merge develop into main

nfdi4health · Aug 3, 2023 · 481b057 · 481b057
2 parents 5b23106 + 070f96f
commit 481b057
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,128 @@
+name: Continuous Integration
+
+on:
+  pull_request: { branches: [ "main","develop" ] }
+  push:
+    branches: [ "main","develop" ]
+    tags: [ "*" ]
+env:
+  KUBECONFIG: .kube/config
+  KUBECONFIG_FILE: ${{ secrets.KUBECONFIG }}
+  GIT_SHA: ${{ github.event.pull_request.head.sha || github.sha }}
+  NPM_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+jobs:
+  build:
+    name: "Build Image"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - id: generate-image-tag
+        name: Generate Image Tag
+        env:
+          ref_name: "${{ github.ref_name }}"
+          head_ref: "${{ github.head_ref }}"
+        run: |
+          head_ref="${head_ref/\//-}"
+          ref_name="${head_ref:-${ref_name/main/latest}}"
+          echo "::set-output name=imageTag::${ref_name#v}"
+      - name: Login to Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Build and Push Backend
+        uses: docker/build-push-action@v2
+        with:
+          context: ./backend
+          push: true
+          tags: |
+            ghcr.io/${{ github.repository }}/backend:${{ steps.generate-image-tag.outputs.imageTag }}
+            ghcr.io/${{ github.repository }}/backend:${{ github.event.pull_request.head.sha || github.sha }}
+          build-args: |
+            COMMIT_SHA=${{ github.sha }}
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '17.x'
+          registry-url: 'https://npm.pkg.github.com/'
+      - run: npm ci --legacy-peer-deps
+        env:
+          NODE_AUTH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        working-directory: ./frontend
+      - run: npm run build
+        env:
+          CI: false
+        working-directory: ./frontend
+      - name: Build and Push Frontend
+        uses: docker/build-push-action@v2
+        with:
+          context: ./frontend
+          push: true
+          tags: |
+            ghcr.io/${{ github.repository }}/frontend:${{ steps.generate-image-tag.outputs.imageTag }}
+            ghcr.io/${{ github.repository }}/frontend:${{ github.event.pull_request.head.sha || github.sha }}
+  deploy_development:
+    needs: build
+    if: github.ref == 'refs/heads/develop'
+    runs-on: ubuntu-latest
+    steps:
+    - id: generate-image-tag
+      name: Generate Image Tag
+      env:
+        ref_name: "${{ github.ref_name }}"
+        head_ref: "${{ github.head_ref }}"
+      run: |
+        head_ref="${head_ref/\//-}"
+        ref_name="${head_ref:-${ref_name/main/latest}}"
+        echo "::set-output name=imageTag::${ref_name#v}"
+    - uses: actions/checkout@v2
+    - run: |
+        mkdir -p .kube
+        echo "${{ env.KUBECONFIG_FILE }}" > $KUBECONFIG
+    - uses: stefanprodan/kube-tools@v1
+      with:
+        helmv3: 3.12.0
+        command: |
+          kubectl get nodes
+          helmv3 repo add mda-deployment https://nfdi4health.github.io/mda-deployment/
+          helmv3 repo update
+          helmv3 upgrade mda-${{ steps.generate-image-tag.outputs.imageTag }} \
+          --install \
+          --set-json='images.backend="ghcr.io/${{ github.repository }}/backend:${{ github.event.pull_request.head.sha || github.sha }}"' \
+          --set-json='images.frontend="ghcr.io/${{ github.repository }}/frontend:${{ github.event.pull_request.head.sha || github.sha }}"'  \
+          --set-json='images.prediction="gitlab.zbmed.de:5050/km/thesis/pierre-ba/backend:a7d3254ee488a236dade40ecedc646861aff9dbe"'  \
+          --set-json='ingress.dns="${{ steps.generate-image-tag.outputs.imageTag }}.mda.qa.km.k8s.zbmed.de"'  \
