Replace organism id with biological replicate (#789)

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

@@ -68,7 +68,7 @@ private Specification<SamplePreview> generateExperimentIdandFilterSpecification(
     Specification<SamplePreview> isBlankSpec = SamplePreviewSpecs.isBlank(filter);
     Specification<SamplePreview> experimentIdSpec = SamplePreviewSpecs.experimentIdEquals(
         experimentId);
-    Specification<SamplePreview> organismIdSpec = SamplePreviewSpecs.organismIdContains(filter);
+    Specification<SamplePreview> biologialReplicateSpec = SamplePreviewSpecs.biologicalReplicateContains(filter);
     Specification<SamplePreview> sampleCodeSpec = SamplePreviewSpecs.sampleCodeContains(filter);
     Specification<SamplePreview> sampleNameSpec = SamplePreviewSpecs.sampleNameContains(filter);
     Specification<SamplePreview> batchLabelSpec = SamplePreviewSpecs.batchLabelContains(filter);
@@ -80,7 +80,7 @@ private Specification<SamplePreview> generateExperimentIdandFilterSpecification(
         filter);
     Specification<SamplePreview> commentSpec = SamplePreviewSpecs.commentContains(filter);
     Specification<SamplePreview> containsFilterSpec = Specification.anyOf(sampleCodeSpec,
-        sampleNameSpec, organismIdSpec, batchLabelSpec, conditionSpec, speciesSpec,
+        sampleNameSpec, biologialReplicateSpec, batchLabelSpec, conditionSpec, speciesSpec,
         specimenSpec, analyteSpec, analysisMethodContains, commentSpec);
     Specification<SamplePreview> isDistinctSpec = SamplePreviewSpecs.isDistinct();
     return Specification.where(experimentIdSpec).and(isBlankSpec)
@@ -158,9 +158,9 @@ private static Specification<SamplePreview> ontologyColumnContains(String col, S
       };
     }
 
-    public static Specification<SamplePreview> organismIdContains(String filter) {
+    public static Specification<SamplePreview> biologicalReplicateContains(String filter) {
       return (root, query, builder) ->
-          builder.like(root.get("organismId"), "%" + filter + "%");
+          builder.like(root.get("biologicalReplicate"), "%" + filter + "%");
     }
 
     public static Specification<SamplePreview> speciesContains(String filter) {

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

@@ -17,16 +17,17 @@ public record SampleUpdateRequest(SampleId sampleId, SampleInformation sampleInf
   /**
    * Sample update request.
    * <p>
-   * @param sampleName          a human-readable semantic descriptor of the sample
-   * @param organismId           optional identifier of the sample's source patient or organism
+   * @param sampleName           a human-readable semantic descriptor of the sample
+   * @param biologicalReplicate  optional identifier of the sample's source patient or organism, to
+   *                             be able to group biological replicates
    * @param analysisMethod       analysis method to be performed
    * @param experimentalGroup    the experimental group the sample is part of
    * @param species              the species the sample belongs to
    * @param specimen             the specimen the sample belongs to.
    * @param analyte              the analyte the sample belongs to
    * @param comment              comment relating to the sample
    */
-  public record SampleInformation(String sampleName, String organismId,
+  public record SampleInformation(String sampleName, String biologicalReplicate,
                                   AnalysisMethod analysisMethod,
                                   ExperimentalGroup experimentalGroup, OntologyTerm species,
                                   OntologyTerm specimen, OntologyTerm analyte,

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

@@ -42,7 +42,7 @@ public class SamplePreview {
   private String sampleName;
 
