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 +6,35 @@
 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.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 +46,7 @@
 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
@@ -65,13 +74,17 @@ public List<ReferralRequest> mapResources(RCMRMT030101UKEhrExtract ehrExtract,
                                               List<Encounter> encounters,
                                               String practiceCode) {
 
-        return mapEhrExtractToFhirResource(ehrExtract, (extract, composition, component) ->
+        var referralRequests = mapEhrExtractToFhirResource(ehrExtract, (extract, composition, component) ->
             extractAllRequestStatements(component)
                 .filter(Objects::nonNull)
                 .filter(this::isNotSelfReferral)
                 .map(requestStatement
-                         -> mapToReferralRequest(ehrExtract, composition, requestStatement, patient, encounters, practiceCode)))
+                    -> mapToReferralRequest(ehrExtract, composition, requestStatement, patient, encounters, practiceCode)))
             .toList();
+
+        populateSupportingInfoWithDocumentReferencesFromLinkSets(ehrExtract, referralRequests);
+
+        return referralRequests;
     }
 
     public ReferralRequest mapToReferralRequest(RCMRMT030101UKEhrExtract ehrExtract,
@@ -274,4 +287,44 @@ private boolean isNotSelfReferral(RCMRMT030101UKRequestStatement requestStatemen
         }
         return true;
     }
+
+    private static void populateSupportingInfoWithDocumentReferencesFromLinkSets(
+        RCMRMT030101UKEhrExtract ehrExtract,
+        List<ReferralRequest> referralRequests
+    ) {
+        extractReferralRequestIdToDocumentReferences(ehrExtract).forEach(
+            (referralRequestId, documentReferences) -> referralRequests.stream()
+                .filter(referralRequest -> referralRequestId.equals(referralRequest.getId()))
+                .findFirst()
+                .ifPresent(referencedReferralRequest -> referencedReferralRequest.setSupportingInfo(documentReferences))
+        );
+    }
+
+    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));
+    }
+
+    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)))
+            .toList();
+
+        return new AbstractMap.SimpleEntry<>(referralRequestId, documentReferences);
+    }
 }

gp2gp-translator/src/main/java/uk/nhs/adaptors/pss/translator/util/ResourceFilterUtil.java

@@ -5,18 +5,26 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import lombok.AccessLevel;
 import lombok.NoArgsConstructor;
+import org.hl7.v3.RCMRMT030101UKComponent;
+import org.hl7.v3.RCMRMT030101UKComponent3;
+import org.hl7.v3.RCMRMT030101UKComponent4;
 import org.hl7.v3.RCMRMT030101UKCompoundStatement;
 import org.hl7.v3.RCMRMT030101UKEhrExtract;
+import org.hl7.v3.RCMRMT030101UKLinkSet;
 import org.hl7.v3.RCMRMT030101UKNarrativeStatement;
 
 @NoArgsConstructor(access = AccessLevel.PRIVATE)
 public class ResourceFilterUtil {
 
     private static final List<String> ALLERGY_CODES = List.of("SN53.00", "14L..00");
     private static final String CODE_SYSTEM_READ_CODE_V2 = "2.16.840.1.113883.2.1.6.2";
+    private static final String SNOMED_CODE_SYSTEM = "2.16.840.1.113883.2.1.3.2.4.15";
+    private static final String UNSPECIFIED_PROBLEM_CODE = "394776006";
     private static final String PATHOLOGY_CODE = "16488004";
     private static final String SPECIMEN_CODE = "123038009";
     private static final String BATTERY_VALUE = "BATTERY";
@@ -82,6 +90,63 @@ public static boolean isTemplate(RCMRMT030101UKCompoundStatement compoundStateme
             && List.of(BATTERY_VALUE, CLUSTER_VALUE).contains(compoundStatement.getClassCode().getFirst());
     }
 
+    public static boolean isReferralRequestToExternalDocumentLinkSet(RCMRMT030101UKEhrExtract ehrExtract, RCMRMT030101UKLinkSet linkSet) {
+        return hasUnspecifiedProblemCodeWithoutQualifierOrOriginalText(linkSet)
+            && !linkSet.getComponent().isEmpty()
+            && hasNamedStatementRefReferencingARequestStatement(ehrExtract, linkSet)
+            && containsOnlyComponentsWithStatementRefReferencingADocument(ehrExtract, linkSet);
+    }
+
+    private static boolean hasUnspecifiedProblemCodeWithoutQualifierOrOriginalText(RCMRMT030101UKLinkSet linkSet) {
+        return linkSet.hasCode()
+            && SNOMED_CODE_SYSTEM.equals(linkSet.getCode().getCodeSystem())
+            && UNSPECIFIED_PROBLEM_CODE.equals(linkSet.getCode().getCode())
+            && linkSet.getCode().getQualifier().isEmpty()
+            && !linkSet.getCode().hasOriginalText();
+    }
+
+    private static boolean containsOnlyComponentsWithStatementRefReferencingADocument(
+        RCMRMT030101UKEhrExtract ehrExtract,
+        RCMRMT030101UKLinkSet linkSet
+    ) {
+        var statementRefIds = linkSet.getComponent()
+            .stream()
+            .map(component -> component.getStatementRef().getId().getRoot())
+            .collect(Collectors.toSet());
+
+        return extractAllEhrCompositionComponentsAsStream(ehrExtract)
+            .flatMap(CompoundStatementResourceExtractors::extractAllNonBloodPressureNarrativeStatements)
+            .filter(Objects::nonNull)
+            .filter(ResourceFilterUtil::isDocumentReference)
+            .map(narrativeStatement -> narrativeStatement.getId().getRoot())
+            .collect(Collectors.toSet())
+            .containsAll(statementRefIds);
+    }
+
+    private static boolean hasNamedStatementRefReferencingARequestStatement(
+        RCMRMT030101UKEhrExtract ehrExtract,
+        RCMRMT030101UKLinkSet linkSet
+    ) {
+        if (linkSet.getConditionNamed() == null) {
+            return false;
+        }
+        var namedStatementRefId = linkSet.getConditionNamed().getNamedStatementRef().getId().getRoot();
+
+        return extractAllEhrCompositionComponentsAsStream(ehrExtract)
+            .flatMap(CompoundStatementResourceExtractors::extractAllRequestStatements)
+            .filter(Objects::nonNull)
+            .anyMatch(requestStatement -> namedStatementRefId.equals(requestStatement.getId().getFirst().getRoot()));
+    }
+
+    private static Stream<RCMRMT030101UKComponent4> extractAllEhrCompositionComponentsAsStream(RCMRMT030101UKEhrExtract ehrExtract) {
+        return ehrExtract.getComponent()
+            .stream()
+            .map(RCMRMT030101UKComponent::getEhrFolder)
+            .flatMap(ehrFolder -> ehrFolder.getComponent().stream())
+            .map(RCMRMT030101UKComponent3::getEhrComposition)
+            .flatMap(ehrComposition -> ehrComposition.getComponent().stream());
+    }
+
     private static boolean hasCode(RCMRMT030101UKCompoundStatement compoundStatement) {
         return compoundStatement.hasCode() && compoundStatement.getCode().hasCode();
     }

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)