6. Replicating the Reference Implementation

The reference implementation is written in python and deployed to Heroku. Data is stored in MongoDB.

Set up a Heroku account

This reference implementation fits within Heroku's base tier.

Set up a MongoDB Atlas account

This reference implementation, including utility data, requires just under 2GB of storage space.

• After creating an account and a project, ascertain the MongoDB Connection String that you will need to insert into the python code in order to access your data (described further below).

• Replicate the data from this instance of the reference implementation over to your MongoDB account:

  • Install MongoDB Database Tools by following the steps mentioned here.
  • Download the Database using the following command: mongodump --uri mongodb+srv://download:[email protected]/FHIRGenomicsData (You may need to include the '--forceTableScan' parameter)
  • Store the downloaded database in your own MongoDB Atlas database using the following command: mongorestore --uri YOUR_MONGODB_ATLAS_DATABASE_URI

• To also grab the data used to drive the utilities:

  • Download the utilities data using the following command: mongodump --uri mongodb+srv://download:[email protected]/UtilitiesData (You may need to include the '--forceTableScan' parameter)

Fork the code

A fork is a copy of a repository. Forking a repository allows you to freely experiment with changes without affecting the original project.

• Note that the connection string (e.g. in common.py) used to call MongoDB must be edited to reflect the connection string of your MongoDB instance
• Deploy the code to your Heroku instance