Merge branch 'release/2.13.0'

.circleci/config.yml

@@ -3,7 +3,7 @@ orbs:
   aws-s3: circleci/aws-s3@3.0.0
   aws-cli: circleci/aws-cli@3.1.1
   slack: circleci/slack@4.4.4
-  browser-tools: circleci/browser-tools@1.4.7
+  browser-tools: circleci/browser-tools@1.4.8
 executors:
   integration_test_exec: # declares a reusable executor
     docker:
@@ -13,7 +13,7 @@ executors:
           password: $DOCKERHUB_PASSWORD
         environment:
           JAVA_TOOL_OPTIONS: -Xmx2g # Java can read cgroup. Sadly the cgroup in CircleCI is wrong. Have to manually set. Using 1/2 memory as heap.
-      - image: cimg/postgres:13.3
+      - image: cimg/postgres:<< pipeline.parameters.postgres-tag >>
         command: postgres -c max_connections=200 -c jit=off
         auth:
           username: dockstoretestuser
@@ -80,6 +80,10 @@ jobs:
             password: $DOCKERHUB_PASSWORD
     steps:
       - setup_nightly_tests
+      - run:
+          name: Reset dockstoretestuser4's resources
+          # Reset user dockstoretestuser4's resources such that it has no registered tools and published workflows
+          command: bash scripts/reset-dockstoretestuser4-resources.sh << parameters.stack >>
       - run:
           name: Run remote verification test against << parameters.stack >> (with auth)
           command: bash -i -c 'npm run test-<< parameters.stack >>-auth'
@@ -89,6 +93,8 @@ jobs:
           name: Reset dockstoretestuser4's resources
           # Reset user dockstoretestuser4's resources such that it has no registered tools and published workflows
           command: bash scripts/reset-dockstoretestuser4-resources.sh << parameters.stack >>
+          # Reset even if the tests failed
+          when: always
       - upload_nightly_artifacts
       - slack/notify:
           channel: $<< parameters.stack >>_id
@@ -131,6 +137,13 @@ jobs:
           command: |
             bash -i -c 'npm run circle-ci-license-test-file'
             bash scripts/detect-package-json-changes.sh
+      # Override the use_snapshot in package.json to instead build against develop webservice
+      - when:
+         condition: << pipeline.parameters.sanity-check-against-develop >>
+         steps:
+          - run:
+              name: set use_snapshot to true (grab snapshot artifacts)
+              command: bash -i -c 'npm config set dockstore-ui2:use_snapshot true'
       - build_ui
       - run:
           name: Install codecov
@@ -211,7 +224,7 @@ jobs:
         auth:
           username: dockstoretestuser
           password: $DOCKERHUB_PASSWORD
-      - image: cimg/python:3.11
+      - image: cimg/python:<< pipeline.parameters.python-tag >>
         auth:
           username: dockstoretestuser
           password: $DOCKERHUB_PASSWORD
@@ -256,17 +269,25 @@ jobs:
         auth:
           username: dockstoretestuser
           password: $DOCKERHUB_PASSWORD
-      - image: cimg/python:3.11
+      - image: cimg/python:<< pipeline.parameters.python-tag >>
         auth:
           username: dockstoretestuser
           password: $DOCKERHUB_PASSWORD
     steps:
-      - get_workspace
-      # Override the webservice version in package.json to instead build against develop webservice
-      - run:
-          name: set webservice to develop
-          command: bash -i -c 'npm config set dockstore-ui2:webservice_version develop'
-      - build_ui
+      - run: # should not need this, but circle ci does not like it when a condition wipes out a whole job https://discuss.circleci.com/t/pipeline-parameters-in-steps-when-conditions-seems-to-have-no-value-using-dynamic-configuration/50524/2
+          name: Java/Maven/Python versions
+          command: |
+            java -version
+            npm --version
+      - when:
+          condition:
+            not: << pipeline.parameters.sanity-check-against-develop >>
+          steps:
+            - get_workspace
+            - run:
+                name: set use_snapshot to true
+                command: bash -i -c 'npm config set dockstore-ui2:use_snapshot true'
+            - build_ui
 
 parameters:
   run_nightly_auth:
@@ -278,6 +299,15 @@ parameters:
   java-tag:
     type: string
     default: "17.0.4-browsers"
+  postgres-tag:
+    type: string
+    default: "16.1"
+  python-tag:
+    type: string
+    default: "3.11"
+  sanity-check-against-develop:
+    type: boolean
+    default: false
 
 workflows:
   version: 2

.eslintrc.json

@@ -19,6 +19,9 @@
         "plugin:@angular-eslint/recommended",
         "plugin:@angular-eslint/template/process-inline-templates"
       ],
+      "plugins": [
+        "@typescript-eslint"
+      ],
       "rules": {
         "@angular-eslint/component-selector": [
           "error",

