Genomie

Genetic visualization application

Please visit our deployed website.

Introduction

Genomie is a web application that provides beautiful data visualizations of hereditary information based on the information received from 23AndMe.com. Providing the user with a varieties of different views, anyone can easily interpret and understand their unique genetic information in an interactive and elegant way. Genomie provides clear and vibrant perspectives in multiple viewing environments for an optimized user experience.

---

## Table of Contents

• Example
• Installation
• Technologies
• Architecture
• API Endpoints
• Contributing
• Meet the Engineers
• Questions and Issues

==========

Example

===============

Installation

Please install Python/Flask dependencies within the root directory

$ virtualenv .
$ source bin/activate
$ pip install -r requirements.txt

Next, install the client-side dependencies

$ sudo npm install -g bower
$ bower install

For testing

$ npm install

You're good to go. Start the server with:

$ npm start

===============

Technologies

Front-end

• AngularJS
• Angular-Material
• D3.js

Back-end

• Python/Flask
• PostgreSQL
• SQLAlchemy

Testing/Automation

• Mocha/Chai
• Karma
• Jasmine
• Grunt

===============

Architecture

High Level Architecture

Database Schema

Database in Postgres, using SQLAlchemy

======

API

Public End Points

Description	Endpoint
Log-in OAuth	GET /receive_code/
Log-in Demo	POST /demo/
Log-out current user	POST /logout
Get User Info	GET /user/basicinfo/
Get User Relatives	POST /user/relativesinfo/
Get User's SNP Data	POST /user/snpinfo/

Admin Only

Description	Endpoint
Access to 23&Me Individual data	GET /1/user/:userID
Access to 23&Me Genotype data	GET /1/genotype/:userID
Access to 23&Me Relative data	GET /1/relatives/:userID

GET /receive_code/

Redirects back to server after acquiring access token after User approves OAuth permissions

Example Request

curl -H 'Accept: auth-url' -H 'Authorization: OAuth <access_token>' \
-X GET https://BASE_API_URL + 
{
  'client_id': CLIENT_ID,
  'client_secret': CLIENT_SECRET,
  'grant_type': 'authorization_code',
  'code': request.args.get('code'),
  'redirect_uri': REDIRECT_URI,
  'scope': DEFAULT_SCOPE
}

POST /demo/

Allows visitors to access site as a demo user

Example Request

{
	'demo_profile_id': 'demo_id',
	'demo_first_name': 'Foo',
	'demo_last_name': 'Bar'
	'demo_data': [
		'sex': 'm/f',
		'rs_id': 'demo_basepairs',
		...
	]
}

POST /logout/

Logs out user from session and clears cookies/cache

Example Request

{
	'user_profile_id': 'profile_id',
	'headers': {
		'cookie': {
			'token': 'asj238xlzhs_uw28hzbhslsm8es9'
		}
	}
}

GET /user/basicinfo/

Fetches the basic information of the current authorized user

Example Response

{
  "user": {
  	"profile_id": 1738,
    "first_name": "Foo",
    "last_name": "Bar",
    "location": "United States",
    "picture_url": ""
    }
}

POST /user/relativesinfo/

Gathers information about the current user's relatives

Example Request

{
	'user_profile_id': 'profile_id',
	'headers': {
		'cookie': {
			'token': 'asj238xlzhs_uw28hzbhslsm8es9'
		}
	}
}

Example Response

{
	"user_profile_id": "profile_id",
	"relatives": [
		{"relative1": {
			"first_name": "Foo",
			"last_name": "Bar",
			"sex": "m/f",
			"residence": "California",
			"similarity": 0.25,
			"maternal_side": "False",
			"paternal_side": "True",
			"birth_year": 1992,
			"relationship": "Brother",
			"birthplace": "United States",
			"ancestry": "Northwestern Europe",
			"picture_url": ""
		}},
		{"relative2": {
			"first_name": "Foo2",
			"last_name": "Bar2",
			"sex": "m/f",
			"residence": "California",
			"similarity": 0.25,
			"maternal_side": "False",
			"paternal_side": "True",
			"birth_year": 1990,
			"relationship": "Sister",
			"birthplace": "United States",
			"ancestry": "Northwestern Europe",
			"picture_url": ""
		}},
		...
	]
}

POST /user/snpinfo/

Gathers DNA information about the current user

Example Request

{
	'user_profile_id': 'profile_id',
	'headers': {
		'cookie': {
			'token': 'asj238xlzhs_uw28hzbhslsm8es9'
		}
	}
}

Example Response

{
	"user_profile_id": "profile_id",
	"body": [
		{"rs270831": {
			"title": "Lactose Intolerance",
			"dna_pair": "AA",
			"outcome": "You have a high likelihood of being lactose intolerant",
			"video": "4UvzSuP_Tzd"
		}},
		{"rs812202": {
			"title": "Cilantro",
			"dna_pair": "GG",
			"outcome": "You are likely to experience a dislike for cilantro, may taste like soap",
			"video": "TZs309snmr"
		}},
		...
	]
}

Admin Routing

GET /1/user/:userID

Requests user's information upon login from 23andMe's designated endpoint

Example Request

curl -H 'Accept: %s%sBASE_API_URL + '/1/user/' + 'user_id'' -H 'Authorization: 'Bearer %s' % access_token' \ -X GET https://auth-url/1/user?email=true

GET /1/genotype/:userID

Requests user's unique genotype information upon login from 23andMe's designated endpoint

Example Request

curl -H 'Accept: %s%sBASE_API_URL + '/1/genotype/' + 'user_id'' -H 'Authorization: 'Bearer %s' % access_token' \ -X GET https://auth-url/1/genotype/

GET /1/relatives/:userID

Requests user's relatives' information upon login from 23andMe's designated endpoint

Example Request

curl -H 'Accept: %s%sBASE_API_URL + '/1/user/' + 'user_id'' -H 'Authorization: 'Bearer %s' % access_token' \ -X GET https://auth-url/1/relatives

=====================

Meet The Engineers

Product Owner

• Gar Lee

Scrum Master

• Alex Anthony

Development Team

• Chris Bassano
• Peter Lollo

===============

Contributing

Genomie was built using waffle.io as the project organization tool. Please visit here for our workflow guidelines.

Questions and Issues

For any issues, please refer to our issues page Please direct any questions regarding Genomie to our wiki page

Thank you!