Merge branch 'master' into v6.3.1-dfci-FIX-10702-SAML

Author: JREastonMarks

.circleci/config.yml

@@ -467,7 +467,6 @@ jobs:
         SUCCESS_COLOR: 'brightgreen'
         FAILURE_MESSAGE: 'Failing'
         FAILURE_COLOR: 'FF0A0A'
-        SEVERITY_THRESHOLD: 'CRITICAL'
         TEST_REPO_URL: '[email protected]:cBioPortal/cbioportal-test.git'
       steps:
         - attach_workspace:
@@ -488,7 +487,7 @@ jobs:
         - run:
             name: Count vulnerabilities and update status badge
             command: |
-              COUNT=$(jq '[.[] | select(.severity == "$SEVERITY_THRESHOLD")] | length' master_report.sbom)
+              COUNT=$(jq '[.[] | select(.severity == "CRITICAL" or .severity == "HIGH")] | length' master_report.sbom)
               cd cbioportal-test
               if [ $COUNT -eq 0 ]; then
                 jq --arg msg "$SUCCESS_MESSAGE" --arg col "$SUCCESS_COLOR" '.message = $msg | .color = $col' security-status.json > temp.json

.github/workflows/core-test.yml

@@ -1,5 +1,19 @@
 name: Core tests
-on: [push, pull_request]
+
+on:
+  push:
+  pull_request_target:
+  workflow_dispatch:
+    inputs:
+      ref:
+        description: 'Branch or PR to test (default: main)'
+        required: false
+        default: 'master'
+
+permissions:
+      id-token: write   # This is required for requesting the JWT
+      contents: read    # This is required for actions/checkout
+
 jobs:
   build:
     name: Setup and Test
@@ -12,6 +26,9 @@ jobs:
         ports:
           - 3306
         options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=10
+    env:
+      TEST_DB_CLICKHOUSE_PASSWORD: ${{ secrets.TEST_DB_CLICKHOUSE_PASSWORD }}
+      TEST_DB_MYSQL_PASSWORD: ${{ secrets.TEST_DB_MYSQL_PASSWORD }}
     steps:
       - name: 'Checkout cbioportal repo'
         uses: actions/checkout@v2
@@ -64,4 +81,8 @@ jobs:
       - name: 'Run integration tests separately'
         working-directory: ./cbioportal
         run: |
-          mvn -U -Ppublic integration-test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword
+          mvn verify -Pintegration-test
+      - name: 'Run e2e tests separately'
+        working-directory: ./cbioportal
+        run: |
+          mvn verify -Pe2e-test

.github/workflows/dockerimage.yml

@@ -128,12 +128,13 @@ jobs:
     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/cbioportal_backend_master.yaml"
+      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: 'apps:Deployment:default/cbioportal-backend-master'
+      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
@@ -164,14 +165,16 @@ jobs:
 
       - name: Update Master Deployment File
         run: |
-          sed -i "s|image:.*|image: $DOCKER_SHA|" $DEPLOYMENT_FILE_PATH
+          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 "[email protected]"
           git config --global user.name "cBioPortal Backend Github Action"
-          if ! git diff --quiet "$DEPLOYMENT_FILE_PATH"; then
-            git add $DEPLOYMENT_FILE_PATH
+          if ! git diff --quiet; then
+            git add -A
             git commit -m "Update master deployment"
           else
             echo "No changes to commit."
@@ -196,4 +199,4 @@ jobs:
         with:
           version: ${{ env.ARGOCD_CLI_VER }}
           command: app sync ${{ env.ARGOCD_APP }}
-          options: --resource ${{ env.ARGOCD_RESOURCE }}
+          options: ${{ env.ARGOCD_RESOURCE_OPTIONS }}

.github/workflows/integration-test.yml

@@ -1,5 +1,5 @@
 name: Integration tests
-on: [push, pull_request]
+on: [push, pull_request_target]
 jobs:
   build:
     name: Integration tests
@@ -45,7 +45,9 @@ jobs:
           cat $PORTAL_SOURCE_DIR/src/main/resources/application.properties | \
               sed 's|spring.datasource.url=.*|spring.datasource.url=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false|' | \
               sed 's|spring.datasource.username=.*|spring.datasource.username=cbio_user|' | \
-              sed 's|spring.datasource.password=.*|spring.datasource.password=somepassword|' \
+              sed 's|spring.datasource.password=.*|spring.datasource.password=somepassword|' | \
+              sed 's|session.service.url=.*|session.service.url=http://cbioportal-session:5001/api/sessions/my_portal/|' | \
+              sed 's|feature.study.export=.*|feature.study.export=true|' \
               > application.properties
       - name: 'Dump Properties'
         working-directory: ./cbioportal-docker-compose
@@ -71,6 +73,11 @@ jobs:
         working-directory: ./cbioportal-docker-compose
         run: |
           $PORTAL_SOURCE_DIR/test/integration/test_load_study.sh
+      - name: 'TEST - Import and Export of study_es_0_import_export'
+        if: steps.startup.conclusion == 'success'
+        working-directory: ./cbioportal-docker-compose
+        run: |
+          $PORTAL_SOURCE_DIR/test/integration/test_import_export.sh
       - name: 'TEST - Add OncoKB annotations to study'
         if: steps.startup.conclusion == 'success'
         working-directory: ./cbioportal-docker-compose

