x1476 include (ancestral) qpcr results comments in release file

src/main/java/uk/ac/sanger/sccp/stan/service/releasefile/ReleaseColumn.java

@@ -48,6 +48,7 @@ public enum ReleaseColumn implements TsvColumn<ReleaseEntry> {
     Tissue_coverage(ReleaseEntry::getCoverage, ReleaseFileOption.Visium),
     Permeabilisation_time(ReleaseEntry::getPermTime, ReleaseFileOption.Visium),
     Cq_value(ReleaseEntry::getCq, ReleaseFileOption.Visium),
+    qPCR_comment(ReleaseEntry::getQpcrComment, ReleaseFileOption.Visium),
     Number_of_amplification_cycles(ReleaseEntry::getAmplificationCycles, ReleaseFileOption.Visium),
     Visium_concentration(ReleaseEntry::getVisiumConcentration, ReleaseFileOption.Visium),
     Visium_concentration_type(ReleaseEntry::getVisiumConcentrationType, ReleaseFileOption.Visium),

src/main/java/uk/ac/sanger/sccp/stan/service/releasefile/ReleaseEntry.java

@@ -31,6 +31,7 @@ public class ReleaseEntry {
     private String reagentPlateType;
     private String reagentSource;
     private String cq;
+    private String qpcrComment;
     private String visiumConcentration;
     private String visiumConcentrationType;
     private String sizeRange;
@@ -186,6 +187,14 @@ public void setCq(String cq) {
         this.cq = cq;
     }
 
+    public String getQpcrComment() {
+        return this.qpcrComment;
+    }
+
+    public void setQpcrComment(String qpcrComment) {
+        this.qpcrComment = qpcrComment;
+    }
+
     public String getVisiumConcentration() {
         return this.visiumConcentration;
     }

src/main/java/uk/ac/sanger/sccp/stan/service/releasefile/ReleaseFileService.java

@@ -132,6 +132,7 @@ public ReleaseFileContent getReleaseFileContent(Collection<Integer> releaseIds,
         if (options.contains(ReleaseFileOption.Visium)) {
             loadVisiumBarcodes(entries, ancestry);
             loadSizeRanges(entries, slotIds);
+            loadQpcrComments(entries, ancestry);
         }
         if (options.contains(ReleaseFileOption.Histology)) {
             loadRnaAnalysis(entries, slotIds);
@@ -984,6 +985,33 @@ public void loadImagingQcComments(Collection<ReleaseEntry> entries, Ancestry anc
         }
     }
 
+
+    /** Loads comments from qpcr operations */
+    public void loadQpcrComments(Collection<ReleaseEntry> entries, Ancestry ancestry) {
+        OperationType qpcrOpType = opTypeRepo.getByName("qPCR results");
+        Set<Integer> allSlotIds = ancestry.keySet().stream().map(SlotSample::slotId).collect(toSet());
+        List<Operation> ops = opRepo.findAllByOperationTypeAndDestinationSlotIdIn(qpcrOpType, allSlotIds);
+        if (ops.isEmpty()) {
+            return;
+        }
+        List<OperationComment> opcoms = opComRepo.findAllByOperationIdIn(ops.stream().map(Operation::getId).collect(toList()));
+        Map<SlotIdSampleId, List<OperationComment>> slotIdComs = opcoms.stream()
+                .collect(groupingBy(oc -> new SlotIdSampleId(oc.getSlotId(), oc.getSampleId())));
+        for (ReleaseEntry entry : entries) {
+            SlotSample key = new SlotSample(entry.getSlot(), entry.getSample());
+            Set<OperationComment> entryOcs = new HashSet<>();
+            for (SlotSample ss : ancestry.ancestors(key)) {
+                List<OperationComment> ocs = slotIdComs.get(new SlotIdSampleId(ss.slotId(), ss.sampleId()));
+                if (!nullOrEmpty(ocs)) {
+                    entryOcs.addAll(ocs);
+                }
+            }
+            if (!nullOrEmpty(entryOcs)) {
+                entry.setQpcrComment(joinComments(entryOcs.stream()));
+            }
+        }
+    }
+
     /**
      * Sets various measurements for the release entries.
      * The measurements may be recorded on the specified slot, or any ancestral slot

