Merge pull request #474 from sanger/sample_risk

x1247 Sample risk

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

@@ -24,13 +24,14 @@ public class OriginalSampleData {
     private String species;
     private LocalDate sampleCollectionDate;
     private String workNumber;
+    private String bioRiskCode;
 
     public OriginalSampleData() {}
 
     public OriginalSampleData(String donorIdentifier, LifeStage lifeStage, String hmdmc, String tissueType,
                               Integer spatialLocation, String replicateNumber, String externalIdentifier,
                               String labwareType, String solution, String fixative, String species,
-                              LocalDate sampleCollectionDate, String workNumber) {
+                              LocalDate sampleCollectionDate, String workNumber, String bioRiskCode) {
         this.donorIdentifier = donorIdentifier;
         this.lifeStage = lifeStage;
         this.hmdmc = hmdmc;
@@ -44,6 +45,7 @@ public OriginalSampleData(String donorIdentifier, LifeStage lifeStage, String hm
         this.species = species;
         this.sampleCollectionDate = sampleCollectionDate;
         this.workNumber = workNumber;
+        this.bioRiskCode = bioRiskCode;
     }
 
     /**
@@ -186,6 +188,14 @@ public void setWorkNumber(String workNumber) {
         this.workNumber = workNumber;
     }
 
+    public String getBioRiskCode() {
+        return this.bioRiskCode;
+    }
+
+    public void setBioRiskCode(String bioRiskCode) {
+        this.bioRiskCode = bioRiskCode;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
@@ -204,6 +214,7 @@ public boolean equals(Object o) {
                 && Objects.equals(this.species, that.species)
                 && Objects.equals(this.sampleCollectionDate, that.sampleCollectionDate)
                 && Objects.equals(this.workNumber, that.workNumber)
+                && Objects.equals(this.bioRiskCode, that.bioRiskCode)
         );
     }
 
@@ -229,6 +240,7 @@ public String toString() {
                 .add("species", species)
                 .add("sampleCollectionDate", sampleCollectionDate)
                 .add("workNumber", workNumber)
+                .add("bioRiskCode", bioRiskCode)
                 .reprStringValues()
                 .toString();
     }

src/main/java/uk/ac/sanger/sccp/stan/service/register/OriginalSampleRegisterServiceImp.java

@@ -49,6 +49,7 @@ public class OriginalSampleRegisterServiceImp implements IRegisterService<Origin
     private final LabwareService labwareService;
     private final OperationService opService;
     private final WorkService workService;
+    private final BioRiskService bioRiskService;
 
     @Autowired
     public OriginalSampleRegisterServiceImp(DonorRepo donorRepo, TissueRepo tissueRepo,
@@ -62,7 +63,7 @@ public OriginalSampleRegisterServiceImp(DonorRepo donorRepo, TissueRepo tissueRe
                                             @Qualifier("hmdmcValidator") Validator<String> hmdmcValidator,
                                             @Qualifier("replicateValidator") Validator<String> replicateValidator,
                                             LabwareService labwareService, OperationService opService,
-                                            WorkService workService) {
+                                            WorkService workService, BioRiskService bioRiskService) {
         this.donorRepo = donorRepo;
         this.tissueRepo = tissueRepo;
         this.tissueTypeRepo = tissueTypeRepo;
@@ -84,6 +85,7 @@ public OriginalSampleRegisterServiceImp(DonorRepo donorRepo, TissueRepo tissueRe
         this.labwareService = labwareService;
         this.opService = opService;
         this.workService = workService;
+        this.bioRiskService = bioRiskService;
     }
 
     @Override
@@ -123,6 +125,7 @@ public RegisterResult register(User user, OriginalSampleRegisterRequest request)
         checkExternalNamesUnique(problems, request);
         checkDonorFieldsAreConsistent(problems, datas);
         checkTissueTypesAndSpatialLocations(problems, datas);
+        checkBioRisks(problems, datas);
 
         if (!problems.isEmpty()) {
             throw new ValidationException("The request validation failed.", problems);
@@ -134,6 +137,7 @@ public RegisterResult register(User user, OriginalSampleRegisterRequest request)
         recordRegistrations(user, datas);
         recordSolutions(datas);
         linkWork(datas);
+        linkBioRisks(datas);
         return makeResult(datas);
     }
 
