x1561: Sectioning order is specified in plan request and saved

src/main/java/uk/ac/sanger/sccp/stan/model/PlanAction.java

@@ -30,6 +30,7 @@ public class PlanAction {
     private String sampleThickness;
     @ManyToOne
     private BioState newBioState;
+    private Integer sectioningOrder;
 
     public PlanAction() {}
 
@@ -113,6 +114,14 @@ public void setNewBioState(BioState newBioState) {
         this.newBioState = newBioState;
     }
 
+    public Integer getSectioningOrder() {
+        return this.sectioningOrder;
+    }
+
+    public void setSectioningOrder(Integer sectioningOrder) {
+        this.sectioningOrder = sectioningOrder;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
@@ -125,7 +134,9 @@ public boolean equals(Object o) {
                 && Objects.equals(this.sample, that.sample)
                 && Objects.equals(this.newSection, that.newSection)
                 && Objects.equals(this.sampleThickness, that.sampleThickness)
-                && Objects.equals(this.newBioState, that.newBioState));
+                && Objects.equals(this.newBioState, that.newBioState)
+                && Objects.equals(this.sectioningOrder, that.sectioningOrder)
+        );
     }
 
     @Override
@@ -144,6 +155,7 @@ public String toString() {
                 .addRepr("newSection", newSection)
                 .add("sampleThickness", sampleThickness)
                 .add("newBioState", newBioState)
+                .add("sectioningOrder", sectioningOrder)
                 .toString();
     }
 }

src/main/java/uk/ac/sanger/sccp/stan/request/plan/PlanRequestAction.java

@@ -17,6 +17,7 @@ public class PlanRequestAction {
     private int sampleId;
     private PlanRequestSource source;
     private String sampleThickness;
+    private Integer sectioningOrder;
 
     public PlanRequestAction() {}
 
@@ -59,6 +60,14 @@ public void setSampleThickness(String sampleThickness) {
         this.sampleThickness = sampleThickness;
     }
 
+    public Integer getSectioningOrder() {
+        return this.sectioningOrder;
+    }
+
+    public void setSectioningOrder(Integer sectioningOrder) {
+        this.sectioningOrder = sectioningOrder;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
@@ -67,7 +76,9 @@ public boolean equals(Object o) {
         return (this.sampleId==that.sampleId
                 && Objects.equals(this.addresses, that.addresses)
                 && Objects.equals(this.source, that.source)
-                && Objects.equals(this.sampleThickness, that.sampleThickness));
+                && Objects.equals(this.sampleThickness, that.sampleThickness)
+                && Objects.equals(this.sectioningOrder, that.sectioningOrder)
+        );
     }
 
     @Override
@@ -82,6 +93,7 @@ public String toString() {
                 .add("sampleId", sampleId)
                 .add("source", source)
                 .add("sampleThickness", sampleThickness)
+                .add("sectioningOrder", sectioningOrder)
                 .toString();
     }
 }

src/main/java/uk/ac/sanger/sccp/stan/service/operation/plan/PlanServiceImp.java

@@ -180,10 +180,12 @@ public List<PlanAction> createActions(PlanRequestLabware requestLabware, int pla
                     .findAny()
                     .orElseThrow(() -> new EntityNotFoundException("Sample " + prac.getSampleId()
                             + " not found in " + prac.getSource()));
+            Integer sectioningOrder = prac.getSectioningOrder();
             for (Address ad : prac.getAddresses()) {
                 Slot slot1 = destination.getSlot(ad);
                 PlanAction action = new PlanAction(null, planId, slot0, slot1, originalSample,
                         null, prac.getSampleThickness(), newBioState);
+                action.setSectioningOrder(sectioningOrder);
                 actions.add(action);
             }
         }

src/main/java/uk/ac/sanger/sccp/stan/service/operation/plan/PlanValidationImp.java

