Simplify the SpecimenMapper observation filtering (#1008)

Now that the filtering of which Observations belong to which
Specimen happens within the DiagnosticReportMapper as of commit
7907883 there is no longer a need to perform the same filtering
within the SpecimenMapper

By moving all grouping, fakery generation and filtering into the
DiagnosticReportMapper this should simplify the complexity of
this part of the adaptor.

Author: Adrian Clay

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

@@ -1,7 +1,5 @@
 package uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport;
 
-import static uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.DiagnosticReportMapper.DUMMY_OBSERVATION_ID_PREFIX;
-import static uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.DiagnosticReportMapper.DUMMY_SPECIMEN_ID_PREFIX;
 import static uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.ObservationMapper.NARRATIVE_STATEMENT_TEMPLATE;
 import static uk.nhs.adaptors.gp2gp.ehr.utils.TextUtils.newLine;
 import static uk.nhs.adaptors.gp2gp.ehr.utils.TextUtils.withSpace;
@@ -64,9 +62,11 @@ public class SpecimenMapper {
     private final RandomIdGeneratorService randomIdGeneratorService;
     private final ConfidentialityService confidentialityService;
 
-    public String mapSpecimenToCompoundStatement(Specimen specimen, List<Observation> observations, DiagnosticReport diagnosticReport) {
+    public String mapSpecimenToCompoundStatement(
+            Specimen specimen, List<Observation> observationsAssociatedWithSpecimen, DiagnosticReport diagnosticReport
+    ) {
         String availabilityTimeElement = StatementTimeMappingUtils.prepareAvailabilityTime(diagnosticReport.getIssuedElement());
-        String mappedObservations = mapObservationsAssociatedWithSpecimen(specimen, observations);
+        String mappedObservations = mapObservationsToCompoundStatements(observationsAssociatedWithSpecimen);
 
         var specimenCompoundStatementTemplateParameters = SpecimenCompoundStatementTemplateParameters.builder()
             .compoundStatementId(messageContext.getIdMapper().getOrNew(ResourceType.Specimen, specimen.getIdElement()))
@@ -135,28 +135,12 @@ private Optional<String> buildSpecimenMaterialType(Specimen specimen) {
         return Optional.empty();
     }
 
-    private String mapObservationsAssociatedWithSpecimen(Specimen specimen, List<Observation> observations) {
-        List<Observation> observationsAssociatedWithSpecimen;
-
-        if (dummySpecimenOrObservationExists(specimen, observations)) {
-            observationsAssociatedWithSpecimen = observations;
-        } else {
-            observationsAssociatedWithSpecimen = observations.stream()
-                .filter(Observation::hasSpecimen)
-                .filter(observation -> observation.getSpecimen().getReference().equals(specimen.getId()))
-                .collect(Collectors.toList());
-        }
-
-        return observationsAssociatedWithSpecimen.stream()
+    private String mapObservationsToCompoundStatements(List<Observation> observations) {
+        return observations.stream()
             .map(observationMapper::mapObservationToCompoundStatement)
             .collect(Collectors.joining());
     }
 
-    private boolean dummySpecimenOrObservationExists(Specimen specimen, List<Observation> observations) {
-        return specimen.getIdElement().getIdPart().contains(DUMMY_SPECIMEN_ID_PREFIX)
-            || (!observations.isEmpty() && observations.getFirst().getIdElement().getIdPart().contains(DUMMY_OBSERVATION_ID_PREFIX));
-    }
-
     private Optional<String> buildSpecimenNarrativeStatement(Specimen specimen, String availabilityTimeElement,
                                                              Boolean emptyMappedObservations) {
         SpecimenNarrativeStatementCommentBuilder specimenNarrativeStatementCommentBuilder = new SpecimenNarrativeStatementCommentBuilder();

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

@@ -50,7 +50,6 @@ class SpecimenMapperTest {
     private static final String DIAGNOSTIC_REPORT_DATE = "2020-10-12T13:33:44Z";
     private static final String FHIR_INPUT_BUNDLE = BASE_DIRECTORY + "fhir_bundle.json";
     private static final String INPUT_OBSERVATION_RELATED_TO_SPECIMEN = "input-observation-related-to-specimen.json";
-    private static final String INPUT_OBSERVATION_NOT_RELATED_TO_SPECIMEN = "input-observation-not-related-to-specimen.json";
     private static final String TEST_ID = "5E496953-065B-41F2-9577-BE8F2FBD0757";
     private static final String ID_FROM_ID_MAPPER = "some-id";
     private static final DiagnosticReport DIAGNOSTIC_REPORT = new DiagnosticReport().setIssuedElement(
@@ -87,8 +86,7 @@ void setUp() {
         when(randomIdGeneratorService.createNewId()).thenReturn(TEST_ID);
 
         observations = List.of(
-            getObservationResourceFromJson(INPUT_OBSERVATION_RELATED_TO_SPECIMEN),
-            getObservationResourceFromJson(INPUT_OBSERVATION_NOT_RELATED_TO_SPECIMEN)
+            getObservationResourceFromJson(INPUT_OBSERVATION_RELATED_TO_SPECIMEN)
         );
     }
 
@@ -126,22 +124,6 @@ public void When_MappingDefaultSpecimenWithDefaultObservation_Expect_DefaultXmlO
         assertThat(actualXml).isEqualTo(expectedXml);
     }
 
-    @Test
-    void When_MappingDefaultSpecimenWithObservation_Expect_DefaultSpecimenAndObservationXmlOutput() {
-        final Specimen specimen = getDefaultSpecimen();
-        final String expectedXml = ResourceTestFileUtils.getFileContent(
-            SPECIMEN_TEST_FILES_DIRECTORY + "expected_output_default_specimen_with_observation.xml");
-
-        when(idMapper.getOrNew(any(ResourceType.class), any(IdType.class)))
-            .thenReturn(ID_FROM_ID_MAPPER);
-        when(observationMapper.mapObservationToCompoundStatement(any())).thenAnswer(mockObservationMapping());
-
-        final String actualXml = specimenMapper.mapSpecimenToCompoundStatement(
-            specimen, observations, DIAGNOSTIC_REPORT);
-
-        assertThat(actualXml).isEqualToIgnoringWhitespace(expectedXml);
-    }
-
     @Test
     void When_MappingDefaultSpecimenWithNoMappableObservations_Expect_EmptySpecimenXmlOutput() {
         final Specimen specimen = getDefaultSpecimen();