Improve software quality and configure Sonarcloud (#917)

Further improves the reliability of the software code and also introduces a Sonarcloud property file, to tell Sonarcloud to exclude
certain contents from the evaluation (template content, etc).

.github/workflows/sonarcloud.yml

@@ -0,0 +1,40 @@
+name: SonarCloud Analysis
+
+# Run this workflow on commits to the development branch
+on:
+  push:
+    branches:
+      - development
+
+jobs:
+  sonarcloud:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu'
+          java-version: '17'
+      - name: Load local Maven repository cache
+        uses: actions/cache@v4
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
+
+      # Build the project using Maven
+      - name: Build with Maven
+        run: mvn clean install
+
+      # Run SonarCloud analysis
+      - name: SonarCloud Scan
+        env:
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} # Use the token stored in GitHub secrets
+        run: mvn sonar:sonar \
+          -Dsonar.projectKey=qbicsoftware_data-manager-app \
+          -Dsonar.organization=qbicsoftware \
+          -Dsonar.host.url=https://sonarcloud.io

pom.xml

@@ -233,6 +233,11 @@
           <target>${maven.compiler.target}</target>
         </configuration>
       </plugin>
+        <plugin>
+          <groupId>org.sonarsource.scanner.maven</groupId>
+          <artifactId>sonar-maven-plugin</artifactId>
+          <version>5.0.0.4389</version>
+        </plugin>
     </plugins>
   </build>
 </project>

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/ontology/TIBTerminologyServiceIntegration.java

@@ -164,6 +164,7 @@ public List<OntologyClass> query(String searchTerm, int offset, int limit)
     } catch (IOException e) {
       throw wrapIO(e);
     } catch (InterruptedException e) {
+      Thread.currentThread().interrupt();
       throw wrapInterrupted(e);
     } catch (Exception e) {
       throw wrapUnknown(e);
@@ -193,6 +194,7 @@ public List<OntologyClass> search(String searchTerm, int offset, int limit)
     } catch (IOException e) {
       throw wrapIO(e);
     } catch (InterruptedException e) {
+      Thread.currentThread().interrupt();
       throw wrapInterrupted(e);
     } catch (Exception e) {
       throw wrapUnknown(e);

project-management/src/main/java/life/qbic/projectmanagement/application/DeletionService.java

@@ -29,7 +29,7 @@
 @Service
 public class DeletionService {
 
-  private ApplicationContext context;
+  private final ApplicationContext context;
 
   private final ProjectInformationService projectInformationService;
   private final ExperimentInformationService experimentInformationService;
@@ -52,6 +52,7 @@ public DeletionService(ProjectInformationService projectInformationService,
         BatchDomainService.class.getSimpleName() + " must not be null");
     this.sampleDomainService = requireNonNull(sampleDomainService,
         SampleDomainService.class.getSimpleName() + " must not be null");
+    this.context = requireNonNull(context);
   }
 
   /**

project-management/src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java

@@ -44,6 +44,7 @@
 import life.qbic.projectmanagement.domain.repository.MeasurementRepository;
 import life.qbic.projectmanagement.domain.service.MeasurementDomainService;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.security.access.prepost.PostAuthorize;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -60,6 +61,7 @@
 public class MeasurementService {
 
   private static final Logger log = logger(MeasurementService.class);
+  private final ApplicationContext context;
   private final MeasurementDomainService measurementDomainService;
   private final MeasurementLookupService measurementLookupService;
   private final SampleInformationService sampleInformationService;
@@ -75,14 +77,16 @@ public MeasurementService(MeasurementDomainService measurementDomainService,
       OrganisationLookupService organisationLookupService,
       MeasurementLookupService measurementLookupService,
       ProjectInformationService projectInformationService,
-      MeasurementRepository measurementRepository) {
+      MeasurementRepository measurementRepository,
+      ApplicationContext context) {
     this.measurementDomainService = Objects.requireNonNull(measurementDomainService);
     this.sampleInformationService = Objects.requireNonNull(sampleInformationService);
     this.speciesLookupService = Objects.requireNonNull(speciesLookupService);
     this.organisationLookupService = Objects.requireNonNull(organisationLookupService);
     this.measurementLookupService = Objects.requireNonNull(measurementLookupService);
     this.projectInformationService = Objects.requireNonNull(projectInformationService);
     this.measurementRepository = Objects.requireNonNull(measurementRepository);
+    this.context = Objects.requireNonNull(context);
   }
 
   /**
@@ -113,7 +117,8 @@ public long countNGSMeasurements(ExperimentId experimentId) {
   @PostAuthorize(
       "hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'READ') ")
   public Collection<ProteomicsMeasurement> findProteomicsMeasurements(String filter,
-      ExperimentId experimentId, int offset, int limit, List<SortOrder> sortOrder, ProjectId projectId) {
+      ExperimentId experimentId, int offset, int limit, List<SortOrder> sortOrder,
+      ProjectId projectId) {
     var result = sampleInformationService.retrieveSamplesForExperiment(experimentId);
     var samplesInExperiment = result.getValue().stream().map(Sample::sampleId).toList();
     return measurementLookupService.queryProteomicsMeasurementsBySampleIds(filter,
@@ -145,7 +150,8 @@ public Collection<NGSMeasurement> findNGSMeasurements(String filter, ExperimentI
 