@@ -70,6 +70,7 @@ public UCMap<Labware> validateSources(OperationType opType) {
         Set<String> releasedBarcodes = new LinkedHashSet<>();
         Set<String> discardedBarcodes = new LinkedHashSet<>();
         Set<String> usedBarcodes = new LinkedHashSet<>();
+        Map<Integer, Set<Integer>> sampleIdSectioningOrders = new HashMap<>();
         for (PlanRequestAction action : (Iterable<PlanRequestAction>) (actions()::iterator)) {
             PlanRequestSource source = action.getSource();
             if (source==null || source.getBarcode()==null || source.getBarcode().isEmpty()) {
@@ -111,11 +112,19 @@ public UCMap<Labware> validateSources(OperationType opType) {
                 addProblem("Slot %s of labware %s does not contain a sample with ID %s.",
                         address, barcode, action.getSampleId());
             }
+            if (action.getSectioningOrder()==null) {
+                addProblem("Missing sectioning order.");
+            }
             if (opType!=null && opType.sourceMustBeBlock() && !slot.isBlock()) {
                 addProblem("Source %s,%s is not a block for operation %s.", action.getSource().getBarcode(), address,
                         opType.getName());
             } else if (opType!=null && !opType.canCreateSection() && sample!=null && sample.getSection()==null) {
                 addProblem("Operation %s cannot create a section of sample %s.", opType.getName(), sample.getId());
+            } else if (sample != null && action.getSectioningOrder() != null) {
+                Set<Integer> secOrders = sampleIdSectioningOrders.computeIfAbsent(sample.getId(), k -> new HashSet<>());
+                if (!secOrders.add(action.getSectioningOrder())) {
+                    addProblem("Repeated sectioning order: %s from sample %s.", action.getSectioningOrder(), sample.getId());
+                }
             }
         }
         if (!unfoundBarcodes.isEmpty()) {

src/main/resources/db/changelog/changelog-4.03.xml

@@ -0,0 +1,14 @@
+<?xml version="1.1" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.1.xsd">
+
+    <changeSet id="4.3.0" author="dr6">
+        <addColumn tableName="plan_action">
+            <column name="sectioning_order" type="INT" afterColumn="sample_thickness">
+                <constraints nullable="true"/>
+            </column>
+        </addColumn>
+    </changeSet>
+
+</databaseChangeLog>

src/main/resources/db/changelog/changelog-master.xml

@@ -47,4 +47,5 @@
     <include relativeToChangelogFile="true" file="changelog-4.00.xml"/>
     <include relativeToChangelogFile="true" file="changelog-4.01.xml"/>
     <include relativeToChangelogFile="true" file="changelog-4.02.xml"/>
+    <include relativeToChangelogFile="true" file="changelog-4.03.xml"/>
 </databaseChangeLog>

src/main/resources/schema.graphqls

@@ -534,6 +534,8 @@ type PlanAction {
     newSection: String
     """The planned thickness of the sample, if any."""
     sampleThickness: String
+    """An indicator for the order sections are taken from their block."""
+    sectioningOrder: Int
 }
 
 """A planned operation."""
@@ -554,6 +556,8 @@ input PlanRequestAction {
     sampleThickness: String
     """The source of the sample (describing a slot in some existing labware)."""
     source: PlanRequestSource!
+    """An indicator for the order sections are taken from their block."""
+    sectioningOrder: Int!
 }
 
 """A specification of new labware to be created for a plan request."""

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

@@ -89,7 +89,7 @@ public void testPlanAndRecordSection() throws Exception {
         String[] expectedPlanDestAddresses = { "A1", "A2", "B2" };
         int[] expectedPlanSampleId = {blockSamples[0].getId(), blockSamples[0].getId(), blockSamples[1].getId()};
         assertEquals(expectedPlanDestAddresses.length, resultActions.size());
-
+        int[] expectedSectioningOrder = {1,1,2};
         for (int i = 0; i < expectedPlanDestAddresses.length; ++i) {
             Map<String, ?> resultAction = resultActions.get(i);
             assertEquals("A1", chainGet(resultAction, "source", "address"));
@@ -99,6 +99,7 @@ public void testPlanAndRecordSection() throws Exception {
             if (i == expectedPlanDestAddresses.length - 1) {
                 assertEquals("2.5", resultAction.get("sampleThickness"));
             }
+            assertEquals(expectedSectioningOrder[i], resultAction.get("sectioningOrder"));
         }
 
         testRetrievePlanData(barcodes);
@@ -120,7 +121,7 @@ private void testRetrievePlanData(String[] barcodes) throws Exception {
         List<Map<String,?>> planActionsData = chainGet(planData, "plan", "planActions");
         assertThat(planActionsData).hasSize(3);
         assertEquals(List.of(List.of("A1", "A2"), List.of("B2")), planData.get("groups"));
-
+        int[] expectedSectioningOrder = {3,4};
         for (int i = 1; i < barcodes.length; ++i) {
             String barcode = barcodes[i]; // fetal waste barcode
             result = tester.post(planQuery.replace("$BARCODE", barcode));
@@ -133,6 +134,7 @@ private void testRetrievePlanData(String[] barcodes) throws Exception {
                     .collect(toList())).containsExactlyInAnyOrder(sources[i-1]);
             planActionsData = chainGet(planData, "plan", "planActions");
             assertThat(planActionsData).hasSize(1);
+            assertEquals(expectedSectioningOrder[i-1], planActionsData.getFirst().get("sectioningOrder"));
         }
         assertEquals(List.of(List.of("A1")), planData.get("groups"));
     }

src/test/java/uk/ac/sanger/sccp/stan/service/operation/plan/TestPlanService.java

@@ -323,11 +323,13 @@ public void testCreateActions(boolean useNewBioState) {
                         new PlanRequestAction(A2, samples.get(0).getId(),
                                 new PlanRequestSource(sourceBarcodes.get(0), null), "1")
                 ));
+        Zip.enumerate(prl.getActions().stream()).forEach((i, a) -> a.setSectioningOrder(i+1));
 
