Release 0.36.0

Release 0.36.0

Author: sven1103

identity/src/main/java/life/qbic/identity/application/token/PersonalAccessTokenServiceImpl.java

@@ -65,7 +65,8 @@ public Collection<PersonalAccessToken> find(String userId) {
 
   @Override
   public void delete(String tokenId, String userId) {
-    tokenRepository.findAllByUserId(userId).stream().filter(token -> token.userId().equals(userId))
+    tokenRepository.findAllByUserId(userId).stream()
+        .filter(token -> token.tokenId().equals(tokenId))
         .findAny().ifPresent(tokenRepository::delete);
   }
 }

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/qualitycontrol/QualityControlJpa.java

@@ -0,0 +1,16 @@
+package life.qbic.projectmanagement.infrastructure.sample.qualitycontrol;
+
+import java.util.List;
+import life.qbic.projectmanagement.domain.model.project.ProjectId;
+import life.qbic.projectmanagement.domain.model.sample.qualitycontrol.QualityControl;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * <b>Quality Control JPA</b>
+ * <p>
+ * JPA interface for {@link QualityControl} items.
+ */
+public interface QualityControlJpa extends CrudRepository<QualityControl, Long> {
+
+  List<QualityControl> findQualityControlAssociationByProjectIdEquals(ProjectId projectId);
+}

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/qualitycontrol/QualityControlStore.java

@@ -0,0 +1,107 @@
+package life.qbic.projectmanagement.infrastructure.sample.qualitycontrol;
+
+import static org.apache.logging.log4j.LogManager.getLogger;
+
+import java.util.Comparator;
+import java.util.List;
+import java.util.Optional;
+import life.qbic.application.commons.ApplicationException;
+import life.qbic.projectmanagement.application.sample.qualitycontrol.QualityControlStorage;
+import life.qbic.projectmanagement.application.sample.qualitycontrol.QualityControlStorageException;
+import life.qbic.projectmanagement.domain.model.project.ProjectId;
+import life.qbic.projectmanagement.domain.model.sample.qualitycontrol.QualityControl;
+import life.qbic.projectmanagement.domain.model.sample.qualitycontrol.QualityControlUpload;
+import org.apache.logging.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+/**
+ * <b>Quality Control Store</b>
+ *
+ * <p>Implementation of the {@link QualityControlStorage} interface.</p>
+ */
+@Component
+public class QualityControlStore implements QualityControlStorage {
+
+  private static final Logger log = getLogger(QualityControlStore.class);
+
+  private final QualityControlJpa persistenceStore;
+
+  @Autowired
+  public QualityControlStore(QualityControlJpa persistenceStore) {
+    this.persistenceStore = persistenceStore;
+  }
+
+  /**
+   * Stores a {@link QualityControl} item persistently.
+   *
+   * @param qualityControl the QualityControlUpload item to store
+   * @throws QualityControlStorageException is thrown if the storage fails
+   * @since 1.0.0
+   */
+  @Override
+  public void storeQualityControl(QualityControl qualityControl)
+      throws QualityControlStorageException {
+    try {
+      persistenceStore.save(qualityControl);
+    } catch (RuntimeException e) {
+      throw new QualityControlStorageException(
+          "Storing the quality control for project %s failed".formatted(qualityControl.project()),
+          e);
+    }
+  }
+
+  @Override
+  public void storeQualityControls(List<QualityControl> qualityControls)
+      throws QualityControlStorageException {
+    try {
+      persistenceStore.saveAll(qualityControls);
+    } catch (RuntimeException e) {
+      throw new QualityControlStorageException((
+          "Storing the quality control for project %s failed".formatted(
+              qualityControls.stream().findFirst().orElseThrow().project())),
+          e);
+    }
+  }
+
+  @Override
+  public List<QualityControlUpload> findQualityControlsForProject(ProjectId projectId) {
+    try {
+      return persistenceStore.findQualityControlAssociationByProjectIdEquals(projectId).stream()
+          .sorted(Comparator.comparing(QualityControl::providedOn)) //ensures same ordering
+          .map(QualityControl::qualityControlUpload).toList();
+    } catch (RuntimeException e) {
+      throw new ApplicationException(
+          "Retrieving quality controls for project %s failed.".formatted(projectId), e);
+    }
+  }
+
+  @Override
+  public void deleteQualityControlForProject(String projectId, long qualityControlId) {
+    List<QualityControl> associations = persistenceStore.findQualityControlAssociationByProjectIdEquals(
+        ProjectId.parse(projectId));
+    List<QualityControl> associationsWithQualityControl = associations.stream()
+        .filter(association -> association.qualityControlUpload().id().equals(qualityControlId))
+        .toList();
+    persistenceStore.deleteAll(associationsWithQualityControl);
+  }
+
+  @Override
+  public Optional<QualityControlUpload> findQualityControlForProject(String projectId,
+      Long qualityControlId) {
+    try {
+      List<QualityControl> associations = persistenceStore.findQualityControlAssociationByProjectIdEquals(
+          ProjectId.parse(projectId));
+      Optional<QualityControlUpload> foundQualityControl = associations.stream()
+          .map(QualityControl::qualityControlUpload)
+          .filter(qualityControl -> qualityControl.id().equals(qualityControlId))
+          .findFirst();
+      foundQualityControl.ifPresent(QualityControlUpload::fileContent); // make sure it is loaded
+      return foundQualityControl;
+    } catch (RuntimeException e) {
+      throw new ApplicationException(
+          "Retrieving quality control %d for project %s failed.".formatted(qualityControlId,
+              projectId), e);
+    }
+  }
+}