src/test/java/uk/ac/sanger/sccp/stan/integrationtest/TestReleaseMutation.java

@@ -76,7 +76,7 @@ public class TestReleaseMutation {
     @Transactional
     public void testRelease() throws Exception {
         Stream.of("Probe hybridisation Xenium", "Probe hybridisation QC", "Xenium analyser",
-                "Xenium analyser QC", "DV200 analysis", "RIN analysis", "Paraffin processing")
+                "Xenium analyser QC", "DV200 analysis", "RIN analysis", "Paraffin processing", "qPCR results")
                         .forEach(name -> entityCreator.createOpType(name, null, OperationTypeFlag.IN_PLACE));
         Work work1 = entityCreator.createWork(null, null, null, null, null);
         Donor donor = entityCreator.createDonor("DONOR1");

src/test/java/uk/ac/sanger/sccp/stan/service/releasefile/TestReleaseFileService.java

@@ -198,6 +198,7 @@ public void testGetReleaseFileContent(StorageDetail detail, boolean includeVisiu
         doNothing().when(service).loadSectionComments(any());
         doNothing().when(service).loadVisiumBarcodes(any(), any());
         doNothing().when(service).loadSizeRanges(any(), any());
+        doNothing().when(service).loadQpcrComments(any(), any());
         doNothing().when(service).loadXeniumFields(any(), any());
         doNothing().when(service).loadSolutions(any());
         doNothing().when(service).loadFlags(any());
@@ -227,6 +228,7 @@ public void testGetReleaseFileContent(StorageDetail detail, boolean includeVisiu
         verify(service).loadSectionComments(entries);
         verify(service, times(includeVisium ? 1 : 0)).loadVisiumBarcodes(entries, ancestry);
         verify(service, times(includeVisium ? 1 : 0)).loadSizeRanges(entries, slotIds);
+        verify(service, times(includeVisium ? 1 : 0)).loadQpcrComments(entries, ancestry);
         verify(service).loadXeniumFields(entries, slotIds);
         verify(service).loadSolutions(entries);
         verify(service).loadFlags(entries);
@@ -814,6 +816,39 @@ public void testLoadStains() {
         verify(service).loadImagingQcComments(entries, ancestry, Set.of(100,101));
     }
 
+    @Test
+    public void testLoadQpcrComments() {
+        setupLabware();
+        OperationType opType = EntityFactory.makeOperationType("qPCR results", null);
+        when(mockOpTypeRepo.getByName(any())).thenReturn(opType);
+        Labware lw3 = EntityFactory.makeLabware(EntityFactory.getTubeType(), sample);
+        Labware lw4 = EntityFactory.makeLabware(EntityFactory.getTubeType(), sample);
+        Ancestry ancestry = makeAncestry(lw3, sample, lw2, sample, lw2, sample, lw1, sample);
+        ancestry.put(new SlotSample(lw4.getFirstSlot(), sample), Set.of());
+        List<Operation> qpcrOps = IntStream.of(3,4).mapToObj(i -> {
+            Operation op = new Operation();
+            op.setId(i);
+            return op;
+        }).toList();
+        when(mockOpRepo.findAllByOperationTypeAndDestinationSlotIdIn(any(), any())).thenReturn(qpcrOps);
+        List<OperationComment> opComs = List.of(
+                new OperationComment(10, new Comment(1, "Banana", "c"), 3, sample.getId(), lw1.getFirstSlot().getId(), null),
+                new OperationComment(11, new Comment(2, "Custard", "c"), 4, sample.getId(), lw2.getFirstSlot().getId(), null)
+        );
+        when(mockOpComRepo.findAllByOperationIdIn(any())).thenReturn(opComs);
+        List<ReleaseEntry> entries = List.of(
+                new ReleaseEntry(lw3, lw3.getFirstSlot(), sample),
+                new ReleaseEntry(lw4, lw4.getFirstSlot(), sample)
+        );
+        service.loadQpcrComments(entries, ancestry);
+        verify(mockOpTypeRepo).getByName("qPCR results");
+        Set<Integer> allSlotIds = ancestry.keySet().stream().map(SlotSample::slotId).collect(toSet());
+        verify(mockOpRepo).findAllByOperationTypeAndDestinationSlotIdIn(opType, allSlotIds);
+        verify(mockOpComRepo).findAllByOperationIdIn(List.of(3,4));
+        assertThat(entries.get(0).getQpcrComment()).isIn("Banana. Custard.", "Custard. Banana.");
+        assertThat(entries.get(1).getQpcrComment()).isNullOrEmpty();
+    }
+
     @Test
     public void testLoadImagingQcComments() {
         setupLabware();