.github/workflows/markdown-links-check.yml

@@ -0,0 +1,15 @@
+name: Markdown links check
+on: [pull_request]
+jobs:
+  build:
+    name: Markdown links check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        # Docs here https://github.com/tcort/github-action-markdown-link-check
+      - uses: tcort/github-action-markdown-link-check@v1
+        continue-on-error: true
+        with:
+          use-quiet-mode: 'yes'
+          use-verbose-mode: 'no'
+          config-file: markdown_links_check_config.json

.github/workflows/retype-action.yml

@@ -19,7 +19,7 @@ jobs:
         with:
           dotnet-version: 7.0.x
 
-      - uses: retypeapp/action-build@latest
+      - uses: retypeapp/action-build@ddc4449f15ae65b75e13198b88200bfd64aef168 # before v3.10.0, which breaks the news on homepage
 
       - uses: retypeapp/action-github-pages@latest
         with:

.github/workflows/security-integration-test.yml

@@ -0,0 +1,40 @@
+name: Update POM for Snapshot Release
+
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  update-pom:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: 'master'
+          token: '${{ secrets.GITHUB_TOKEN }}'
+
+      - name: Setup Git identity
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "github-actions"
+
+      - name: Download semver management tool
+        run: |
+          wget -q https://raw.githubusercontent.com/fsaintjacques/semver-tool/master/src/semver
+          chmod +x semver
+
+      - name: Update pom with snapshot release version
+        run: |
+          TAG=${{ github.event.release.tag_name }}
+          VERSION=${TAG#v}
+          SNAPSHOT_VERSION=$(./semver bump patch $VERSION)
+          SNAPSHOT_TAG=v"$SNAPSHOT_VERSION"-SNAPSHOT
+          sed -i "s|<version>\(.*\)-SNAPSHOT</version>|<version>$SNAPSHOT_TAG</version>|" pom.xml
+          git add pom.xml
+          git commit -m "Prepare for $SNAPSHOT_TAG"
+          git push

.github/workflows/snapshot-release.yml

@@ -3,12 +3,15 @@ on:
   push:
     branches:
       - master
-  pull_request:
+  pull_request_target:
     types: [opened, synchronize, reopened]
 jobs:
   build:
     name: sonarcloud
     runs-on: ubuntu-latest
+    env:
+      TEST_DB_CLICKHOUSE_PASSWORD: ${{ secrets.TEST_DB_CLICKHOUSE_PASSWORD }}
+      TEST_DB_MYSQL_PASSWORD: ${{ secrets.TEST_DB_MYSQL_PASSWORD }}
     steps:
       - uses: actions/checkout@v2
         with:
@@ -43,8 +46,11 @@ jobs:
       - name: 'Run integration tests'
         run: |
           mvn verify -Pintegration-test
+      - name: 'Run e2e tests'
+        run: |
+          mvn verify -Pe2e-test
       - name: Code Coverage
         env:
           SONAR_TOKEN:  de1b5cc660cd210dde840f492c371da6cc801763
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: mvn sonar:sonar -Pcoverage
+        run: mvn sonar:sonar -Pcoverage

.github/workflows/sonarcloud.yml

@@ -28,7 +28,7 @@ From the [GitHub Help Page of Using Pull Requests](https://help.github.com/artic
 
 ### Programming
  * Make sure you have a [GitHub account](https://github.com/signup/free).
- * Familiarize yourself with the [project documentation](https://docs.cbioportal.org), including the [Feature Development Guide](https://docs.cbioportal.org/development/feature-development-guide/), the [Architecture docs](https://docs.cbioportal.org/2.1-deployment/architecture-overview), the [backend code organization](docs/Backend-Code-Organization.md) and [backend development guidelines](docs/Backend-Development-Guidelines.md).
+ * Familiarize yourself with the [project documentation](https://docs.cbioportal.org), including the [Feature Development Guide](https://docs.cbioportal.org/development/feature-development-guide/), the [Architecture docs](https://docs.cbioportal.org/2.1-deployment/architecture-overview), the [backend code organization](https://docs.cbioportal.org/development/backend-code-organization/) and [backend development guidelines](https://docs.cbioportal.org/development/backend-development-guidelines/).
  * Find a [good first issue](https://github.com/cBioPortal/cbioportal/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc+label%3A%22good+first+issue%22) to start with
  * Check if the issue will require frontend or backend changes. If it is for the frontend look at how to set up the [frontend repo](https://github.com/cbioPortal/cbioportal-frontend/) instead
  * Fork the cbioportal or cbioportal-frontend project on GitHub depending on what your working on.  For general instructions on forking a GitHub project, see [Forking a Repo](https://help.github.com/articles/fork-a-repo/) and [Syncing a fork](https://help.github.com/articles/syncing-a-fork/).