Merge pull request #953 from qbicsoftware/development

Release PR

Author: KochTobi

.github/workflows/sonarcloud.yml

@@ -0,0 +1,40 @@
+name: SonarCloud Analysis
+
+# Run this workflow on commits to the development branch
+on:
+  push:
+    branches:
+      - development
+  pull_request:
+    branches:
+      - development
+      - main
+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

domain-concept/src/main/java/life/qbic/domain/concepts/DomainEventPublisher.java

@@ -24,6 +24,7 @@
 public class ProjectManagementEmailServiceProvider implements EmailService {
 
   private static final Logger log = logger(ProjectManagementEmailServiceProvider.class);
+  public static final String EMAIL_SUBMISSION_FAILED = "Email submission failed";
 
   private final EmailServiceProvider emailServiceProvider;
 
@@ -39,7 +40,7 @@ public void send(Subject subject, Recipient recipient, Content content)
           MessageTranslator.translate(content));
     } catch (EmailSubmissionException e) {
       log.error("Email submission failed!", e);
-      throw new CommunicationException("Email submission failed");
+      throw new CommunicationException(EMAIL_SUBMISSION_FAILED);
     }
   }
 
@@ -50,8 +51,8 @@ public void send(Subject subject, Recipient recipient, Content content, Attachme
       emailServiceProvider.send(MessageTranslator.translate(subject), MessageTranslator.translate(recipient),
           MessageTranslator.translate(content), MessageTranslator.translate(attachment));
     } catch (EmailSubmissionException e) {
-      log.error("Email submission failed", e);
-      throw new CommunicationException("Email submission failed");
+      log.error(EMAIL_SUBMISSION_FAILED, e);
+      throw new CommunicationException(EMAIL_SUBMISSION_FAILED);
     }
   }
 

email-service-provider/src/main/java/life/qbic/infrastructure/email/project/ProjectManagementEmailServiceProvider.java

@@ -36,6 +36,9 @@
     <jakarta.persistence.version>3.2.0</jakarta.persistence.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <jackson.version>2.18.1</jackson.version>
+    <sonar.projectKey>qbicsoftware_data-manager-app</sonar.projectKey>
+    <sonar.organization>qbicsoftware</sonar.organization>
+    <sonar.host.url>https://sonarcloud.io</sonar.host.url>
   </properties>
 
   <parent>
@@ -233,6 +236,11 @@
           <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>

pom.xml

@@ -20,7 +20,6 @@
 import life.qbic.logging.api.Logger;
 import life.qbic.projectmanagement.application.OrganisationRepository;
 import life.qbic.projectmanagement.domain.Organisation;
-import org.springframework.stereotype.Component;
 
 /**
  * <b>Cached Organisation Repository</b>
@@ -35,7 +34,6 @@
  *
  * @since 1.0.0s
  */
-@Component
 public class CachedOrganisationRepository implements OrganisationRepository {
 
   private static final Logger log = logger(CachedOrganisationRepository.class);
@@ -53,7 +51,6 @@ public CachedOrganisationRepository(int cacheSize) {
     this.configuredCacheSize = cacheSize;
   }
 
-
   public CachedOrganisationRepository() {
     this.configuredCacheSize = DEFAULT_CACHE_SIZE;
   }

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

@@ -22,8 +22,9 @@ public interface AppContextProvider {
    * Returns a resolvable URL to the target project's sample page resource in the application.
    *
    * @param projectId the project id
+   * @param experimentId the experiment id
    * @return a fully resolvable URL
    * @since 1.0.0
    */
-  String urlToSamplePage(String projectId);
+  String urlToSamplePage(String projectId, String experimentId);
 }

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

@@ -17,7 +17,7 @@
  */
 public class QbicOidcUser extends DefaultOidcUser {
 
-  private final QbicUserInfo qbicUserInfo;
+  private final transient QbicUserInfo qbicUserInfo;
   private final String originalAuthName;
 
   public record QbicUserInfo(String userId, String fullName, String email, boolean active) {