@@ -397,6 +401,21 @@ void checkWorks(Collection<String> problems, List<DataStruct> datas) {
         }
     }
 
+    /**
+     * Checks bio risk codes are specified and correspond to known bio risks
+     * @param problems receptacle for problems
+     * @param datas data in progress
+     */
+    void checkBioRisks(Collection<String> problems, List<DataStruct> datas) {
+        UCMap<BioRisk> riskMap = bioRiskService.loadAndValidateBioRisks(problems, datas.stream().map(DataStruct::getOriginalSampleData),
+                OriginalSampleData::getBioRiskCode, OriginalSampleData::setBioRiskCode);
+        if (!riskMap.isEmpty()) {
+            for (DataStruct data : datas) {
+                data.setBioRisk(riskMap.get(data.originalSampleData.getBioRiskCode()));
+            }
+        }
+    }
+
     /**
      * Loads any existing donors matching given donor names.
      * The donors are placed in the appropriate field in the DataStructs.
@@ -493,6 +512,16 @@ void linkWork(List<DataStruct> datas) {
         workService.linkWorkOps(workOps);
     }
 
+    /**
+     * Link samples and operations to the indicated bio risk
+     * @param datas created data
+     */
+    void linkBioRisks(List<DataStruct> datas) {
+        for (DataStruct data : datas) {
+            bioRiskService.recordSampleBioRisks(Map.of(data.sample.getId(), data.bioRisk), data.operation.getId());
+        }
+    }
+
     /**
      * Creates labware for each data element
      * @param datas the data under construction
@@ -548,6 +577,7 @@ static class DataStruct {
         Fixative fixative;
         Species species;
         Work work;
+        BioRisk bioRisk;
 
         Donor donor;
         Sample sample;
@@ -585,5 +615,9 @@ void setSpecies(Species species) {
         public void setWork(Work work) {
             this.work = work;
         }
+
+        void setBioRisk(BioRisk risk) {
+            this.bioRisk = risk;
+        }
     }
 }

src/main/java/uk/ac/sanger/sccp/stan/service/register/filereader/OriginalSampleRegisterFileReader.java

@@ -26,6 +26,7 @@ enum Column implements IColumn {
         Life_stage,
         Collection_date(LocalDate.class, Pattern.compile("(if.*)?(date.*collection|collection.*date).*", Pattern.CASE_INSENSITIVE), false),
         Species,
+        Bio_risk(Pattern.compile("bio\\w*\\s+risk.*", Pattern.CASE_INSENSITIVE)),
         HuMFre(Pattern.compile("humfre\\s*(number)?", Pattern.CASE_INSENSITIVE), false),
         Tissue_type,
         External_identifier(Pattern.compile("external\\s*id.*", Pattern.CASE_INSENSITIVE), false),

src/main/java/uk/ac/sanger/sccp/stan/service/register/filereader/OriginalSampleRegisterFileReaderImp.java

@@ -43,6 +43,7 @@ public OriginalSampleData createSampleData(Collection<String> problems, Map<Colu
         data.setLifeStage(valueToLifeStage(problems, (String) row.get(Column.Life_stage)));
         data.setSampleCollectionDate((LocalDate) row.get(Column.Collection_date));
         data.setSpecies((String) row.get(Column.Species));
+        data.setBioRiskCode((String) row.get(Column.Bio_risk));
         data.setHmdmc((String) row.get(Column.HuMFre));
         data.setTissueType((String) row.get(Column.Tissue_type));
         data.setExternalIdentifier((String) row.get(Column.External_identifier));

src/main/resources/schema.graphqls

@@ -405,6 +405,8 @@ input OriginalSampleData {
     sampleCollectionDate: Date
     """The optional work number to link to the registration."""
     workNumber: String
+    """The biological risk number for this sample."""
+    bioRiskCode: String!
 }
 
 """A request to register one or more original samples of tissue."""

