Merge pull request #445 from sanger/metric_run

x1224: add run name to SampleMetricsRequest

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

@@ -13,15 +13,17 @@ public class SampleMetricsRequest {
     private String operationType;
     private String barcode;
     private String workNumber;
+    private String runName;
     private List<SampleMetric> metrics = List.of();
 
     // Deserialisation constructor
     public SampleMetricsRequest() {}
 
-    public SampleMetricsRequest(String operationType, String barcode, String workNumber, List<SampleMetric> metrics) {
+    public SampleMetricsRequest(String operationType, String barcode, String workNumber, String runName, List<SampleMetric> metrics) {
         setOperationType(operationType);
         setBarcode(barcode);
         setWorkNumber(workNumber);
+        setRunName(runName);
         setMetrics(metrics);
     }
 
@@ -52,6 +54,15 @@ public void setWorkNumber(String workNumber) {
         this.workNumber = workNumber;
     }
 
+    /** The run name to link to the operation. */
+    public String getRunName() {
+        return this.runName;
+    }
+
+    public void setRunName(String runName) {
+        this.runName = runName;
+    }
+
     /** The metrics to save. */
     public List<SampleMetric> getMetrics() {
         return this.metrics;
@@ -67,6 +78,7 @@ public String toString() {
                 .add("operationType", operationType)
                 .add("barcode", barcode)
                 .add("workNumber", workNumber)
+                .add("runName", runName)
                 .add("metrics", metrics)
                 .reprStringValues()
                 .toString();
@@ -80,13 +92,14 @@ public boolean equals(Object o) {
         return (Objects.equals(this.operationType, that.operationType)
                 && Objects.equals(this.barcode, that.barcode)
                 && Objects.equals(this.workNumber, that.workNumber)
+                && Objects.equals(this.runName, that.runName)
                 && Objects.equals(this.metrics, that.metrics)
         );
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(operationType, barcode, workNumber, metrics);
+        return barcode==null ? 0 : barcode.hashCode();
     }
 
     /**

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

@@ -4,7 +4,8 @@
 import uk.ac.sanger.sccp.utils.UCMap;
 
 import javax.persistence.EntityNotFoundException;
-import java.util.*;
+import java.util.Collection;
+import java.util.Set;
 
 /**
  * Service helping with {@link uk.ac.sanger.sccp.stan.model.LabwareNote labware notes}
@@ -27,13 +28,31 @@ public interface LabwareNoteService {
      */
     UCMap<Set<String>> findNoteValuesForLabware(Collection<Labware> labware, String name);
 
+    /**
+     * Gets the labware note values for one item of labware with the given note name
+     * @param lw the labware
+     * @param name the name of the note
+     * @return the set of note values
+     */
+    Set<String> findNoteValuesForLabware(Labware lw, String name);
+
     /**
      * Records specified notes
      * @param name the name of the notes
      * @param lwMap map to look up labware by barcode
      * @param opMap map to look up operation by labware barcode
-     * @param values of labware barcode to note value
+     * @param values map of labware barcode to note value
      * @return the created notes
      */
     Iterable<LabwareNote> createNotes(String name, UCMap<Labware> lwMap, UCMap<Operation> opMap, UCMap<String> values);
+
+    /**
+     * Records a note
+     * @param name name of the note
+     * @param lw the labware
+     * @param op the operation to link with the note
+     * @param value note value
+     * @return the created note
+     */
+    LabwareNote createNote(String name, Labware lw, Operation op, String value);
 }

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

@@ -30,9 +30,7 @@ public LabwareNoteServiceImp(LabwareRepo lwRepo, LabwareNoteRepo lwNoteRepo) {
     @Override
     public Set<String> findNoteValuesForBarcode(String barcode, String name) throws EntityNotFoundException {
         Labware lw = lwRepo.getByBarcode(barcode);
-        return lwNoteRepo.findAllByLabwareIdInAndName(List.of(lw.getId()), name).stream()
-                .map(LabwareNote::getValue)
-                .collect(toLinkedHashSet());
+        return findNoteValuesForLabware(lw, name);
     }
 
     @Override
@@ -50,6 +48,14 @@ public UCMap<Set<String>> findNoteValuesForLabware(Collection<Labware> labware,
         return bcNotes;
     }
 
