Adds the project id to measurements

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

@@ -116,7 +116,7 @@ public Collection<ProteomicsMeasurement> findProteomicsMeasurement(String filter
   }
 
   private Result<MeasurementId, ResponseCode> registerNGS(
-      NGSMeasurementMetadata ngsMeasurementMetadata) {
+      ProjectId projectId, NGSMeasurementMetadata ngsMeasurementMetadata) {
 
     var associatedSampleCodes = ngsMeasurementMetadata.associatedSamples();
     var selectedSampleCode = MeasurementCode.createNGS(
@@ -134,6 +134,7 @@ private Result<MeasurementId, ResponseCode> registerNGS(
     }
 
     var measurement = NGSMeasurement.create(
+        projectId,
         sampleIdCodeEntries.stream().map(SampleIdCodeEntry::sampleId).toList(),
         selectedSampleCode,
         instrumentQuery.get());
@@ -150,7 +151,7 @@ private Result<MeasurementId, ResponseCode> registerNGS(
   }
 
   private Result<MeasurementId, ResponseCode> registerPxP(
-      ProteomicsMeasurementMetadata metadata) {
+      ProjectId projectId, ProteomicsMeasurementMetadata metadata) {
     var associatedSampleCodes = metadata.associatedSamples();
     var selectedSampleCode = MeasurementCode.createMS(
         String.valueOf(metadata.associatedSamples().get(0).code()));
@@ -183,6 +184,7 @@ private Result<MeasurementId, ResponseCode> registerPxP(
         label.sampleCode(), label.labelType(), label.label())).toList();
 
     var measurement = ProteomicsMeasurement.create(
+        projectId,
         sampleIdCodeEntries.stream().map(SampleIdCodeEntry::sampleId).toList(),
         selectedSampleCode,
         organisationQuery.get(),
@@ -213,10 +215,10 @@ public Result<MeasurementId, ResponseCode> register(ProjectId projectId,
       return Result.fromError(ResponseCode.MISSING_ASSOCIATED_SAMPLES);
     }
     if (measurementMetadata instanceof ProteomicsMeasurementMetadata proteomicsMeasurementMetadata) {
-      return registerPxP(proteomicsMeasurementMetadata);
+      return registerPxP(projectId, proteomicsMeasurementMetadata);
     }
     if (measurementMetadata instanceof NGSMeasurementMetadata ngsMeasurementMetadata) {
-      return registerNGS(ngsMeasurementMetadata);
+      return registerNGS(projectId, ngsMeasurementMetadata);
     }
     return Result.fromError(ResponseCode.FAILED);
   }

project-management/src/main/java/life/qbic/projectmanagement/domain/model/measurement/NGSMeasurement.java

@@ -1,12 +1,21 @@
 package life.qbic.projectmanagement.domain.model.measurement;
 
-import jakarta.persistence.*;
+import static java.util.Objects.requireNonNull;
 
+import jakarta.persistence.AttributeOverride;
+import jakarta.persistence.CollectionTable;
+import jakarta.persistence.Column;
+import jakarta.persistence.Convert;
+import jakarta.persistence.ElementCollection;
+import jakarta.persistence.Embedded;
+import jakarta.persistence.EmbeddedId;
+import jakarta.persistence.Entity;
+import jakarta.persistence.JoinColumn;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Objects;
 import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
 import life.qbic.projectmanagement.domain.model.OntologyTerm;
+import life.qbic.projectmanagement.domain.model.project.ProjectId;
 import life.qbic.projectmanagement.domain.model.sample.SampleId;
 
 /**
@@ -29,6 +38,10 @@ public class NGSMeasurement implements MeasurementMetadata {
   @AttributeOverride(name = "uuid", column = @Column(name = "measurement_id"))
   private MeasurementId id;
 
+  @Embedded
+  @Column(nullable = false)
+  private ProjectId projectId;
+
   @Embedded
   private OntologyTerm instrument;
 
@@ -44,9 +57,11 @@ protected NGSMeasurement() {
     // Needed for JPA
   }
 
-  private NGSMeasurement(Collection<SampleId> sampleIds, MeasurementCode measurementCode, OntologyTerm instrument) {
+  private NGSMeasurement(ProjectId projectId, Collection<SampleId> sampleIds,
+      MeasurementCode measurementCode, OntologyTerm instrument) {
     measuredSamples = new ArrayList<>();
     measuredSamples.addAll(sampleIds);
+    this.projectId = requireNonNull(projectId, "projectId must not be null");
     this.instrument = instrument;
     this.measurementCode = measurementCode;
   }
@@ -55,6 +70,7 @@ private NGSMeasurement(Collection<SampleId> sampleIds, MeasurementCode measureme
    * Creates a new {@link NGSMeasurement} object instance, that describes an NGS measurement entity
    * with many describing properties about provenance and instrumentation.
    *
+   * @param projectId
    * @param sampleIds  the sample ids of the samples the measurement was performed on. If more than
    *                   one sample id is provided, the measurement is considered to be performed on a
    *                   pooled sample
@@ -63,17 +79,18 @@ private NGSMeasurement(Collection<SampleId> sampleIds, MeasurementCode measureme
    * @return
    * @since 1.0.0
    */
-  public static NGSMeasurement create(Collection<SampleId> sampleIds, MeasurementCode measurementCode, OntologyTerm instrument) {
+  public static NGSMeasurement create(ProjectId projectId, Collection<SampleId> sampleIds,
+      MeasurementCode measurementCode, OntologyTerm instrument) {
     if (sampleIds.isEmpty()) {
       throw new IllegalArgumentException(
           "No sample ids provided. At least one sample id must provided for a measurement.");
     }
-    Objects.requireNonNull(instrument);
-    Objects.requireNonNull(measurementCode);
+    requireNonNull(instrument);
+    requireNonNull(measurementCode);
     if (!measurementCode.isNGSDomain()) {
       throw new IllegalArgumentException("NGSMeasurementMetadata code is not from the NGS domain for: \"" + measurementCode + "\"");
     }
-    return new NGSMeasurement(sampleIds, measurementCode, instrument);
+    return new NGSMeasurement(projectId, sampleIds, measurementCode, instrument);
   }
 
