Improve SonarQube workflow and refine project config

Added debug steps to SonarQube GitHub Actions workflow for both backend and frontend to show directory structure and file counts. Enabled verbose output for SonarQube scans. Updated sonar-project.properties to specify backend source directories and refined exclusions for more accurate analysis.

Author: TheSinnerAR

.github/workflows/sonarqube.yaml

@@ -17,6 +17,19 @@ jobs:
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
 
+      - name: Debug - Show directory structure
+        run: |
+          echo "=== Current directory ==="
+          pwd
+          echo "=== Root files ==="
+          ls -la
+          echo "=== src/ directory ==="
+          ls -la src/
+          echo "=== Python files count ==="
+          find src/ -name "*.py" -type f | grep -v __pycache__ | grep -v migrations | wc -l
+          echo "=== First 20 Python files ==="
+          find src/ -name "*.py" -type f | grep -v __pycache__ | grep -v migrations | head -20
+
       - name: SonarQube Scan - Backend
         uses: SonarSource/sonarqube-scan-action@v6
         env:
@@ -27,6 +40,7 @@ jobs:
           args: >
             -Dsonar.projectKey=omics-datascience_multiomix-backend
             -Dsonar.organization=omics-datascience
+            -Dsonar.verbose=true
 
   sonarqube-frontend:
     name: SonarQube Frontend Analysis
@@ -47,6 +61,17 @@ jobs:
       - name: Run linter and type checks
         run: npm --prefix src/frontend/static/frontend run check-all
 
+      - name: Debug - Show frontend structure
+        run: |
+          echo "=== Frontend directory ==="
+          pwd
+          echo "=== Frontend src files ==="
+          ls -la src/frontend/static/frontend/
+          echo "=== TypeScript files count ==="
+          find src/frontend/static/frontend/src -type f \( -name "*.ts" -o -name "*.tsx" \) | wc -l
+          echo "=== First 20 TypeScript files ==="
+          find src/frontend/static/frontend/src -type f \( -name "*.ts" -o -name "*.tsx" \) | head -20
+
       - name: SonarQube Scan - Frontend
         uses: SonarSource/sonarqube-scan-action@v6
         env:
@@ -57,3 +82,4 @@ jobs:
           args: >
             -Dsonar.projectKey=omics-datascience_multiomix-frontend
             -Dsonar.organization=omics-datascience
+            -Dsonar.verbose=true

sonar-project.properties

@@ -6,24 +6,17 @@ sonar.organization=omics-datascience
 sonar.projectName=Multiomix Backend
 sonar.projectVersion=1.0
 
-# Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
-sonar.sources=src
+# Path is relative to the sonar-project.properties file
+sonar.sources=src/api_service,src/biomarkers,src/common,src/datasets_synchronization,src/differential_expression,src/feature_selection,src/genes,src/inferences,src/institutions,src/molecules_details,src/multiomics_intermediate,src/statistical_properties,src/tags,src/user_files,src/users,src/websockets
 
-# Exclude frontend, tests, migrations, and other non-backend code
-sonar.exclusions=**/node_modules/**,**/frontend/**,**/migrations/**,**/tests/**,**/__pycache__/**,**/venv/**,**/*.pyc,**/.venv/**,**/staticfiles/**,**/static/frontend/**
-
-# Test files (commented out to avoid empty test issues)
-# sonar.tests=src
-# sonar.test.inclusions=**/tests/**,**/*_test.py,**/test_*.py
+# Exclude migrations, tests, cache, virtual env, and frontend
+sonar.exclusions=**/migrations/**,**/tests/**,**/__pycache__/**,**/venv/**,**/*.pyc,**/.venv/**,**/staticfiles/**,**/node_modules/**,**/frontend/**,**/htmlcov/**,**/email/**
 
 # Python specific settings
 sonar.python.version=3.7,3.8,3.9,3.10,3.11
 
 # Coverage reports (if you generate them)
 # sonar.python.coverage.reportPaths=src/.coverage
 
-# Encoding of the source code. Default is default system encoding
+# Encoding of the source code
 sonar.sourceEncoding=UTF-8
-
-# Language
-sonar.language=py