]:Rosswell/variant-search-app.git

React installation & setup

React is not dockerized, so the React app is run locally.

Navigate to the client directory and install the libraries from package.lock with yarn:

$ cd variant-search-app/services/client
$ yarn install

or with npm:

$ cd variant-search-app/services/client
$ npm install

Standing up the app

Spin up the postgres/flask docker container. This will serve the API endpoints at 0.0.0.0:5001.

$ cd variant-search-app
$ docker-compose -f docker-compose-dev.yml up -d --build

Create and fill the DB

$ docker-compose -f docker-compose-dev.yml run genes python manage.py recreate-db
$ chmod +x load_data.sh && ./load_data.sh

Start the React app

$ cd variant-search-app/services/client
$ npm start
# or, with yarn:
$ yarn start

Run the few tests that I had time to write

Flask tests

$ cd variant-search-app
$ docker-compose -f docker-compose-dev.yml run genes python manage.py test

React tests

$ cd variant-search-app/services/client
$ npm test
# with yarn:
$ yarn test

The Process

1. Build a static API route
2. Attach API to sqlite DB, make API dynamic
3. Serve API through Docker
4. Discover sqlite table is empty, put postgres in Docker as well
5. Serve data from postgres to gene query endpoint
6. Start actually inspecting data, discover some intricacies there not previously considered
   • Lists represented as strings
   • Variable null value nomenclatures
   • At least 10 different shorthand ways of representing a variant
   • Relationships between other_mappings and other fields
7. Stand up frontend
8. Create MVP dynamically rendered components
9. Create table components and associated subcomponents
10. Style table components
11. Backfill python tests
12. Write React tests

Finally

Please let me know if there are any issues! I think I'm going to continue to work on this since I wasn't able to dockerize the React app or host on AWS or any fun things like that