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

@@ -45,6 +45,8 @@ public class TestRegisterOriginalSamplesMutation {
     private OperationRepo opRepo;
     @Autowired
     private OperationSolutionRepo opSolRepo;
+    @Autowired
+    private BioRiskRepo bioRiskRepo;
     @MockBean
     private StorelightClient mockStorelight;
 
@@ -55,6 +57,7 @@ public void testRegisterOriginalSamples(boolean hasExternalName) throws Exceptio
         stubStorelightUnstore(mockStorelight);
 
         User user = entityCreator.createUser("user1");
+        BioRisk risk1 = entityCreator.createBioRisk("risk1");
         tester.setUser(user);
         Solution solution = solutionRepo.save(new Solution(null, "Glue"));
         String externalName = (hasExternalName ? "EXT1" : null);
@@ -105,6 +108,7 @@ public void testRegisterOriginalSamples(boolean hasExternalName) throws Exceptio
         Map<String, String> lwSol = lwSolData.get(0);
         assertEquals(lw.getBarcode(), lwSol.get("barcode"));
         assertEquals(solution.getName(), lwSol.get("solutionName"));
+        assertThat(bioRiskRepo.loadBioRiskForSampleId(sample.getId())).contains(risk1);
 
         Work work = entityCreator.createWork(null, null, null, null, null);
         Labware block = testBlockProcessing(barcode, work);

src/test/java/uk/ac/sanger/sccp/stan/service/register/TestOriginalSampleRegisterService.java

@@ -74,6 +74,8 @@ public class TestOriginalSampleRegisterService {
     private OperationService mockOpService;
     @Mock
     private WorkService mockWorkService;
+    @Mock
+    private BioRiskService mockBioRiskService;
 
     OriginalSampleRegisterServiceImp service;
 
@@ -87,7 +89,8 @@ void setup() {
                 mockSampleRepo, mockBsRepo, mockSlotRepo, mockHmdmcRepo, mockSpeciesRepo, mockFixativeRepo,
                 mockMediumRepo, mockSolutionRepo, mockLtRepo, mockOpTypeRepo, mockOpSolRepo, mockDonorNameValidator,
                 mockExternalNameValidator,
-                mockHmdmcValidator, mockReplicateValidator, mockLabwareService, mockOpService, mockWorkService));
+                mockHmdmcValidator, mockReplicateValidator, mockLabwareService, mockOpService, mockWorkService,
+                mockBioRiskService));
     }
 
     @AfterEach
@@ -111,7 +114,7 @@ public void testRegister_noSamples() {
     @Test
     public void testRegister_validationErrors() {
         OriginalSampleData data = new OriginalSampleData("DONOR1", LifeStage.adult, "HMDMC1", "TISSUE1", 5,
-                "R1", "EXT1", "LT1", "SOL1", "FIX1", "SPEC1", LocalDate.of(2022,1,1), "TODO");
+                "R1", "EXT1", "LT1", "SOL1", "FIX1", "SPEC1", LocalDate.of(2022,1,1), "TODO", "RISK1");
         OriginalSampleRegisterRequest request = new OriginalSampleRegisterRequest(List.of(data));
 
         doAnswer(invocation -> {
@@ -134,6 +137,7 @@ public void testRegister_validationErrors() {
 
         doNothing().when(service).checkExternalNamesUnique(any(), any());
         doNothing().when(service).checkDonorFieldsAreConsistent(any(), any());
+        doNothing().when(service).checkBioRisks(any(), any());
 
         User user = EntityFactory.getUser();
 
