Merge pull request #397 from sanger/stain_reagent_type

x1192 Stain reagent types

src/main/java/uk/ac/sanger/sccp/stan/GraphQLDataFetchers.java

@@ -80,6 +80,7 @@ public class GraphQLDataFetchers extends BaseGraphQLResource {
     final FlagLookupService flagLookupService;
     final MeasurementService measurementService;
     final GraphService graphService;
+    final CommentRepo commentRepo;
 
     @Autowired
     public GraphQLDataFetchers(ObjectMapper objectMapper, AuthenticationComponent authComp, UserRepo userRepo,
@@ -104,7 +105,7 @@ public GraphQLDataFetchers(ObjectMapper objectMapper, AuthenticationComponent au
                                SlotRegionService slotRegionService, RecentOpService recentOpService,
                                CleanedOutSlotService cleanedOutSlotService,
                                FlagLookupService flagLookupService, MeasurementService measurementService,
-                               GraphService graphService) {
+                               GraphService graphService, CommentRepo commentRepo) {
         super(objectMapper, authComp, userRepo);
         this.sessionConfig = sessionConfig;
         this.versionInfo = versionInfo;
@@ -150,6 +151,7 @@ public GraphQLDataFetchers(ObjectMapper objectMapper, AuthenticationComponent au
         this.flagLookupService = flagLookupService;
         this.measurementService = measurementService;
         this.graphService = graphService;
+        this.commentRepo = commentRepo;
     }
 
     public DataFetcher<User> getUser() {
@@ -484,6 +486,10 @@ public DataFetcher<List<StainType>> getEnabledStainTypes() {
         return dfe -> stainService.getEnabledStainTypes();
     }
 
+    public DataFetcher<List<Comment>> getStainReagentTypes() {
+        return dfe -> commentRepo.findAllByCategoryInAndEnabled(StainType.H_AND_E_MEASUREMENTS, true);
+    }
+
     public DataFetcher<VisiumPermData> getVisiumPermData() {
         return dfe -> visiumPermDataService.load(dfe.getArgument("barcode"));
     }

src/main/java/uk/ac/sanger/sccp/stan/GraphQLProvider.java

@@ -102,6 +102,7 @@ private RuntimeWiring buildWiring() {
                         .dataFetcher("worksSummary", graphQLDataFetchers.worksSummary())
                         .dataFetcher("listFiles", graphQLDataFetchers.listStanFiles())
                         .dataFetcher("stainTypes", graphQLDataFetchers.getEnabledStainTypes())
+                        .dataFetcher("stainReagentTypes", graphQLDataFetchers.getStainReagentTypes())
                         .dataFetcher("visiumPermData", graphQLDataFetchers.getVisiumPermData())
                         .dataFetcher("extractResult", graphQLDataFetchers.getExtractResult())
                         .dataFetcher("passFails", graphQLDataFetchers.getPassFails())

src/main/java/uk/ac/sanger/sccp/stan/repo/CommentRepo.java

@@ -11,6 +11,7 @@
  */
 public interface CommentRepo extends CrudRepository<Comment, Integer> {
     List<Comment> findAllByCategory(String category);
+    List<Comment> findAllByCategoryInAndEnabled(List<String> categories, boolean enabled);
     List<Comment> findAllByCategoryAndEnabled(String category, boolean enabled);
     Optional<Comment> findByCategoryAndText(String category, String text);
 

src/main/java/uk/ac/sanger/sccp/stan/request/stain/StainRequest.java

@@ -4,6 +4,7 @@
 import java.util.Objects;
 
 import static uk.ac.sanger.sccp.utils.BasicUtils.describe;
+import static uk.ac.sanger.sccp.utils.BasicUtils.nullToEmpty;
 
 /**
  * A request to perform a stain operation
@@ -12,15 +13,18 @@
 public class StainRequest {
     private String stainType;
     private List<String> barcodes;
-    private List<TimeMeasurement> timeMeasurements;
+    private List<TimeMeasurement> timeMeasurements = List.of();
     private String workNumber;
+    private List<Integer> commentIds = List.of();
 
     public StainRequest() {}
 
-    public StainRequest(String stainType, List<String> barcodes, List<TimeMeasurement> timeMeasurements) {
+    public StainRequest(String stainType, List<String> barcodes, List<TimeMeasurement> timeMeasurements,
+                        List<Integer> commentIds) {
         this.stainType = stainType;
         this.barcodes = barcodes;
-        this.timeMeasurements = timeMeasurements;
+        setTimeMeasurements(timeMeasurements);
+        setCommentIds(commentIds);
     }
 
     public String getStainType() {
@@ -44,7 +48,7 @@ public List<TimeMeasurement> getTimeMeasurements() {
     }
 
     public void setTimeMeasurements(List<TimeMeasurement> timeMeasurements) {
-        this.timeMeasurements = timeMeasurements;
+        this.timeMeasurements = nullToEmpty(timeMeasurements);
     }
 
     public String getWorkNumber() {
@@ -55,6 +59,14 @@ public void setWorkNumber(String workNumber) {
         this.workNumber = workNumber;
     }
 
