Merge pull request #1582 from ScilifelabDataCentre/dev

New release: December 18th 2024

Author: i-oden

.github/workflows/codeql-analysis.yml

@@ -51,11 +51,11 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # 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.
@@ -66,7 +66,7 @@ jobs:
       # Autobuild attempts to build any compiled languages  (C/C++, C#, 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.
       # 📚 https://git.io/JvXDl
@@ -80,4 +80,4 @@ jobs:
       #   make release
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3

.github/workflows/docker-compose-tests.yml

@@ -19,7 +19,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Run tests against database container
         run: docker compose -f docker-compose.yml -f tests/docker-compose-test.yml up --build --exit-code-from backend
@@ -31,7 +31,7 @@ jobs:
           ## If no one connects after 5 minutes, shut down server.
           wait-timeout-minutes: 5
 
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage/report.xml

.github/workflows/lint-yaml.yml

@@ -13,7 +13,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: yaml-lint
         uses: ibiqlik/action-yamllint@v3
         with:

.github/workflows/prettier.yml

@@ -9,9 +9,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier

.github/workflows/python-black.yml

@@ -15,7 +15,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: psf/black@stable
         with:
           version: ${{ env.INPUT_VERSION }}

.github/workflows/snyk-scan.yml

@@ -30,7 +30,7 @@ jobs:
           command: code test
           args: --sarif-file-output=snyk.sarif
       - name: Upload result to GitHub Code Scanning
-        uses: github/codeql-action/upload-sarif@v2
+        uses: github/codeql-action/upload-sarif@v3
         with:
           sarif_file: snyk.sarif
           category: snyk

.github/workflows/trivy-scan-branch.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Run Trivy vulnerability scanner
         uses: aquasecurity/trivy-action@master

.github/workflows/trivy-scheduled-dev.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Ensure lowercase name
         run: echo REPOSITORY_OWNER=$(echo ${{ github.repository_owner }} | tr "[:upper:]" "[:lower:]") >> $GITHUB_ENV

.github/workflows/trivy-scheduled-master.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: master
 

CHANGELOG.rst

@@ -1,6 +1,24 @@
 Changelog
 ==========
 
+.. _2.9.0:
+
+2.9.0 - 2024-12-18
+~~~~~~~~~~~~~~~~~~
+
+- New features:
+    - Delivery directory names now include 'Upload' or 'Download' for clarity.
+    - Monitor usage now sends warnings to the affected unit and Data Centre when approaching the allocated quota.
+- Bugs fixed:
+    - Improved error message for downloads after a password reset.
+    - Fixed the dds ls --tree command.
+    - Pinned mariadb-client version in backend Dockerfile for stability.
+    - Resolved Node.js vulnerabilities with npm audit fix.
+- Logging:
+    - Removed invalid token exceptions from logs.
+    - Logged usernames for password resets.
+    - Filtered out MaintenanceModeException from logs.
+
 .. _2.8.1:
 
 2.8.1 - 2024-10-23