NIAD-3401: DUMMY instances replacement in DiagnosticReportMapper

CHANGELOG.md

@@ -18,7 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * The GP2GP Adaptor now throws an exception when the Access Structure Record is empty, thereby rejecting the transfer
 
 ### Fixed
-* When DiagnosticReport doesn't contain a Specimen reference, instead of "DUMMY" "NOT-PRESENT" value is used
+* When DiagnosticReport doesn't contain a Specimen or Observation reference, instead of "DUMMY" "NOT-PRESENT" value is used
 
 ### Update
 

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

@@ -53,7 +53,7 @@
 public class DiagnosticReportMapper {
 
     public static final String NOT_PRESENT_SPECIMEN_ID_PREFIX = "NOT-PRESENT-SPECIMEN-";
-    public static final String DUMMY_OBSERVATION_ID_PREFIX = "DUMMY-OBSERVATION-";
+    public static final String NOT_PRESENT_OBSERVATION_ID_PREFIX = "NOT-PRESENT-OBSERVATION-";
 
     private static final Mustache DIAGNOSTIC_REPORT_COMPOUND_STATEMENT_TEMPLATE =
         TemplateUtils.loadTemplate("diagnostic_report_compound_statement_template.mustache");
@@ -80,25 +80,25 @@ public String mapDiagnosticReportToCompoundStatement(DiagnosticReport diagnostic
         final IdMapper idMapper = messageContext.getIdMapper();
         markObservationsAsProcessed(idMapper, observations);
 
-        List<Observation> observationsWithAttachedDummySpecimens =
-                new ArrayList<>(assignDummySpecimensToObservationsWithNoSpecimen(observations, specimens));
+        List<Observation> observationsWithAttachedNotPresentSpecimens =
+                new ArrayList<>(assignNotPresentSpecimensToObservationsWithNoSpecimen(observations, specimens));
 
-        observations = addDummyObservationsToObservationList(
-                observationsWithAttachedDummySpecimens,
+        observations = addNotPresentObservationsToObservationList(
+                observationsWithAttachedNotPresentSpecimens,
                 specimens,
                 diagnosticReport);
 
-        List<Observation> observationsWithDummySpecimensAndDummyObservations = observations;
+        List<Observation> observationsWithNotPresentSpecimensAndNotPresentObservations = observations;
 
         String mappedSpecimens = specimens.stream()
             .map(specimen -> specimenMapper.mapSpecimenToCompoundStatement(specimen,
-                    observationsForSpecimen(specimen, observationsWithDummySpecimensAndDummyObservations),
+                    observationsForSpecimen(specimen, observationsWithNotPresentSpecimensAndNotPresentObservations),
                     diagnosticReport))
             .collect(Collectors.joining());
 
         String reportLevelNarrativeStatements = prepareReportLevelNarrativeStatements(
                 diagnosticReport,
-                observationsWithDummySpecimensAndDummyObservations);
+                observationsWithNotPresentSpecimensAndNotPresentObservations);
 
         var diagnosticReportCompoundStatementTemplateParameters = DiagnosticReportCompoundStatementTemplateParameters.builder()
             .compoundStatementId(idMapper.getOrNew(ResourceType.DiagnosticReport, diagnosticReport.getIdElement()))
@@ -146,14 +146,14 @@ private List<Specimen> fetchSpecimens(DiagnosticReport diagnosticReport, List<Ob
         }
 
         var inputBundleHolder = messageContext.getInputBundleHolder();
-        List<Specimen> nonDummySpecimens = diagnosticReport.getSpecimen()
+        List<Specimen> nonNotPresentSpecimens = diagnosticReport.getSpecimen()
             .stream()
             .map(specimenReference -> inputBundleHolder.getResource(specimenReference.getReferenceElement()))
             .flatMap(Optional::stream)
             .map(Specimen.class::cast)
             .toList();
 
-        specimens.addAll(nonDummySpecimens);
+        specimens.addAll(nonNotPresentSpecimens);
 
         return specimens;
     }
@@ -166,9 +166,9 @@ private boolean hasObservationsWithoutSpecimen(List<Observation> observations) {
     }
 
