Merge pull request #473 from qbicsoftware/release/0.34.0

Release 0.34.0

Author: KochTobi

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

@@ -41,14 +41,15 @@ public List<OntologyClassEntity> query(int offset, int limit) {
   private String buildSearchTerm(String searchString) {
     StringBuilder searchTermBuilder = new StringBuilder();
     for(String word : searchString.split(" ")) {
-      searchTermBuilder.append(" +" + word);
+      searchTermBuilder.append(" +").append(word);
     }
     searchTermBuilder.append("*");
     return searchTermBuilder.toString().trim();
   }
 
   @Override
-  public List<OntologyClassEntity> query(String searchString, List<String> ontologyAbbreviations,
+  public List<OntologyClassEntity> query(String searchString,
+      List<String> ontologyAbbreviations,
       int offset,
       int limit, List<SortOrder> sortOrders) {
     List<Order> orders = sortOrders.stream().map(it -> {

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

@@ -19,9 +19,5 @@ public interface OntologyTermRepository extends
       countQuery = "SELECT count(*) FROM ontology_classes WHERE MATCH(label) AGAINST(?1 IN BOOLEAN MODE) AND ontology in (?2);",
       nativeQuery = true)
   Page<OntologyClassEntity> findByLabelFulltextMatching(
-      String termFilter, List<String> ontology, Pageable pageable);
-
-  Page<OntologyClassEntity> findByLabelNotNullAndOntologyIn(List<String> ontologies, Pageable pageable);
-
-  Page<OntologyClassEntity> findByLabelStartingWithIgnoreCaseAndOntologyIn(String filter, List<String> ontology, Pageable pageable);
+      String termFilter, List<String> ontologyAbbreviations, Pageable pageable);
 }

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

@@ -38,7 +38,7 @@ public OntologyTermRepositoryImpl(QbicOntologyTermRepo ontologyTermRepo) {
 
   @Override
   public List<OntologyClassEntity> find(String name) {
-    return ontologyTermRepo.findOntologyTermByName(name);
+    return ontologyTermRepo.findOntologyClassEntitiesByClassName(name);
   }
 
   @Override

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

@@ -17,5 +17,5 @@
  */
 public interface QbicOntologyTermRepo extends CrudRepository<OntologyClassEntity, Long> {
 
-  List<OntologyClassEntity> findOntologyTermByName(String name);
+  List<OntologyClassEntity> findOntologyClassEntitiesByClassName(String name);
 }

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

@@ -0,0 +1,29 @@
+package life.qbic.projectmanagement.application;
+
+import java.util.List;
+import life.qbic.projectmanagement.domain.model.project.Contact;
+import org.springframework.stereotype.Component;
+
+@Component
+public class ContactRepository {
+
+  public List<Contact> findAll() {
+    //TODO implement
+    return dummyContacts();
+  }
+
+  private static List<Contact> dummyContacts() {
+    return List.of(
+        new Contact("Max Mustermann", "[email protected]"),
+        new Contact("David Müller", "[email protected]"),
+        new Contact("John Koch", "[email protected]"),
+        new Contact("Trevor Noah", "[email protected]"),
+        new Contact("Sarah Connor", "[email protected]"),
+        new Contact("Anna Bell", "[email protected]"),
+        new Contact("Sophia Turner", "[email protected]"),
+        new Contact("Tylor Smith", "[email protected]")
+    );
+  }
+
+
+}

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

@@ -97,19 +97,19 @@ public BatchId deleteBatch(ProjectId projectId, BatchId batchId) {
     deletedBatchId.onError(error -> {
       throw new ApplicationException("Could not delete batch " + batchId);
     });
-    deleteSamples(projectId, samples);
+    deleteSamples(projectId, batchId, samples);
     return deletedBatchId.getValue();
   }
 
 
   @Transactional
   public void deleteSamples(
-      ProjectId projectId, Collection<SampleId> samplesCollection) {
+      ProjectId projectId, BatchId batchId, Collection<SampleId> samplesCollection) {
     var project = projectInformationService.find(projectId);
     if (project.isEmpty()) {
       throw new IllegalArgumentException("Could not find project " + projectId);
     }
-    sampleDomainService.deleteSamples(project.get(), samplesCollection);
+    sampleDomainService.deleteSamples(project.get(), batchId, samplesCollection);
   }
 
   /**

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

@@ -1,5 +1,6 @@
 package life.qbic.projectmanagement.application;
 
+import jakarta.persistence.Column;
 import jakarta.persistence.Entity;
 import jakarta.persistence.GeneratedValue;
 import jakarta.persistence.Id;
@@ -10,18 +11,19 @@
 @Table(name = "ontology_classes")
 public class OntologyClassEntity {
 
-  String ontology;
-
+  @Column(name = "ontology")
+  String ontologyAbbreviation;
+  @Column(name = "ontologyVersion")
   String ontologyVersion;
-
+  @Column(name = "ontologyIri")
   String ontologyIri;
-
-  String label;
-
-  String name;
-
+  @Column(name = "label")
+  String classLabel;
+  @Column(name = "name")
+  String className;
+  @Column(name = "description", length = 2000)
   String description;
-
+  @Column(name = "classIri")
   String classIri;
 
