Extend database and domain for 'analysis performed' and 'comment' (#311)

projectmanagement/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java

@@ -44,6 +44,9 @@ public class SamplePreview {
   private String bioReplicateLabel;
   @Column(name = "label")
   private String sampleLabel;
+  private String comment;
+  @Column(name = "analysis_type")
+  private String analysisType;
   @OneToOne(cascade = CascadeType.ALL)
   @JoinColumn(name = "experimentalGroupId")
   private ExperimentalGroup experimentalGroup;
@@ -58,7 +61,7 @@ protected SamplePreview() {
   private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampleCode,
       String batchLabel, String bioReplicateLabel,
       String sampleLabel, ExperimentalGroup experimentalGroup, String species, String specimen,
-      String analyte) {
+      String analyte, String analysisType, String comment) {
     Objects.requireNonNull(experimentId);
     Objects.requireNonNull(sampleId);
     Objects.requireNonNull(sampleCode);
@@ -79,6 +82,9 @@ private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampl
     this.species = species;
     this.specimen = specimen;
     this.analyte = analyte;
+    // optional columns
+    this.comment = comment;
+    this.analysisType = analysisType;
   }
 
   /**
@@ -100,15 +106,17 @@ private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampl
    *                          preview
    * @param analyte           the {@link Analyte} for the {@link Sample} associated with this
    *                          preview
+   * @param analysisType      the type of analysis to be performed for this {@link Sample}
+   * @param comment           an optional comment pertaining to the associated {@link Sample}
    * @return the sample preview
    */
   public static SamplePreview create(ExperimentId experimentId, SampleId sampleId,
       String sampleCode,
       String batchLabel, String bioReplicateLabel,
       String sampleLabel, ExperimentalGroup experimentalGroup, String species, String specimen,
-      String analyte) {
+      String analyte, String analysisType, String comment) {
     return new SamplePreview(experimentId, sampleId, sampleCode, batchLabel, bioReplicateLabel,
-        sampleLabel, experimentalGroup, species, specimen, analyte);
+        sampleLabel, experimentalGroup, species, specimen, analyte, analysisType, comment);
   }
 
   public ExperimentId experimentId() {
@@ -146,6 +154,12 @@ public String specimen() {
   public String analyte() {
     return analyte;
   }
+  public String analysisType() {
+    return analysisType;
+  }
+  public String comment() {
+    return comment;
+  }
 
   public ExperimentalGroup experimentalGroup() {
     return experimentalGroup;
@@ -167,14 +181,15 @@ public boolean equals(Object o) {
         that.sampleLabel)
         && Objects.equals(species, that.species) && Objects.equals(specimen,
         that.specimen) && Objects.equals(analyte, that.analyte) && Objects.equals(
-        experimentalGroup, that.experimentalGroup);
+        experimentalGroup, that.experimentalGroup) && Objects.equals(analysisType,
+        that.analysisType) && Objects.equals(comment, that.comment);
   }
 
   @Override
   public int hashCode() {
     return Objects.hash(experimentId, sampleCode, sampleId, batchLabel, bioReplicateLabel,
         sampleLabel,
-        species, specimen, analyte, experimentalGroup);
+        species, specimen, analyte, experimentalGroup, analysisType, comment);
   }
 
   @Override
@@ -189,6 +204,8 @@ public String toString() {
         ", species='" + species + '\'' +
         ", specimen='" + specimen + '\'' +
         ", analyte='" + analyte + '\'' +
+        ", analysisType='" + analysisType + '\'' +
+        ", comment='" + comment + '\'' +
         ", conditions=" + experimentalGroup +
         '}';
   }

projectmanagement/src/main/java/life/qbic/projectmanagement/domain/project/sample/Sample.java

@@ -6,6 +6,7 @@
 import jakarta.persistence.EmbeddedId;
 import jakarta.persistence.Entity;
 import java.util.Objects;
+import java.util.Optional;
 import life.qbic.projectmanagement.domain.project.experiment.BiologicalReplicateId;
 import life.qbic.projectmanagement.domain.project.experiment.ExperimentId;
 
@@ -37,14 +38,17 @@ public class Sample {
   @AttributeOverride(name = "uuid", column = @Column(name = "sample_id"))
   private SampleId id;
   private String label;
+  private String comment;
+  @Column(name = "analysis_type")
+  private String analysisType;
   @Embedded
   private SampleCode sampleCode;
   @Embedded
   private SampleOrigin sampleOrigin;
 
   private Sample(SampleId id, SampleCode sampleCode, BatchId assignedBatch, String label,
       ExperimentId experimentId, Long experimentalGroupId, SampleOrigin sampleOrigin,
-      BiologicalReplicateId replicateReference
+      BiologicalReplicateId replicateReference, String analysisType, String comment
   ) {
     this.id = id;
     this.sampleCode = Objects.requireNonNull(sampleCode);
@@ -54,6 +58,8 @@ private Sample(SampleId id, SampleCode sampleCode, BatchId assignedBatch, String
     this.sampleOrigin = sampleOrigin;
     this.biologicalReplicateId = replicateReference;
     this.assignedBatch = assignedBatch;
+    this.analysisType = analysisType;
+    this.comment = comment;
   }
 