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

@@ -57,6 +57,10 @@ public String getUsername() {
     return user.id();
   }
 
+  public String fullName() {
+    return user.fullName();
+  }
+
   @Override
   public boolean isAccountNonExpired() {
     return true;

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

@@ -0,0 +1,42 @@
+package life.qbic.projectmanagement.application.sample.qualitycontrol;
+
+import java.util.Arrays;
+import java.util.Objects;
+import java.util.StringJoiner;
+import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
+
+/**
+ * <b>Simple quality control information exchange object</b>
+ */
+public record QualityControlReport(String fileName, ExperimentId experimentId, byte[] content) {
+
+  @Override
+  public boolean equals(Object o) {
+    if (this == o) {
+      return true;
+    }
+    if (o == null || getClass() != o.getClass()) {
+      return false;
+    }
+    QualityControlReport qualityControlReport = (QualityControlReport) o;
+    return Objects.equals(fileName, qualityControlReport.fileName) && Objects.equals(experimentId,
+        qualityControlReport.experimentId)
+        && Arrays.equals(content, qualityControlReport.content);
+  }
+
+  @Override
+  public int hashCode() {
+    int result = Objects.hash(experimentId, fileName);
+    result = 31 * result + Arrays.hashCode(content);
+    return result;
+  }
+
+  @Override
+  public String toString() {
+    return new StringJoiner(", ", QualityControlReport.class.getSimpleName() + "[", "]")
+        .add("fileName='" + fileName + "'")
+        .add("experimentId='" + experimentId + "'")
+        .add("content=" + Arrays.toString(content))
+        .toString();
+  }
+}

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

@@ -0,0 +1,99 @@
+package life.qbic.projectmanagement.application.sample.qualitycontrol;
+
+import static java.util.Objects.requireNonNull;
+import static life.qbic.logging.service.LoggerFactory.logger;
+
+import java.time.Instant;
+import java.util.List;
+import java.util.Optional;
+import life.qbic.application.commons.ApplicationException;
+import life.qbic.logging.api.Logger;
+import life.qbic.projectmanagement.application.api.PurchaseStoreException;
+import life.qbic.projectmanagement.domain.model.project.ProjectId;
+import life.qbic.projectmanagement.domain.model.sample.qualitycontrol.QualityControl;
+import life.qbic.projectmanagement.domain.model.sample.qualitycontrol.QualityControlUpload;
+import org.springframework.stereotype.Service;
+
+/**
+ * <b>Quality Control Service</b>
+ * <p>
+ * A service that enables actions on quality control services.
+ *
+ * @since 1.0.0
+ */
+@Service
+public class QualityControlService {
+
+  private static final Logger log = logger(QualityControlService.class);
+  private final QualityControlStorage storage;
+
+  public QualityControlService(QualityControlStorage storage) {
+    this.storage = storage;
+  }
+
+  /**
+   * Adds a quality controls to a project.
+   *
+   * @param projectId      the project the quality control is related to
+   * @param qualityControl the quality control information item
+   */
+  public void addQualityControl(String projectId, QualityControlReport qualityControl) {
+    addQualityControls(projectId, List.of(qualityControl));
+  }
+
+  /**
+   * Adds a list of quality controls to a project.
+   *
+   * @param projectId           the project the quality control is related to
+   * @param qualityControlsList list of quality controls information items to be added
+   */
+  public void addQualityControls(String projectId, List<QualityControlReport> qualityControlsList) {
+    var projectReference = ProjectId.parse(projectId);
+    var qualityControlUploadDate = Instant.now();
+    List<QualityControl> qualityControls = qualityControlsList.stream()
+        .map(it -> QualityControlUpload.create(it.fileName(), it.experimentId(), it.content()))
+        .map(it -> QualityControl.create(projectReference, qualityControlUploadDate, it))
+        .toList();
+    try {
+      storage.storeQualityControls(qualityControls);
+    } catch (PurchaseStoreException e) {
+      throw ApplicationException.wrapping(e);
+    }
+  }
+
+  /**
+   * Lists all quality controls files linked to a project
+   *
+   * @param projectId the projectId for which to search quality controls for
+   * @return a list of all linked quality controls, can be empty, never null.
+   */
+  public List<QualityControlUpload> linkedQualityControls(String projectId) {
+    ProjectId parsedId = ProjectId.parse(projectId);
+    return requireNonNull(storage.findQualityControlsForProject(parsedId),
+        "Provided quality controls must not be null");
+  }
+
+  /**
+   * Triggers the deletion of a {@link QualityControl} item.
+   *
+   * @param projectId        the projectId for which the {@link QualityControl} should be deleted
+   * @param qualityControlId the id of the quality control to be deleted
+   */
+  public void deleteQualityControl(String projectId, long qualityControlId) {
+    storage.deleteQualityControlForProject(projectId, qualityControlId);
+  }
+
+  /**
+   * Returns a {@link QualityControlUpload} item with the provided qualityControlId which is
+   * associated with the provided {@link ProjectId} from the database.
+   *
+   * @param projectId        the projectId for which the {@link QualityControl} should be
+   *                         returned
+   * @param qualityControlId the id of the quality control to be returned
+   */
+  public Optional<QualityControlUpload> getQualityControlWithContent(String projectId,
+      Long qualityControlId) {
+    return storage.findQualityControlForProject(projectId, qualityControlId);
+  }
+
+}

