x1238 Xenium analyser decoding consumables lot

src/main/java/uk/ac/sanger/sccp/stan/config/FieldValidation.java

@@ -290,6 +290,21 @@ public Validator<String> reagentPlateBarcodeValidator() {
         return new StringValidator("Reagent plate barcode", 24, 24, charTypes);
     }
 
+    @Bean
+    public Validator<String> samplePrepReagentLotValidator() {
+        return new StringValidator("Sample prep reagent lot", 6, 6, CharacterType.DIGIT);
+    }
+
+    @Bean
+    public Validator<String> reagentLotValidator() {
+        return new StringValidator("Reagent lot", 6, 6, CharacterType.DIGIT);
+    }
+
+    @Bean
+    public Validator<String> decodingConsumablesLotValidator() {
+        return new StringValidator("Decoding consumables lot number", 6, 6, CharacterType.DIGIT);
+    }
+
     @Bean
     public Validator<String> cytAssistBarcodeValidator() {
         Set<CharacterType> charTypes = EnumSet.of(CharacterType.DIGIT, CharacterType.ALPHA, CharacterType.HYPHEN);

src/main/java/uk/ac/sanger/sccp/stan/request/AnalyserRequest.java

@@ -96,14 +96,17 @@ public static class AnalyserLabware {
         private String barcode;
         private String workNumber;
         private CassettePosition position;
+        private String decodingConsumablesLot;
         private List<SampleROI> samples = List.of();
 
         public AnalyserLabware() {}
 
-        public AnalyserLabware(String barcode, String workNumber, CassettePosition position, List<SampleROI> samples) {
+        public AnalyserLabware(String barcode, String workNumber, CassettePosition position,
+                               String decodingConsumablesLot, List<SampleROI> samples) {
             this.barcode = barcode;
             this.workNumber = workNumber;
             this.position = position;
+            this.decodingConsumablesLot = decodingConsumablesLot;
             setSamples(samples);
         }
 
@@ -140,6 +143,15 @@ public void setPosition(CassettePosition position) {
             this.position = position;
         }
 
+        /** The decoding consumables lot number. */
+        public String getDecodingConsumablesLot() {
+            return this.decodingConsumablesLot;
+        }
+
+        public void setDecodingConsumablesLot(String decodingConsumablesLot) {
+            this.decodingConsumablesLot = decodingConsumablesLot;
+        }
+
         /**
          * The sample regions of interest in this labware.
          */
@@ -153,7 +165,25 @@ public void setSamples(List<SampleROI> samples) {
 
         @Override
         public String toString() {
-            return String.format("{%s: %s, %s, %s}", position, repr(barcode), repr(workNumber), samples);
+            return String.format("{%s: %s, %s, %s, %s}", position, repr(barcode), repr(workNumber),
+                    repr(decodingConsumablesLot), samples);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+            if (this == o) return true;
+            if (o == null || getClass() != o.getClass()) return false;
+            AnalyserLabware that = (AnalyserLabware) o;
+            return (Objects.equals(this.barcode, that.barcode)
+                    && Objects.equals(this.workNumber, that.workNumber)
+                    && this.position == that.position
+                    && Objects.equals(this.decodingConsumablesLot, that.decodingConsumablesLot)
+                    && Objects.equals(this.samples, that.samples));
+        }
+
+        @Override
+        public int hashCode() {
+            return barcode==null ? 0 : barcode.hashCode();
         }
     }
     // endregion

src/main/java/uk/ac/sanger/sccp/stan/request/ProbeOperationRequest.java

@@ -24,14 +24,16 @@ public static class ProbeOperationLabware {
         private String barcode;
         private String workNumber;
         private SlideCosting kitCosting;
+        private String samplePrepReagentLot;
         private List<ProbeLot> probes = List.of();
 
         public ProbeOperationLabware() {}
 
-        public ProbeOperationLabware(String barcode, String workNumber, SlideCosting kitCosting, List<ProbeLot> probes) {
+        public ProbeOperationLabware(String barcode, String workNumber, SlideCosting kitCosting, String samplePrepReagentLot, List<ProbeLot> probes) {
             setBarcode(barcode);
             setWorkNumber(workNumber);
             setKitCosting(kitCosting);
+            setSamplePrepReagentLot(samplePrepReagentLot);
             setProbes(probes);
         }
 
