Merge pull request #166 from uc-cdis/dep/vadca

dep(vadc): update base image; add psycopg2

.github/workflows/build_vadc_notebook_image.yml

@@ -7,109 +7,16 @@ on:
     - .github/workflows/build_vadc_notebook_image.yml
 
 jobs:
-  push-image:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Maximize build space
-        uses: easimon/maximize-build-space@master
-        with:
-          root-reserve-mb: 30000
-          swap-size-mb: 1024
-          remove-dotnet: 'true'
-          remove-android: 'true'
-          remove-haskell: 'true'
-
-      - name: clean
-        run: sudo apt clean
-
-      - name: Extract branch name
-        shell: bash
-        run: echo "branch=$(echo $(echo ${GITHUB_REF#refs/heads/} | tr  / _))" >> $GITHUB_OUTPUT
-        id: extract_branch
-
-      - name: Checkout repo
-        uses: actions/checkout@v2
-
-      - name: Get changed files
-        id: get_changed_files
-        uses: jitterbit/get-changed-files@v1
-        with:
-          format: 'json'
-
-      - name: Determine image to build
-        id: parse_image
-        shell: python
-        env:
-          CHANGES: ${{ steps.get_changed_files.outputs.added_modified }}
-        run: |
-          import os, json, re
-
-          notebook_dir = "jupyter-vadc"
-          changed_vadc_notebook_files = json.loads(os.environ['CHANGES'])
-          print(f"Changed files {changed_vadc_notebook_files}")
-
-          # build an image for every subdir of jupyter-vadc with a changed file
-          subdirs = list(
-            filter(
-              lambda d: os.path.isdir(f"{os.environ['GITHUB_WORKSPACE']}/{notebook_dir}/{d}"),
-              os.listdir(notebook_dir)
-            )
-          )
-
-          print(f"Scanning subdirs for changed files: {subdirs}")
-
-          buildable_images = list(
-            filter(
-              lambda subdir: any(
-                changed_file.startswith(f"{notebook_dir}/{subdir}")
-                for changed_file in changed_vadc_notebook_files
-              ),
-              subdirs
-            )
-          )
-
-          if not len(buildable_images):
-            print(f"None of {changed_vadc_notebook_files} triggers a build for any of {subdirs}. Done.")
-            exit(0)
-          elif len(buildable_images) > 1:
-            print("Found multiple notebook directories with changes: {buildable_images}")
-            print("Only one image can be built at a time. Exiting.")
-            exit(1)
-
-          build_target = buildable_images[0]
-          print(f"Will trigger build for: {build_target}")
-          with open(os.environ['GITHUB_OUTPUT'], 'a') as fh:
-            print(f'build_target={build_target}', file=fh)
-
-      - if: ${{ steps.parse_image.outputs.build_target }}
-        name: Sanitize image name
-        id: sanitize_name
-        run: |
-          IMAGE_NAME=$( sed 's/[^[:alnum:]]/_/g' <<< ${{ steps.parse_image.outputs.build_target }} );
-          echo "image_name=$IMAGE_NAME" >> $GITHUB_OUTPUT
-
-      - if: ${{ steps.parse_image.outputs.build_target }}
-        name: Build image
-        id: build-image
-        uses: redhat-actions/buildah-build@v2
-        with:
-          image: jupyter-vadc
-          context: ./jupyter-vadc/
-          tags:
-            ${{ steps.sanitize_name.outputs.image_name }}__${{ steps.extract_branch.outputs.branch }}
-            ${{ steps.sanitize_name.outputs.image_name }}__${{ github.sha }}
-            ${{ steps.sanitize_name.outputs.image_name }}__latest
-          dockerfiles: ./jupyter-vadc/Dockerfile
-          build-args:
-            NOTEBOOK_DIR=jupyter-vadc/${{ steps.parse_image.outputs.build_target }}
-
-      - if: ${{ steps.parse_image.outputs.build_target }}
-        name: Push To quay.io
-        id: push-to-quay
-        uses: redhat-actions/push-to-registry@v2
-        with:
-          image: ${{ steps.build-image.outputs.image }}
-          tags: ${{ steps.build-image.outputs.tags }}
-          registry: quay.io/cdis
-          username: ${{ secrets.QUAY_SERVICE_ACCOUNT_USER }}
-          password: ${{ secrets.QUAY_SERVICE_ACCOUNT_PASSWORD }}
+  jupyter-vadc:
+    name: Build and Push jupyter-vadc
+    uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    with:
+      DOCKERFILE_LOCATION: "./jupyter-vadc/Dockerfile"
+      DOCKERFILE_BUILD_CONTEXT: "./jupyter-vadc"
+      OVERRIDE_REPO_NAME: "jupyter-vadc"
+      OVERRIDE_TAG_NAME: "vadc-$(echo ${GITHUB_REF#refs/*/} | tr / _)"
+    secrets:
+      ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
+      ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
+      QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
+      QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }}

jupyter-vadc/Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/cdis/datascience-notebook:2023-04-10
+FROM quay.io/cdis/datascience-notebook:2024-02-26
 
 USER root
 

jupyter-vadc/resources/requirements.txt

@@ -1,3 +1,4 @@
-tqdm
 pqdm
+psycopg2
 pymssql
+tqdm