Merge pull request #2 from HarryHung/feature/auto-deployment

Auto image test and deployment

.github/workflows/docker-image-build-to-test.yml

@@ -0,0 +1,19 @@
+name: Docker Image Build to Test
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+  workflow_call:
+
+jobs:
+  build-to-test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository 
+      uses: actions/checkout@v4
+
+    - name: Build the Docker image to test
+      run: docker build . --file Dockerfile --tag spn-pbp-amr:$(date +%s) --target test

.github/workflows/docker-image-publish-on-release.yml

@@ -0,0 +1,53 @@
+name: Docker Image Publish on Release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build-to-test:
+    uses: ./.github/workflows/docker-image-build-to-test.yml
+
+  build-and-push-image:
+    needs: build-to-test
+
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            ${{ secrets.DOCKER_USERNAME }}/${{ github.event.repository.name }}
+            ghcr.io/${{ github.repository }}
+          tags: |
+            type=semver,pattern={{version}}
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          target: app
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -1,7 +1,9 @@
-FROM ubuntu:18.04
+FROM ubuntu:18.04 as app
 
 ARG DEBIAN_FRONTEND=noninteractive
 
+RUN mkdir ~/.gnupg && echo "disable-ipv6" >> ~/.gnupg/dirmngr.conf
+
 RUN apt update \
       && apt install -y -q apt-transport-https software-properties-common \
       && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
@@ -82,3 +84,19 @@ RUN cd /predictor \
 ENV PATH /predictor:$PATH
 
 ENV PATH /predictor/bLactam_MIC_Rscripts/:$PATH
+
+
+# new base for testing
+FROM app as test
+
+RUN mkdir -p /test_data
+
+COPY test_data /test_data
+
+RUN spn_pbp_amr /test_data/contigs.fasta > result.json
+
+RUN apt update && apt install -y -q jq
+
+RUN jq --sort-keys . result.json > sorted_result.json && jq --sort-keys . /test_data/expected_result.json > sorted_expected_result.json
+
+RUN cmp sorted_result.json sorted_expected_result.json