update-ncov-case-counts.yaml

name: COVID-19 case counts

on:
  schedule:
    - cron: '0 16 * * *'
  workflow_dispatch:
    inputs:
      slack_channel:
        description: 'Slack channel to push update alerts. Default channel is nextstrain-counts-updates.'
        required: false
      trial_name:
        description: 'Short name for a trial run. WARNING: without this we will overwrite files in s3://nextstrain-data/files/workflows/forecasts-ncov/cases.'
        required: false

jobs:
  case_counts:
    runs-on: ubuntu-latest
    env:
      SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }}
      SLACK_CHANNELS: ${{ github.event.inputs.slack_channel || 'nextstrain-counts-updates' }}
    defaults:
      run:
        # Login shell is required to include changes by conda init bash.
        shell: bash -l -eo pipefail {0}
    steps:
    - uses: actions/checkout@v2
    - uses: conda-incubator/setup-miniconda@v2
      with:
        python-version: "3.9"
        miniforge-variant: Mambaforge
        channels: conda-forge,bioconda

    - name: setup
      run: mamba install "csvtk>=0.23.0"

    - name: download case counts
      run: |
        ./ingest/bin/fetch-ncov-global-case-counts > global_case_counts.tsv

    - name: upload to S3
      run: |
        S3_DST=s3://nextstrain-data/files/workflows/forecasts-ncov/cases
        CLOUDFRONT_DOMAIN="data.nextstrain.org"

        if [[ "$TRIAL_NAME" ]]; then
          S3_DST+=/trial/"$TRIAL_NAME"
        fi

        ./ingest/vendored/upload-to-s3 global_case_counts.tsv "$S3_DST"/global.tsv.gz $CLOUDFRONT_DOMAIN
      env:
        AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
        TRIAL_NAME: ${{ github.event.inputs.trial_name }}

    - name: notify_pipeline_failed
      if: ${{ failure() }}
      run: ./ingest/vendored/notify-on-job-fail "Case counts ingest" "nextstrain/forecasts-ncov"