     /**
-     * For correct display in EMIS, any observation without a specimen must be assigned a dummy specimen.
+     * For correct display in EMIS, any observation without a specimen must be assigned a not present specimen.
      */
-    List<Observation> assignDummySpecimensToObservationsWithNoSpecimen(List<Observation> observations, List<Specimen> specimens) {
+    List<Observation> assignNotPresentSpecimensToObservationsWithNoSpecimen(List<Observation> observations, List<Specimen> specimens) {
 
         List<Observation> filingComments = getFilingComments(observations);
         List<Observation> nonFilingObservations = new ArrayList<>(stripFilingComments(observations));
@@ -178,7 +178,7 @@ List<Observation> assignDummySpecimensToObservationsWithNoSpecimen(List<Observat
             return nonFilingObservations;
         }
 
-        // The assumption was made that all test results without a specimen will have the same dummy specimen referenced
+        // The assumption was made that all test results without a specimen will have the same not present specimen referenced
         Specimen notPresentSpecimen = specimens.stream()
             .filter(specimen -> specimen.getId().contains(NOT_PRESENT_SPECIMEN_ID_PREFIX))
             .toList().getFirst();
@@ -219,21 +219,21 @@ private List<Observation> fetchObservations(DiagnosticReport diagnosticReport) {
     }
 
     /**
-     * For correct display in EMIS, any specimen without an observation must be assigned a dummy observation.
+     * For correct display in EMIS, any specimen without an observation must be assigned a not present observation.
      */
-    private List<Observation> addDummyObservationsToObservationList(
+    private List<Observation> addNotPresentObservationsToObservationList(
             List<Observation> observations,
             List<Specimen> specimens,
             DiagnosticReport diagnosticReport) {
         List<Observation> completeObservations = new ArrayList<>();
         completeObservations.addAll(observations);
 
-        // Generate a dummy Observation for each Specimen without an Observation
+        // Generate a not present Observation for each Specimen without an Observation
         for (String specimenWithoutObservations : getSpecimenIdsWithoutObservation(specimens, observations)) {
-            Observation dummyObservation = generateDummyObservation(diagnosticReport);
+            Observation notPresentObservation = generateNotPresentObservation(diagnosticReport);
             Reference specimenReference = new Reference(specimenWithoutObservations);
-            dummyObservation.setSpecimen(specimenReference);
-            completeObservations.add(dummyObservation);
+            notPresentObservation.setSpecimen(specimenReference);
+            completeObservations.add(notPresentObservation);
         }
 
         return completeObservations;
@@ -243,7 +243,7 @@ private List<String> getSpecimenIdsWithoutObservation(List<Specimen> specimens,
         List<String> specimenIDList = new ArrayList<>();
         List<String> nonOrphanSpecimenIDList = new ArrayList<>();
         for (Specimen specimen : specimens) {
-            // Dummy Specimens should not have a dummy observation attached.
+            // Not present Specimens should not have a not present observation attached.
             if (!specimen.getId().contains(NOT_PRESENT_SPECIMEN_ID_PREFIX)) {
                 specimenIDList.add(specimen.getId());
             }
@@ -264,10 +264,10 @@ private List<String> getSpecimenIdsWithoutObservation(List<Specimen> specimens,
         return specimensWithoutObservations;
     }
 
-    private Observation generateDummyObservation(DiagnosticReport diagnosticReport) {
+    private Observation generateNotPresentObservation(DiagnosticReport diagnosticReport) {
         Observation observation = new Observation();
 
-        observation.setId(DUMMY_OBSERVATION_ID_PREFIX + randomIdGeneratorService.createNewId());
+        observation.setId(NOT_PRESENT_OBSERVATION_ID_PREFIX + randomIdGeneratorService.createNewId());
 
         return observation
             .setIssuedElement(diagnosticReport.getIssuedElement())

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

@@ -1,6 +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 java.util.List;
 import java.util.Objects;
@@ -46,6 +45,8 @@
 import uk.nhs.adaptors.gp2gp.ehr.utils.StatementTimeMappingUtils;
 import uk.nhs.adaptors.gp2gp.ehr.utils.TemplateUtils;
 
