Improve software quality by addressing some reliability issues (#931)

Improves the reliability and maintenance of the software by addressing various issues.

---------

Co-authored-by: Steffengreiner <steffen.greiner@qbic.uni-tuebingen.de>

Author: sven1103

.github/workflows/sonarcloud.yml

@@ -5,7 +5,10 @@ on:
   push:
     branches:
       - development
-
+  pull_request:
+    branches:
+      - development
+      - main
 jobs:
   sonarcloud:
     runs-on: ubuntu-latest

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

@@ -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

@@ -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

@@ -219,7 +219,7 @@ public CompletableFuture<List<Result<MeasurementId, ErrorCode>>> registerAll(
   @PreAuthorize(
       "hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'WRITE')")
   @Transactional
-  protected List<MeasurementId> performRegistration(
+  public List<MeasurementId> performRegistration(
       List<? extends MeasurementMetadata> measurementMetadataList, ProjectId projectId) {
     if (measurementMetadataList.isEmpty()) {
       return new ArrayList<>(); // Nothing to do
@@ -243,7 +243,6 @@ private List<MeasurementId> performRegistrationNGS(
         ngsMeasurementMetadata.add(ngsMetadata);
       }
     }
-    Map<NGSMeasurement, Collection<SampleIdCodeEntry>> ngsMeasurementsMapping = new HashMap<>();
 
     // Start with the pooled measurements first and group the metadata entries by pool
     Map<String, List<NGSMeasurementMetadata>> measurementsByPool = ngsMeasurementMetadata.stream()
@@ -255,7 +254,8 @@ private List<MeasurementId> performRegistrationNGS(
         .filter(metadata -> metadata.assignedSamplePoolGroup().isEmpty()).toList();
 
     // Then merge and prepare the domain objects by pool
-    ngsMeasurementsMapping.putAll(mergeByPoolNGS(measurementsByPool, projectId));
+    Map<NGSMeasurement, Collection<SampleIdCodeEntry>> ngsMeasurementsMapping = new HashMap<>(
+        mergeByPoolNGS(measurementsByPool, projectId));
     // and last but not least also the single sample measurements
     singleMeasurements.stream()
         .map(singleMeasurement -> buildNGS(List.of(singleMeasurement), projectId))
@@ -273,7 +273,6 @@ private List<MeasurementId> performRegistrationPxP(
         proteomicsMeasurements.add(proteomicsMetadata);
       }
     }
-    Map<ProteomicsMeasurement, Collection<SampleIdCodeEntry>> proteomicsMeasurementsMapping = new HashMap<>();
 
     // Start with the pooled measurements first and group the metadata entries by pool
     Map<String, List<ProteomicsMeasurementMetadata>> measurementsByPool = proteomicsMeasurements.stream()
@@ -285,7 +284,8 @@ private List<MeasurementId> performRegistrationPxP(
         .filter(metadata -> metadata.assignedSamplePoolGroup().isEmpty()).toList();
 
     // Then merge and prepare the domain objects by pool
-    proteomicsMeasurementsMapping.putAll(mergeByPoolPxP(measurementsByPool, projectId));
+    Map<ProteomicsMeasurement, Collection<SampleIdCodeEntry>> proteomicsMeasurementsMapping = new HashMap<>(
+        mergeByPoolPxP(measurementsByPool, projectId));
     // and last but not least also the single sample measurements
     singleMeasurements.stream()
         .map(singleMeasurement -> buildPxP(List.of(singleMeasurement), projectId))
@@ -346,7 +346,7 @@ private Map<NGSMeasurement, Collection<SampleIdCodeEntry>> buildNGS(
     NGSMeasurement measurement;
     if (firstMetadataEntry.assignedSamplePoolGroup().isPresent()) {
       measurement = NGSMeasurement.createWithPool(projectId,
-          firstMetadataEntry.assignedSamplePoolGroup().get(), assignedMeasurementCode,
+          firstMetadataEntry.assignedSamplePoolGroup().orElseThrow(), assignedMeasurementCode,
           organisationQuery.get(), method, specificMetadata);
     } else {
       measurement = NGSMeasurement.createSingleMeasurement(projectId, assignedMeasurementCode,

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

@@ -20,6 +20,8 @@
  */
 public class PropertyConversion {
 
+  private PropertyConversion(){}
+
   private static final String CONDITION_VARIABLE_LEVEL_UNIT_TEMPLATE = "%s: %s %s"; // <variable name>: <value> [unit]
 
   private static final String CONDITION_VARIABLE_LEVEL_NO_UNIT_TEMPLATE = "%s: %s"; // <variable name>: <value>
@@ -72,7 +74,7 @@ public static String toString(VariableLevel variableLevel) {
     if (variableLevel.experimentalValue().unit().isPresent()) {
       return CONDITION_VARIABLE_LEVEL_UNIT_TEMPLATE.formatted(variableLevel.variableName().value(),
           variableLevel.experimentalValue().value(),
-          variableLevel.experimentalValue().unit().get());
+          variableLevel.experimentalValue().unit().orElseThrow());
     } else {
       return CONDITION_VARIABLE_LEVEL_NO_UNIT_TEMPLATE.formatted(
           variableLevel.variableName().value(), variableLevel.experimentalValue().value());

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

@@ -80,4 +80,8 @@ public String fractionName() {
     return fractionName;
   }
 
+  public String comment() {
+    return comment;
+  }
+
 }