+          mda-deployment/metadata-annotation
+  deploy_main:
+    needs: build
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    steps:
+    - id: generate-image-tag
+      name: Generate Image Tag
+      env:
+        ref_name: "${{ github.ref_name }}"
+        head_ref: "${{ github.head_ref }}"
+      run: |
+        head_ref="${head_ref/\//-}"
+        ref_name="${head_ref:-${ref_name/main/latest}}"
+        echo "::set-output name=imageTag::${ref_name#v}"
+    - uses: actions/checkout@v2
+    - run: |
+        mkdir -p .kube
+        echo "${{ env.KUBECONFIG_FILE }}" > $KUBECONFIG
+    - uses: stefanprodan/kube-tools@v1
+      with:
+        helmv3: 3.12.0
+        command: |
+          kubectl get nodes
+          helmv3 repo add mda-deployment https://nfdi4health.github.io/mda-deployment/
+          helmv3 repo update
+          helmv3 upgrade mda-${{ steps.generate-image-tag.outputs.imageTag }} \
+          --install \
+          --set-json='images.backend="ghcr.io/${{ github.repository }}/backend:${{ github.event.pull_request.head.sha || github.sha }}"' \
+          --set-json='images.frontend="ghcr.io/${{ github.repository }}/frontend:${{ github.event.pull_request.head.sha || github.sha }}"'  \
+          --set-json='images.prediction="gitlab.zbmed.de:5050/km/thesis/pierre-ba/backend:a7d3254ee488a236dade40ecedc646861aff9dbe"'  \
+          --set-json='ingress.dns="${{ steps.generate-image-tag.outputs.imageTag }}.mda.qa.km.k8s.zbmed.de"'  \
+          mda-deployment/metadata-annotation
diff --git a/.github/workflows/deployment_production.yml b/.github/workflows/deployment_production.yml
@@ -0,0 +1,37 @@
+name: Deployment to production
+concurrency: production
+on:
+   workflow_dispatch:
+    inputs:
+      tags:
+        description: 'Do you really want to update the production instance'
+        required: false
+        type: boolean
+      image_sha:
+        description: 'Image SHA ID, Optional '
+        type: string
+        required: false
+env:
+  KUBECONFIG: .kube/config
+  KUBECONFIG_FILE: ${{ secrets.KUBECONFIG_PROD }}
+jobs:
+  deployment:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - run: |
+        mkdir -p .kube
+        echo "${{ env.KUBECONFIG_FILE }}" > $KUBECONFIG
+    - uses: stefanprodan/kube-tools@v1
+      with:
+        helmv3: 3.12.0
+        command: |
+          helmv3 repo add mda-deployment https://nfdi4health.github.io/mda-deployment/
+          helmv3 repo update
+          helmv3 upgrade mda-main  \
+          --install \
+          --set-json='images.backend="ghcr.io/${{ github.repository }}/backend:${{ github.event.pull_request.head.sha || github.sha }}"' \
+          --set-json='images.frontend="ghcr.io/${{ github.repository }}/frontend:${{ github.event.pull_request.head.sha || github.sha }}"'  \
+          --set-json='images.prediction="gitlab.zbmed.de:5050/km/thesis/pierre-ba/backend:a7d3254ee488a236dade40ecedc646861aff9dbe"'  \
+          --set-json='ingress.dns="mda.main.prod.km.k8s.zbmed.de"'  \
+          mda-deployment/metadata-annotation
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
diff --git a/README.md b/README.md
@@ -59,7 +59,7 @@ export DB_PASSWORD=postgres
 export DB_HOST=localhost
 export API_SEMLOOKP=https://semanticlookup.zbmed.de/ols/api/
 export INSTRUMENTS=instruments
-export API_PREDICT=http://172.29.0.3:5000
+export API_PREDICT=http://172.29.0.5:5000
 flask run
 ```
 

diff --git a/backend/Dockerfile b/backend/Dockerfile
@@ -6,5 +6,6 @@ ENV FLASK_APP="restapi"
 ARG COMMIT_SHA
 ENV COMMIT_SHA=$COMMIT_SHA
 RUN python -m pip install -r requirements.txt
+RUN python -m pip install -U pydantic spacy
 RUN python -m spacy download en_core_web_sm
 CMD ["flask","run","--host=0.0.0.0"]