main.yml

##### ------------------------------------------------------------------------------------------------ #####
##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most   #####
##### recent version of Freyja and downloading the most recent variant information.                    #####
##### It takes no manual input.                                                                        #####
##### ------------------------------------------------------------------------------------------------ #####

name: Update Freyja

on: 
  workflow_dispatch:
  schedule:
    - cron: '30 7 * * *'

run-name: Updating Freyja

jobs:
  update:
    runs-on: ubuntu-latest
    steps:

# Keeping here in case we want to use it to keep Freyja's version up-to-date as well
#      - name: Get latest release
#        uses: rez0n/actions-github-release@main
#        id: latest_release
#        with:
#          token: ${{ secrets.GITHUB_TOKEN }}
#          repository: andersen-lab/Freyja
#          type: "stable"
#      - name: Remove V
#        id: strip
#        run: |
#          version=$(echo "${{ steps.latest_release.outputs.release }}" | sed 's/V//g' | sed 's/v//g' )
#          echo "The version is $version"
#          echo "version=$version" >> $GITHUB_OUTPUT
          
      - name: pull repo
        uses: actions/checkout@v3

# Keeping here in case we want to figure out why this doesn't work      
#      - name: get latest version of freyja in docker-builds repo
#        id: latest_version
#        run: | 
#          file=$(git log -1 --name-only --format=%cd --date=iso freyja/*/Dockerfile | grep Dockerfile | head -n 1 )
#          echo "the latest file is $file"
#          echo "file=$file" >> $GITHUB_OUTPUT
#
#          version=$(echo $file | cut -f 2 -d "/" | cut -f 1 -d "_")
#          echo "the latest version is $version"
#          echo "version=$version" >> $GITHUB_OUTPUT      

      - name: set freyja version
        id: latest_version
        run: |
          version=1.4.8
          echo "version=$version" >> $GITHUB_OUTPUT 
          
          file=freyja/$version/Dockerfile
          ls $file
          echo "file=$file" >> $GITHUB_OUTPUT
      - name: set up docker buildx
        id: buildx
        uses: docker/setup-buildx-action@v2

      - name: cache docker layers
        uses: actions/cache@v3
        with:
          path: /tmp/.buildx-cache-freyja
          key: ${{ runner.os }}-buildx-freyja-${{ github.sha }}
          restore-keys: ${{ runner.os }}-buildx-freyja

      - name: build to test
        id: docker_build_to_test
        uses: docker/build-push-action@v3
        with:
          file: ${{ steps.latest_version.outputs.file }}
          target: test
          load: true
          push: false
          cache-from: type=local,src=/tmp/.buildx-cache-freyja
          cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new
          tags: freyja:update

      - name: get freyja database version
        id: db_version
        run: |
          docker run freyja:update freyja demix --version
          version=$(docker run freyja:update freyja demix --version | grep . | grep -v Barcode | head -n 1)
          echo "the latest version is $version"
          echo "version=$version" >> $GITHUB_OUTPUT
      - name: Get current date
        id: date
        run: |
          date=$(date '+%Y-%m-%d')
          echo "the date is $date"
          echo "date=$date" >> $GITHUB_OUTPUT
      
      # - name: Login to DockerHub
      #   uses: docker/login-action@v2
      #   with:
      #     username: ${{ secrets.DOCKER_HUB_USERNAME }}
      #     password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

      - name: Login to Quay
        uses: docker/login-action@v2
        with:
          registry: quay.io
          username: ${{ secrets.QUAY_USERNAME }}
          password: ${{ secrets.QUAY_ROBOT_TOKEN }}

      - name: Build and push user-defined tag to DockerHub
        id: docker_build_user_defined_tag
        uses: docker/build-push-action@v3
        with:
          file: ${{ steps.latest_version.outputs.file }}
          target: app
          push: true
          cache-from: type=local,src=/tmp/.buildx-cache-freyja
          cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new # mode=max means export layers from all stage to cache
          tags: staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
            
      - name: Build and push to Quay
        id: build
        uses: docker/build-push-action@v3
        with:
          file: ${{ steps.latest_version.outputs.file }}
          target: app
          push: true
          cache-from: type=local,src=/tmp/.buildx-cache-freyja
          cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new # mode=max means export 
          tags: quay.io/staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}

      - name: Move cache # apparently prevents the cache from growing in size forever
        run: |
          rm -rf /tmp/.buildx-cache-freyja
          mv /tmp/.buildx-cache-freyja-new /tmp/.buildx-cache-freyja
      - name: Image digest