Update branch with master

.githooks/spotless_pre_commit_hook.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+HOOK_FILE=".git/hooks/pre-commit"
+
+# Ensure hooks directory exists
+mkdir -p .git/hooks
+
+# If the pre-commit hook doesn't exist, create it with a shebang line
+if [[ ! -f "$HOOK_FILE" ]]; then
+    echo "#!/bin/bash" > "$HOOK_FILE"
+    echo "set -e" >> "$HOOK_FILE"
+fi
+
+# Check if Spotless is already in the pre-commit hook, and add it if missing
+if ! grep -qxF "mvn spotless:apply" "$HOOK_FILE"; then
+    echo "echo 'Running Spotless on staged files...'" >> "$HOOK_FILE"
+    echo "mvn spotless:apply" >> "$HOOK_FILE"
+fi
+
+# Check if `git add -u` is already in the pre-commit hook, and add it if missing
+if ! grep -qxF "git add -u" "$HOOK_FILE"; then
+    echo "echo 'Adding formatted files back to commit...'" >> "$HOOK_FILE"
+    echo "git add -u" >> "$HOOK_FILE"
+fi
+
+# Make sure the pre-commit hook is executable
+chmod +x "$HOOK_FILE"
+
+echo "✅ Spotless pre-commit hook installed successfully!"

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,27 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: bug, triage
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: "[FEATURE REQUEST]"
+labels: feature, triage
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is.
+
+**Describe the solution you'd like**
+What would you want to happen?
+
+**Describe alternatives you've considered**
+Any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/question-for-cbioportal-team.md

@@ -0,0 +1,16 @@
+---
+name: Question for cBioPortal team
+about: Submit questions related to cBioPortal data or your cBioPortal deployment
+title: "[USER SUPPORT]"
+labels: support, triage
+assignees: dippindots
+
+---
+
+**How can we help**
+What kind of support are you looking for? e.g.
+- Data submitssion (have new data and want us to host data)
+- Installation support (get questions when installing your cBioPortal instance)
+
+**Describe the your question**
+A clear description of what the question is.

.github/workflows/auto-label.yml

@@ -0,0 +1,22 @@
+name: Auto Label New Issues
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  add-label:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Add default label to new issues or pull requests
+        uses: actions/github-script@v6
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            // Add default label 'triage' to new issues so that new issues can be added to the project board automatically
+            await github.rest.issues.addLabels({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.payload.issue.number,
+              labels: ['triage']
+            });

.github/workflows/core-test.yml

@@ -23,7 +23,7 @@ jobs:
           website: oracle.com
           release: 21
       - name: 'Cache Maven packages'
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
@@ -45,19 +45,23 @@ jobs:
         working-directory: ./cbioportal
         run: |
           cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties
+      - name: 'Create settings.xml for github packages'
+        working-directory: ./cbioportal
+        run: |
+          echo "<settings><servers><server><id>github</id><username>${{ github.actor }}</username><password>${{ secrets.GITHUB_TOKEN }}</password></server></servers></settings>" > settings.xml
       - name: 'Build cBioPortal once without tests'
         working-directory: ./cbioportal
         run: |
-          mvn -q -U -Ppublic -DskipTests clean install
+          mvn --settings settings.xml -q -U -Ppublic -DskipTests clean install
       - name: 'Build cbioportal with tests'
         working-directory: ./cbioportal
         run: |
-          mvn -q -U -Ppublic clean install
+          mvn --settings settings.xml -q -U -Ppublic clean install
       - name: 'Run tests separately'
         working-directory: ./cbioportal
         run: |
           mvn -U -Ppublic test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword
       - name: 'Run integration tests separately'
         working-directory: ./cbioportal
         run: |
-          mvn -U -Ppublic integration-test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword
+          mvn -U -Ppublic integration-test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword

.github/workflows/dockerimage.yml

@@ -3,12 +3,6 @@ on:
   push:
     branches:
       - master
-      - release-*
-      - rc
-      - rfc*
-      - demo-*
-      - fusion-sv-migration
-      - redis-branch-up-to-date
     tags: '*'
 
 jobs:
@@ -46,7 +40,7 @@ jobs:
         uses: docker/setup-buildx-action@v3
 
       - name: Publish Docker Image on Tag
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true
@@ -93,7 +87,7 @@ jobs:
           uses: docker/setup-buildx-action@v3
 
