code and test refactoring

Author: ORybak5

service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/DiagnosticReportMapper.java

@@ -142,7 +142,7 @@ private List<Specimen> fetchSpecimens(DiagnosticReport diagnosticReport, List<Ob
 
         // At least one specimen is required to exist for any DiagnosticReport, according to the mim
         if (!diagnosticReport.hasSpecimen() || hasObservationsWithoutSpecimen(observations)) {
-            specimens.add(generateDummySpecimen(diagnosticReport));
+            specimens.add(generateNotPresentSpecimen(diagnosticReport));
         }
 
         var inputBundleHolder = messageContext.getInputBundleHolder();
@@ -179,21 +179,21 @@ List<Observation> assignDummySpecimensToObservationsWithNoSpecimen(List<Observat
         }
 
         // The assumption was made that all test results without a specimen will have the same dummy specimen referenced
-        Specimen dummySpecimen = specimens.stream()
+        Specimen notPresentSpecimen = specimens.stream()
             .filter(specimen -> specimen.getId().contains(NOT_PRESENT_SPECIMEN_ID_PREFIX))
             .toList().getFirst();
 
-        Reference dummySpecimenReference = new Reference(dummySpecimen.getId());
+        Reference notPresentSpecimenReference = new Reference(notPresentSpecimen.getId());
 
         nonFilingObservations.stream()
             .filter(obs -> !obs.hasSpecimen() && !isFilingComment(obs))
-            .forEach(obs -> obs.setSpecimen(dummySpecimenReference));
+            .forEach(obs -> obs.setSpecimen(notPresentSpecimenReference));
 
         nonFilingObservations.addAll(filingComments);
         return nonFilingObservations;
     }
 
-    private Specimen generateDummySpecimen(DiagnosticReport diagnosticReport) {
+    private Specimen generateNotPresentSpecimen(DiagnosticReport diagnosticReport) {
         Specimen specimen = new Specimen();
 
         specimen.setId(NOT_PRESENT_SPECIMEN_ID_PREFIX + randomIdGeneratorService.createNewId());

service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/DiagnosticReportMapperTest.java

@@ -1,17 +1,21 @@
 package uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport;
 
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.AssertionsForClassTypes.assertThatThrownBy;
+import static org.junit.Assert.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertAll;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.when;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.NoSuchElementException;
 import java.util.Optional;
 import java.util.stream.Stream;
 
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
+import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.DiagnosticReport;
 import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.Observation;
@@ -62,6 +66,7 @@ class DiagnosticReportMapperTest {
 
     private static final String TEST_ID = "5E496953-065B-41F2-9577-BE8F2FBD0757";
     public static final String NOT_PRESENT_SPECIMEN_ID_PREFIX = "NOT-PRESENT-SPECIMEN-";
+    private static final String COMMENT_NOTE = "37331000000100";
 
     private static final String INPUT_JSON_REQUIRED_DATA = "diagnostic-report-with-required-data.json";
     private static final String INPUT_JSON_EMPTY_SPECIMENS = "diagnostic-report-with-empty-specimens.json";
@@ -130,6 +135,53 @@ public void tearDown() {
         messageContext.resetMessageContext();
     }
 
+    @Test
+    void shouldAssignDummySpecimenOnlyToNonFilingObservationsWithoutSpecimen() {
+
+        Observation obsWithoutSpecimen = new Observation();
+        obsWithoutSpecimen.setId("obs1");
+
+        Observation obsWithSpecimen = new Observation();
+        obsWithSpecimen.setId("obs2");
+        obsWithSpecimen.setSpecimen(new Reference("real-specimen"));
+
+        Observation filingCommentObs = new Observation();
+        filingCommentObs.setId("obs3");
+        filingCommentObs.getCode().addCoding(new Coding().setCode(COMMENT_NOTE));
+
+        List<Observation> observations = List.of(obsWithoutSpecimen, obsWithSpecimen, filingCommentObs);
+
+        Specimen dummySpecimen = new Specimen();
+        dummySpecimen.setId(NOT_PRESENT_SPECIMEN_ID_PREFIX + "123");
+        List<Specimen> specimens = List.of(dummySpecimen);
+
+        List<Observation> result = mapper.assignDummySpecimensToObservationsWithNoSpecimen(observations, specimens);
+
+        assertThat(obsWithoutSpecimen.getSpecimen())
+            .isNotNull()
+            .extracting(Reference::getReference)
+            .isEqualTo(dummySpecimen.getId());
+
+        assertThat(obsWithSpecimen.getSpecimen())
+            .extracting(Reference::getReference)
+            .isEqualTo("real-specimen");
+
+        assertFalse(filingCommentObs.hasSpecimen());
+        assertThat(result).containsExactlyInAnyOrder(obsWithoutSpecimen, obsWithSpecimen, filingCommentObs);
+    }
+
+    @Test
+    void shouldThrowIfNoDummySpecimenFound() {
+
+        Observation obsWithoutSpecimen = new Observation();
+        List<Observation> observations = List.of(obsWithoutSpecimen);
+
+        List<Specimen> specimens = List.of();
+
+        assertThatThrownBy(() -> mapper.assignDummySpecimensToObservationsWithNoSpecimen(observations, specimens))
+            .isInstanceOf(NoSuchElementException.class);
+    }
+
     @Test
     void shouldAssignDummySpecimenToObservationsWithoutSpecimen() {