@@ -67,6 +69,15 @@ public void setKitCosting(SlideCosting kitCosting) {
             this.kitCosting = kitCosting;
         }
 
+        /** Sample prep reagent lot number. */
+        public String getSamplePrepReagentLot() {
+            return this.samplePrepReagentLot;
+        }
+
+        public void setSamplePrepReagentLot(String samplePrepReagentLot) {
+            this.samplePrepReagentLot = samplePrepReagentLot;
+        }
+
         /**
          * The probes used on this labware.
          */
@@ -86,6 +97,7 @@ public boolean equals(Object o) {
             return (Objects.equals(this.barcode, that.barcode)
                     && Objects.equals(this.workNumber, that.workNumber)
                     && this.kitCosting==that.kitCosting
+                    && Objects.equals(this.samplePrepReagentLot, that.samplePrepReagentLot)
                     && Objects.equals(this.probes, that.probes)
             );
         }
@@ -97,7 +109,8 @@ public int hashCode() {
 
         @Override
         public String toString() {
-            return String.format("(%s, %s, workNumber: %s, probes: %s)", repr(barcode), kitCosting, repr(workNumber), probes);
+            return String.format("(%s, %s, workNumber: %s, samplePrepReagentLot: %s, probes: %s)",
+                    repr(barcode), kitCosting, repr(workNumber), repr(samplePrepReagentLot), probes);
         }
     }
 

src/main/java/uk/ac/sanger/sccp/stan/request/SegmentationRequest.java

@@ -78,6 +78,7 @@ public static class SegmentationLabware {
         private List<Integer> commentIds = List.of();
         private SlideCosting costing;
         private LocalDateTime performed;
+        private String reagentLot;
 
         /**
          * The barcode of the labware.
@@ -134,6 +135,14 @@ public void setPerformed(LocalDateTime performed) {
             this.performed = performed;
         }
 
+        public String getReagentLot() {
+            return this.reagentLot;
+        }
+
+        public void setReagentLot(String reagentLot) {
+            this.reagentLot = reagentLot;
+        }
+
         @Override
         public String toString() {
             return BasicUtils.describe(this)
@@ -142,6 +151,7 @@ public String toString() {
                     .add("commentIds", commentIds)
                     .add("costing", costing)
                     .add("performed", performed==null ? null : performed.toString())
+                    .add("reagentLot", reagentLot)
                     .reprStringValues()
                     .toString();
         }
@@ -155,7 +165,9 @@ public boolean equals(Object o) {
                     && Objects.equals(this.workNumber, that.workNumber)
                     && Objects.equals(this.commentIds, that.commentIds)
                     && this.costing == that.costing
-                    && Objects.equals(this.performed, that.performed));
+                    && Objects.equals(this.performed, that.performed)
+                    && Objects.equals(this.reagentLot, that.reagentLot)
+            );
         }
 
         @Override

src/main/java/uk/ac/sanger/sccp/stan/service/ProbeServiceImp.java

@@ -14,6 +14,7 @@
 
 import java.time.*;
 import java.util.*;
+import java.util.function.Consumer;
 import java.util.stream.Stream;
 
 import static uk.ac.sanger.sccp.utils.BasicUtils.*;
@@ -24,6 +25,7 @@
 @Service
 public class ProbeServiceImp implements ProbeService {
     public static final String KIT_COSTING_NAME = "kit costing";
+    public static final String SAMPLE_PREP_REAGENT_LOT_NAME = "sample prep reagent lot";
 
     private final LabwareValidatorFactory lwValFac;
     private final LabwareRepo lwRepo;
@@ -35,6 +37,7 @@ public class ProbeServiceImp implements ProbeService {
     private final OperationService opService;
     private final WorkService workService;
     private final Validator<String> probeLotValidator;
+    private final Validator<String> samplePrepReagentLotValidator;
     private final Clock clock;
 