+import static uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.DiagnosticReportMapper.NOT_PRESENT_OBSERVATION_ID_PREFIX;
+
 @Component
 @RequiredArgsConstructor(onConstructor = @__(@Autowired))
 @Slf4j
@@ -240,7 +241,7 @@ private String mapObservationToObservationStatement(MultiStatementObservationHol
     private Optional<String> prepareNarrativeStatements(MultiStatementObservationHolder holder, boolean interpretationCodeMapped) {
         Observation observation = holder.getObservation();
 
-        if (observation.getIdElement().getIdPart().contains(DUMMY_OBSERVATION_ID_PREFIX)) {
+        if (observation.getIdElement().getIdPart().contains(NOT_PRESENT_OBSERVATION_ID_PREFIX)) {
             return Optional.of(
                 mapObservationToNarrativeStatement(holder, observation.getComment(), CommentType.AGGREGATE_COMMENT_SET.getCode())
             );

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

@@ -155,7 +155,7 @@ void shouldAssignDummySpecimenOnlyToNonFilingObservationsWithoutSpecimen() {
         dummySpecimen.setId(NOT_PRESENT_SPECIMEN_ID_PREFIX + "123");
         List<Specimen> specimens = List.of(dummySpecimen);
 
-        List<Observation> result = mapper.assignDummySpecimensToObservationsWithNoSpecimen(observations, specimens);
+        List<Observation> result = mapper.assignNotPresentSpecimensToObservationsWithNoSpecimen(observations, specimens);
 
         assertThat(obsWithoutSpecimen.getSpecimen())
             .isNotNull()
@@ -178,7 +178,7 @@ void shouldThrowIfNoDummySpecimenFound() {
 
         List<Specimen> specimens = List.of();
 
-        assertThatThrownBy(() -> mapper.assignDummySpecimensToObservationsWithNoSpecimen(observations, specimens))
+        assertThatThrownBy(() -> mapper.assignNotPresentSpecimensToObservationsWithNoSpecimen(observations, specimens))
             .isInstanceOf(NoSuchElementException.class);
     }
 
@@ -197,7 +197,7 @@ void shouldAssignDummySpecimenToObservationsWithoutSpecimen() {
         realSpecimen.setId("real-specimen");
         List<Specimen> specimens = List.of(realSpecimen, dummySpecimen);
 
-        List<Observation> result = mapper.assignDummySpecimensToObservationsWithNoSpecimen(observations, specimens);
+        List<Observation> result = mapper.assignNotPresentSpecimensToObservationsWithNoSpecimen(observations, specimens);
 
         assertThat(result).hasSize(2);
         assertThat(result.get(0).getSpecimen().getReference()).contains(dummySpecimen.getId());
@@ -412,7 +412,7 @@ void When_DiagnosticReport_Has_MultipleSpecimensAndOneObservation_Expect_ADummyO
 
         assertThat(actualXml).containsIgnoringWhitespaces(
                 "<!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-1 "
-                        + "with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->");
+                        + "with linked Observations: NOT-PRESENT-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->");
 
     }
 
@@ -438,11 +438,11 @@ void When_DiagnosticReport_Has_ThreeSpecimensAndOneObservation_Expect_DummyObser
 
         assertThat(actualXml).containsIgnoringWhitespaces(
                 "<!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-1 "
-                        + "with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->");
+                        + "with linked Observations: NOT-PRESENT-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->");
 
         assertThat(actualXml).containsIgnoringWhitespaces(
                 "<!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-2 "
-                        + "with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->");
+                        + "with linked Observations: NOT-PRESENT-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->");
     }
 
     /**
@@ -472,7 +472,7 @@ void When_DiagnosticReport_Has_TwoLinkedSpecimensOneUnlinkedSpecimenAndOneObserv
 
         assertThat(actualXml).containsIgnoringWhitespaces(
                 "<!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-2 "
-                        + "with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->");
+                        + "with linked Observations: NOT-PRESENT-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->");
     }
 
