Merge in master

.github/workflows/build_and_push_nf_base_images.yml

@@ -17,14 +17,13 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v3
         with:
-          path: containers
-
+          path: containers       
 
       - name: Checkout other private repository
         uses: actions/checkout@v3
         with:
           repository: uc-cdis/base-images
-          token: ${{ secrets.PLANXCYBORG_TOKEN }}
+          token: ${{ secrets.PLANXCYBORG_PAT }}
           path: base-images
 
       - name: Set up Docker Buildx
@@ -62,7 +61,7 @@ jobs:
 
       - name: Trigger `get_layer_info_for_nf_imgs.yml` workflow
         env:
-          GH_TOKEN: ${{ secrets.PLANXCYBORG_TOKEN }}
+          GH_TOKEN: ${{ secrets.PLANXCYBORG_PAT }}
         run: |
               gh api \
               --method POST \

.github/workflows/build_jupyter_bih_image.yml

@@ -0,0 +1,22 @@
+name: Build and Push Jupyter-BIH image
+
+on:
+  push:
+    paths:
+    - jupyter-bih/**
+    - .github/workflows/build_jupyter_bih_image.yml
+
+jobs:
+  jupyter-midrc-bih:
+    name: Build and Push jupyter-bih image
+    uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    with:
+      DOCKERFILE_LOCATION: "./jupyter-bih/Dockerfile"
+      DOCKERFILE_BUILD_CONTEXT: "./jupyter-bih"
+      OVERRIDE_REPO_NAME: "jupyter-notebook"
+      OVERRIDE_TAG_NAME: "bih-$(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 }}

.github/workflows/build_jupyter_midrc_image.yml

@@ -0,0 +1,22 @@
+name: Build and Push Jupyter-MIDRC image
+
+on:
+  push:
+    paths:
+    - jupyter-midrc/**
+    - .github/workflows/build_jupyter_midrc_image.yml
+
+jobs:
+  jupyter-midrc:
+    name: Build and Push jupyter-midrc image
+    uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    with:
+      DOCKERFILE_LOCATION: "./jupyter-midrc/Dockerfile"
+      DOCKERFILE_BUILD_CONTEXT: "./jupyter-midrc"
+      OVERRIDE_REPO_NAME: "jupyter-notebook"
+      OVERRIDE_TAG_NAME: "midrc-$(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 }}

.github/workflows/build_push_jupyterlab_generic.yml

@@ -0,0 +1,44 @@
+name: Push Jupyterlab Generic Image to quay
+
+on:
+  push:
+    paths:
+      - jupyterlab-generic/**
+      - .github/workflows/build_push_jupyterlab_generic.yml
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Extract branch name
+        id: extract_branch
+        run: |
+          echo "IMAGE_TAG=$(echo ${GITHUB_REF#refs/*/} | tr / _)"
+          echo "IMAGE_TAG=$(echo ${GITHUB_REF#refs/*/} | tr / _)" >> $GITHUB_ENV
+
+      - name: Login to Quay.io
+        id: login
+        uses: docker/login-action@v3
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_ROBOT_TOKEN }}
+
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            quay.io/cdis/jupyterlab-generic:${{ env.IMAGE_TAG }}
+
+      - name: Build and Push Image
+        uses: docker/build-push-action@v6
+        with:
+          context: ./jupyterlab-generic
+          file: "./jupyterlab-generic/Dockerfile"
+          push: true
+          tags: |
+            quay.io/cdis/jupyterlab-generic:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/build_utils_image.yml

@@ -0,0 +1,23 @@
+name: Build and push utilities image
+
+on:
+  push:
+    paths:
+    - utilities/**
+    - .github/workflows/build_utils_image.yml
+
+jobs:
+  utils:
+    name: Build and Push jupyter-vadc
+    uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    with:
+      DOCKERFILE_LOCATION: "./utilities/Dockerfile"
+      DOCKERFILE_BUILD_CONTEXT: "./utilities"
+      OVERRIDE_REPO_NAME: "utilities"
+      USE_QUAY_ONLY: true
+      # 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 }}