   @Column(name = "organism_id")
-  private String organismId;
+  private String biologicalReplicate;
   private String comment;
   @Column(name = "analysis_method")
   private String analysisMethod;
@@ -58,7 +58,7 @@ protected SamplePreview() {
   }
 
   private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampleCode,
-      String batchLabel, String sampleName, String organismId,
+      String batchLabel, String sampleName, String biologicalReplicate,
       ExperimentalGroup experimentalGroup, OntologyTerm species,
       OntologyTerm specimen, OntologyTerm analyte, String analysisMethod, String comment) {
     Objects.requireNonNull(experimentId);
@@ -83,40 +83,40 @@ private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampl
     this.analysisMethod = analysisMethod;
     // optional columns
     this.comment = comment;
-    this.organismId = organismId;
+    this.biologicalReplicate = biologicalReplicate;
   }
 
   /**
    * Creates a new instance of a SamplePreview object.
    *
-   * @param experimentId      the {@link ExperimentId} of the associated experiment
-   * @param sampleId          the {@link SampleId} from which this preview was created
-   * @param sampleCode        the {@link SampleCode} associated with this SamplePreview
-   * @param batchLabel        the label of the {@link Batch} which contains the {@link Sample}
-   *                          associated with this preview
-   *                          associated with this preview
-   * @param sampleName       the name of the {@link Sample} associated with this preview
-   * @param organismId        optional identifier of the patient or organism a {@link Sample} was taken of
-   * @param experimentalGroup the {@link ExperimentalGroup} for the {@link Sample} associated with
-   *                          this preview
-   * @param species           the {@link OntologyTerm} for the species of this {@link Sample}
-   *                          associated with this preview
-   * @param specimen          the {@link OntologyTerm} for the specimen of this {@link Sample}
-   *                          associated with this preview
-   * @param analyte           the {@link OntologyTerm} for the analyte of this {@link Sample}
-   *                          associated with this preview
-   * @param analysisMethod    the analysis method to be performed for this {@link Sample}
-   * @param comment           an optional comment pertaining to the associated {@link Sample}
+   * @param experimentId        the {@link ExperimentId} of the associated experiment
+   * @param sampleId            the {@link SampleId} from which this preview was created
+   * @param sampleCode          the {@link SampleCode} associated with this SamplePreview
+   * @param batchLabel          the label of the {@link Batch} which contains the {@link Sample}
+   *                            associated with this preview
+   * @param sampleName          the name of the {@link Sample} associated with this preview
+   * @param biologicalReplicate optional identifier of the patient or organism a {@link Sample}
+   *                            was taken of. Used to group biological replicates
+   * @param experimentalGroup   the {@link ExperimentalGroup} for the {@link Sample} associated with
+   *                            this preview
+   * @param species             the {@link OntologyTerm} for the species of this {@link Sample}
+   *                            associated with this preview
+   * @param specimen            the {@link OntologyTerm} for the specimen of this {@link Sample}
+   *                            associated with this preview
+   * @param analyte             the {@link OntologyTerm} for the analyte of this {@link Sample}
+   *                            associated with this preview
+   * @param analysisMethod      the analysis method 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 sampleName, String organismId, ExperimentalGroup experimentalGroup,
+      String sampleName, String biologicalReplicate, ExperimentalGroup experimentalGroup,
       OntologyTerm species, OntologyTerm specimen, OntologyTerm analyte,
       String analysisMethod, String comment) {
     return new SamplePreview(experimentId, sampleId, sampleCode, batchLabel,
-        sampleName, organismId, experimentalGroup, species, specimen, analyte, analysisMethod,
+        sampleName, biologicalReplicate, experimentalGroup, species, specimen, analyte, analysisMethod,
         comment);
   }
 
