Get covid clade counts and upload them to the AWS S3 bucket #12
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| 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: | |
| 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: 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=$(date +'%Y-%m-%d') | |
| - 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 |