Merge branch 'master' into erin-vigor4

StaPH-B · Aug 30, 2024 · ddff8de · ddff8de
2 parents e6df4b4 + 213dbc7
commit ddff8de
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diff --git a/.github/workflows/build-to-deploy.yml b/.github/workflows/build-to-deploy.yml
@@ -51,7 +51,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Check Out Repo (+ download Git LFS dependencies)  # each job runs in an isolated environment, so need to check out the repo in each job
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 
@@ -61,10 +61,10 @@ jobs:
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Cache Docker layers  # also need to set up the cache in each job, using the same prefix (here ${{ runner.os }}-buildx) makes it sharable between jobs
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /tmp/.buildx-cache-${{ inputs.cache }}
           key: ${{ runner.os }}-buildx-${{ inputs.cache }}-${{ github.sha }}
@@ -73,7 +73,7 @@ jobs:
 
       - name: Docker meta
         id: meta
-        uses: docker/metadata-action@v4 # trying this to resolve issues with pushing identical images to quay. info here: https://github.com/docker/build-push-action/issues/452
+        uses: docker/metadata-action@v5 # trying this to resolve issues with pushing identical images to quay. info here: https://github.com/docker/build-push-action/issues/452
         with:
           images: |
             ${{ inputs.repository_name }}/${{ inputs.container_name }}:${{ inputs.tag }}
@@ -82,13 +82,13 @@ jobs:
             quay.io/${{ inputs.repository_name }}/${{ inputs.container_name }}:latest
 
       - name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.docker_username }}
           password: ${{ secrets.docker_access_token }}
 
       - name: Login to Quay
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         if: ${{ inputs.push_quay }}
         with:
           registry: quay.io
@@ -97,7 +97,7 @@ jobs:
 
       - name: Build and push user-defined tag to DockerHub
         id: docker_build_user_defined_tag
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: ${{ inputs.path_to_context }}
           file: ${{ inputs.path_to_context }}/${{ inputs.dockerfile_name }}
@@ -111,7 +111,7 @@ jobs:
 
       - name: Build and push latest tag to DockerHub
         id: docker_build_latest_tag
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         if: ${{ inputs.push_latest_tag }}
         with:
           context: ${{ inputs.path_to_context }}
@@ -126,7 +126,7 @@ jobs:
 
       - name: Build and push user-defined tag to Quay
         id: quay_build_user_defined_tag
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         if: ${{ inputs.push_quay }}
         with:
           context: ${{ inputs.path_to_context }}
@@ -141,7 +141,7 @@ jobs:
 
       - name: Build and push latest tag to Quay
         id: quay_build_latest_tag
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         if: ${{ inputs.push_quay && inputs.push_latest_tag }}
         with:
           context: ${{ inputs.path_to_context }}
@@ -160,4 +160,4 @@ jobs:
           mv /tmp/.buildx-cache-${{ inputs.cache }}-new /tmp/.buildx-cache-${{ inputs.cache }}
 
       - name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
+        run: echo ${{ steps.docker_build_user_defined_tag.outputs.digest }}
diff --git a/.github/workflows/build-to-test.yml b/.github/workflows/build-to-test.yml
@@ -22,17 +22,17 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Check Out Repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Cache Docker layers
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /tmp/.buildx-cache-${{ inputs.cache }}
           key: ${{ runner.os }}-buildx-${{ inputs.cache }}-${{ github.sha }}
@@ -41,7 +41,7 @@ jobs:
 
       - name: Build to test
         id: docker_build_to_test
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: ${{ inputs.path_to_context }}
           file: ${{ inputs.path_to_context }}/${{ inputs.dockerfile_name }}
@@ -56,4 +56,4 @@ jobs:
           mv /tmp/.buildx-cache-${{ inputs.cache }}-new /tmp/.buildx-cache-${{ inputs.cache }}
 
       - name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
+        run: echo ${{ steps.docker_build_to_test.outputs.digest }}
diff --git a/.github/workflows/run-singularity.yml b/.github/workflows/run-singularity.yml
@@ -23,7 +23,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Check out Repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Singularity
         uses: eWaterCycle/setup-singularity@v7

diff --git a/.github/workflows/test-PR-dockerfiles.yml b/.github/workflows/test-PR-dockerfiles.yml
@@ -15,9 +15,9 @@ jobs:
     outputs:
       json: ${{ steps.files.outputs.added_modified }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - id: files
-        uses: Ana06/get-changed-files@v2.2.0
+        uses: Ana06/get-changed-files@v2.3.0
         with:
           format: 'json'
           filter: 'Dockerfile' 
@@ -54,27 +54,27 @@ jobs:
 ##### --------------------------------------------------------------------------- ##### 
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Layer check
         run: |
           #checking layers
           warning=''
-          app_layer=$(grep FROM ./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }}/Dockerfile | grep "as app")
-          tst_layer=$(grep FROM ./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }}/Dockerfile | grep "as test")
+          app_layer=$(grep FROM ./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }}/Dockerfile | grep -E "as app|AS app")
+          tst_layer=$(grep FROM ./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }}/Dockerfile | grep -E "as test|AS test")
           if [ -z "$app_layer" ] ; then echo "FATAL : app layer is missing" ; warning='warning' ; fi
           if [ -z "$tst_layer" ] ; then echo "FATAL : test layer is missing" ; warning='warning' ; fi
           if [ -n "$warning" ] ; then echo "Please see template for recommended format https://github.com/StaPH-B/docker-builds/blob/master/dockerfile-template/Dockerfile" ; exit 1 ; fi
       
