NIAD-3220: Detect Referral + Document LinkSets and not create a Problem (Condition) from them

CHANGELOG.md

@@ -5,6 +5,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+### Fixed
+
+* When a `LinkSet` which is a linkage between a `ReferralRequest` and one or more `DocumentReferences` is mapped then a
+  `Condition` will no longer be mapped for this `Linkset`.
+  Instead, the `statementRef`s will be added to the `supportingInfo` when mapping the `ReferralRequest`
+  as `DocumentReferences`
+
 ## [3.0.7] - 2024-11-19
 
 ### Fixed

gp2gp-translator/src/integrationTest/resources/e2e-mapping/output-json/PWTP7_vis-output.json

@@ -2073,6 +2073,11 @@
         } ],
         "text": "Referral to private doctor"
       } ],
+      "supportingInfo": [ {
+        "reference": "DocumentReference/BFBF038A-F142-4C67-B05B-D155E2C89990"
+      }, {
+        "reference": "DocumentReference/6DC83A17-4DFD-4C1C-A452-45F8F8A8FBA1"
+      } ],
       "note": [ {
         "text": "Priority: Routine"
       }, {
@@ -2623,61 +2628,6 @@
       } ],
       "comment": "This is a dry eyes problem {Episodicity : code=255217005, displayName=First}"
     }
-  }, {
-    "resource": {
-      "resourceType": "Condition",
-      "id": "E0EF416A-A513-4668-B454-1F3002573B80",
-      "meta": {
-        "profile": [ "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-ProblemHeader-Condition-1" ]
-      },
-      "extension": [ {
-        "url": "https://fhir.hl7.org.uk/STU3/StructureDefinition/Extension-CareConnect-ProblemSignificance-1",
-        "valueCode": "minor"
-      }, {
-        "url": "https://fhir.hl7.org.uk/STU3/StructureDefinition/Extension-CareConnect-ActualProblem-1",
-        "valueReference": {
-          "reference": "ReferralRequest/E63AF323-919F-4D5F-9A1D-BA933BC230BC"
-        }
-      }, {
-        "url": "https://fhir.hl7.org.uk/STU3/StructureDefinition/Extension-CareConnect-RelatedClinicalContent-1",
-        "valueReference": {
-          "reference": "DocumentReference/BFBF038A-F142-4C67-B05B-D155E2C89990"
-        }
-      }, {
-        "url": "https://fhir.hl7.org.uk/STU3/StructureDefinition/Extension-CareConnect-RelatedClinicalContent-1",
-        "valueReference": {
-          "reference": "DocumentReference/6DC83A17-4DFD-4C1C-A452-45F8F8A8FBA1"
-        }
-      } ],
-      "identifier": [ {
-        "system": "https://PSSAdaptor/B83002",
-        "value": "E0EF416A-A513-4668-B454-1F3002573B80"
-      } ],
-      "clinicalStatus": "active",
-      "category": [ {
-        "coding": [ {
-          "system": "https://fhir.hl7.org.uk/STU3/CodeSystem/CareConnect-ConditionCategory-1",
-          "code": "problem-list-item",
-          "display": "Problem List Item"
-        } ]
-      } ],
-      "subject": {
-        "reference": "Patient/00000000-0000-0000-0000-000000000012"
-      },
-      "context": {
-        "reference": "Encounter/7626FAAD-8562-478D-B79C-598520953E86"
-      },
-      "onsetDateTime": "2010-01-19T11:32:00+00:00",
-      "assertedDate": "2010-01-19T11:32:30+00:00",
-      "asserter": {
-        "reference": "Practitioner/1E473786-E7FA-785E-C911-A8D38FB56F20"
-      },
-      "note": [ {
-        "text": "Defaulted status to active : Unknown status at source"
-      }, {
-        "text": "Unspecified Significance: Defaulted to Minor"
-      } ]
-    }
   }, {
     "resource": {
       "resourceType": "Condition",

gp2gp-translator/src/main/java/uk/nhs/adaptors/pss/translator/mapper/ConditionMapper.java

@@ -58,6 +58,7 @@
 import uk.nhs.adaptors.pss.translator.service.ConfidentialityService;
 import uk.nhs.adaptors.pss.translator.util.CompoundStatementResourceExtractors;
 import uk.nhs.adaptors.pss.translator.util.DegradedCodeableConcepts;
+import uk.nhs.adaptors.pss.translator.util.ResourceFilterUtil;
 import static uk.nhs.adaptors.common.util.CodeableConceptUtils.createCodeableConcept;
 