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

@@ -21,7 +21,7 @@
 public class QbicUserDetails implements UserDetails {
   @Serial
   private static final long serialVersionUID = 5812210012669790933L;
-  private final User user;
+  private final transient User user;
   private final List<GrantedAuthority> grantedAuthorities;
 
   /**

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

@@ -43,6 +43,7 @@
 public class ProjectAccessServiceImpl implements ProjectAccessService {
 
   private static final Logger log = logger(ProjectAccessServiceImpl.class);
+  public static final String SELECT_IDENTITY = "SELECT @@IDENTITY";
   private final MutableAclService aclService;
   private final JdbcTemplate jdbcTemplate;
 
@@ -59,8 +60,8 @@ private static MutableAcl getAclForProject(ProjectId projectId, List<Sid> sids,
     JdbcMutableAclService serviceImpl = (JdbcMutableAclService) mutableAclService;
     // these settings are necessary for MySQL to correctly throw several types of exceptions
     // instead of an unrelated exception related to the identity function
-    serviceImpl.setClassIdentityQuery("SELECT @@IDENTITY");
-    serviceImpl.setSidIdentityQuery("SELECT @@IDENTITY");
+    serviceImpl.setClassIdentityQuery(SELECT_IDENTITY);
+    serviceImpl.setSidIdentityQuery(SELECT_IDENTITY);
     try {
       acl = (MutableAcl) serviceImpl.readAclById(objectIdentity, sids);
     } catch (NotFoundException e) {
@@ -75,8 +76,8 @@ private static MutableAcl createAclForProject(ProjectId projectId,
     JdbcMutableAclService serviceImpl = (JdbcMutableAclService) mutableAclService;
     // these settings are necessary for MySQL to correctly throw several types of exceptions
     // instead of an unrelated exception related to the identity function
-    serviceImpl.setClassIdentityQuery("SELECT @@IDENTITY");
-    serviceImpl.setSidIdentityQuery("SELECT @@IDENTITY");
+    serviceImpl.setClassIdentityQuery(SELECT_IDENTITY);
+    serviceImpl.setSidIdentityQuery(SELECT_IDENTITY);
     return serviceImpl.createAcl(objectIdentity);
   }
 

project-management/src/main/java/life/qbic/projectmanagement/application/authorization/acl/ProjectAccessServiceImpl.java

@@ -15,6 +15,7 @@
 import life.qbic.projectmanagement.application.sample.SampleRegistrationService;
 import life.qbic.projectmanagement.domain.model.batch.Batch;
 import life.qbic.projectmanagement.domain.model.batch.BatchId;
+import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
 import life.qbic.projectmanagement.domain.model.project.ProjectId;
 import life.qbic.projectmanagement.domain.model.sample.Sample;
 import life.qbic.projectmanagement.domain.model.sample.SampleId;
@@ -70,21 +71,23 @@ public BatchRegistrationService(BatchRepository batchRepository,
    *                  are usually followed by a complete batch that represents the measurements of
    *                  the complete experiment.
    * @param projectId id of the project this batch is added to
+   * @param experimentId id of the experiment this batch is added to
    * @return a result object with the response. If the registration failed, a response code will be
    * provided.
    * @since 1.0.0
    */
   @PreAuthorize("hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE')")
   public Result<BatchId, ResponseCode> registerBatch(String label, boolean isPilot,
-      ProjectId projectId) {
+      ProjectId projectId, ExperimentId experimentId) {
     var project = projectInformationService.find(projectId);
     if (project.isEmpty()) {
       log.error(
           "Batch registration aborted. Reason: project with id:" + projectId + " was not found");
       return Result.fromError(ResponseCode.BATCH_CREATION_FAILED);
     }
     String projectTitle = project.get().getProjectIntent().projectTitle().title();
-    var result = batchDomainService.register(label, isPilot, projectTitle, projectId);
+    var result = batchDomainService.register(label, isPilot, projectTitle, projectId,
+        experimentId);
     if (result.isError()) {
       return Result.fromError(ResponseCode.BATCH_REGISTRATION_FAILED);
     }