deploy-private-nextflu.yaml

name: Deploy private.nextflu.org

on:
  workflow_dispatch:
    inputs:
      aws_batch_job_id:
        description: The AWS Batch Job ID for the private nextflu seasonal flu builds.
        type: string
        required: true
      deploy_to_staging:
        description: Deploy to the staging website at https://staging-private-nextflu.netlify.app
        type: boolean
        required: true

env:
  # Everything should run from within the nextflu/auspice directory
  # https://github.com/blab/nextflu/tree/e672eba6d2e0ad5e10b0775f94fc87ffc75d6005/auspice
  WORKING_DIR: auspice
  AUSPICE_DIR: auspice-who

defaults:
  run:
    # Cannot use contexts or expressions for this top level defaults, so must
    # hard-code the path instead of using env.WORKING_DIR
    # https://docs.github.com/en/actions/using-jobs/setting-default-values-for-jobs#setting-default-shell-and-working-directory
    working-directory: auspice

jobs:
  deploy_to_netlify:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          repository: blab/nextflu
          sparse-checkout: |
            ${{ env.WORKING_DIR }}

      - uses: ruby/setup-ruby@v1
        with:
          ruby-version: '2.3.7'
          bundler-cache: true
          # `uses` does not respect the default working-directory
          # Luckily, the setup-ruby action has a `working-directory` input
          # https://github.com/ruby/setup-ruby#working-directory
          #
          # Must be set to access the Gemfile.lock file in the auspice directory
          # https://github.com/blab/nextflu/blob/12c5645d990f53c553d6f04e293e2f12b4ad3575/auspice/Gemfile.lock
          working-directory: ${{ env.WORKING_DIR }}

      - uses: nextstrain/.github/actions/setup-nextstrain-cli@master

      - name: Download builds from AWS Batch
        run: |
          nextstrain build \
          --aws-batch \
          --attach "$AWS_BATCH_JOB_ID" \
          --download "$AUSPICE_DIR/*.json" \
          --no-logs \
          .
        env:
          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
          AWS_BATCH_JOB_ID: ${{ inputs.aws_batch_job_id }}

      - name: Move Auspice JSONs
        run: |
          mkdir data
          mv "$AUSPICE_DIR"/*.json data/
          rm -r "$AUSPICE_DIR"

      - name: Create index files
        run: python provision_directories.py

      - name: Build site
        run: bundle exec jekyll build

      - uses: actions/setup-node@v4
        with:
          # Minimum node version to install Netlify CLI
          # https://docs.netlify.com/cli/get-started/#installation
          node-version: 18

      - name: Install Netlify CLI
        run: npm install netlify-cli@17.2.2 -g

      - name: Deploy to Netlify
        run: netlify deploy --build --prod
        env:
          NETLIFY_SITE_ID: ${{ inputs.deploy_to_staging && secrets.NETLIFY_SITE_ID_STAGING || secrets.NETLIFY_SITE_ID }}
          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}