Merge pull request #438 from sanger/average_size

x1221 change: max/min size -> average size
sanger · Jul 23, 2024 · 17ba414 · 17ba414
2 parents 6b0af1e + 517066d
commit 17ba414
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Showing 3 changed files with 6 additions and 7 deletions.
diff --git a/src/main/java/uk/ac/sanger/sccp/stan/service/OpWithSlotMeasurementsServiceImp.java b/src/main/java/uk/ac/sanger/sccp/stan/service/OpWithSlotMeasurementsServiceImp.java
@@ -31,7 +31,7 @@ public class OpWithSlotMeasurementsServiceImp implements OpWithSlotMeasurementsS
             OP_QPCR = "qPCR results";
     public static final String MEAS_CQ = "Cq value", MEAS_CDNA = "cDNA concentration",
             MEAS_LIBR = "Library concentration", MEAS_CYC = "Cycles",
-            MEAS_MIN_SIZE = "Minimum size", MEAS_MAX_SIZE = "Maximum size", MEAS_PEAK_SIZE = "Main peak size"
+            AVERAGE_SIZE = "Average size", MEAS_PEAK_SIZE = "Main peak size"
     ;
 
     private final MeasurementRepo measurementRepo;
@@ -66,7 +66,7 @@ public OpWithSlotMeasurementsServiceImp(MeasurementRepo measurementRepo, Operati
         this.valHelperFactory = valHelperFactory;
         UCMap<List<String>> opTypeMeasurements = new UCMap<>(3);
         opTypeMeasurements.put(OP_AMP, List.of(MEAS_CQ, MEAS_CYC));
-        opTypeMeasurements.put(OP_VISIUM_CONC, List.of(MEAS_CDNA, MEAS_LIBR, MEAS_MIN_SIZE, MEAS_MAX_SIZE, MEAS_PEAK_SIZE));
+        opTypeMeasurements.put(OP_VISIUM_CONC, List.of(MEAS_CDNA, MEAS_LIBR, AVERAGE_SIZE, MEAS_PEAK_SIZE));
         opTypeMeasurements.put(OP_QPCR, List.of(MEAS_CQ));
         this.opTypeMeasurements = Collections.unmodifiableMap(opTypeMeasurements);
     }
@@ -268,7 +268,7 @@ public String sanitiseMeasurementName(OperationType opType, String name) {
     public String sanitiseMeasurementValue(Collection<String> problems, String name, String value) {
         return switch (name) {
             case MEAS_CDNA, MEAS_LIBR -> concentrationSanitiser.sanitise(problems, value);
-            case MEAS_MIN_SIZE, MEAS_MAX_SIZE, MEAS_PEAK_SIZE -> sizeSanitiser.sanitise(problems, value);
+            case AVERAGE_SIZE, MEAS_PEAK_SIZE -> sizeSanitiser.sanitise(problems, value);
             case MEAS_CQ -> cqSanitiser.sanitise(problems, value);
             case MEAS_CYC -> cycleSanitiser.sanitise(problems, value);
             default -> null;

diff --git a/src/main/java/uk/ac/sanger/sccp/stan/service/history/HistoryServiceImp.java b/src/main/java/uk/ac/sanger/sccp/stan/service/history/HistoryServiceImp.java
@@ -29,7 +29,7 @@
 public class HistoryServiceImp implements HistoryService {
     static final String RELEASE_EVENT_TYPE = "Release", DESTRUCTION_EVENT_TYPE = "Destruction",
             SOLUTION_TRANSFER_OP_NAME = "Solution transfer";
-    static final Pattern SIZE_BP_PTN = Pattern.compile("^M((in|ax)imum|ain peak) size$", Pattern.CASE_INSENSITIVE);
+    static final Pattern SIZE_BP_PTN = Pattern.compile("^(Average|Main peak) size$", Pattern.CASE_INSENSITIVE);
 
     private final OperationRepo opRepo;
     private final OperationTypeRepo opTypeRepo;

diff --git a/src/test/java/uk/ac/sanger/sccp/stan/service/TestOpWithSlotMeasurementsService.java b/src/test/java/uk/ac/sanger/sccp/stan/service/TestOpWithSlotMeasurementsService.java
@@ -441,15 +441,14 @@ public void testValidateComments() {
             "Sploop,20,,",
             "Cq value,20,x!,,Bad value",
             "Cycles,024,24,",
-            "Minimum size,20,20,",
-            "Maximum size,40,40,",
+            "Average size,20,20,",
             "Main peak size,30,30,",
     })
     public void testSanitiseMeasurementValue(String name, String value, String sanValue, String problem) {
         List<Sanitiser<String>> sans = List.of(mockConcSan, mockCqSan, mockCycSan);
         Sanitiser<String> san = switch (name) {
             case "cDNA concentration", "Library concentration" -> mockConcSan;
-            case "Minimum size", "Maximum size", "Main peak size" -> mockSizeSan;
+            case "Average size", "Main peak size" -> mockSizeSan;
             case "Cq value" -> mockCqSan;
             case "Cycles" -> mockCycSan;
             default -> null;