 @Service
@@ -96,6 +97,7 @@ public List<Condition> mapResources(RCMRMT030101UKEhrExtract ehrExtract, Patient
         return mapEhrExtractToFhirResource(ehrExtract, (extract, composition, component) ->
                 extractAllLinkSets(component)
                     .filter(Objects::nonNull)
+                    .filter(linkSet -> !ResourceFilterUtil.isReferralRequestToExternalDocumentLinkSet(ehrExtract, linkSet))
                     .map(linkSet -> getCondition(
                         patient,
                         encounters,

gp2gp-translator/src/main/java/uk/nhs/adaptors/pss/translator/mapper/ReferralRequestMapper.java

@@ -6,27 +6,36 @@
 import static uk.nhs.adaptors.pss.translator.util.CompoundStatementResourceExtractors.extractAllRequestStatements;
 import static uk.nhs.adaptors.pss.translator.util.ResourceUtil.buildIdentifier;
 
+import java.util.AbstractMap;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
+import java.util.function.BinaryOperator;
+import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.dstu3.model.Annotation;
 import org.hl7.fhir.dstu3.model.DateTimeType;
 import org.hl7.fhir.dstu3.model.Encounter;
+import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.Meta;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.Reference;
 import org.hl7.fhir.dstu3.model.ReferralRequest;
 import org.hl7.fhir.dstu3.model.ReferralRequest.ReferralCategory;
 import org.hl7.fhir.dstu3.model.ReferralRequest.ReferralRequestStatus;
+import org.hl7.fhir.dstu3.model.ResourceType;
 import org.hl7.v3.CD;
 import org.hl7.v3.CR;
 import org.hl7.v3.CV;
 import org.hl7.v3.IVLTS;
+import org.hl7.v3.RCMRMT030101UKComponent;
+import org.hl7.v3.RCMRMT030101UKComponent3;
+import org.hl7.v3.RCMRMT030101UKComponent4;
 import org.hl7.v3.RCMRMT030101UKEhrComposition;
 import org.hl7.v3.RCMRMT030101UKEhrExtract;
+import org.hl7.v3.RCMRMT030101UKLinkSet;
 import org.hl7.v3.RCMRMT030101UKPart;
 import org.hl7.v3.RCMRMT030101UKRequestStatement;
 import org.hl7.v3.RCMRMT030101UKResponsibleParty3;
@@ -38,6 +47,7 @@
 import uk.nhs.adaptors.pss.translator.util.DateFormatUtil;
 import uk.nhs.adaptors.pss.translator.util.DegradedCodeableConcepts;
 import uk.nhs.adaptors.pss.translator.util.ParticipantReferenceUtil;
+import uk.nhs.adaptors.pss.translator.util.ResourceFilterUtil;
 
 @Service
 @AllArgsConstructor
@@ -57,6 +67,18 @@ public class ReferralRequestMapper extends AbstractMapper<ReferralRequest> {
     );
     private static final String SNOMED_CODE_SYSTEM = "2.16.840.1.113883.2.1.3.2.4.15";
 
+    private static final BinaryOperator<List<Reference>> DOCUMENT_REFERENCE_MERGE_FUNCTION = (existing, added) -> {
+        added.forEach(addedReference -> {
+            if (existing.stream().noneMatch(
+                existingReference -> addedReference.getReference().equals(existingReference.getReference())
+            )) {
+                existing.add(addedReference);
+            }
+        });
+
+        return existing;
+    };
+
     private CodeableConceptMapper codeableConceptMapper;
     private ConfidentialityService confidentialityService;
 
@@ -65,12 +87,27 @@ public List<ReferralRequest> mapResources(RCMRMT030101UKEhrExtract ehrExtract,
                                               List<Encounter> encounters,
                                               String practiceCode) {
 
+        var referralRequestToDocumentReferences = extractReferralRequestIdToDocumentReferences(ehrExtract);
+
         return mapEhrExtractToFhirResource(ehrExtract, (extract, composition, component) ->
             extractAllRequestStatements(component)
                 .filter(Objects::nonNull)
                 .filter(this::isNotSelfReferral)
-                .map(requestStatement
-                         -> mapToReferralRequest(ehrExtract, composition, requestStatement, patient, encounters, practiceCode)))
+                .map(requestStatement -> {
+                    var documentReferences = referralRequestToDocumentReferences.getOrDefault(
+                        requestStatement.getId().getFirst().getRoot(),
+                        List.of()
+                    );
+                    return mapToReferralRequest(
+                        ehrExtract,
+                        composition,
+                        requestStatement,
+                        patient,
+                        encounters,
+                        documentReferences,
+                        practiceCode
+                    );
+                }))
             .toList();
     }
 
