pathogen-repo-build.yml

name: Ingest to phylogenetic

defaults:
  run:
    # This is the same as GitHub Action's `bash` keyword as of 20 June 2023:
    # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell
    #
    # Completely spelling it out here so that GitHub can't change it out from under us
    # and we don't have to refer to the docs to know the expected behavior.
    shell: bash --noprofile --norc -eo pipefail {0}

on:
  schedule:
    # Note times are in UTC, which is 1 or 2 hours behind CET depending on daylight savings.
    #
    # Note the actual runs might be late.
    # Numerous people were confused, about that, including me:
    #  - https://github.community/t/scheduled-action-running-consistently-late/138025/11
    #  - https://github.com/github/docs/issues/3059
    #
    # Note, '*' is a special character in YAML, so you have to quote this string.
    #
    # Docs:
    #  - https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows#schedule
    #
    # Tool that deciphers this particular format of crontab string:
    #  - https://crontab.guru/
    #
    # Runs at 5pm UTC (1pm EDT/10am PDT) since curation by NCBI happens on the East Coast.
    # We were running into invalid zip archive errors at 9am PDT, so hoping an hour
    # delay will lower the error frequency
    - cron: '0 17 * * *'

  workflow_dispatch:
    inputs:
      ingest_image:
        description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")'
        required: false
      phylogenetic_image:
        description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")'
        required: false

jobs:
  ingest:
    permissions:
      id-token: write
    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
    secrets: inherit
    with:
      # Starting with the default docker runtime
      # We can migrate to AWS Batch when/if we need to for more resources or if
      # the job runs longer than the GH Action limit of 6 hours.
      runtime: docker
      env: |
        NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.ingest_image }}
      run: |
        nextstrain build \
          ingest \
            all \
            --configfile config/config.yaml config/optional.yaml
      # Specifying artifact name to differentiate ingest build outputs from
      # the phylogenetic build outputs
      artifact-name: ingest-build-output
      artifact-paths: |
        ingest/results/
        ingest/benchmarks/
        ingest/logs/
        ingest/.snakemake/log/

  # Check if ingest results include new data by checking for the cache
  # of the file with the results' Metadata.sh256sum (which should have been added within upload-to-s3)
  # GitHub will remove any cache entries that have not been accessed in over 7 days,
  # so if the workflow has not been run over 7 days then it will trigger phylogenetic.
  check-new-data:
    needs: [ingest]
    runs-on: ubuntu-latest
    outputs:
      cache-hit: ${{ steps.check-cache.outputs.cache-hit }}
    steps:
      - name: Get sha256sum
        id: get-sha256sum
        env:
          AWS_DEFAULT_REGION: ${{ vars.AWS_DEFAULT_REGION }}
        run: |
          s3_urls=(
            "s3://nextstrain-data/files/workflows/hmpv/metadata.tsv.gz"
            "s3://nextstrain-data/files/workflows/hmpv/sequences.fasta.xz"
          )

          # Code below is modified from ingest/upload-to-s3
          # https://github.com/nextstrain/ingest/blob/c0b4c6bb5e6ccbba86374d2c09b42077768aac23/upload-to-s3#L23-L29


          no_hash=0000000000000000000000000000000000000000000000000000000000000000

          for s3_url in "${s3_urls[@]}"; do
            s3path="${s3_url#s3://}"
            bucket="${s3path%%/*}"
            key="${s3path#*/}"

            s3_hash="$(aws s3api head-object --no-sign-request --bucket "$bucket" --key "$key" --query Metadata.sha256sum --output text 2>/dev/null || echo "$no_hash")"
            echo "${s3_hash}" | tee -a ingest-output-sha256sum
          done

      - name: Check cache
        id: check-cache
        uses: actions/cache@v4
        with:
          path: ingest-output-sha256sum
          key: ingest-output-sha256sum-${{ hashFiles('ingest-output-sha256sum') }}
          lookup-only: true

  phylogenetic:
    needs: [check-new-data]
    if: ${{ needs.check-new-data.outputs.cache-hit != 'true' }}
    permissions:
      id-token: write
    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
    secrets: inherit
    with:
      # Starting with the default docker runtime
      # We can migrate to AWS Batch when/if we need to for more resources or if
      # the job runs longer than the GH Action limit of 6 hours.
      runtime: docker
      env: |
        NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.phylogenetic_image }}
      run: |
        nextstrain build \
          phylogenetic \
            deploy \
            --configfile defaults/config.yaml
      # Specifying artifact name to differentiate ingest build outputs from
      # the phylogenetic build outputs
      artifact-name: phylogenetic-build-output
      artifact-paths: |
        phylogenetic/auspice/
        phylogenetic/results/
        phylogenetic/benchmarks/
        phylogenetic/logs/
        phylogenetic/.snakemake/log/