+    @Override
+    public Set<String> findNoteValuesForLabware(Labware lw, String name) {
+        List<LabwareNote> notes = lwNoteRepo.findAllByLabwareIdInAndName(List.of(lw.getId()), name);
+        return notes.stream()
+                .map(LabwareNote::getValue)
+                .collect(toLinkedHashSet());
+    }
+
     @Override
     public Iterable<LabwareNote> createNotes(String name, UCMap<Labware> lwMap, UCMap<Operation> opMap, UCMap<String> values) {
         List<LabwareNote> notes = new ArrayList<>(values.size());
@@ -68,4 +74,9 @@ public Iterable<LabwareNote> createNotes(String name, UCMap<Labware> lwMap, UCMa
         }
         return lwNoteRepo.saveAll(notes);
     }
+
+    @Override
+    public LabwareNote createNote(String name, Labware lw, Operation op, String value) {
+        return lwNoteRepo.save(new LabwareNote(null, lw.getId(), op.getId(), name, value));
+    }
 }

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

@@ -23,22 +23,27 @@
  */
 @Service
 public class RoiMetricServiceImp implements RoiMetricService {
+    public static final String RUN_NAME = "run";
+
     private final Clock clock;
     private final ValidationHelperFactory valFactory;
     private final RoiMetricValidationService valService;
     private final OperationService opService;
     private final WorkService workService;
     private final RoiMetricRepo roiMetricRepo;
+    private final LabwareNoteService lwNoteService;
 
     @Autowired
     public RoiMetricServiceImp(Clock clock, ValidationHelperFactory valFactory,
                                RoiMetricValidationService valService, OperationService opService,
-                               WorkService workService, RoiMetricRepo roiMetricRepo) {
+                               WorkService workService, LabwareNoteService lwNoteService,
+                               RoiMetricRepo roiMetricRepo) {
         this.clock = clock;
         this.valFactory = valFactory;
         this.valService = valService;
         this.opService = opService;
         this.workService = workService;
+        this.lwNoteService = lwNoteService;
         this.roiMetricRepo = roiMetricRepo;
     }
 
@@ -67,16 +72,41 @@ MetricValidation validate(User user, SampleMetricsRequest request) {
             val.addProblem("No request supplied.");
             return val;
         }
+
         UCMap<Labware> lwMap = helper.checkLabware(Collections.singletonList(request.getBarcode()));
         if (!lwMap.isEmpty()) {
             val.labware = lwMap.values().iterator().next();
+            val.runName = validateRunName(val.problems, val.labware, request.getRunName());
         }
         val.work = helper.checkWork(request.getWorkNumber());
         val.opType = helper.checkOpType(request.getOperationType(), OperationTypeFlag.IN_PLACE);
         val.metrics = valService.validateMetrics(val.problems, val.labware, request.getMetrics());
         return val;
     }
 
+    /**
+     * Checks for problems with the given run name.
+     * @param problems receptacle for problems
+     * @param lw the indicated labware
+     * @param runName the given run name
+     * @return sanitised run name
+     */
+    public String validateRunName(Collection<String> problems, Labware lw, String runName) {
+        if (runName==null) {
+            return null;
+        }
+        runName = runName.trim();
+        if (runName.isEmpty()) {
+            return null;
+        }
+        Set<String> runNames = lwNoteService.findNoteValuesForLabware(lw, RUN_NAME);
+        if (!runNames.contains(runName)) {
+            problems.add(String.format("%s is not a recorded run-name for labware %s.",
+                    runName, lw.getBarcode()));
+        }
+        return runName;
+    }
+
     /**
      * Records the given request
      * @param user the user responsible for the request
@@ -88,9 +118,12 @@ OperationResult record(User user, MetricValidation val) {
         Operation op = opService.createOperationInPlace(val.opType, user, lw, null, null);
 
         deprecateOldMetrics(clock, lw.getId(), val.metrics);
-
         recordMetrics(lw.getId(), op.getId(), val.metrics);
 