@@ -79,14 +116,20 @@ public ReferralRequest mapToReferralRequest(RCMRMT030101UKEhrExtract ehrExtract,
                                                 RCMRMT030101UKRequestStatement requestStatement,
                                                 Patient patient,
                                                 List<Encounter> encounters,
-                                                String practiceCode) {
+                                                List<Reference> documentReferences,
+                                                String practiceCode
+    ) {
 
         var referralRequest = initializeReferralRequest(ehrComposition, requestStatement, patient, practiceCode);
 
         setReferralRequestContext(referralRequest, ehrComposition, encounters);
         setReferralRequestRecipient(ehrExtract, requestStatement, referralRequest);
         setReferralRequestReasonCode(referralRequest, requestStatement.getCode());
 
+        if (!documentReferences.isEmpty()) {
+            referralRequest.setSupportingInfo(documentReferences);
+        }
+
         return referralRequest;
     }
 
@@ -274,4 +317,32 @@ private boolean isNotSelfReferral(RCMRMT030101UKRequestStatement requestStatemen
         }
         return true;
     }
+
+    private static Map<String, List<Reference>> extractReferralRequestIdToDocumentReferences(
+        RCMRMT030101UKEhrExtract ehrExtract) {
+
+        return ehrExtract.getComponent()
+            .stream()
+            .map(RCMRMT030101UKComponent::getEhrFolder)
+            .flatMap(ehrFolder -> ehrFolder.getComponent().stream())
+            .map(RCMRMT030101UKComponent3::getEhrComposition)
+            .flatMap(ehrComposition -> ehrComposition.getComponent().stream())
+            .map(RCMRMT030101UKComponent4::getLinkSet)
+            .filter(Objects::nonNull)
+            .filter(linkSet -> ResourceFilterUtil.isReferralRequestToExternalDocumentLinkSet(ehrExtract, linkSet))
+            .map(ReferralRequestMapper::buildReferralRequestToDocumentReferenceSimpleEntry)
+            .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue, DOCUMENT_REFERENCE_MERGE_FUNCTION));
+    }
+
+    private static AbstractMap.SimpleEntry<String, List<Reference>> buildReferralRequestToDocumentReferenceSimpleEntry(
+        RCMRMT030101UKLinkSet linkSet
+    ) {
+        var referralRequestId = linkSet.getConditionNamed().getNamedStatementRef().getId().getRoot();
+        var documentReferences = linkSet.getComponent().stream()
+            .map(component -> component.getStatementRef().getId().getRoot())
+            .map(id -> new Reference(new IdType(ResourceType.DocumentReference.name(), id)))
+            .collect(Collectors.toCollection(ArrayList::new));
+
+        return new AbstractMap.SimpleEntry<>(referralRequestId, documentReferences);
+    }
 }

gp2gp-translator/src/test/java/uk/nhs/adaptors/pss/translator/mapper/ConditionMapperTest.java

@@ -363,6 +363,18 @@ void When_Condition_With_NopatConfidentialityCodeInEhrComposition_Expect_MetaFro
         );
     }
 
+    @Test
+    void When_MappingLinksetWhichIsAReferralRequestToExternalDocumentLinkSet_Expect_ConditionNotToBeMapped() {
+        final var ehrExtract = unmarshallEhrExtract(
+            "ResourceFilter",
+            "ehr_extract_with_referral_request_to_external_document_linkset.xml"
+        );
+
+        final List<Condition> conditions = conditionMapper.mapResources(ehrExtract, patient, Collections.emptyList(), PRACTISE_CODE);
+
+        assertThat(conditions).hasSize(0);
+    }
+
     private void addMedicationRequestsToBundle(Bundle bundle) {
         var planMedicationRequest = new MedicationRequest().setId(AUTHORISE_ID);
         var orderMedicationRequest = new MedicationRequest().setId(PRESCRIBE_ID);
@@ -448,11 +460,16 @@ private void assertAllConditionsHaveMeta(List<Condition> conditions, Meta expect
     }
 
     @SneakyThrows
-    private RCMRMT030101UKEhrExtract unmarshallEhrExtract(String filename) {
-        final File file = FileFactory.getXmlFileFor(TEST_FILES_DIRECTORY, filename);
+    private RCMRMT030101UKEhrExtract unmarshallEhrExtract(String testFilesDirectory, String filename) {
+        final File file = FileFactory.getXmlFileFor(testFilesDirectory, filename);
         return unmarshallFile(file, RCMRMT030101UKEhrExtract.class);
     }
 
+    @SneakyThrows
+    private RCMRMT030101UKEhrExtract unmarshallEhrExtract(String filename) {
+        return unmarshallEhrExtract(TEST_FILES_DIRECTORY, filename);
+    }
+
     private void configureCommonStubs() {
         Mockito.lenient().when(dateTimeMapper.mapDateTime(
             any(String.class)

gp2gp-translator/src/test/java/uk/nhs/adaptors/pss/translator/mapper/ReferralRequestMapperTest.java