         - name: Publish Docker Image on Tag
-          uses: docker/build-push-action@v3
+          uses: docker/build-push-action@v6
           with:
             context: .
             push: true
@@ -128,3 +122,81 @@ jobs:
             image: ${{ steps.meta.outputs.tags }}
             dependency-snapshot: 'true'
             github-token: '${{ secrets.GITHUB_TOKEN }}'
+
+  update_master_k8s_deployment:
+    needs: build_and_publish_web
+    if: github.repository == 'cBioPortal/cbioportal' && github.ref == 'refs/heads/master'
+    runs-on: ubuntu-latest
+    env:
+      DEPLOYMENT_FILE_PATH: "argocd/aws/203403084713/clusters/cbioportal-prod/apps/cbioportal"
+      DEPLOYMENT_FILE_NAMES: "cbioportal_backend_master_blue.yaml cbioportal_backend_master_green.yaml"
+      K8S_REPO: 'knowledgesystems/knowledgesystems-k8s-deployment'
+      ARGOCD_CLI_VER: '2.13.3'
+      ARGOCD_SERVER: 'argocd.cbioportal.org'
+      ARGOCD_APP: 'cbioportal'
+      ARGOCD_RESOURCE_OPTIONS: '--resource apps:Deployment:default/cbioportal-backend-master-blue --resource apps:Deployment:default/cbioportal-backend-master-green'
+    steps:
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: |
+            cbioportal/cbioportal
+          # Do not generate latest tag
+          flavor: |
+            latest=false
+            suffix=-web-shenandoah
+          tags: |
+            type=ref,event=branch
+            type=semver,pattern={{version}}
+
+      - name: Extract Image Tag
+        run: |
+          DOCKER_TAG=${{ steps.meta.outputs.tags }}
+          docker pull $DOCKER_TAG
+          DOCKER_SHA=$(docker inspect --format="{{index .RepoDigests 0}}" $DOCKER_TAG)
+          echo "DOCKER_SHA=$DOCKER_SHA" >> $GITHUB_ENV
+
+      - name: Checkout K8s Repo
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ env.K8S_REPO }}
+          token: ${{ secrets.K8S_REPO_TOKEN }}
+
+      - name: Update Master Deployment File
+        run: |
+          for FILE in $DEPLOYMENT_FILE_NAMES; do
+            sed -i "s|image:.*|image: $DOCKER_SHA|" $DEPLOYMENT_FILE_PATH/$FILE
+          done
+
+      - name: Add and commit changes to deployment file
+        run: |
+          git config --global user.email "cBioPortal-Action@github.com"
+          git config --global user.name "cBioPortal Backend Github Action"
+          if ! git diff --quiet; then
+            git add -A
+            git commit -m "Update master deployment"
+          else
+            echo "No changes to commit."
+          fi
+
+      - name: Push changes to K8s repo
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: '${{ secrets.K8S_REPO_TOKEN }}'
+          repository: ${{ env.K8S_REPO }}
+          branch: master
+
+      - name: Setup ArgoCD
+        uses: clowdhaus/argo-cd-action/@main
+        with:
+          version: ${{ env.ARGOCD_CLI_VER }}
+          command: login ${{ env.ARGOCD_SERVER }}
+          options: --username ${{ secrets.ARGOCD_2034_USERNAME }} --password ${{ secrets.ARGOCD_2034_PASSWORD }}
+
+      - name: Sync master deployment
+        uses: clowdhaus/argo-cd-action/@main
+        with:
+          version: ${{ env.ARGOCD_CLI_VER }}
+          command: app sync ${{ env.ARGOCD_APP }}
+          options: ${{ env.ARGOCD_RESOURCE_OPTIONS }}

.github/workflows/integration-test.yml

@@ -19,7 +19,7 @@ jobs:
           website: oracle.com
           release: 21
       - name: 'Cache Maven packages'
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
@@ -31,7 +31,8 @@ jobs:
       - name: 'Build cbioportal'
         working-directory: ./cbioportal
         run: |
-          mvn -DskipTests clean install
+          echo "<settings><servers><server><id>github</id><username>${{ github.actor }}</username><password>${{ secrets.GITHUB_TOKEN }}</password></server></servers></settings>" > settings.xml
+          mvn --settings settings.xml -DskipTests clean install
       - name: 'Checkout cbioportal-docker-compose repo'
         uses: actions/checkout@master
         with:
@@ -46,8 +47,6 @@ jobs:
               sed 's|spring.datasource.username=.*|spring.datasource.username=cbio_user|' | \
               sed 's|spring.datasource.password=.*|spring.datasource.password=somepassword|' \
               > application.properties
-      - name: 'Copy cgds.sql file into Docker Compose'
-        run: cp ./cbioportal/src/main/resources/db-scripts/cgds.sql ./cbioportal-docker-compose/data/.
       - name: 'Dump Properties'
         working-directory: ./cbioportal-docker-compose
         run: cat config/application.properties

.github/workflows/label-check.yml

@@ -32,20 +32,27 @@ jobs:
         id: check_labels
         run: |
           PR_NUMBER=$(jq -r ".number" $GITHUB_EVENT_PATH)
-          PR_LABELS=$(curl -s "https://api.github.com/repos/${{ github.repository }}/pulls/$PR_NUMBER" | \
+          PR_LABELS_STRING=$(curl -s "https://api.github.com/repos/${{ github.repository }}/pulls/$PR_NUMBER" | \
                        jq -r '.labels[].name')
+          mapfile -t PR_LABELS <<< "$PR_LABELS_STRING"
           mapfile -t AVAILABLE_LABELS < labels.txt
-          for LABEL in ${PR_LABELS[@]}; do
-            if [[ "$LABEL" == "skip-changelog" ]]; then
+          pr_label_index=0
+          while [ $pr_label_index -lt ${#PR_LABELS[@]} ] ; do
+            pr_label="${PR_LABELS[$pr_label_index]}"
+            if [[ "$pr_label" == "skip-changelog" ]] ; then
               echo "PR contains a valid label: skip-changelog"
               exit 0  # Valid label found, exit successfully
             fi
-            for AVAILABLE_LABEL in "${AVAILABLE_LABELS[@]}"; do
-              if [[ "$AVAILABLE_LABEL" == "$LABEL" ]]; then
-                echo "PR contains a valid label: $LABEL"
+            available_label_index=0
+            while [ $available_label_index -lt ${#AVAILABLE_LABELS[@]} ] ; do
+              available_label="${AVAILABLE_LABELS[$available_label_index]}"
+              if [[ "$available_label" == "$pr_label" ]] ; then
+                echo "PR contains a valid label: $pr_label"
                 exit 0  # Valid label found, exit successfully
               fi
+              available_label_index=$(($available_label_index+1))
             done
+            pr_label_index=$(($pr_label_index+1))
           done
           echo "No valid label found on PR."
           echo "Available label options from release-drafter.yml:"