@@ -165,11 +169,12 @@ public void testRegister_validationErrors() {
     public void testRegister_valid() {
         User user = EntityFactory.getUser();
         OriginalSampleData data = new OriginalSampleData("DONOR1", LifeStage.adult, "HMDMC1", "TISSUE1", 5,
-                "R1", "EXT1", "LT1", "SOL1", "FIX1", "SPEC1", LocalDate.of(2022,1,1), "TODO");
+                "R1", "EXT1", "LT1", "SOL1", "FIX1", "SPEC1", LocalDate.of(2022,1,1), "TODO", "risk1");
         OriginalSampleRegisterRequest request = new OriginalSampleRegisterRequest(List.of(data));
         doNothing().when(service).checkFormat(any(), any(), any(), any(), anyBoolean(), any());
         doNothing().when(service).checkHmdmcsForSpecies(any(), any());
         doNothing().when(service).checkCollectionDates(any(), any());
+        doNothing().when(service).checkBioRisks(any(), any());
 
         doNothing().when(service).checkExistence(any(), any(), any(), any(), any(), any());
 
@@ -184,6 +189,7 @@ public void testRegister_valid() {
         doNothing().when(service).createNewLabware(any());
         doNothing().when(service).recordRegistrations(any(), any());
         doNothing().when(service).recordSolutions(any());
+        doNothing().when(service).linkBioRisks(any());
         final RegisterResult expectedResult = new RegisterResult(List.of(EntityFactory.getTube()));
         doReturn(expectedResult).when(service).makeResult(any());
 
@@ -196,6 +202,7 @@ public void testRegister_valid() {
         verify(service).recordRegistrations(same(user), same(datas));
         verify(service).recordSolutions(same(datas));
         verify(service).linkWork(same(datas));
+        verify(service).linkBioRisks(same(datas));
         verify(service).makeResult(same(datas));
     }
 
@@ -229,6 +236,7 @@ private List<DataStruct> verifyValidationMethods(OriginalSampleRegisterRequest r
         verify(service).checkDonorFieldsAreConsistent(same(problems), same(datas));
 
         verify(service).checkTissueTypesAndSpatialLocations(same(problems), same(datas));
+        verify(service).checkBioRisks(same(problems), same(datas));
         return datas;
     }
 
@@ -607,6 +615,36 @@ public void testCheckWorks_ok(boolean errors) {
         verify(mockWorkService).validateUsableWorks(any(), eq(Set.of("SGP1", "SGP2")));
     }
 
+    @SuppressWarnings("unchecked")
+    @Test
+    public void testCheckBioRisks() {
+        BioRisk risk1 = new BioRisk(1, "risk1");
+        BioRisk risk2 = new BioRisk(2, "risk2");
+        UCMap<BioRisk> riskMap = UCMap.from(BioRisk::getCode, risk1, risk2);
+        List<DataStruct> datas = Stream.of("RISK1","", "risk2")
+                .map(code -> {
+                    OriginalSampleData osd = new OriginalSampleData();
+                    osd.setBioRiskCode(code);
+                    return new DataStruct(osd);
+                })
+                .toList();
+        when(mockBioRiskService.loadAndValidateBioRisks(any(), any(), any(), any())).thenReturn(riskMap);
+
+        ArgumentCaptor<Function<OriginalSampleData, String>> getterCaptor = ArgumentCaptor.forClass(Function.class);
+        ArgumentCaptor<BiConsumer<OriginalSampleData, String>> setterCaptor = ArgumentCaptor.forClass(BiConsumer.class);
+        ArgumentCaptor<Stream<OriginalSampleData>> streamCaptor = ArgumentCaptor.forClass(Stream.class);
+        final List<String> problems = new ArrayList<>();
+        service.checkBioRisks(problems, datas);
+        verify(mockBioRiskService).loadAndValidateBioRisks(same(problems), streamCaptor.capture(), getterCaptor.capture(), setterCaptor.capture());
+        // Test the correct stream and getter were passed
+        assertThat(streamCaptor.getValue().map(getterCaptor.getValue())).containsExactly("RISK1","", "risk2");
+        OriginalSampleData osd = new OriginalSampleData();
+        // Test the correct setter was passed
+        setterCaptor.getValue().accept(osd, "Banana");
+        assertEquals("Banana", osd.getBioRiskCode());
+        assertThat(datas.stream().map(data -> data.bioRisk)).containsExactly(risk1, null, risk2);
+    }
+
     @Test
     public void testLoadDonors_none() {
         List<DataStruct> datas = Stream.of(osdWithDonor(""), osdWithDonor(null))
@@ -679,6 +717,37 @@ static DataStruct dataStructOf(String donorName, Donor donor, Species species, L
         return data;
     }
 