     @Autowired
@@ -43,6 +46,7 @@ public ProbeServiceImp(LabwareValidatorFactory lwValFac,
                            ProbePanelRepo probePanelRepo, LabwareProbeRepo lwProbeRepo, LabwareNoteRepo noteRepo,
                            OperationService opService, WorkService workService,
                            @Qualifier("probeLotNumberValidator") Validator<String> probeLotValidator,
+                           @Qualifier("samplePrepReagentLotValidator") Validator<String> samplePrepReagentLotValidator,
                            Clock clock) {
         this.lwValFac = lwValFac;
         this.lwRepo = lwRepo;
@@ -54,6 +58,7 @@ public ProbeServiceImp(LabwareValidatorFactory lwValFac,
         this.opService = opService;
         this.workService = workService;
         this.probeLotValidator = probeLotValidator;
+        this.samplePrepReagentLotValidator = samplePrepReagentLotValidator;
         this.clock = clock;
     }
 
@@ -79,6 +84,7 @@ public OperationResult recordProbeOperation(User user, ProbeOperationRequest req
                 .toList();
         UCMap<Work> work = workService.validateUsableWorks(problems, workNumbers);
         checkKitCostings(problems, request.getLabware());
+        checkSamplePrepReagentLots(problems, request.getLabware());
         UCMap<ProbePanel> probes = validateProbes(problems, request.getLabware());
         if (request.getPerformed()!=null) {
             validateTimestamp(problems, request.getPerformed(), labware);
@@ -160,6 +166,28 @@ public void checkKitCostings(Collection<String> problems, Collection<ProbeOperat
         }
     }
 
+    /**
+     * Checks sample prep reagent lots.
+     * Lots are trimmed; empty lots are nulled; missing lots are skipped.
+     * @param problems receptacle for problems
+     * @param pols details of the request
+     */
+    public void checkSamplePrepReagentLots(Collection<String> problems, Collection<ProbeOperationLabware> pols) {
+        if (pols != null) {
+            final Consumer<String> addProblem = problems::add;
+            for (ProbeOperationLabware pol : pols) {
+                String lot = pol.getSamplePrepReagentLot();
+                if (lot != null) {
+                    lot = emptyToNull(lot.trim());
+                    pol.setSamplePrepReagentLot(lot);
+                    if (lot != null) {
+                        samplePrepReagentLotValidator.validate(lot, addProblem);
+                    }
+                }
+            }
+        }
+    }
+
     /**
      * Loads and checks the probes indicated in the request, their lot numbers and plexes.
      * @param problems receptacle for problems
@@ -240,6 +268,7 @@ public OperationResult perform(User user, Collection<ProbeOperationLabware> pols
                                    UCMap<Work> workMap) {
         UCMap<Operation> lwOps = makeOps(user, opType, pols, lwMap, time);
         saveKitCostings(pols, lwMap, lwOps);
+        saveSamplePrepReagentLots(pols, lwMap, lwOps);
         linkWork(pols, lwOps, workMap);
         saveProbes(pols, lwOps, lwMap, probeMap);
         return assembleResult(pols, lwMap, lwOps);
@@ -324,6 +353,29 @@ public void saveProbes(Collection<ProbeOperationLabware> pols, UCMap<Operation>
         lwProbeRepo.saveAll(lwProbes);
     }
 
+    /**
+     * Saves the indicated sample prep reagent lots against the indicated labware and ops
+     * @param pols request details
+     * @param lwMap map to look up labware by barcode
+     * @param lwOps map to look up operation by labware barcode
+     */
+    public void saveSamplePrepReagentLots(Collection<ProbeOperationLabware> pols,
+                                          UCMap<Labware> lwMap, UCMap<Operation> lwOps) {
+        List<LabwareNote> notes = new ArrayList<>();
+        for (ProbeOperationLabware pol : pols) {
+            String lot = pol.getSamplePrepReagentLot();
+            if (!nullOrEmpty(lot)) {
+                String barcode = pol.getBarcode();
+                Labware lw = lwMap.get(barcode);
+                Operation op = lwOps.get(barcode);
+                notes.add(new LabwareNote(null, lw.getId(), op.getId(), SAMPLE_PREP_REAGENT_LOT_NAME, lot));
+            }
+        }
+        if (!notes.isEmpty()) {
+            noteRepo.saveAll(notes);
+        }
+    }
+
     /**
      * Assembles an operation result whose order matches the order given in the request.
      * @param pols the request specifying labware barcodes

src/main/java/uk/ac/sanger/sccp/stan/service/SegmentationServiceImp.java

@@ -1,5 +1,6 @@
 package uk.ac.sanger.sccp.stan.service;
 