+    public List<Integer> getCommentIds() {
+        return this.commentIds;
+    }
+
+    public void setCommentIds(List<Integer> commentIds) {
+        this.commentIds = nullToEmpty(commentIds);
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
@@ -63,12 +75,14 @@ public boolean equals(Object o) {
         return (Objects.equals(this.stainType, that.stainType)
                 && Objects.equals(this.barcodes, that.barcodes)
                 && Objects.equals(this.timeMeasurements, that.timeMeasurements)
-                && Objects.equals(this.workNumber, that.workNumber));
+                && Objects.equals(this.workNumber, that.workNumber)
+                && Objects.equals(this.commentIds, that.commentIds)
+        );
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(stainType, barcodes, timeMeasurements, workNumber);
+        return Objects.hash(stainType, barcodes, timeMeasurements, workNumber, commentIds);
     }
 
     @Override
@@ -78,6 +92,7 @@ public String toString() {
                 .add("barcodes", barcodes)
                 .add("timeMeasurements", timeMeasurements)
                 .add("workNumber", workNumber)
+                .add("commentIds", commentIds)
                 .toString();
     }
 }

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

@@ -15,6 +15,7 @@
 
 import static java.util.stream.Collectors.toList;
 import static java.util.stream.Collectors.toSet;
+import static uk.ac.sanger.sccp.utils.BasicUtils.nullOrEmpty;
 import static uk.ac.sanger.sccp.utils.BasicUtils.repr;
 
 /**
@@ -26,22 +27,26 @@ public class StainServiceImp implements StainService {
     private final LabwareRepo labwareRepo;
     private final OperationTypeRepo opTypeRepo;
     private final MeasurementRepo measurementRepo;
+    private final OperationCommentRepo opComRepo;
 
     private final LabwareValidatorFactory labwareValidatorFactory;
     private final WorkService workService;
     private final OperationService opService;
+    private final CommentValidationService commentValidationService;
 
     public StainServiceImp(StainTypeRepo stainTypeRepo, LabwareRepo labwareRepo, OperationTypeRepo opTypeRepo,
-                           MeasurementRepo measurementRepo,
+                           MeasurementRepo measurementRepo, OperationCommentRepo opComRepo,
                            LabwareValidatorFactory labwareValidatorFactory, WorkService workService,
-                           OperationService opService) {
+                           OperationService opService, CommentValidationService commentValidationService) {
         this.stainTypeRepo = stainTypeRepo;
         this.labwareRepo = labwareRepo;
         this.opTypeRepo = opTypeRepo;
         this.measurementRepo = measurementRepo;
+        this.opComRepo = opComRepo;
         this.labwareValidatorFactory = labwareValidatorFactory;
         this.workService = workService;
         this.opService = opService;
+        this.commentValidationService = commentValidationService;
     }
 
     @Override
@@ -194,20 +199,42 @@ public Iterable<Measurement> recordMeasurements(Collection<Operation> ops, Colle
         return measurementRepo.saveAll(measurements);
     }
 
+    /**
+     * Records the given comments against every slot/sample in the given operations.
+     * @param ops the created operations
+     * @param comments the comments to record
+     */
+    public void recordComments(List<Operation> ops, List<Comment> comments) {
+        List<OperationComment> opComs = ops.stream()
+                .flatMap(op -> op.getActions().stream())
+                .flatMap(ac -> comments.stream()
+                        .map(com -> new OperationComment(null, com, ac.getOperationId(), ac.getSample().getId(), ac.getDestination().getId(), null))
+                ).toList();
+        opComRepo.saveAll(opComs);
+    }
+
     @Override
     public OperationResult recordStain(User user, StainRequest request) {
         Collection<String> problems = new LinkedHashSet<>();
         Work work = workService.validateUsableWork(problems, request.getWorkNumber());
         Collection<Labware> labware = validateLabware(problems, request.getBarcodes());
         StainType stainType = validateStainType(problems, request.getStainType());
         List<TimeMeasurement> measurements = validateMeasurements(problems, stainType, request.getTimeMeasurements());
-
+        List<Comment> comments;
+        if (nullOrEmpty(request.getCommentIds())) {
+            comments = List.of();
+        } else {
+            comments = commentValidationService.validateCommentIds(problems, request.getCommentIds().stream());
+        }
         if (!problems.isEmpty()) {
             throw new ValidationException("The stain request could not be validated.", problems);
         }
 
         List<Operation> ops = createOperations(user, labware, List.of(stainType));
         recordMeasurements(ops, measurements);
+        if (!comments.isEmpty()) {
+            recordComments(ops, comments);
+        }
         if (work!=null) {
             workService.link(work, ops);
         }

src/main/resources/schema.graphqls

@@ -1173,6 +1173,8 @@ input StainRequest {
     timeMeasurements: [TimeMeasurement!]!
     """An optional work number to associate with this operation."""
     workNumber: String
+    """Comment ids indicating reagent types used in stain."""
+    commentIds: [Int!]
 }
 
 """The panel used with a stain."""
@@ -1957,6 +1959,8 @@ type Query {
     planData(barcode: String!): PlanData!
     """Get the available stain types."""
     stainTypes: [StainType!]!
+    """Get the reagent types for H&E staining."""
+    stainReagentTypes: [Comment!]!
     """Event types."""
     eventTypes: [String!]!
     """Get an item of labware and the visium permeabilisation data recorded on it, if any."""