+    @Test
+    public void testLinkBioRisks() {
+        Operation[] ops = IntStream.range(100,103)
+                .mapToObj(id -> {
+                    Operation op = new Operation();
+                    op.setId(id);
+                    return op;
+                }).toArray(Operation[]::new);
+        Sample[] samples = EntityFactory.makeSamples(ops.length);
+        BioRisk risk1 = new BioRisk(201, "risk1");
+        BioRisk risk2 = new BioRisk(202, "risk2");
+        List<DataStruct> datas = List.of(
+                dataForRisk(ops[0], samples[0], risk1),
+                dataForRisk(ops[1], samples[1], risk2),
+                dataForRisk(ops[2], samples[2], risk1)
+        );
+        service.linkBioRisks(datas);
+        verify(mockBioRiskService, times(datas.size())).recordSampleBioRisks(any(), any());
+        verify(mockBioRiskService).recordSampleBioRisks(Map.of(samples[0].getId(), risk1), ops[0].getId());
+        verify(mockBioRiskService).recordSampleBioRisks(Map.of(samples[1].getId(), risk2), ops[1].getId());
+        verify(mockBioRiskService).recordSampleBioRisks(Map.of(samples[2].getId(), risk1), ops[2].getId());
+    }
+
+    private static DataStruct dataForRisk(Operation op, Sample sample, BioRisk risk) {
+        DataStruct data = new DataStruct(null);
+        data.operation = op;
+        data.sample = sample;
+        data.bioRisk = risk;
+        return data;
+    }
+
     @Test
     public void testCreateNewSamples() {
         Species human = EntityFactory.getHuman();

src/test/java/uk/ac/sanger/sccp/stan/service/register/filereader/TestOriginalSampleRegisterFileReader.java

@@ -36,7 +36,7 @@ void testColumns() {
     void testHeadings() {
         OriginalSampleRegisterFileReaderImp reader = spy(new OriginalSampleRegisterFileReaderImp());
         String[] headings = {"mandatory whatever", "SGP number", "donor identifier", "life stage",
-                "if such and such date of collection", "species", "humfre", "tissue type", "external identifier",
+                "if such and such date of collection", "species", "bio risk", "humfre", "tissue type", "external identifier",
                 "spatial location", "replicate", "labware type",
                 "fixative", "solution of things", "information about whatever"};
         Row row = mockRow(headings);
@@ -58,7 +58,7 @@ void testCreateSampleData() {
         final LocalDate date = LocalDate.of(2023, 1, 2);
         Object[] values = {
                 "junk", "SGP15", "DONOR1", "fetal", date,
-                "human", "12345", "tt1", "EXT1", 12, "11A", "bowl", "fix1", "sol1", "junkyjunk"
+                "human", "risk1", "12345", "tt1", "EXT1", 12, "11A", "bowl", "fix1", "sol1", "junkyjunk"
         };
         Column[] columns = Column.values();
         for (int i = 0; i < values.length; ++i) {
@@ -74,6 +74,7 @@ void testCreateSampleData() {
         assertEquals(LifeStage.fetal, data.getLifeStage());
         assertEquals(date, data.getSampleCollectionDate());
         assertEquals("human", data.getSpecies());
+        assertEquals("risk1", data.getBioRiskCode());
         assertEquals("12345", data.getHmdmc());
         assertEquals("tt1", data.getTissueType());
         assertEquals("EXT1", data.getExternalIdentifier());

src/test/resources/graphql/registeroriginal.graphql

@@ -6,6 +6,7 @@ mutation {
                 donorIdentifier:"DONOR1"
                 species: "Human"
                 lifeStage:adult
+                bioRiskCode: "risk1"
                 hmdmc:"20/0002"
                 spatialLocation:0
                 tissueType:"Bone"