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.stereotype.Service;
 import uk.ac.sanger.sccp.stan.model.*;
 import uk.ac.sanger.sccp.stan.repo.*;
@@ -14,11 +15,11 @@
 
 import java.time.*;
 import java.util.*;
+import java.util.function.Consumer;
 import java.util.stream.Stream;
 
 import static java.util.stream.Collectors.toSet;
-import static uk.ac.sanger.sccp.utils.BasicUtils.inMap;
-import static uk.ac.sanger.sccp.utils.BasicUtils.nullOrEmpty;
+import static uk.ac.sanger.sccp.utils.BasicUtils.*;
 
 /**
  * @author dr6
@@ -39,10 +40,13 @@ public class SegmentationServiceImp implements SegmentationService {
     private final OperationCommentRepo opComRepo;
     private final LabwareNoteRepo noteRepo;
 
+    private final Validator<String> reagentLotValidator;
+
     public SegmentationServiceImp(Clock clock, ValidationHelperFactory valHelperFactory,
                                   OperationService opService, WorkService workService,
                                   OperationRepo opRepo, OperationTypeRepo opTypeRepo,
-                                  OperationCommentRepo opComRepo, LabwareNoteRepo noteRepo) {
+                                  OperationCommentRepo opComRepo, LabwareNoteRepo noteRepo,
+                                  @Qualifier("reagentLotValidator") Validator<String> reagentLotValidator) {
         this.clock = clock;
         this.valHelperFactory = valHelperFactory;
         this.opService = opService;
@@ -51,6 +55,7 @@ public SegmentationServiceImp(Clock clock, ValidationHelperFactory valHelperFact
         this.opTypeRepo = opTypeRepo;
         this.opComRepo = opComRepo;
         this.noteRepo = noteRepo;
+        this.reagentLotValidator = reagentLotValidator;
     }
 
     @Override
@@ -92,6 +97,7 @@ SegmentationData validate(User user, SegmentationRequest request) {
         checkCostings(problems, data.opType, request.getLabware());
         UCMap<LocalDateTime> priorOpTimes = checkPriorOps(problems, data.opType, data.labware.values());
         checkTimestamps(val, clock, request.getLabware(), data.labware, priorOpTimes);
+        checkReagentLots(problems, request.getLabware());
         return data;
     }
 
@@ -221,6 +227,25 @@ void checkTimestamps(ValidationHelper val, Clock clock, List<SegmentationLabware
         }
     }
 
+    /**
+     * Checks the reagent lots
+     * @param problems receptacle for problems
+     * @param lwReqs details of the request
+     */
+    void checkReagentLots(final Collection<String> problems, final Collection<SegmentationLabware> lwReqs) {
+        final Consumer<String> problemAdd = problems::add;
+        for (SegmentationLabware lwReq : lwReqs) {
+            String lot = lwReq.getReagentLot();
+            if (lot != null) {
+                lot = emptyToNull(lot.trim());
+                lwReq.setReagentLot(lot);
+            }
+            if (lot != null) {
+                reagentLotValidator.validate(lot, problemAdd);
+            }
+        }
+    }
+
     /**
      * Records the operations and all associated information for the request
      * @param lwReqs details of the request
@@ -281,6 +306,9 @@ Operation recordOp(User user, SegmentationData data, SegmentationLabware lwReq,
             newNotes.add(new LabwareNote(null, lw.getId(), op.getId(), "costing",
                     lwReq.getCosting().name()));
         }
+        if (lwReq.getReagentLot()!=null) {
+            newNotes.add(new LabwareNote(null, lw.getId(), op.getId(), "reagent lot", lwReq.getReagentLot()));
+        }
         if (!lwReq.getCommentIds().isEmpty()) {
             lwReq.getCommentIds().stream()
                     .map(data.comments::get)