         List<PlanAction> expectedActions = List.of(
                 new PlanAction(21, planId, sources.get(0).getFirstSlot(), destination.getFirstSlot(), samples.get(0), null, null, bioState),
                 new PlanAction(22, planId, sources.get(0).getFirstSlot(), destination.getSlot(A2), samples.get(0), null, "1", bioState)
         );
+        Zip.enumerate(expectedActions.stream()).forEach((i, a) -> a.setSectioningOrder(i+1));
 
         final int[] planActionIdCounter = {20};
         when(mockPlanActionRepo.saveAll(any())).then(invocation -> {

src/test/java/uk/ac/sanger/sccp/stan/service/operation/plan/TestPlanValidation.java

@@ -158,7 +158,7 @@ public void testValidatePrebarcode(String barcode, boolean xenium, boolean preba
 
     @ParameterizedTest
     @MethodSource("sourcesData")
-    public void testValidateSources(Object sourceBarcodes, Object sourceAddresses, Integer sampleId,
+    public void testValidateSources(Object sourceBarcodes, Object sourceAddresses, Integer sampleId, Integer sectioningOrder,
                                     Labware existingLabware, OperationType opType, Object expectedProblems) {
         when(mockLabwareRepo.findByBarcode(any())).thenReturn(Optional.empty());
         if (existingLabware!=null) {
@@ -173,6 +173,9 @@ public void testValidateSources(Object sourceBarcodes, Object sourceAddresses, I
                             new PlanRequestSource(bc, sourceAddressIter.hasNext() ? sourceAddressIter.next() : null), null)
                     )
                     .collect(toList());
+        if (sectioningOrder != null) {
+            prActions.forEach(a -> a.setSectioningOrder(sectioningOrder));
+        }
 
         PlanRequest request = new PlanRequest(
                 opType.getName(),
@@ -418,27 +421,29 @@ static Stream<Arguments> sourcesData() {
         OperationType otherOpType = EntityFactory.makeOperationType("Other", null);
 