   @PostAuthorize(
       "hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'READ') ")
-  public Collection<NGSMeasurement> findNGSMeasurements(ExperimentId experimentId, ProjectId projectId) {
+  public Collection<NGSMeasurement> findNGSMeasurements(ExperimentId experimentId,
+      ProjectId projectId) {
     var result = sampleInformationService.retrieveSamplesForExperiment(experimentId);
     var samplesInExperiment = result.getValue().stream().map(Sample::sampleId).toList();
     return measurementLookupService.queryAllNGSMeasurement(samplesInExperiment);
@@ -192,7 +198,7 @@ public CompletableFuture<List<Result<MeasurementId, ErrorCode>>> registerAll(
       return CompletableFuture.completedFuture(List.of(Result.fromError(e.reason)));
     }
     try {
-      results = performRegistration(measurementMetadataList, projectId).stream()
+      results = context.getBean(MeasurementService.class).performRegistration(measurementMetadataList, projectId).stream()
           .map(Result::<MeasurementId, ErrorCode>fromValue).toList();
     } catch (MeasurementRegistrationException e) {
       log.error("Failed to register measurement", e);
@@ -202,7 +208,7 @@ public CompletableFuture<List<Result<MeasurementId, ErrorCode>>> registerAll(
       return CompletableFuture.completedFuture(List.of(Result.fromError(ErrorCode.FAILED)));
     }
     // if the creation worked, we forward the events, otherwise it will be rolled back
-    if(results.stream().allMatch(Result::isValue)) {
+    if (results.stream().allMatch(Result::isValue)) {
       domainEventsCache.forEach(
           domainEvent -> DomainEventDispatcher.instance().dispatch(domainEvent));
     }
@@ -529,21 +535,21 @@ public CompletableFuture<List<Result<MeasurementId, ErrorCode>>> updateAll(
 
   private void handleUpdateEvents(List<DomainEvent> domainEventsCache,
       List<Result<MeasurementId, ErrorCode>> results) {
-    if(results.stream().anyMatch(Result::isError)) {
+    if (results.stream().anyMatch(Result::isError)) {
       return;
     }
     Set<MeasurementId> dispatchedIDs = new HashSet<>();
-    for(DomainEvent event : domainEventsCache) {
-      if(event instanceof MeasurementUpdatedEvent measurementUpdatedEvent) {
+    for (DomainEvent event : domainEventsCache) {
+      if (event instanceof MeasurementUpdatedEvent measurementUpdatedEvent) {
         MeasurementId id = measurementUpdatedEvent.measurementId();
-        if(dispatchedIDs.contains(id)) {
+        if (dispatchedIDs.contains(id)) {
           continue;
         }
         DomainEventDispatcher.instance().dispatch(event);
         dispatchedIDs.add(id);
       }
     }
-   
+
   }
 
   /**
@@ -803,7 +809,7 @@ public Result<Void, MeasurementDeletionException> deletePxPMeasurements(ProjectI
       Set<ProteomicsMeasurement> selectedMeasurements) {
     try {
       measurementDomainService.deletePxP(selectedMeasurements);
-      if(!selectedMeasurements.isEmpty()) {
+      if (!selectedMeasurements.isEmpty()) {
         dispatchProjectChangedOnMeasurementDeleted(projectId);
       }
       return Result.fromValue(null);
@@ -817,7 +823,7 @@ public Result<Void, MeasurementDeletionException> deleteNGSMeasurements(ProjectI
       Set<NGSMeasurement> selectedMeasurements) {
     try {
       measurementDomainService.deleteNGS(selectedMeasurements);
-      if(!selectedMeasurements.isEmpty()) {
+      if (!selectedMeasurements.isEmpty()) {
         dispatchProjectChangedOnMeasurementDeleted(projectId);
       }
       return Result.fromValue(null);
@@ -829,7 +835,8 @@ public Result<Void, MeasurementDeletionException> deleteNGSMeasurements(ProjectI
   private void dispatchProjectChangedOnMeasurementDeleted(ProjectId projectId) {
     ProjectChanged projectChanged = ProjectChanged.create(projectId);
     DomainEventDispatcher.instance().dispatch(projectChanged);
-}
+  }
+
   public enum DeletionErrorCode {
     FAILED, DATA_ATTACHED
   }

sonar-project.properties

@@ -0,0 +1,3 @@
+sonar.projectKey=qbicsoftware_data-manager-app
+sonar.organization=qbicsoftware
+sonar.exclusions=src/test/**,build/**,node_modules/**, **/DataPrivacyAgreement.html, **/LegalNotice.html

user-interface/src/main/java/life/qbic/datamanager/RejectedExecutionHandlerImplementation.java

@@ -38,6 +38,7 @@ public void rejectedExecution(Runnable r, ThreadPoolExecutor executor) {
           "Thread " + Thread.currentThread().getId() + " rejected, because the queue was full.");
       executor.getQueue().put(r);
     } catch (InterruptedException e) {
+      Thread.currentThread().interrupt();
       throw new RejectedExecutionException("Unexpected InterruptedException", e);
     }
   }

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/experiments/experiment/ExperimentDetailsComponent.java

@@ -603,11 +603,12 @@ private void addExperimentalVariables(
   }
 
   public void setContext(Context context) {
+    this.context = requireNonNull(context);
+    if (context.projectId().isEmpty()) {
+      throw new ApplicationException("no project id in context " + context);
+    }
     ExperimentId experimentId = context.experimentId()
         .orElseThrow(() -> new ApplicationException("no experiment id in context " + context));
-    context.projectId()
-        .orElseThrow(() -> new ApplicationException("no project id in context " + context));
-    this.context = context;
     reloadExperimentInfo(experimentId);
   }