@@ -160,8 +160,8 @@ public String comment() {
     return comment;
   }
 
-  public String organismId() {
-    return organismId;
+  public String biologicalReplicate() {
+    return biologicalReplicate;
   }
 
   public ExperimentalGroup experimentalGroup() {
@@ -180,7 +180,7 @@ public boolean equals(Object o) {
     return Objects.equals(experimentId, that.experimentId) && Objects.equals(
         sampleCode, that.sampleCode) && Objects.equals(sampleId, that.sampleId)
         && Objects.equals(batchLabel, that.batchLabel) && Objects.equals(sampleName,
-        that.sampleName) && Objects.equals(organismId, that.organismId)
+        that.sampleName) && Objects.equals(biologicalReplicate, that.biologicalReplicate)
         && Objects.equals(species, that.species) && Objects.equals(specimen,
         that.specimen) && Objects.equals(analyte, that.analyte) && Objects.equals(
         experimentalGroup, that.experimentalGroup) && Objects.equals(analysisMethod,
@@ -190,7 +190,7 @@ public boolean equals(Object o) {
   @Override
   public int hashCode() {
     return Objects.hash(experimentId, sampleCode, sampleId, batchLabel,
-        sampleName, organismId,
+        sampleName, biologicalReplicate,
         species, specimen, analyte, experimentalGroup, analysisMethod, comment);
   }
 
@@ -202,7 +202,7 @@ public String toString() {
         ", sampleId='" + sampleId + '\'' +
         ", batchLabel='" + batchLabel + '\'' +
         ", sampleName='" + sampleName + '\'' +
-        ", organismId='" + organismId + '\'' +
+        ", biologicalReplicate='" + biologicalReplicate + '\'' +
         ", species='" + species + '\'' +
         ", specimen='" + specimen + '\'' +
         ", analyte='" + analyte + '\'' +

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

@@ -44,7 +44,7 @@ public class Sample {
   private SampleId id;
   private String label;
   @Column(name = "organism_id")
-  private String organismId;
+  private String biologicalReplicate;
   private String comment;
 
   @Column(name = "analysis_method")
@@ -58,13 +58,13 @@ public class Sample {
   private SampleOrigin sampleOrigin;
 
   private Sample(SampleId id, SampleCode sampleCode, BatchId assignedBatch, String label,
-      String organismId, ExperimentId experimentId, Long experimentalGroupId,
+      String biologicalReplicate, ExperimentId experimentId, Long experimentalGroupId,
       SampleOrigin sampleOrigin,
       AnalysisMethod analysisMethod, String comment) {
     this.id = id;
     this.sampleCode = Objects.requireNonNull(sampleCode);
     this.label = label;
-    this.organismId = organismId;
+    this.biologicalReplicate = biologicalReplicate;
     this.experimentId = experimentId;
     this.experimentalGroupId = experimentalGroupId;
     this.sampleOrigin = sampleOrigin;
@@ -89,7 +89,7 @@ public static Sample create(SampleCode sampleCode,
     Objects.requireNonNull(sampleRegistrationRequest);
     SampleId sampleId = SampleId.create();
     return new Sample(sampleId, sampleCode, sampleRegistrationRequest.assignedBatch(),
-        sampleRegistrationRequest.label(), sampleRegistrationRequest.organismId(),
+        sampleRegistrationRequest.label(), sampleRegistrationRequest.biologicalReplicate(),
         sampleRegistrationRequest.experimentId(), sampleRegistrationRequest.experimentalGroupId(),
         sampleRegistrationRequest.sampleOrigin(),
         sampleRegistrationRequest.analysisMethod(), sampleRegistrationRequest.comment());
@@ -119,8 +119,8 @@ public String label() {
     return this.label;
   }
 
-  public String organismId() {
-    return this.organismId;
+  public String biologicalReplicate() {
+    return this.biologicalReplicate;
   }
 
   public Optional<String> comment() {
@@ -147,8 +147,8 @@ public void setLabel(String label) {
     this.label = label;
   }
 
-  public void setOrganismId(String organismId) {
-    this.organismId = organismId;
+  public void setBiologicalReplicate(String biologicalReplicate) {
+    this.biologicalReplicate = biologicalReplicate;
   }
 
   public void setComment(String comment) {
@@ -165,7 +165,7 @@ public void setSampleOrigin(SampleOrigin sampleOrigin) {
 
   public void update(SampleUpdateRequest sampleInfo) {
     setLabel(sampleInfo.sampleInformation().sampleName());
-    setOrganismId(sampleInfo.sampleInformation().organismId());
+    setBiologicalReplicate(sampleInfo.sampleInformation().biologicalReplicate());
     setAnalysisMethod(sampleInfo.sampleInformation().analysisMethod());
     setSampleOrigin(SampleOrigin.create(sampleInfo.sampleInformation().species(),
         sampleInfo.sampleInformation().specimen(), sampleInfo.sampleInformation().analyte()));