         return Stream.of(
-                Arguments.of(List.of(), List.of(), null, null, sectionOpType, null),
-                Arguments.of(block.getBarcode(), A1, blockSampleId, block, sectionOpType, null),
-                Arguments.of(block.getBarcode(), null, blockSampleId, block, sectionOpType, null),
-                Arguments.of(nonBlock.getBarcode(), null, sectionSampleId, nonBlock, otherOpType, null),
-
-                Arguments.of(destroyedLw.getBarcode(), A1, sectionSampleId, destroyedLw, otherOpType, "Labware already destroyed: ["+destroyedLw.getBarcode()+"]"),
-                Arguments.of(releasedLw.getBarcode(), A1, sectionSampleId, releasedLw, otherOpType, "Labware already released: ["+releasedLw.getBarcode()+"]"),
-                Arguments.of(discardedLw.getBarcode(), A1, sectionSampleId, discardedLw, otherOpType, "Labware already discarded: ["+discardedLw.getBarcode()+"]"),
-                Arguments.of(null, A1, blockSampleId, null, sectionOpType, "Missing source barcode."),
-                Arguments.of("", A1, blockSampleId, null, sectionOpType, "Missing source barcode."),
-                Arguments.of("404", A1, blockSampleId, null, sectionOpType, "Unknown labware barcode: [404]"),
-                Arguments.of(block.getBarcode(), new Address(2,3), blockSampleId, block, sectionOpType,
+                Arguments.of(List.of(), List.of(), null, 1, null, sectionOpType, null),
+                Arguments.of(block.getBarcode(), A1, blockSampleId, 1, block, sectionOpType, null),
+                Arguments.of(block.getBarcode(), null, blockSampleId, 1, block, sectionOpType, null),
+                Arguments.of(nonBlock.getBarcode(), null, sectionSampleId, 1, nonBlock, otherOpType, null),
+
+                Arguments.of(List.of(block.getBarcode(), block.getBarcode()), List.of(A1, A1), blockSampleId, 1, block, sectionOpType, "Repeated sectioning order: 1 from sample "+ blockSampleId+"."),
+                Arguments.of(block.getBarcode(), A1, blockSampleId, null, block, sectionOpType, "Missing sectioning order."),
+                Arguments.of(destroyedLw.getBarcode(), A1, sectionSampleId, 1, destroyedLw, otherOpType, "Labware already destroyed: ["+destroyedLw.getBarcode()+"]"),
+                Arguments.of(releasedLw.getBarcode(), A1, sectionSampleId, 1, releasedLw, otherOpType, "Labware already released: ["+releasedLw.getBarcode()+"]"),
+                Arguments.of(discardedLw.getBarcode(), A1, sectionSampleId, 1, discardedLw, otherOpType, "Labware already discarded: ["+discardedLw.getBarcode()+"]"),
+                Arguments.of(null, A1, blockSampleId, 1, null, sectionOpType, "Missing source barcode."),
+                Arguments.of("", A1, blockSampleId, 1, null, sectionOpType, "Missing source barcode."),
+                Arguments.of("404", A1, blockSampleId, 1, null, sectionOpType, "Unknown labware barcode: [404]"),
+                Arguments.of(block.getBarcode(), new Address(2,3), blockSampleId, 1, block, sectionOpType,
                         "Labware "+block.getBarcode()+" ("+lt.getName()+") has no slot at address B3."),
-                Arguments.of(block.getBarcode(), null, blockSampleId+1, block, sectionOpType,
+                Arguments.of(block.getBarcode(), null, blockSampleId+1, 1, block, sectionOpType,
                         "Slot A1 of labware "+block.getBarcode()+" does not contain a sample with ID "+(blockSampleId+1)+"."),
-                Arguments.of(block.getBarcode(), null, blockSampleId, block, nonSectionOpType,
+                Arguments.of(block.getBarcode(), null, blockSampleId, 1, block, nonSectionOpType,
                         "Operation Nonsection cannot create a section of sample "+blockSampleId+"."),
-                Arguments.of(nonBlock.getBarcode(), null, sectionSampleId, nonBlock, sectionOpType,
+                Arguments.of(nonBlock.getBarcode(), null, sectionSampleId, 1, nonBlock, sectionOpType,
                         "Source "+nonBlock.getBarcode()+",A1 is not a block for operation "+sectionOpType.getName()+"."),
-                Arguments.of(List.of("404", "404"), List.of(), blockSampleId, null, sectionOpType, "Unknown labware barcode: [404]"),
-                Arguments.of(List.of("404", "405"), List.of(), blockSampleId, null, sectionOpType, "Unknown labware barcodes: [404, 405]")
+                Arguments.of(List.of("404", "404"), List.of(), blockSampleId, 1, null, sectionOpType, "Unknown labware barcode: [404]"),
+                Arguments.of(List.of("404", "405"), List.of(), blockSampleId, 1, null, sectionOpType, "Unknown labware barcodes: [404, 405]")
         );
     }
 

src/test/resources/graphql/plan.graphql

@@ -10,12 +10,14 @@ mutation {
                     source:{ barcode:"STAN-B70C" }
                     addresses: ["A1", "A2"]
                     sampleId: 55555
+                    sectioningOrder: 1
                 }
                 {
                     source: { barcode: "STAN-B70D" }
                     addresses: ["B2"]
                     sampleId: 55556
                     sampleThickness: "2.5"
+                    sectioningOrder: 2
                 }
             ]
         }, {
@@ -25,6 +27,7 @@ mutation {
                     source:{ barcode:"STAN-B70C" }
                     addresses: ["A1"]
                     sampleId: 55555
+                    sectioningOrder: 3
                 }
             ]
         }, {
@@ -34,6 +37,7 @@ mutation {
                     source:{ barcode:"STAN-B70D" }
                     addresses: ["A1"]
                     sampleId: 55556
+                    sectioningOrder: 4
                 }
             ]
         }]
@@ -58,6 +62,7 @@ mutation {
                 sample { id }
                 newSection
                 sampleThickness
+                sectioningOrder
             }
         }
     }

src/test/resources/graphql/plan_simple.graphql

@@ -8,6 +8,7 @@ mutation {
                     source:{ barcode:"BARCODE0" }
                     addresses: ["A1"]
                     sampleId: 55555
+                    sectioningOrder: 1
                 }
             ]
         }]

src/test/resources/graphql/plandata.graphql

@@ -7,6 +7,7 @@ query {
                     labwareId
                     address
                 }
+                sectioningOrder
             }
         }
         destination {