x1403 Support complex block registration

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

@@ -44,7 +44,7 @@
 public class GraphQLMutation extends BaseGraphQLResource {
     Logger log = LoggerFactory.getLogger(GraphQLMutation.class);
     final AuthService authService;
-    final IRegisterService<RegisterRequest> registerService;
+    final IRegisterService<BlockRegisterRequest> blockRegisterService;
     final IRegisterService<SectionRegisterRequest> sectionRegisterService;
     final PlanService planService;
     final LabelPrintService labelPrintService;
@@ -115,7 +115,7 @@ public class GraphQLMutation extends BaseGraphQLResource {
     @Autowired
     public GraphQLMutation(ObjectMapper objectMapper, AuthenticationComponent authComp,
                            AuthService authService,
-                           IRegisterService<RegisterRequest> registerService,
+                           IRegisterService<BlockRegisterRequest> blockRegisterService,
                            IRegisterService<SectionRegisterRequest> sectionRegisterService,
                            PlanService planService, LabelPrintService labelPrintService,
                            ConfirmOperationService confirmOperationService,
@@ -150,7 +150,7 @@ public GraphQLMutation(ObjectMapper objectMapper, AuthenticationComponent authCo
                            ProteinPanelAdminService proteinPanelAdminService) {
         super(objectMapper, authComp, userRepo);
         this.authService = authService;
-        this.registerService = registerService;
+        this.blockRegisterService = blockRegisterService;
         this.sectionRegisterService = sectionRegisterService;
         this.planService = planService;
         this.labelPrintService = labelPrintService;
@@ -245,12 +245,12 @@ public DataFetcher<LoginResult> userSelfRegister(final User.Role role) {
         };
     }
 
-    public DataFetcher<RegisterResult> register() {
+    public DataFetcher<RegisterResult> blockRegister() {
         return dfe -> {
             User user = checkUser(dfe, User.Role.normal);
-            RegisterRequest request = arg(dfe, "request", RegisterRequest.class);
-            logRequest("Register", user, request);
-            return registerService.register(user, request);
+            BlockRegisterRequest request = arg(dfe, "request", BlockRegisterRequest.class);
+            logRequest("Block register", user, request);
+            return blockRegisterService.register(user, request);
         };
     }
 

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

@@ -153,7 +153,7 @@ private RuntimeWiring buildWiring() {
                         .dataFetcher("registerAsEndUser", graphQLMutation.userSelfRegister(User.Role.enduser)) // internal transaction
                         .dataFetcher("login", graphQLMutation.logIn())
                         .dataFetcher("logout", graphQLMutation.logOut())
-                        .dataFetcher("register", transact(graphQLMutation.register()))
+                        .dataFetcher("registerBlocks", transact(graphQLMutation.blockRegister()))
                         .dataFetcher("plan", transact(graphQLMutation.recordPlan()))
                         .dataFetcher("printLabware", graphQLMutation.printLabware()) // not transacted
                         .dataFetcher("confirmOperation", transact(graphQLMutation.confirmOperation()))

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

@@ -71,16 +71,16 @@ public Validator<String> externalNameValidator() {
         Set<CharacterType> charTypes = EnumSet.of(
                 CharacterType.ALPHA, CharacterType.DIGIT, CharacterType.HYPHEN,
                 CharacterType.UNDERSCORE, CharacterType.FULL_STOP
-        ) ;
+        );
         return new StringValidator("External identifier", 3, 64, charTypes);
     }
 
     @Bean
     public Validator<String> externalBarcodeValidator() {
         Set<CharacterType> charTypes = EnumSet.of(
                 CharacterType.ALPHA, CharacterType.DIGIT, CharacterType.HYPHEN,
-                CharacterType.UNDERSCORE
-        ) ;
+                CharacterType.UNDERSCORE, CharacterType.FULL_STOP
+        );
         return new StringValidator("External barcode", 3, 32, charTypes);
     }
 

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

@@ -24,6 +24,9 @@ default Labware getByBarcode(final String barcode) throws EntityNotFoundExceptio
     @Query("select barcode from Labware where barcode in (?1)")
     Set<String> findBarcodesByBarcodeIn(Collection<String> barcodes);
 
+    @Query("select externalBarcode from Labware where externalBarcode in (?1)")
+    Set<String> findExternalBarcodesIn(Collection<String> barcodes);
+
     default Labware getById(final Integer id) throws EntityNotFoundException {
         return findById(id).orElseThrow(() -> new EntityNotFoundException("No labware found with id "+id));
     }

src/main/java/uk/ac/sanger/sccp/stan/request/register/BlockRegisterLabware.java

@@ -0,0 +1,94 @@
+package uk.ac.sanger.sccp.stan.request.register;
+
+import java.util.List;
+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 register in a piece of labware containing one or more block-samples.
+ * @author dr6
+ */
+public class BlockRegisterLabware {
+    private String labwareType;
+    private String medium;
+    private String fixative;
+    private String externalBarcode;
+    private List<BlockRegisterSample> samples = List.of();
+
+    /** The name of the type of labware containing the block. */
+    public String getLabwareType() {
+        return this.labwareType;
+    }
+
+    public void setLabwareType(String labwareType) {
+        this.labwareType = labwareType;
+    }
+
+    /** The medium used for the tissue. */
+    public String getMedium() {
+        return this.medium;
+    }
+
+    public void setMedium(String medium) {
+        this.medium = medium;
+    }
+
+    /** The fixative used for the tissue. */
+    public String getFixative() {
+        return this.fixative;
+    }
+
+    public void setFixative(String fixative) {
+        this.fixative = fixative;
+    }
+
+    /** The external barcode of the labware. */
+    public String getExternalBarcode() {
+        return this.externalBarcode;
+    }
+
+    public void setExternalBarcode(String externalBarcode) {
+        this.externalBarcode = externalBarcode;
+    }
+
+    /** The samples in this block. */
+    public List<BlockRegisterSample> getSamples() {
+        return this.samples;
+    }
+
+    public void setSamples(List<BlockRegisterSample> samples) {
+        this.samples = nullToEmpty(samples);
+    }
+
+    @Override
+    public String toString() {
+        return describe(this)
+                .add("labwareType", labwareType)
+                .add("medium", medium)
+                .add("fixative", fixative)
+                .add("externalBarcode", externalBarcode)
+                .add("samples", samples)
+                .reprStringValues()
+                .toString();
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || o.getClass() != this.getClass()) return false;
+        BlockRegisterLabware that = (BlockRegisterLabware) o;
+        return (Objects.equals(this.labwareType, that.labwareType)
+                && Objects.equals(this.medium, that.medium)
+                && Objects.equals(this.fixative, that.fixative)
+                && Objects.equals(this.externalBarcode, that.externalBarcode)
+                && Objects.equals(this.samples, that.samples)
+        );
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(labwareType, medium, fixative, externalBarcode, samples);
+    }
+}