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

@@ -0,0 +1,65 @@
+package life.qbic.projectmanagement.application.sample.qualitycontrol;
+
+import java.util.List;
+import java.util.Optional;
+import life.qbic.projectmanagement.domain.model.project.ProjectId;
+import life.qbic.projectmanagement.domain.model.sample.qualitycontrol.QualityControl;
+import life.qbic.projectmanagement.domain.model.sample.qualitycontrol.QualityControlUpload;
+
+/**
+ * <b>QualityControlUpload Storage</b>
+ * <p>
+ * Quality Control storage interface, that enables storing of {@link QualityControl}
+ * items.
+ * <p>
+ */
+public interface QualityControlStorage {
+
+  /**
+   * Stores a {@link QualityControl} item persistently.
+   *
+   * @param qualityControl the QualityControl item to store
+   * @throws QualityControlStorageException is thrown if the storage fails
+   */
+  void storeQualityControl(QualityControl qualityControl)
+      throws QualityControlStorageException;
+
+  /**
+   * Stores a list of {@link QualityControl} item persistently.
+   *
+   * @param qualityControls the QualityControl item list to store
+   * @throws QualityControlStorageException is thrown if the storage fails
+   */
+  void storeQualityControls(List<QualityControl> qualityControls)
+      throws QualityControlStorageException;
+
+  /**
+   * Returns a list of {@link QualityControlUpload} items associated with the provided
+   * {@link ProjectId} from the database.
+   *
+   * @param projectId the projectId for which the {@link QualityControl} should be returned
+   */
+  List<QualityControlUpload> findQualityControlsForProject(ProjectId projectId);
+
+  /**
+   * Deletes {@link QualityControl} item persistently.
+   *
+   * @param projectId        the projectId for which the {@link QualityControl} should be
+   *                         deleted
+   * @param qualityControlId the id of the quality control to be deleted
+   */
+  void deleteQualityControlForProject(String projectId, long qualityControlId);
+
+
+  /**
+   * Returns a {@link QualityControlUpload} item with the provided qualityControlId which is
+   * associated with the provided {@link ProjectId} from the database.
+   *
+   * @param projectId        the projectId for which the {@link QualityControl} should be
+   *                         returned
+   * @param qualityControlId the id of the quality control to be returned
+   */
+  Optional<QualityControlUpload> findQualityControlForProject(String projectId,
+      Long qualityControlId);
+
+}

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

@@ -0,0 +1,38 @@
+package life.qbic.projectmanagement.application.sample.qualitycontrol;
+
+import java.io.Serial;
+import life.qbic.projectmanagement.domain.model.sample.qualitycontrol.QualityControlUpload;
+
+/**
+ * <b>QualityControlStorageException</b>
+ * <p>
+ * Exception that shall be thrown if a {@link QualityControlUpload} item cannot be stored in the
+ * persistence storage implementation.
+ *
+ * @since 1.0.0
+ */
+public class QualityControlStorageException extends RuntimeException {
+
+  @Serial
+  private static final long serialVersionUID = -3283512159754153169L;
+
+  public QualityControlStorageException() {
+  }
+
+  public QualityControlStorageException(String message) {
+    super(message);
+  }
+
+  public QualityControlStorageException(String message, Throwable cause) {
+    super(message, cause);
+  }
+
+  public QualityControlStorageException(Throwable cause) {
+    super(cause);
+  }
+
+  public QualityControlStorageException(String message, Throwable cause, boolean enableSuppression,
+      boolean writableStackTrace) {
+    super(message, cause, enableSuppression, writableStackTrace);
+  }
+}