uniprot_s3_dump.yml

name: Uniprot to S3

on:
#   schedule:
#     - cron: '0 0 1 * *' # Runs on the 1st of every month at midnight
  workflow_dispatch: # Allows manual triggering

jobs:
  fetch-and-upload:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@v4
      
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.x'

      - name: Install Poetry
        uses: snok/install-poetry@v1

      - name: Install project dependencies
        run: poetry install --no-interaction

      - name: Install additional dependencies
        run: |
          poetry add requests
          poetry add boto3
          poetry add aws
      
      - name: Fetch data from Uniprot API
        run: poetry run kg get-via-api -a uniprot
      
      - name: Upload to S3
        uses: aws-actions/configure-aws-credentials@v1
        with:
          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
          aws-region: us-east-1
      - name: Sync files to S3 bucket
        run: |
          poetry run aws s3 sync data/raw/uniprot/test s3://${{ secrets.AWS_BUCKET_NAME }} --delete