   @Id
@@ -31,23 +33,24 @@ public class OntologyClassEntity {
   public OntologyClassEntity() {
   }
 
-  public OntologyClassEntity(String ontology, String ontologyVersion, String ontologyIri,
-      String label, String name, String description, String classIri) {
-    this.ontology = ontology;
+  public OntologyClassEntity(String ontologyAbbreviation, String ontologyVersion,
+      String ontologyIri,
+      String classLabel, String className, String description, String classIri) {
+    this.ontologyAbbreviation = ontologyAbbreviation;
     this.ontologyVersion = ontologyVersion;
     this.ontologyIri = ontologyIri;
-    this.label = label;
-    this.name = name;
+    this.classLabel = classLabel;
+    this.className = className;
     this.description = description;
     this.classIri = classIri;
   }
 
-  public String getOntology() {
-    return ontology;
+  public String getOntologyAbbreviation() {
+    return ontologyAbbreviation;
   }
 
-  public void setOntology(String ontology) {
-    this.ontology = ontology;
+  public void setOntologyAbbreviation(String ontology) {
+    this.ontologyAbbreviation = ontology;
   }
 
   public String getOntologyVersion() {
@@ -66,20 +69,20 @@ public void setOntologyIri(String ontologyIri) {
     this.ontologyIri = ontologyIri;
   }
 
-  public String getLabel() {
-    return label;
+  public String getClassLabel() {
+    return classLabel;
   }
 
-  public void setLabel(String label) {
-    this.label = label;
+  public void setClassLabel(String label) {
+    this.classLabel = label;
   }
 
-  public String getName() {
-    return name;
+  public String getClassName() {
+    return className;
   }
 
-  public void setName(String name) {
-    this.name = name;
+  public void setClassName(String name) {
+    this.className = name;
   }
 
   public String getDescription() {
@@ -107,16 +110,17 @@ public boolean equals(Object o) {
       return false;
     }
     OntologyClassEntity that = (OntologyClassEntity) o;
-    return Objects.equals(ontology, that.ontology) && Objects.equals(
+    return Objects.equals(ontologyAbbreviation, that.ontologyAbbreviation) && Objects.equals(
         ontologyVersion, that.ontologyVersion) && Objects.equals(ontologyIri,
-        that.ontologyIri) && Objects.equals(label, that.label) && Objects.equals(
-        name, that.name) && Objects.equals(description, that.description)
+        that.ontologyIri) && Objects.equals(classLabel, that.classLabel) && Objects.equals(
+        className, that.className) && Objects.equals(description, that.description)
         && Objects.equals(classIri, that.classIri);
   }
 
   @Override
   public int hashCode() {
-    return Objects.hash(ontology, ontologyVersion, ontologyIri, label, name, description, classIri);
+    return Objects.hash(ontologyAbbreviation, ontologyVersion, ontologyIri, classLabel, className,
+        description, classIri);
   }
 
   public Long getId() {
@@ -126,4 +130,4 @@ public Long getId() {
   public void setId(Long id) {
     this.id = id;
   }
-}
+}

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

@@ -45,7 +45,7 @@ public List<OntologyClassEntity> queryOntologyTerm(String termFilter, List<Strin
       int offset, int limit, List<SortOrder> sortOrders) {
     // returned by JPA -> UnmodifiableRandomAccessList
     List<OntologyClassEntity> termList = ontologyTermLookup.query(termFilter, ontologyAbbreviations, offset,
-        50, sortOrders);
+        limit, sortOrders);
     // the list must be modifiable for spring security to filter it
     return new ArrayList<>(termList);
   }

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

@@ -98,6 +98,21 @@ public Result<BatchId, ResponseCode> addSampleToBatch(SampleId sampleId, BatchId
     }
   }
 
+  public Result<BatchId, ResponseCode> deleteSampleFromBatch(SampleId sampleId, BatchId batchId) {
+    var searchResult = batchRepository.find(batchId);
+    if (searchResult.isEmpty()) {
+      return Result.fromError(ResponseCode.BATCHES_COULD_NOT_BE_RETRIEVED);
+    } else {
+      Batch batch = searchResult.get();
+      batch.removeSample(sampleId);
+      var result = batchRepository.update(batch);
+      if (result.isError()) {
+        return Result.fromError(ResponseCode.BATCH_UPDATE_FAILED);
+      }
+      return Result.fromValue(batch.batchId());
+    }
+  }
+
   /**
    * Edits the information contained within a {@link Batch} and its corresponding registered
    * {@link Sample}
@@ -150,7 +165,7 @@ public Result<BatchId, ResponseCode> editBatch(BatchId batchId, String batchLabe
       sampleRegistrationService.updateSamples(projectId, editedSamples);
     }
     if (!deletedSamples.isEmpty()) {
-      deletionService.deleteSamples(projectId, deletedSamples);
+      deletionService.deleteSamples(projectId, batchId, deletedSamples);
     }
     return Result.fromValue(batch.batchId());
   }