     @Test

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

@@ -90,6 +90,8 @@ class ObservationMapperTest {
         "observation_test_group_header.json";
     private static final String OBSERVATION_TEST_RESULT_JSON =
         "observation_test_result.json";
+    private static final String NOT_PRESENT_OBSERVATION_RESULT_JSON =
+        "not_present_observation.json";
     private static final String OBSERVATION_FILING_COMMENT_JSON =
         "observation_filing_comment.json";
     private static final String OBSERVATION_ASSOCIATED_WITH_IGNORED_MEMBER_JSON =
@@ -273,6 +275,21 @@ void When_MappingTestResult_With_NopatMetaSecurity_Expect_ConfidentialityCodeWit
         assertThatXml(actualXml).containsXPath(OBSERVATION_STATEMENT_CONFIDENTIALITY_CODE_XPATH);
     }
 
+    @Test
+    void When_ObservationDoesNotContainNotPresentElements_Expect_MappedObservetionNotContainAggregateComments() {
+        final Observation not_present_observation = getObservationResourceFromJson(NOT_PRESENT_OBSERVATION_RESULT_JSON);
+        String expression = "//component/NarrativeStatement/text[contains(normalize-space(.), 'AGGREGATE COMMENT SET')]";
+
+        ConfidentialityCodeUtility.appendNopatSecurityToMetaForResource(not_present_observation);
+        when(confidentialityService.generateConfidentialityCode(not_present_observation))
+            .thenReturn(Optional.of(NOPAT_HL7_CONFIDENTIALITY_CODE));
+
+        final String actualXml = observationMapper.mapObservationToCompoundStatement(not_present_observation);
+        String wrappedXml = "<root>" + actualXml + "</root>";
+
+        assertThatXml(wrappedXml).containsXPath(expression);
+    }
+
     @Test
     void When_MappingTestResult_With_NoscrubMetaSecurity_Expect_ConfidentialityCodeNotPresent() {
         final Observation observation = getObservationResourceFromJson(OBSERVATION_TEST_RESULT_JSON);

service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-multi-specimens.xml

@@ -20,8 +20,8 @@ Status: unknown</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
-        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-0 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
-        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-1 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
-        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-2 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
+        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-0 with linked Observations: NOT-PRESENT-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
+        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-1 with linked Observations: NOT-PRESENT-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
+        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-2 with linked Observations: NOT-PRESENT-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
     </CompoundStatement>
 </component>

service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-one-specimen.xml

@@ -20,6 +20,6 @@ Status: unknown</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
-        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-0 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
+        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-0 with linked Observations: NOT-PRESENT-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
     </CompoundStatement>
 </component>

service/src/test/resources/ehr/mapper/diagnosticreport/observation/not_present_observation.json

@@ -0,0 +1,55 @@
+{
+  "resourceType": "Observation",
+  "id": "NOT-PRESENT-OBSERVATION-32685afe-1d46-4d98-8279-39b9e96ee914",
+  "meta":
+  {
+    "profile": [
+      "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-Observation-1"
+    ]
+  },
+  "identifier": [
+    {
+      "system": "https://tools.ietf.org/html/rfc4122",
+      "value": "2af46949-4938-4c57-bad4-c4363e1965d7"
+    }
+  ],
+  "status": "final",
+  "category": [
+    {
+      "coding": [
+        {
+          "system": "http://snomed.info/sct",
+          "code": "394595002",
+          "display": "Pathology"
+        }
+      ]
+    }
+  ],
+  "code": {
+    "coding": [
+      {
+        "system": "http://snomed.info/sct",
+        "code": "1022451000000103",
+        "display": "Red blood cell count"
+      }
+    ]
+  },
+  "subject": {
+    "reference": "Patient/11",
+    "display": "SKELLY, Horace"
+  },
+  "issued": "2019-04-06T12:00:00+00:00",
+  "performer": [
+    {
+      "reference": "Organization/7",
+      "display": "COXWOLD Surgery"
+    }
+  ],
+  "valueQuantity": {
+    "value": 4.5700000000000003,
+    "unit": "10*12/L"
+  },
+  "specimen": {
+    "reference": "Specimen/756a8361-79ce-4561-afcb-a91fe19df123"
+  }
+}