@@ -29,6 +29,7 @@
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.ReferralRequest;
 import org.hl7.fhir.dstu3.model.ReferralRequest.ReferralRequestStatus;
+import org.hl7.fhir.dstu3.model.ResourceType;
 import org.hl7.v3.CV;
 import org.hl7.v3.RCMRMT030101UKEhrComposition;
 import org.hl7.v3.RCMRMT030101UKEhrExtract;
@@ -552,6 +553,63 @@ void When_MapToReferralRequest_With_NopatConfidentialityCodeWithinEhrComposition
         );
     }
 
+    @Test
+    void When_MappingReferralRequestReferencedByReferralRequestToExternalDocumentLinkSet_Expect_SupportingInfoReferencesLinksetDocuments() {
+        final RCMRMT030101UKEhrExtract ehrExtract = unmarshallEhrExtractElement(
+            "ResourceFilter",
+            "ehr_extract_with_referral_request_to_external_document_linkset.xml"
+        );
+
+        final var referralRequests = referralRequestMapper.mapResources(
+            ehrExtract,
+            (Patient) new Patient().setId(PATIENT_ID),
+            List.of(),
+            PRACTISE_CODE
+        );
+        final var referralRequest = referralRequests.getFirst();
+
+        assertAll(
+            () -> assertThat(referralRequest.getSupportingInfo())
+                .hasSize(2),
+            () -> assertThat(referralRequest.getSupportingInfo().getFirst().getReferenceElement().getResourceType())
+                .isEqualTo(ResourceType.DocumentReference.name()),
+            () -> assertThat(referralRequest.getSupportingInfo().getFirst().getReferenceElement().getIdPart())
+                .isEqualTo("narrative-statement-1"),
+            () -> assertThat(referralRequest.getSupportingInfo().getLast().getReferenceElement().getResourceType())
+                .isEqualTo(ResourceType.DocumentReference.name()),
+            () -> assertThat(referralRequest.getSupportingInfo().getLast().getReferenceElement().getIdPart())
+                .isEqualTo("narrative-statement-2")
+        );
+    }
+
+    @Test
+    void When_ReferralRequestReferencedByMultipleLinkSets_Expect_AllRelatedDocumentReferencesAddedAsSupportingInfo() {
+        final var expectedSize = 3;
+        final RCMRMT030101UKEhrExtract ehrExtract = unmarshallEhrExtractElement(
+            "ehr_extract_with_multiple_request_statement_to_external_document_linksets.xml"
+        );
+
+
+        final var referralRequests = referralRequestMapper.mapResources(
+            ehrExtract,
+            (Patient) new Patient().setId(PATIENT_ID),
+            List.of(),
+            PRACTISE_CODE
+        );
+        final var referralRequest = referralRequests.getFirst();
+        assertAll(
+            () -> assertThat(referralRequest.getSupportingInfo()).hasSize(expectedSize),
+            () -> assertThat(referralRequest.getSupportingInfo())
+                .extracting(reference -> reference.getReferenceElement().getIdPart())
+                .containsExactly(
+                    "narrative-statement-1",
+                    "narrative-statement-2",
+                    "narrative-statement-3"
+                )
+        );
+
+    }
+
     private RCMRMT030101UKRequestStatement getNestedRequestStatement(RCMRMT030101UKEhrComposition ehrComposition) {
         return ehrComposition.getComponent()
             .getFirst()
@@ -595,6 +653,7 @@ private static ReferralRequest mapReferralRequest(RCMRMT030101UKEhrExtract ehrEx
                 requestStatement,
                 patient,
                 List.of(encounter),
+                List.of(),
                 PRACTISE_CODE);
     }
 
@@ -618,10 +677,17 @@ private RCMRMT030101UKEhrComposition unmarshallStringToEhrCompositionElement(Str
 
     @SneakyThrows
     private RCMRMT030101UKEhrExtract unmarshallEhrExtractElement(String fileName) {
-        final File file = FileFactory.getXmlFileFor(TEST_DIRECTORY_NAME, fileName);
+        return unmarshallEhrExtractElement(TEST_DIRECTORY_NAME, fileName);
+    }
+
+    @SneakyThrows
+    private RCMRMT030101UKEhrExtract unmarshallEhrExtractElement(String testDirectory, String fileName) {
+        final File file = FileFactory.getXmlFileFor(testDirectory, fileName);
         return unmarshallFile(file, RCMRMT030101UKEhrExtract.class);
     }
 
+
+
     @SneakyThrows
     private RCMRMT030101UKEhrExtract unmarshallStringToEhrExtractElement(String inputXml) {
         return unmarshallString(inputXml, RCMRMT030101UKEhrExtract.class);