x1499 more than one sample in a block

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/model/Sample.java

@@ -20,6 +20,7 @@ public class Sample {
     private Tissue tissue;
     @ManyToOne
     private BioState bioState;
+    private Integer blockHighestSection;
 
     public Sample() {}
 
@@ -62,6 +63,24 @@ public void setBioState(BioState bioState) {
         this.bioState = bioState;
     }
 
+    public Integer getBlockHighestSection() {
+        return this.blockHighestSection;
+    }
+
+    public void setBlockHighestSection(Integer blockHighestSection) {
+        this.blockHighestSection = blockHighestSection;
+    }
+
+    public boolean isBlock() {
+        return blockHighestSection != null;
+    }
+
+    public static Sample newBlock(Integer id, Tissue tissue, BioState bs, Integer blockHighestSection) {
+        Sample sample = new Sample(id, null, tissue, bs);
+        sample.setBlockHighestSection(blockHighestSection);
+        return sample;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
@@ -70,7 +89,9 @@ public boolean equals(Object o) {
         return (Objects.equals(this.id, that.id)
                 && Objects.equals(this.section, that.section)
                 && Objects.equals(this.tissue, that.tissue)
-                && Objects.equals(this.bioState, that.bioState));
+                && Objects.equals(this.bioState, that.bioState)
+                && Objects.equals(this.blockHighestSection, that.blockHighestSection)
+        );
     }
 
     @Override
@@ -85,6 +106,7 @@ public String toString() {
                 .addRepr("section", section)
                 .add("tissue", tissue)
                 .add("bioState", bioState)
+                .addIfNotNull("blockHighestSection", blockHighestSection)
                 .toString();
     }
 }

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

@@ -12,7 +12,6 @@
  * @author dr6
  */
 @Entity
-@SecondaryTable(name = "block_info", pkJoinColumns = @PrimaryKeyJoinColumn(name = "slot_id"))
 public class Slot {
     @Id
     @GeneratedValue(strategy = GenerationType.IDENTITY)
@@ -25,22 +24,14 @@ public class Slot {
     @JoinTable(name = "slot_sample", inverseJoinColumns = @JoinColumn(name="sample_id"))
     private List<Sample> samples;
 
-    @Column(table = "block_info", name = "sample_id")
-    private Integer blockSampleId;
-    @Column(table = "block_info", name = "highest_section")
-    private Integer blockHighestSection;
-
     public Slot() {
         this.samples = new ArrayList<>();
     }
 
-    public Slot(Integer id, Integer labwareId, Address address, List<Sample> samples, Integer blockSampleId,
-                Integer blockHighestSection) {
+    public Slot(Integer id, Integer labwareId, Address address, List<Sample> samples) {
         this.id = id;
         this.labwareId = labwareId;
         this.address = address;
-        this.blockSampleId = blockSampleId;
-        this.blockHighestSection = blockHighestSection;
         setSamples(samples);
     }
 
@@ -83,24 +74,8 @@ public void addSample(Sample sample) {
         this.samples.add(sample);
     }
 
-    public Integer getBlockSampleId() {
-        return this.blockSampleId;
-    }
-
-    public void setBlockSampleId(Integer blockSampleId) {
-        this.blockSampleId = blockSampleId;
-    }
-
-    public Integer getBlockHighestSection() {
-        return this.blockHighestSection;
-    }
-
-    public void setBlockHighestSection(Integer blockHighestSection) {
-        this.blockHighestSection = blockHighestSection;
-    }
-
     public boolean isBlock() {
-        return (this.blockSampleId != null);
+        return (this.samples.stream().anyMatch(Sample::isBlock));
     }
 
     @Override
@@ -112,8 +87,7 @@ public boolean equals(Object o) {
                 && Objects.equals(this.address, that.address)
                 && Objects.equals(this.labwareId, that.labwareId)
                 && Objects.equals(this.samples, that.samples)
-                && Objects.equals(this.blockSampleId, that.blockSampleId)
-                && Objects.equals(this.blockHighestSection, that.blockHighestSection));
+        );
     }
 
     @Override
@@ -128,8 +102,6 @@ public String toString() {
                 .add("labwareId", labwareId)
                 .add("address", address)
                 .add("samples", samples)
-                .add("blockSampleId", blockSampleId)
-                .add("blockHighestSection", blockHighestSection)
                 .toString();
     }
 }

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));
     }