Removed filtering of filing comments from Specimen mapper and added it to diagnostic report mapper

Author: Alex-Nita

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

@@ -12,6 +12,7 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
+import java.util.function.Predicate;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -121,7 +122,7 @@ private List<Specimen> fetchSpecimens(DiagnosticReport diagnosticReport, List<Ob
 
         List<Specimen> specimens = new ArrayList<>();
 
-        // At least one specimen is required to exist for any DiagnosticReport
+        // At least one specimen is required to exist for any DiagnosticReport, according to the mim
         if (!diagnosticReport.hasSpecimen() || hasOrphanedTestResults(observations)) {
             specimens.add(generateDummySpecimen(diagnosticReport));
         }
@@ -143,6 +144,7 @@ private List<Specimen> fetchSpecimens(DiagnosticReport diagnosticReport, List<Ob
     private boolean hasOrphanedTestResults(List<Observation> observations) {
         return observations
                 .stream()
+                .filter(observation -> !isFilingComment(observation))
                 .anyMatch(observation -> !observation.hasSpecimen());
     }
 
@@ -161,7 +163,7 @@ private List<Observation> assignDummySpecimensToOrphanedTestResults(
         Reference dummySpecimenReference = new Reference(dummySpecimen.getId());
 
         for (Observation observation : observations) {
-            if (!observation.hasSpecimen()) {
+            if (!observation.hasSpecimen() && !isFilingComment(observation)) {
                 observation.setSpecimen(dummySpecimenReference);
             }
         }

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

@@ -149,7 +149,6 @@ private String mapObservationsAssociatedWithSpecimen(Specimen specimen, List<Obs
         }
 
         return observationsAssociatedWithSpecimen.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

@@ -90,9 +90,6 @@ class DiagnosticReportMapperTest {
     private static final String OUTPUT_XML_EXTENSION_ID = "diagnostic-report-with-extension-id.xml";
     private static final String OUTPUT_XML_MULTIPLE_RESULTS = "diagnostic-report-with-multiple-results.xml";
     private static final String OUTPUT_XML_UNRELATED_TEST_RESULT = "diagnostic-report-with-one-specimen-and-one-unrelated-observation.xml";
-    private static final String REGEXP_UUID = "[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}";
-    private static final String MOCKED_SPECIMEN_PREFIX = "Mapped Specimen with id";
-    private static final String MOCKED_SPECIMEN_LINKED_OBSERVATION = "with linked Observations";
 
     @Mock
     private CodeableConceptCdMapper codeableConceptCdMapper;
@@ -307,20 +304,15 @@ void When_DiagnosticReport_Has_SpecimenAndUnlinkedTestResult_Expect_ADummySpecim
         final DiagnosticReport diagnosticReport = getDiagnosticReportResourceFromJson(diagnosticReportFileName);
         final Bundle bundle = getBundleResourceFromJson(INPUT_JSON_BUNDLE);
         final InputBundle inputBundle = new InputBundle(bundle);
-        final String expectObservation = "Observation/TestResult-WithoutSpecimenReference";
-        final String dummyNamePrefix = DiagnosticReportMapper.DUMMY_SPECIMEN_ID_PREFIX;
 
         when(messageContext.getInputBundleHolder()).thenReturn(inputBundle);
 
         final String actualXml = mapper.mapDiagnosticReportToCompoundStatement(diagnosticReport);
 
         // This checks that the unlinked test result is given a dummy specimen.
-        assertThat(actualXml).matches("(?s).*<!-- " + MOCKED_SPECIMEN_PREFIX + ": " + dummyNamePrefix
-                + REGEXP_UUID
-                + " " + MOCKED_SPECIMEN_LINKED_OBSERVATION + ": "
-                + expectObservation
-                + "-->.*"
-        );
+        assertThat(actualXml).containsIgnoringWhitespaces(
+                "<!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 "
+                        + "with linked Observations: Observation/TestResult-WithoutSpecimenReference-->");
     }
 
     @Test
@@ -330,25 +322,13 @@ void When_DiagnosticReport_Has_SpecimenALinkedTestResultAndAnUnlinkedTestResult_
         final DiagnosticReport diagnosticReport = getDiagnosticReportResourceFromJson(diagnosticReportFileName);
         final Bundle bundle = getBundleResourceFromJson(INPUT_JSON_BUNDLE);
         final InputBundle inputBundle = new InputBundle(bundle);
-        final String expectObservation = "Observation/TestResult-WithoutSpecimenReference";
-        final String dummyNamePrefix = DiagnosticReportMapper.DUMMY_SPECIMEN_ID_PREFIX;
         when(messageContext.getInputBundleHolder()).thenReturn(inputBundle);
 
         final String actualXml = mapper.mapDiagnosticReportToCompoundStatement(diagnosticReport);
         // This checks that the unlinked test result is given a dummy specimen.
-        assertThat(actualXml).matches("(?s).*<!-- " + MOCKED_SPECIMEN_PREFIX + ": " + dummyNamePrefix
-                + REGEXP_UUID
-                + " " + MOCKED_SPECIMEN_LINKED_OBSERVATION + ": "
-                + expectObservation
-                + "-->.*"
-        );
-        // This checks that the linked test result has its correct specimen.
-        assertThat(actualXml).containsIgnoringWhitespaces("<!-- " + MOCKED_SPECIMEN_PREFIX + ": "
-                + "Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-0"
-                + MOCKED_SPECIMEN_LINKED_OBSERVATION + ":"
-                + "Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2"
-                + " -->"
-        );
+        assertThat(actualXml).containsIgnoringWhitespaces(
+                "<!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 "
+                        + "with linked Observations: Observation/TestResult-WithoutSpecimenReference-->");
 
     }
 
@@ -412,10 +392,9 @@ private Answer<String> mockSpecimenMapping() {
             }
 
             if (linkedObservations.isEmpty()) {
-                return String.format("<!-- " + MOCKED_SPECIMEN_PREFIX + ": %s -->", specimen.getId());
+                return String.format("<!-- Mapped Specimen with id: %s -->", specimen.getId());
             }
-            return String.format("<!-- " + MOCKED_SPECIMEN_PREFIX + ": %s "
-                    + MOCKED_SPECIMEN_LINKED_OBSERVATION + ": %s-->",
+            return String.format("<!-- Mapped Specimen with id: %s with linked Observations: %s-->",
                     specimen.getId(),
                     String.join(",", linkedObservations));
         };

service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-multiple-results.xml

@@ -62,6 +62,6 @@ CommentDate:20100225154100
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
-            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 with linked Observations: Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2-COMM,Observation/6E30A9E3-FF9A-4868-8FCD-7DAC26A16E78-COMM,Observation/D0A358C9-4833-4827-B14B-E8515C25CB12-COMM-->
+            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757-->
     </CompoundStatement>
 </component>

service/src/test/resources/ehr/mapper/diagnosticreport/specimen/expected_output_default_specimen_with_observation.xml

@@ -31,6 +31,6 @@ Received Date: 2010-02-24 15:41
         <availabilityTime value="20201012143344"/>
     </NarrativeStatement>
 </component>
-            <!-- Mapped Observation with id: Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2 -->
+            <!-- Mapped Observation with id: Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2 --><!-- Mapped Observation with id: Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2-COMM -->
     </CompoundStatement>
 </component>