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Cache Docker layers
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /tmp/.buildx-cache-${{ steps.parse.outputs.tool }}
           key: ${{ runner.os }}-buildx-${{ steps.parse.outputs.tool }}-${{ github.sha }}
@@ -83,7 +83,7 @@ jobs:
       
       - name: Build to test
         id: docker_build_to_test
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: ./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }}
           file: ./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }}/Dockerfile
@@ -123,4 +123,4 @@ jobs:
           mv /tmp/.buildx-cache-${{ steps.parse.outputs.tool }}-new /tmp/.buildx-cache-${{ steps.parse.outputs.tool }}
       
       - name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
+        run: echo ${{ steps.docker_build_to_test.outputs.digest }}
diff --git a/.github/workflows/update_freyja.yml b/.github/workflows/update_freyja.yml
@@ -0,0 +1,89 @@
+##### ------------------------------------------------------------------------------------------------ #####
+##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most   #####
+##### recent version of Freyja and downloading the most recent variant information.                    #####
+##### It takes no manual input.                                                                        #####
+##### ------------------------------------------------------------------------------------------------ #####
+
+name: Update Freyja
+
+on: 
+  workflow_dispatch:
+  schedule:
+    - cron: '30 7 1 * *'
+
+run-name: Updating Freyja
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    steps:    
+      - name: pull repo
+        uses: actions/checkout@v4     
+
+      - name: set freyja version
+        id: latest_version
+        run: |
+          version=1.5.1
+          echo "version=$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@v3
+
+      - name: build to test
+        id: docker_build_to_test
+        uses: docker/build-push-action@v5
+        with:
+          file: ${{ steps.latest_version.outputs.file }}
+          target: test
+          load: true
+          push: false
+          tags: freyja:update
+
+      - name: get freyja database version
+        id: db_version
+        run: |
+          docker run freyja:update freyja demix --version
+          version=$(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@v3
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Login to Quay
+        uses: docker/login-action@v3
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_ROBOT_TOKEN }}
+
+      - name: Build and push Dockerfile
+        id: docker_build_and_push
+        uses: docker/build-push-action@v5
+        with:
+          file: ${{ steps.latest_version.outputs.file }}
+          target: app
+          push: true
+          tags: |
+            staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
+            staphb/freyja:latest
+            quay.io/staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
+            quay.io/staphb/freyja:latest
+
+      - name: Image digest
+        run: echo ${{ steps.docker_build_user_defined_tag.outputs.digest }}
diff --git a/.github/workflows/update_mlst.yml b/.github/workflows/update_mlst.yml
@@ -0,0 +1,87 @@
+##### ------------------------------------------------------------------------------------------------ #####
+##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most   #####
+##### recent version of MLST and downloads the current MLST schemes.                                   #####
+##### It takes no manual input.                                                                        #####
+##### ------------------------------------------------------------------------------------------------ #####
+
+name: Update MLST
+
+on: 
+  workflow_dispatch:
+  schedule:
+    - cron: '30 7 1 * *'
+
+run-name: Updating MLST
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: pull repo
+        uses: actions/checkout@v4
+
+      - name: set mlst version
+        id: latest_version
+        run: |
+          version=2.23.0
+          echo "version=$version" >> $GITHUB_OUTPUT 
+          
+          file=mlst/2.23.0-2024-03/Dockerfile
+          ls $file
+          echo "file=$file" >> $GITHUB_OUTPUT
+
+      - name: set up docker buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: build to test
+        id: docker_build_to_test
+        uses: docker/build-push-action@v5
+        with:
+          context: mlst/${{ steps.latest_version.outputs.version }}
+          target: test
+          load: true
+          push: false
+          tags: mlst:update
+
+      - 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@v3
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Login to Quay
+        uses: docker/login-action@v3
+        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@v5
+        with:
+          file: ${{ steps.latest_version.outputs.file }}
+          target: app
+          push: true
+          tags: staphb/mlst:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
+
+      - name: Build and push to Quay
+        id: build
+        uses: docker/build-push-action@v5
+        with:
+          file: ${{ steps.latest_version.outputs.file }}
+          target: app
+          push: true
+          tags: quay.io/staphb/mlst:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
+
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}