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

@@ -9,7 +9,8 @@
  * Serves as a parameter object for sample creation.
  *
  * @param label               a human-readable semantic descriptor of the sample
- * @param organismId          optional identifier of the patient or organism a sample was taken of
+ * @param biologicalReplicate optional identifier of the patient or organism a sample was taken of.
+ *                            Used to group biological replicates
  * @param assignedBatch       the assigned batch
  * @param experimentId        the experiment reference
  * @param experimentalGroupId the experimental group id the sample is part of
@@ -19,16 +20,16 @@
  *
  * @since 1.0.0
  */
-public record SampleRegistrationRequest(String label, String organismId, BatchId assignedBatch,
+public record SampleRegistrationRequest(String label, String biologicalReplicate, BatchId assignedBatch,
                                         ExperimentId experimentId, Long experimentalGroupId,
                                         SampleOrigin sampleOrigin, AnalysisMethod analysisMethod,
                                         String comment) {
 
-  public SampleRegistrationRequest(String label, String organismId, BatchId assignedBatch,
+  public SampleRegistrationRequest(String label, String biologicalReplicate, BatchId assignedBatch,
       ExperimentId experimentId, Long experimentalGroupId,
       SampleOrigin sampleOrigin, AnalysisMethod analysisMethod, String comment) {
     this.label = Objects.requireNonNull(label);
-    this.organismId = organismId;
+    this.biologicalReplicate = biologicalReplicate;
     this.assignedBatch = Objects.requireNonNull(assignedBatch);
     this.experimentId = Objects.requireNonNull(experimentId);
     this.experimentalGroupId = Objects.requireNonNull(experimentalGroupId);

project-management/src/main/java/life/qbic/projectmanagement/domain/service/SampleDomainService.java

@@ -86,7 +86,7 @@ public void updateSamples(Project project, Collection<SampleUpdateRequest> updat
           .filter(sampleUpdateRequest -> sampleUpdateRequest.sampleId().equals(sample.sampleId()))
           .findFirst().orElseThrow();
       sample.setLabel(sampleInfo.sampleInformation().sampleName());
-      sample.setOrganismId(sampleInfo.sampleInformation().organismId());
+      sample.setBiologicalReplicate(sampleInfo.sampleInformation().biologicalReplicate());
       sample.setAnalysisMethod(sampleInfo.sampleInformation().analysisMethod());
       sample.setSampleOrigin(SampleOrigin.create(sampleInfo.sampleInformation().species(),
           sampleInfo.sampleInformation().specimen(), sampleInfo.sampleInformation().analyte()));

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java

@@ -104,10 +104,10 @@ private static Grid<SamplePreview> createSampleGrid() {
         .setTooltipGenerator(SamplePreview::sampleName)
         .setAutoWidth(true)
         .setResizable(true);
-    sampleGrid.addColumn(SamplePreview::organismId)
-        .setHeader("Organism ID")
-        .setSortProperty("organismId")
-        .setTooltipGenerator(SamplePreview::organismId)
+    sampleGrid.addColumn(SamplePreview::biologicalReplicate)
+        .setHeader("Biological Replicate")
+        .setSortProperty("biologicalReplicate")
+        .setTooltipGenerator(SamplePreview::biologicalReplicate)
         .setAutoWidth(true)
         .setResizable(true);
     sampleGrid.addColumn(SamplePreview::batchLabel)