   protected Sample() {
@@ -75,7 +81,8 @@ public static Sample create(
         sampleRegistrationRequest.assignedBatch(),
         sampleRegistrationRequest.label(), sampleRegistrationRequest.experimentId(),
         sampleRegistrationRequest.experimentalGroupId(),
-        sampleRegistrationRequest.sampleOrigin(), sampleRegistrationRequest.replicateReference());
+        sampleRegistrationRequest.sampleOrigin(), sampleRegistrationRequest.replicateReference(),
+        sampleRegistrationRequest.analysisType(), sampleRegistrationRequest.comment());
   }
 
   public BatchId assignedBatch() {
@@ -98,6 +105,14 @@ public String label() {
     return this.label;
   }
 
+  public Optional<String> analysisType() {
+    return Optional.ofNullable(analysisType);
+  }
+
+  public Optional<String> comment() {
+    return Optional.ofNullable(comment);
+  }
+
   public Long experimentalGroupId() {
     return this.experimentalGroupId;
   }

projectmanagement/src/main/java/life/qbic/projectmanagement/domain/project/sample/SampleRegistrationRequest.java

@@ -1,6 +1,7 @@
 package life.qbic.projectmanagement.domain.project.sample;
 
 import java.util.Objects;
+import java.util.Optional;
 import life.qbic.projectmanagement.domain.project.experiment.BiologicalReplicateId;
 import life.qbic.projectmanagement.domain.project.experiment.ExperimentId;
 
@@ -15,21 +16,26 @@
  * @param experimentalGroupId the experimental group id the sample is part of
  * @param replicateReference  the biological replicated reference the sample has been taken from
  * @param sampleOrigin        information about the sample origin.
+ * @param analysisType        analysis to be performed
+ * @param comment             comment relating to the sample
  * @since 1.0.0
  */
 public record SampleRegistrationRequest(String label, BatchId assignedBatch,
                                         ExperimentId experimentId, Long experimentalGroupId,
                                         BiologicalReplicateId replicateReference,
-                                        SampleOrigin sampleOrigin) {
+                                        SampleOrigin sampleOrigin, String analysisType, String comment) {
 
   public SampleRegistrationRequest(String label, BatchId assignedBatch, ExperimentId experimentId,
       Long experimentalGroupId, BiologicalReplicateId replicateReference,
-      SampleOrigin sampleOrigin) {
+      SampleOrigin sampleOrigin, String analysisType, String comment) {
     this.label = Objects.requireNonNull(label);
     this.assignedBatch = Objects.requireNonNull(assignedBatch);
     this.experimentId = Objects.requireNonNull(experimentId);
     this.experimentalGroupId = Objects.requireNonNull(experimentalGroupId);
     this.replicateReference = Objects.requireNonNull(replicateReference);
     this.sampleOrigin = Objects.requireNonNull(sampleOrigin);
+    this.comment = comment;
+    this.analysisType = analysisType;
   }
+
 }

projectmanagement/src/test/groovy/life/qbic/projectmanagement/application/SampleRegistrationServiceSpec.groovy

@@ -33,7 +33,7 @@ class SampleRegistrationServiceSpec extends Specification {
     def "Invalid SampleRegistrationRequests returns a Result containing a SAMPLE_REGISTRATION_FAILED response code"() {
         given:
         SampleOrigin sampleOrigin = SampleOrigin.create(new Species("species"), new Specimen("specimen"), new Analyte("analyte"))
-        SampleRegistrationRequest sampleRegistrationRequest = new SampleRegistrationRequest("my_label", BatchId.create(), ExperimentId.create(), 5, BiologicalReplicateId.create(), sampleOrigin)
+        SampleRegistrationRequest sampleRegistrationRequest = new SampleRegistrationRequest("my_label", BatchId.create(), ExperimentId.create(), 5, BiologicalReplicateId.create(), sampleOrigin, "mytype", "no comment")
         SampleCode sampleCode = SampleCode.create("QABCDE")
         sampleCodeService.generateFor(projectId) >> Result.fromValue(sampleCode)
         Map<SampleCode, SampleRegistrationRequest> sampleCodesToRegistrationRequests = new HashMap<>()
@@ -53,7 +53,7 @@ class SampleRegistrationServiceSpec extends Specification {
     def "Valid SampleRegistrationRequests returns a Result with the list of registered Samples"() {
         given:
         SampleOrigin sampleOrigin = SampleOrigin.create(new Species("species"), new Specimen("specimen"), new Analyte("analyte"))
-        SampleRegistrationRequest sampleRegistrationRequest = new SampleRegistrationRequest("my_label", BatchId.create(), ExperimentId.create(), 4, BiologicalReplicateId.create(), sampleOrigin)
+        SampleRegistrationRequest sampleRegistrationRequest = new SampleRegistrationRequest("my_label", BatchId.create(), ExperimentId.create(), 4, BiologicalReplicateId.create(), sampleOrigin, "this analysis type", "a comment")
         SampleCode sampleCode = SampleCode.create("QABCDE")
         Sample sample = Sample.create(sampleCode, sampleRegistrationRequest)
         sampleCodeService.generateFor(projectId) >> Result.fromValue(sampleCode)

projectmanagement/src/test/groovy/life/qbic/projectmanagement/domain/project/service/SampleDomainServiceSpec.groovy

