AMI update and DNS Configuration for Neo4j

Description

This PR includes major changes for gfe-db including a new AMI, SSL, refactoring of User Data and DNS configuration.

Major Changes

New AMI from Bitnami
- Neo4j recently suspended support of their Community Edition AMI
- New AMI available at https://aws.amazon.com/marketplace/pp/prodview-v47qqrn2yy7ie?sr=0-3&ref_=beagle&applicationId=AWS-Marketplace-Console
CloudWatch Logs Agent, SSM Agent, and CloudFormation Helpers are installed on EC2 during deployment
User Data creates an environment file env.sh for Neo4j setup, database loading and other tasks.
Neo4j setup is handled by Makefile on the database instance
- Automatically provisions SSL cert
- Updates config
- Installs plugins
- Runs queries to create constraints and indexes
- Retrieves and stores the password in Secrets Manager
SSL and DNS configuration for Neo4j
- Browser access over HTTPS on self-hosted domain

Deployment Notes

Bitnami AMI

The Bitnami AMI requires a subscription through AWS Marketplace: https://aws.amazon.com/marketplace/pp/prodview-v47qqrn2yy7ie?sr=0-3&ref_=beagle&applicationId=AWS-Marketplace-Console

Once you have subscribed to the AMI, make sure to add the correct AMI ID to the root Makefile under the NEO4J_AMI_ID variable.

DNS Configuration

Neo4j browser can now be accessed using HTTPS at a custom domain name. To configure your domain for Neo4j follow these steps.

Update ./gfe-db/database/neo4j/neo4j.conf with your domain name:
```
dbms.default_advertised_address=<subdomain name>.<domain>.com
```
Update the Hosted variable HOSTED_ZONE_ID in the root Makefile
Deploy the project to AWS

Alternatively, if you are not using Route 53 for your hosting, you must manually create an A record for your DNS. You can indicate a subdomain if you want. Make sure to point it to Neo4j's static IP.

  Subdomain name: <subdomain name>.<domain>.com
  Type: A
  TTL: 300
  Resource: <Neo4j IP>

Quickstart

Subscribe to the Bitnami Neo4j AMI (as described above)
Configure neo4j.conf and update the Hosted Zone ID (as described above)
Install prerequisites and dependencies (see README)

Create .env with necessary environment variables

# ./.env
STAGE=<dev or prod>
APP_NAME=gfe-db
REGION=<AWS region>
GITHUB_PERSONAL_ACCESS_TOKEN=<secret>
HOST_DOMAIN=<fqdn>
ADMIN_EMAIL=<email>
APOC_VERSION=4.4.0.3
GDS_VERSION=2.0.1

Check the JSON input parameters and edit the values as desired.

// ./gfe-db/pipeline/config/pipeline-input.json
{
  "align": "False",
  "kir": "False",
  "mem_profile": "False",
  "limit": "1000"
}

Run make deploy to deploy the stacks to AWS.
Run make database.load release=<version> to load Neo4j.
Run make database.get-credentials to get the password for Neo4j.
Navigate to the Neo4j browser at https://<your domain>:7473/browser/

nmdp-bioinformatics / gfe-db