upload.yaml

name: Upload data from fauna to S3

# Only support manual trigger of this workflow.
on:
  workflow_dispatch:
    inputs:
      triggerAvianFlu:
        description: "Trigger nextstrain/avian-flu GenoFLU workflow"
        type: boolean
        required: true
      triggerPublic:
        description: "Trigger Nextstrain public builds"
        required: true
        type: boolean
      publicDockerImage:
        description: "Specific container image to use for Nextstrain public builds"
        required: false
        type: string
      triggerNextfluPrivate:
        description: "Trigger nextflu-private group builds"
        required: true
        type: boolean
      nextfluPrivateDockerImage:
        description: "Specific container image to use for nextflu-private group builds"
        required: false
        type: string
      triggerForecastsFlu:
        description: "Trigger forecasts-flu models"
        required: true
        type: boolean
      forecastsFluDockerImage:
        description: "Specific container image to use for forecasts-flu models"
        required: false
        type: string

concurrency:
  group: ${{ github.workflow }}
  # Only cancel in progress workflow if the workflow is running on the default branch
  cancel-in-progress: ${{ github.ref_name == github.event.repository.default_branch }}

jobs:
  ingest:
    permissions:
      id-token: write
    uses: ./.github/workflows/ingest.yaml
    with:
      # Trigger avian flu in a separate job to prevent error from failing
      # the rest of the upload workflow
      triggerAvianFlu: false
      artifact-name: build-outputs-ingest
    secrets: inherit

  trigger_avian_flu:
    needs: [ingest]
    continue-on-error: true
    runs-on: ubuntu-latest
    steps:
      - if: ${{ inputs.triggerAvianFlu }}
        name: Trigger avian-flu/genoflu-gisaid.yaml
        run: |
          gh workflow run \
            genoflu-gisaid.yaml \
            --repo nextstrain/avian-flu
        env:
          GITHUB_TOKEN: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH }}
     
  upload_titers:
    # Depends on ingest since titer should be checked against sequence strains
    needs: [ingest]
    permissions:
      id-token: write
    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
    secrets: inherit
    with:
      artifact-name: build-outputs-upload
      runtime: docker
      run: |
        nextstrain build \
          --env RETHINK_AUTH_KEY \
          --env RETHINK_HOST \
          . \
          -j 4 \
          upload_all_titers \
          --configfile profiles/upload.yaml

  trigger:
    needs: [upload_titers]
    strategy:
      matrix:
        include:
          - trigger: ${{ inputs.triggerPublic }}
            repo: seasonal-flu
            workflow: run-public-builds.yaml
            image: ${{ inputs.publicDockerImage }}
          - trigger: ${{ inputs.triggerNextfluPrivate }}
            repo: seasonal-flu
            workflow: run-nextflu-private-builds.yaml
            image: ${{ inputs.nextfluPrivateDockerImage }}
          - trigger: ${{ inputs.triggerForecastsFlu }}
            repo: forecasts-flu
            workflow: run-models.yaml
            image: ${{ inputs.forecastsFluDockerImage }}
    runs-on: ubuntu-latest
    steps:
      - if: ${{ matrix.trigger }}
        name: Trigger ${{ matrix.workflow }}
        run: |
          gh workflow run \
            ${{ matrix.workflow }} \
            --repo nextstrain/${{ matrix.repo }} \
            -f dockerImage=${{ matrix.image }}
        env:
          GITHUB_TOKEN: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH }}