FlaskApp

NGS 360 Front-End Web Application

Motivation

We needed an easy way for everyone to access NGS data and pipelines. This app provides that interface.

Architecture

This app is deployed via Amazon Elastic BeanStalk as a Python Flask application in Docker.

This application was originally modeled after https://blog.miguelgrinberg.com/post/the-flask-mega-tutorial-part-i-hello-world

Configuration Settings

Default configuration settings are loaded from config.py, then can be overridden by setting the environment variable, NGS360_SETTINGS, to the full path of a config file. Config files are python files and only values in uppercase are actually stored. This provides a way to maintain multiple app configurations external to the application.

Build, Test, Run

Makefile targets are used to make this easy:

build - Build the Docker image for this app
test - Run unit tests (currently this is done on outside of Docker.  This may be a problem due to local host machine settings)
make - Run the app in Docker

Development

NGS360 uses 'A successful Git branching model' for development:

• master branch is the current production version

• develop branch is the active development version targetted for production

• Feature branches are forked from the develop branch

• Branch names should be Jira ticket ids

We also aim to achieve https://12factor.net

CI/CD Pipeline

Jenkins handles the CI/CD pipeline.

Deployment to elastic beanstalk is done using the deploy-eb branch, which sets up the elastic beanstalk environment.

When a merge/commit is performed on the develop or master branch, Jenkins runs unit tests, the merges the branch with deploy-eb and deploys to ngsdev or ngsstaging.