.github/snapshot-mvn-settings.xml

@@ -0,0 +1,31 @@
+<!--This is not currently used, but has been tested to work with github packages -->
+<settings>
+  <servers>
+    <server>
+      <id>github-packages</id>
+      <username>DockstoreTestUser</username>
+      <password>${env.GITHUB_TOKEN}</password>
+    </server>
+  </servers>
+
+
+  <activeProfiles>
+    <activeProfile>github-packages</activeProfile>
+  </activeProfiles>
+
+  <profiles>
+    <profile>
+      <id>github-packages</id>
+      <repositories>
+        <repository>
+          <id>github-packages</id>
+          <url>https://maven.pkg.github.com/dockstore/dockstore</url>
+          <snapshots>
+            <enabled>true</enabled>
+          </snapshots>
+        </repository>
+      </repositories>
+    </profile>
+  </profiles>
+
+</settings>

.github/workflows/accessibility_test.yml

@@ -12,11 +12,11 @@ jobs:
     # Uses if/else expression evaluation workaround from https://github.com/actions/runner/issues/409#issuecomment-752775072
     # 'matrix.branch == github.base_ref' is the condition, 'base' is the true value and 'current' is the false value
     name: Accessibility test (${{ matrix.branch == github.base_ref && 'base' || 'current' }} branch)
-  
+
     runs-on: ubuntu-20.04
     services:
       postgres:
-        image: postgres:13.3
+        image: postgres:16.1
         env:
           POSTGRES_USER: postgres
           POSTGRES_DB: postgres
@@ -56,7 +56,7 @@ jobs:
 
       - name: Cache dependencies
         id: cache-dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           cache-version: version1
         with:
@@ -97,17 +97,17 @@ jobs:
           if [[ "${{ matrix.branch }}" == "$GITHUB_BASE_REF" ]]; then
             echo "Running accessibility test for base branch"
             npm run accessibility-test -- -RB
-          else 
+          else
             echo "Running accessibility test for current branch"
             npm run accessibility-test -- -R
           fi
-          
+
       - name: Save accessibility results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: accessibility-results
+          name: accessibility-results-${{ matrix.branch == github.base_ref && 'base' || 'current' }}
           path: accessibility-results/
-  
+
   compare_accessibility_results:
     needs: run-accessibility-test
     runs-on: ubuntu-20.04
@@ -120,12 +120,12 @@ jobs:
           node-version-file: '.nvmrc'
 
       - name: Download accessibility results
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: accessibility-results
           # Download to this directory because this is the directory that the accessibility script looks at for the results
-          path: accessibility-results 
-
+          path: accessibility-results
+          pattern: accessibility-results-*
+          merge-multiple: true
+
       - name: Compare accessibility results
         run: npm run accessibility-test -- -A
-

.github/workflows/codeql.yml

@@ -40,7 +40,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -54,7 +54,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -67,6 +67,6 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
       with:
         category: "/language:${{matrix.language}}"

README.md

@@ -139,7 +139,33 @@ Run `ng g component component-name` to generate a new component. You can also us
 
 ## Build
 
+When building against artifactory, the build should use the latest SNAPSHOT. In this scenario, the package.json will look like
+```
+ "config": {
+    "webservice_version_prefix": "1.16.0",
+    "webservice_version": "1.16.0-alpha.10",
+    "use_snapshot": true
+```
+
 Optionally override the webservice version using `npm config set dockstore-ui2:webservice_version ${WEBSERVICE_VERSION}`
+
+For example, to build against a specific branch, edit the package.json with
+```
+  "config": {
+    "webservice_version_prefix": "1.16.0",
+    "webservice_version": "feature/seab-6420/modify-endpoint-description-for-new-health-checks",
+    "use_snapshot": false
+  },
+```
+For example, to build against a specific commit, edit the package.json with
+```
+  "config": {
+    "webservice_version_prefix": "1.16.0",
+    "webservice_version": "1550b549c45b2f4ba7f205e2f64502d523417dcd",
+    "use_snapshot": false
+  },
+```
+
 Run `npm run build` to build the project. The build artifacts will be stored in the `dist/` directory. 
 
 ### Angular Production Build