get-covid-clade-counts.yaml

name: Get covid clade counts and upload them to the AWS S3 bucket

on:
  schedule:
    - cron: "37 04 * * 1" # 4:37 AM UTC every Mon
  workflow_dispatch:
    inputs:
      as_of:
        description: "Get clade counts as of 11:59 UTC on this date (YYYY-MM-DD)"
        required: true
        default: $(date +'%Y-%m-%d')

env:
  # Hubverse AWS account number
  AWS_ACCOUNT: 312560106906

permissions:
  contents: read
  # id-token write required for AWS auth
  id-token: write

jobs:
  get-covid-clade-counts:
    runs-on: ubuntu-latest

    steps:

    - name: Get --as-of date 🕰️
      run: |
        if [[ ${{ github.event_name == 'workflow_dispatch' }} == true ]]; then
          AS_OF=${{ inputs.as_of }}
        else
          AS_OF=$(date +'%Y-%m-%d')
        fi
        echo "as_of date is set to $AS_OF"
        echo "AS_OF=$AS_OF" >> $GITHUB_ENV

    - name: Checkout
      uses: actions/checkout@v4

    - name: Configure AWS credentials
      # request credentials to assume the hub's AWS role via OpenID Connect
      uses: aws-actions/configure-aws-credentials@v4
      with:
        role-to-assume: arn:aws:iam::312560106906:role/covid-clade-counts-action
        aws-region: us-east-1

    - name: Install uv 🐍
      uses: astral-sh/setup-uv@v2
      with:
        version: "0.4.9"
        enable-cache: true

    - name: Get covid clade counts
      run: |
        uv run get_covid_clade_counts.py --as-of="$AS_OF"

    - name: Install rclone
      run: |
        curl https://rclone.org/install.sh | sudo bash
        rclone version

    - name: Copy to cloud storage
      # copy the created file to S3
      run: |
        rclone copy ./data/ ":s3,provider=AWS,env_auth:covid-clade-counts" \
          --checksum --verbose --stats-one-line --config=/dev/null
      shell: bash