@@ -25,7 +25,7 @@ class SampleDomainServiceSpec extends Specification {
 
     def "When a sample has been successfully registered, a sample registered event is dispatched"() {
         given:
-        Sample testSample = Sample.create(SampleCode.create("test"), new SampleRegistrationRequest("test sample", BatchId.create(), ExperimentId.create(), 1L, BiologicalReplicateId.create(), new SampleOrigin(new Species("test"), new Specimen("test"), new Analyte("test"))))
+        Sample testSample = Sample.create(SampleCode.create("test"), new SampleRegistrationRequest("test sample", BatchId.create(), ExperimentId.create(), 1L, BiologicalReplicateId.create(), new SampleOrigin(new Species("test"), new Specimen("test"), new Analyte("test")), "DNA analysis", ""))
 
         and:
         SampleRepository testRepo = Mock(SampleRepository)
@@ -54,7 +54,7 @@ class SampleDomainServiceSpec extends Specification {
 
         when:
         Result<Sample, SampleDomainService.ResponseCode> result = sampleDomainService.registerSample(SampleCode.create("test"),
-                new SampleRegistrationRequest("test sample", BatchId.create(), ExperimentId.create(), 1L, BiologicalReplicateId.create(), new SampleOrigin(new Species("test"), new Specimen("test"), new Analyte("test"))))
+                new SampleRegistrationRequest("test sample", BatchId.create(), ExperimentId.create(), 1L, BiologicalReplicateId.create(), new SampleOrigin(new Species("test"), new Specimen("test"), new Analyte("test")), "DNA analysis", ""))
 
         then:
         sampleRegistered.batchIdOfEvent.equals(result.getValue().assignedBatch())

vaadinfrontend/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleOverviewComponent.java

@@ -61,7 +61,7 @@
  * Sample Overview Component
  * <p>
  * Component embedded within the {@link SampleInformationPage} in the {@link ProjectViewPage}. It
- * allows the user to see the information associated for all {@link Batch} and {@link Sample} of
+ * allows the user to see the information associated for each {@link Batch} and {@link Sample} of
  * each
  * {@link Experiment within a {@link life.qbic.projectmanagement.domain.project.Project}
  * Additionally it enables the user to register new {@link Batch} and {@link Sample} via the
@@ -289,6 +289,8 @@ private Grid<SamplePreview> createSampleGrid() {
       sampleGrid.addColumn(SamplePreview::species).setHeader("Species");
       sampleGrid.addColumn(SamplePreview::specimen).setHeader("Specimen");
       sampleGrid.addColumn(SamplePreview::analyte).setHeader("Analyte");
+      sampleGrid.addColumn(SamplePreview::analysisType).setHeader("Analysis to Perform");
+      sampleGrid.addColumn(SamplePreview::comment).setHeader("Comment");
       return sampleGrid;
     }
 
@@ -377,7 +379,8 @@ private List<SampleRegistrationRequest> createSampleRegistrationRequests(BatchId
             return new SampleRegistrationRequest(sampleRegistrationContent.label(), batchId,
                 experimentId,
                 sampleRegistrationContent.experimentalGroupId(),
-                sampleRegistrationContent.biologicalReplicateId(), sampleOrigin);
+                sampleRegistrationContent.biologicalReplicateId(), sampleOrigin,
+                sampleRegistrationContent.analysisType(), sampleRegistrationContent.comment());
           }).toList();
     }
 

vaadinfrontend/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/SampleRegistrationContent.java

@@ -15,12 +15,13 @@
  * @param species               String representation of the {@link Species}
  * @param specimen              String representation of the {@link Specimen}
  * @param analyte               String representation of the {@link Analyte}
+ * @param analysisType          The analysis to be performed
  * @param comment               Sample specific comments
  */
 
 public record SampleRegistrationContent(String label, BiologicalReplicateId biologicalReplicateId,
                                         Long experimentalGroupId,
-                                        String species, String specimen, String analyte,
+                                        String species, String specimen, String analyte, String analysisType,
                                         String comment) {
 
 }

vaadinfrontend/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/SampleSpreadsheetLayout.java

@@ -168,7 +168,7 @@ private List<SampleRegistrationContent> getContent() {
         SampleRegistrationContent sampleRegistrationContent = new SampleRegistrationContent(
             row.sampleLabel(), row.bioReplicateID(), row.experimentalGroupId(), row.species(),
             row.specimen(),
-            row.analyte(), row.customerComment());
+            row.analyte(), row.analysisType(), row.customerComment());
         samplesToRegister.add(sampleRegistrationContent);
       });
       return samplesToRegister;