+        if (val.runName!=null) {
+            lwNoteService.createNote(RUN_NAME, lw, op, val.runName);
+        }
+
         List<Operation> ops = List.of(op);
         workService.link(val.work, ops);
         return new OperationResult(ops, List.of(lw));
@@ -128,6 +161,7 @@ static class MetricValidation {
         Labware labware;
         Work work;
         OperationType opType;
+        String runName;
         List<SampleMetric> metrics;
 
         public MetricValidation(Set<String> problems) {

src/main/resources/schema.graphqls

@@ -1944,6 +1944,8 @@ input SampleMetricsRequest {
     barcode: String!
     """The work number to link to the operation."""
     workNumber: String!
+    """The run name to link to the operation."""
+    runName: String
     """The metrics to save."""
     metrics: [SampleMetric!]!
 }

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

@@ -180,5 +180,13 @@ private void testSampleMetrics(Labware lw, Work work) throws Exception {
             assertEquals("n"+j, rm.getName());
             assertEquals("v"+j, rm.getValue());
         }
+
+        List<LabwareNote> notes = lwNoteRepo.findAllByOperationIdIn(List.of(opId));
+        assertThat(notes).hasSize(1);
+        LabwareNote note = notes.getFirst();
+        assertEquals(lw.getId(), note.getLabwareId());
+        assertEquals(opId, note.getOperationId());
+        assertEquals("run", note.getName());
+        assertEquals("RUN1", note.getValue());
     }
 }

src/test/java/uk/ac/sanger/sccp/stan/service/TestLabwareNoteService.java

@@ -14,6 +14,7 @@
 
 import static java.util.stream.Collectors.toSet;
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.junit.jupiter.api.Assertions.assertSame;
 import static org.mockito.Mockito.*;
 import static uk.ac.sanger.sccp.stan.Matchers.sameElements;
 
@@ -55,6 +56,19 @@ void testFindNoteValuesForBarcode() {
         assertThat(service.findNoteValuesForBarcode(bc, name)).containsExactly("val1", "val2");
     }
 
+    @Test
+    void testFindNoteValuesForLabware_single() {
+        Labware lw = EntityFactory.getTube();
+        String name = "Bananas";
+        List<LabwareNote> notes = List.of(
+                new LabwareNote(1, lw.getId(), 11, name, "val1"),
+                new LabwareNote(2, lw.getId(), 12, name, "val2"),
+                new LabwareNote(3, lw.getId(), 13, name, "val1")
+        );
+        when(mockLwNoteRepo.findAllByLabwareIdInAndName(List.of(lw.getId()), name)).thenReturn(notes);
+        assertThat(service.findNoteValuesForLabware(lw, name)).containsExactly("val1", "val2");
+    }
+
     @Test
     void testFindNoteValueForLabware_none() {
         assertThat(service.findNoteValuesForLabware(List.of(), "Bananas")).isEmpty();
@@ -115,4 +129,17 @@ void testCreateNotes_none() {
         service.createNotes("Bananas", new UCMap<>(), new UCMap<>(), new UCMap<>());
         verifyNoInteractions(mockLwNoteRepo);
     }
+
+    @Test
+    void testCreateNote() {
+        String name = "Bananas";
+        String value = "Alpha";
+        Labware lw = EntityFactory.getTube();
+        Operation op = new Operation();
+        op.setId(10);
+        LabwareNote createdNote = mock(LabwareNote.class);
+        when(mockLwNoteRepo.save(any())).thenReturn(createdNote);
+        assertSame(createdNote, service.createNote(name, lw, op, value));
+        verify(mockLwNoteRepo).save(new LabwareNote(null, lw.getId(), op.getId(), name, value));
+    }
 }

src/test/java/uk/ac/sanger/sccp/stan/service/TestQCLabwareService.java

@@ -309,7 +309,7 @@ public void testCheckRunNames(boolean valid) {
         UCMap<Set<String>> bcValues = new UCMap<>(2);
         bcValues.put(lws[0].getBarcode(), Set.of("run1", "runA"));
         bcValues.put(lws[1].getBarcode(), Set.of("run2", "runB"));
-        when(mockLwNoteService.findNoteValuesForLabware(any(), any())).thenReturn(bcValues);
+        when(mockLwNoteService.findNoteValuesForLabware(anyCollection(), any())).thenReturn(bcValues);
 
         Set<Labware> lwSet;
         if (valid) {