P*R*O*P

Prerequisites

• Docker & docker compose
  • https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-on-ubuntu-18-04
  • https://www.digitalocean.com/community/tutorials/how-to-install-docker-compose-on-ubuntu-18-04
• npm
  • curl -sL https://deb.nodesource.com/setup_12.x | sudo -E bash -
  • sudo apt install nodejs

Development

Frontend & Backend

1. Pull this repo
2. cd PROP
3. copy .env.example to .env
4. in frontend/src/environments/environment.ts set the env vars for development:
   • set production to false
   • set baseUrl to http://localhost:5004
   • set apiKey to DUMMY
   • set fileSizeLimit to the file size limit
5. make sure Docker is running
6. PYTHON=python3.8 ./dc_script.sh
   • NOTES:
     • this script will prune ALL existing Docker volumes, images and containers
     • it is necessary to set PYTHON=python3.8 so that the dc_script runs correctly
7. wait for the script to finish
8. open the website on https://localhost:4200/
9. make changes to the frontend/backend code. Hot reload is enabled

NOTE:

• If you want to run the frontend/backend separately, you can do so by running sudo ./dc_script.sh --frontend-only or sudo ./dc_script.sh --backend-only

Production

Build

Frontend (static)

1. Pull this repo
2. cd PROP
3. Ensure the .env file in the root directory contains the following variables:
   • PRODUCTION=true
   • BASE_URL (set to the API Gateway URL)
   • BACKEND_APIKEY (set to the Python backend API key)
   • FILE_SIZE_LIMIT (set to the desired file size limit)
4. cd frontend
5. npm install
6. Build production version
   1. non-prop environments: npm run build:prod
   2. prop environment: npm run build:prod:prop
7. Host the resulting /docs folder on a hosting platform

Backend

1. Pull this repo
2. aws sso login --profile [PROFILE] (if not already logged in)
3. In the .env file:
   • set AWS_ACCOUNT_ID and AWS_REGION
4. cd PROP
5. ./build_and_upload_backend_images_production.sh [AWS SSO PROFILE]
6. wait for the script to finish

NOTE:

• the script builds the Docker images and uploads them to AWS ECR repositories
  • access to that repository / AWS account is required

Deploy

Frontend

1. Host the docs folder created during the build process on a hosting platform

Backend

Pre-requisites:

• make sure that the VPC endpoints ecr.dkr, ecr.api and aws_ec2_instance_connect_endpoint are created using the repository PROP-infra

1. SSH into the EC2 instance via the management console
   1. access to the EC2 instance / AWS account is required
2. copy compose_deploy.yml to the instance
3. ensure the .env file is present and contains the following variables:
   • AWS_ACCOUNT_ID
   • AWS_REGION
   • BACKEND_APIKEY
   • MAFFT_ARRAY_COUNT
   • MAFFT_ARRAY_LENGTH
   • CLUSTALW_ARRAY_COUNT
   • CLUSTALW_ARRAY_LENGTH
   • NO_ALIGNMENT_ARRAY_COUNT
   • NO_ALIGNMENT_ARRAY_LENGTH
   • FILE_SIZE_LIMIT
4. aws ecr get-login-password | docker login --username AWS --password-stdin 151247720829.dkr.ecr.ap-northeast-1.amazonaws.com
5. docker compose -f compose_deploy.yml up -d

How to update

MAFFT / ClustalW variables

• array length and count variables can be set in ./.env.fixedVariables
  • can set:
    • MAFFT array length & count
    • ClustalW array length & count

frontend only

1. sudo ./dc_script.sh --frontend-only

backend only

1. sudo ./dc_script.sh --backend-only

re-build / update everything

1. Rebuild: sudo ./dc_script.sh

Usage via browser

• local environment: https://localhost:4200/

• static hosting: domain provided by the hosting platform

This software is released under the MIT License, see LICENSE.txt.