   /**

project-management/src/main/java/life/qbic/projectmanagement/domain/model/measurement/ProteomicsMeasurement.java

@@ -1,5 +1,7 @@
 package life.qbic.projectmanagement.domain.model.measurement;
 
+import static java.util.Objects.requireNonNull;
+
 import jakarta.persistence.AttributeOverride;
 import jakarta.persistence.CollectionTable;
 import jakarta.persistence.Column;
@@ -14,13 +16,13 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
-import java.util.Objects;
 import java.util.Optional;
 import java.util.Set;
 import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
 import life.qbic.projectmanagement.domain.Organisation;
 import life.qbic.projectmanagement.domain.model.OntologyTerm;
 import life.qbic.projectmanagement.domain.model.measurement.MeasurementCode.MeasurementCodeConverter;
+import life.qbic.projectmanagement.domain.model.project.ProjectId;
 import life.qbic.projectmanagement.domain.model.sample.SampleId;
 
 /**
@@ -43,6 +45,10 @@ public class ProteomicsMeasurement implements MeasurementMetadata {
   @AttributeOverride(name = "uuid", column = @Column(name = "measurement_id"))
   private MeasurementId id;
 
+  @Embedded
+  @Column(nullable = false)
+  ProjectId projectId;
+
   @Column(name = "instrument", columnDefinition = "longtext CHECK (json_valid(`instrument`))")
   private OntologyTerm instrument;
 
@@ -97,9 +103,11 @@ protected ProteomicsMeasurement() {
     // Needed for JPA
   }
 
-  private ProteomicsMeasurement(MeasurementId id, Collection<SampleId> sampleIds,
+  private ProteomicsMeasurement(ProjectId projectId, MeasurementId id,
+      Collection<SampleId> sampleIds,
       MeasurementCode measurementCode,
       Organisation organisation, ProteomicsMethodMetadata method, Instant registration) {
+    this.projectId = requireNonNull(projectId, "projectId must not be null");
     evaluateMandatorMetadata(
         method); // throws IllegalArgumentException if required properties are missing
     measuredSamples = new ArrayList<>();
@@ -155,35 +163,38 @@ private static void evaluateMandatorMetadata(ProteomicsMethodMetadata method)
    * Creates a new {@link ProteomicsMeasurement} object instance, that describes an NGS measurement
    * entity with many describing properties about provenance and instrumentation.
    *
+   * @param projectId
    * @param sampleIds the sample ids of the samples the measurement was performed on. If more than
    *                  one sample id is provided, the measurement is considered to be performed on a
    *                  pooled sample
    * @return
    * @throws IllegalArgumentException in case there are missing required metadata.
    * @since 1.0.0
    */
-  public static ProteomicsMeasurement create(Collection<SampleId> sampleIds,
+  public static ProteomicsMeasurement create(ProjectId projectId, Collection<SampleId> sampleIds,
       MeasurementCode measurementCode, Organisation organisation, ProteomicsMethodMetadata method)
       throws IllegalArgumentException {
     if (sampleIds.isEmpty()) {
       throw new IllegalArgumentException(
           "No sample ids provided. At least one sample id must provided for a measurement.");
     }
-    Objects.requireNonNull(method.instrument());
-    Objects.requireNonNull(measurementCode);
+    requireNonNull(method.instrument());
+    requireNonNull(measurementCode);
     if (!measurementCode.isMSDomain()) {
       throw new IllegalArgumentException(
           "Proteomics code is not from the Proteomics domain for: \"" + measurementCode + "\"");
     }
     var measurementId = MeasurementId.create();
-    return new ProteomicsMeasurement(measurementId, sampleIds, measurementCode, organisation,
+    return new ProteomicsMeasurement(projectId, measurementId, sampleIds, measurementCode,
+        organisation,
         method, Instant.now());
   }
 
-  public static ProteomicsMeasurement create(Collection<SampleId> sampleIds, MeasurementCode code,
+  public static ProteomicsMeasurement create(ProjectId projectId, Collection<SampleId> sampleIds,
+      MeasurementCode code,
       Organisation organisation, ProteomicsMethodMetadata method,
       ProteomicsSamplePreparation samplePreparation) {
-    var measurement = create(sampleIds, code, organisation, method);
+    var measurement = create(projectId, sampleIds, code, organisation, method);
     measurement.setSamplePreparation(samplePreparation);
     return measurement;
   }