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

@@ -19,6 +19,7 @@ public record SampleUpdateRequest(SampleId sampleId, SampleInformation sampleInf
    * Sample update request.
    * <p>
    * @param sampleLabel          a human-readable semantic descriptor of the sample
+   * @param organismId           optional identifier of the sample's source patient or organism
    * @param analysisMethod       analysis method to be performed
    * @param biologicalReplicate  the biological replicate the sample has been taken from
    * @param experimentalGroup    the experimental group the sample is part of
@@ -27,7 +28,8 @@ public record SampleUpdateRequest(SampleId sampleId, SampleInformation sampleInf
    * @param analyte              the analyte the sample belongs to
    * @param comment              comment relating to the sample
    */
-  public record SampleInformation(String sampleLabel, AnalysisMethod analysisMethod,
+  public record SampleInformation(String sampleLabel, String organismId,
+                                  AnalysisMethod analysisMethod,
                                   BiologicalReplicate biologicalReplicate,
                                   ExperimentalGroup experimentalGroup, OntologyClassDTO species,
                                   OntologyClassDTO specimen, OntologyClassDTO analyte,

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

@@ -0,0 +1,36 @@
+package life.qbic.projectmanagement.application.policy;
+
+import life.qbic.domain.concepts.DomainEventDispatcher;
+import life.qbic.projectmanagement.application.policy.directive.DeleteSampleFromBatch;
+import life.qbic.projectmanagement.domain.model.batch.Batch;
+import life.qbic.projectmanagement.domain.model.sample.event.SampleDeleted;
+
+/**
+ * <b>Policy: Sample Deleted</b>
+ * <p>
+ * A collection of all directives that need to be executed after a sample has been deleted
+ * <p>
+ * The policy subscribes to events of type
+ * {@link SampleDeleted} and ensures the
+ * registration of all business required directives.
+ *
+ * @since 1.0.0
+ */
+public class SampleDeletedPolicy {
+
+  private final DeleteSampleFromBatch deleteSampleFromBatch;
+
+  /**
+   * Creates an instance of a {@link SampleDeletedPolicy} object.
+   * <p>
+   * All directives will be created and subscribed upon instantiation.
+   *
+   * @param deleteSampleFromBatch directive to remove the affected sample from
+   *                         {@link Batch}
+   * @since 1.0.0
+   */
+  public SampleDeletedPolicy(DeleteSampleFromBatch deleteSampleFromBatch) {
+    this.deleteSampleFromBatch = deleteSampleFromBatch;
+    DomainEventDispatcher.instance().subscribe(this.deleteSampleFromBatch);
+  }
+}

project-management/src/main/java/life/qbic/projectmanagement/application/policy/directive/DeleteSampleFromBatch.java

@@ -0,0 +1,56 @@
+package life.qbic.projectmanagement.application.policy.directive;
+
+import static life.qbic.logging.service.LoggerFactory.logger;
+
+import life.qbic.domain.concepts.DomainEvent;
+import life.qbic.domain.concepts.DomainEventSubscriber;
+import life.qbic.logging.api.Logger;
+import life.qbic.projectmanagement.application.batch.BatchRegistrationService;
+import life.qbic.projectmanagement.domain.model.batch.BatchId;
+import life.qbic.projectmanagement.domain.model.sample.SampleId;
+import life.qbic.projectmanagement.domain.model.sample.event.SampleDeleted;
+import org.jobrunr.jobs.annotations.Job;
+import org.jobrunr.scheduling.JobScheduler;
+import org.springframework.stereotype.Component;
+
+/**
+ * <b>Directive: Delete Sample from Batch</b>
+ * <p>
+ * After a sample has been deleted, we need to update the batch and remove
+ * the sample reference of the deleted sample.
+ *
+ * @since 1.0.0
+ */
+@Component
+public class DeleteSampleFromBatch implements DomainEventSubscriber<SampleDeleted> {
+
+  private static final Logger log = logger(DeleteSampleFromBatch.class);
+  private final BatchRegistrationService batchRegistrationService;
+  private final JobScheduler jobScheduler;
+
+  public DeleteSampleFromBatch(BatchRegistrationService batchRegistrationService,
+      JobScheduler jobScheduler) {
+    this.batchRegistrationService = batchRegistrationService;
+    this.jobScheduler = jobScheduler;
+  }
+
+  @Override
+  public Class<? extends DomainEvent> subscribedToEventType() {
+    return SampleDeleted.class;
+  }
+
+  @Override
+  public void handleEvent(SampleDeleted event) {
+    jobScheduler.enqueue(() -> deleteSampleFromBatch(event.deletedSample(), event.assignedBatch()));
+  }
+
+  @Job(name = "Delete_Sample_From_Batch")
+  public void deleteSampleFromBatch(SampleId sample, BatchId batch) throws RuntimeException {
+    batchRegistrationService.deleteSampleFromBatch(sample, batch).onError(responseCode -> {
+      throw new RuntimeException(
+          String.format("Deletion of sample %s from batch %s failed, response code was %s ", sample,
+              batch,
+              responseCode));
+    });
+  }
+}