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java

@@ -233,7 +233,7 @@ private List<SampleRegistrationRequest> generateSampleRequestsFromSampleInfo(Bat
     List<SampleRegistrationRequest> sampleRegistrationRequests;
     sampleRegistrationRequests = sampleInfos.stream()
         .map(sample -> new SampleRegistrationRequest(
-            sample.getSampleName(), sample.getOrganismId(),
+            sample.getSampleName(), sample.getBiologicalReplicate(),
             batchId,
             context.experimentId().orElseThrow(),
             sample.getExperimentalGroup().id(),
@@ -247,7 +247,7 @@ private List<SampleRegistrationRequest> generateSampleRequestsFromSampleInfo(Bat
   private SampleUpdateRequest generateSampleUpdateRequestFromSampleInfo(
       SampleInfo sampleInfo) {
     return new SampleUpdateRequest(sampleInfo.getSampleId(), new SampleInformation(
-        sampleInfo.getSampleName(), sampleInfo.getOrganismId(),
+        sampleInfo.getSampleName(), sampleInfo.getBiologicalReplicate(),
         sampleInfo.getAnalysisToBePerformed(),
         sampleInfo.getExperimentalGroup(),
         sampleInfo.getSpecies(), sampleInfo.getSpecimen(), sampleInfo.getAnalyte(),
@@ -353,7 +353,7 @@ private SampleBatchInformationSpreadsheet.SampleInfo convertSampleToSampleInfo(S
     /*We currently allow replicates independent of experimental groups which is why we have to parse all replicates */
     return SampleBatchInformationSpreadsheet.SampleInfo.create(sample.sampleId(),
         sample.sampleCode(), sample.analysisMethod(),
-        sample.label(), sample.organismId(), experimentalGroup, sample.sampleOrigin()
+        sample.label(), sample.biologicalReplicate(), experimentalGroup, sample.sampleOrigin()
             .getSpecies(), sample.sampleOrigin().getSpecimen(), sample.sampleOrigin().getAnalyte(),
         sample.comment().orElse(""));
   }

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java

@@ -32,7 +32,7 @@ public byte[] getContent() {
     TSVBuilder<SamplePreview> tsvBuilder = new TSVBuilder<>(samples);
     tsvBuilder.addColumn("Sample ID", SamplePreview::sampleCode);
     tsvBuilder.addColumn("Sample Name", SamplePreview::sampleName);
-    tsvBuilder.addColumn("Organism ID", SamplePreview::organismId);
+    tsvBuilder.addColumn("Biological Replicate", SamplePreview::biologicalReplicate);
     tsvBuilder.addColumn("Batch", SamplePreview::batchLabel);
     tsvBuilder.addColumn("Species", sample -> sample.species().getLabel());
     tsvBuilder.addColumn("Specimen", sample -> sample.specimen().getLabel());

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java

@@ -119,8 +119,8 @@ private void createSampleInfoEntry(SamplePreview sample, Row sampleRow,
     var labelCol = sampleRow.createCell(SamplePreviewColumn.LABEL.column());
     labelCol.setCellValue(sample.sampleName());
 
-    var organismIdCol = sampleRow.createCell(SamplePreviewColumn.ORGANISM_ID.column());
-    organismIdCol.setCellValue(sample.organismId());
+    var bioRepCol = sampleRow.createCell(SamplePreviewColumn.BIOLOGICAL_REPLICATE.column());
+    bioRepCol.setCellValue(sample.biologicalReplicate());
 
     var batchCol = sampleRow.createCell(SamplePreviewColumn.BATCH.column());
     batchCol.setCellValue(sample.batchLabel());
@@ -162,7 +162,7 @@ enum SamplePreviewColumn {
 
     SAMPLE_ID("Sample ID", 0),
     LABEL("Sample Name", 1),
-    ORGANISM_ID("Organism ID", 2),
+    BIOLOGICAL_REPLICATE("Biological Replicate", 2),
     BATCH("Batch", 3),
     SPECIES("Species", 4),
     SPECIMEN("Specimen", 5),