Fixed test data

Added placeholder for new linking between specimen and observation, and removed the old one.

Added test for the second scenario and fixed the test data.

Author: Alex-Nita

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

@@ -111,13 +111,15 @@ private String fetchExtensionId(List<Identifier> identifiers) {
 
     private List<Specimen> fetchSpecimens(DiagnosticReport diagnosticReport) {
 
-        //if there are any orphan diagnostic reports, add a dummy specimen to each of them
+        //if there are any orphan observations, add a dummy specimen to each of them
 
         if (!diagnosticReport.hasSpecimen()) {
             return Collections.singletonList(generateDefaultSpecimen(diagnosticReport));
         }
 
-        var inputBundleHolder = messageContext.getInputBundleHolder();
+        fixOrphanedTestResults(diagnosticReport);
+
+        InputBundle inputBundleHolder = messageContext.getInputBundleHolder();
         return diagnosticReport.getSpecimen()
             .stream()
             .map(specimenReference -> inputBundleHolder.getResource(specimenReference.getReferenceElement()))
@@ -126,6 +128,22 @@ private List<Specimen> fetchSpecimens(DiagnosticReport diagnosticReport) {
             .collect(Collectors.toList());
     }
 
+    private void fixOrphanedTestResults(DiagnosticReport diagnosticReport) {
+
+
+        if (diagnosticReport.hasResult()){
+            List<Reference> results = diagnosticReport.getResult();
+            List<Reference> specimens = diagnosticReport.getSpecimen();
+            for (Reference specimen : specimens){
+
+            }
+            for (Reference result : results) {
+                //
+                    //check each test result one by one, and if it doesn't have a dummy assigned to it, assign it.
+            }
+        }
+    }
+
     private Specimen generateDefaultSpecimen(DiagnosticReport diagnosticReport) {
         Specimen specimen = new Specimen();
 

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

@@ -137,18 +137,8 @@ private Optional<String> buildSpecimenMaterialType(Specimen specimen) {
     }
 
     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()
+        return observations.stream()
             .filter(Predicate.not(DiagnosticReportMapper::isFilingComment))
             .map(observationMapper::mapObservationToCompoundStatement)
             .collect(Collectors.joining());

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

@@ -308,6 +308,19 @@ void When_DiagnosticReport_Has_SpecimenAndUnlinkedTestResult_ExpectADummySpecime
         assertThat(actualXml).contains("Mapped Specimen with id: DUMMY-SPECIMEN-");
     }
 
+    @Test
+    void When_DiagnosticReport_Has_SpecimenAndUnlinkedTestResult_ExpectScenario2() {
+        final String diagnosticReportFileName = "diagnostic-report-with-one-specimen-one-linked-observation-and-one-unlinked-observation.json";
+        final DiagnosticReport diagnosticReport = getDiagnosticReportResourceFromJson(diagnosticReportFileName);
+        final Bundle bundle = getBundleResourceFromJson(INPUT_JSON_BUNDLE);
+        final InputBundle inputBundle = new InputBundle(bundle);
+
+        when(messageContext.getInputBundleHolder()).thenReturn(inputBundle);
+
+        final String actualXml = mapper.mapDiagnosticReportToCompoundStatement(diagnosticReport);
+        assertThat(actualXml).contains("Mapped Specimen with id: DUMMY-SPECIMEN-");
+    }
+
     private Bundle getBundleResourceFromJson(String filename) {
         final String filePath = TEST_FILE_DIRECTORY + filename;
         return FileParsingUtility.parseResourceFromJsonFile(filePath, Bundle.class);
@@ -359,7 +372,18 @@ private Answer<String> mockIdForReference() {
     private Answer<String> mockSpecimenMapping() {
         return invocation -> {
             Specimen specimen = invocation.getArgument(0);
-            return String.format("<!-- Mapped Specimen with id: %s -->", specimen.getId());
+            List<Observation> observations = invocation.getArgument(1);
+
+            String linkedObservations = "";
+
+            for (Observation observation : observations) {
+                if(observation.getSpecimen().getReference() != null && observation.getSpecimen().getReference().equals(specimen.getId())){
+                    linkedObservations = linkedObservations + observation.getId() + ", ";
+                }
+            }
+
+
+            return String.format("<!-- Mapped Specimen with id: %s with linked Observations: %s-->", specimen.getId(), linkedObservations);
         };
     }
 }