Refactor AllergyStructureMapper

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

@@ -0,0 +1,167 @@
+package uk.nhs.adaptors.gp2gp.ehr.mapper;
+
+import lombok.RequiredArgsConstructor;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.dstu3.model.AllergyIntolerance;
+import org.hl7.fhir.dstu3.model.Annotation;
+import org.hl7.fhir.dstu3.model.Condition;
+import org.hl7.fhir.dstu3.model.RelatedPerson;
+import org.hl7.fhir.dstu3.model.ResourceType;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+import uk.nhs.adaptors.gp2gp.ehr.utils.DateFormatUtil;
+
+import java.util.List;
+import java.util.Optional;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static uk.nhs.adaptors.gp2gp.ehr.mapper.AllergyStructureExtractor.extractReaction;
+import static uk.nhs.adaptors.gp2gp.ehr.utils.DateFormatUtil.toTextFormat;
+import static uk.nhs.adaptors.gp2gp.ehr.utils.ExtensionMappingUtils.filterExtensionByUrl;
+
+@RequiredArgsConstructor(onConstructor = @__(@Autowired))
+@Component
+public class PertinentInformationAllergyMapper {
+    private static final String ALLERGY_INTOLERANCE_END_URL =
+        "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-AllergyIntoleranceEnd-1";
+    private static final String END_DATE = "End Date: ";
+    private static final String STATUS = "Status: ";
+    private static final String TYPE = "Type: ";
+    private static final String CRITICALITY = "Criticality: ";
+    private static final String PATIENT_ASSERTER = "Asserted By Patient";
+    private static final String RELATED_PERSON_ASSERTER = "Asserted By: Related Person";
+    private static final String LAST_OCCURRENCE = "Last Occurred: ";
+    private static final String PATIENT_RECORDER = "Recorded By Patient";
+    private static final String COMMA = ", ";
+
+
+    private final MessageContext messageContext;
+
+    public String buildPertinentInformation(AllergyIntolerance allergyIntolerance) {
+        return retrievePertinentInformation(allergyIntolerance)
+            .stream()
+            .filter(StringUtils::isNotEmpty)
+            .collect(Collectors.joining(StringUtils.SPACE));
+    }
+
+    private List<String> retrievePertinentInformation(AllergyIntolerance allergyIntolerance) {
+        return List.of(
+            buildExtensionReasonEndPertinentInformation(allergyIntolerance),
+            buildClinicalStatusPertinentInformation(allergyIntolerance),
+            buildTypePertinentInformation(allergyIntolerance),
+            buildCriticalityPertinentInformation(allergyIntolerance),
+            buildAsserterPertinentInformation(allergyIntolerance),
+            buildLastOccurrencePertinentInformation(allergyIntolerance),
+            buildRecorderPertinentInformation(allergyIntolerance),
+            buildReactionPertinentInformation(allergyIntolerance),
+            buildNotePertinentInformation(allergyIntolerance),
+            buildEndDatePertinentInformation(allergyIntolerance)
+        );
+    }
+
+    private String buildExtensionReasonEndPertinentInformation(AllergyIntolerance allergyIntolerance) {
+        return filterExtensionByUrl(allergyIntolerance, ALLERGY_INTOLERANCE_END_URL)
+            .map(AllergyStructureExtractor::extractReasonEnd)
+            .orElse(StringUtils.EMPTY);
+    }
+
+    private String buildClinicalStatusPertinentInformation(AllergyIntolerance allergyIntolerance) {
+        return allergyIntolerance.hasClinicalStatus()
+            ? buildClinicalStatusNotePertinentInformation(allergyIntolerance)
+            : StringUtils.EMPTY;
+    }
+
+    private String buildClinicalStatusNotePertinentInformation(AllergyIntolerance allergyIntolerance) {
+        return allergyIntolerance.hasNote()
+            ? STATUS + StringUtils.capitalize(allergyIntolerance.getClinicalStatus().toCode())
+            : STATUS + allergyIntolerance.getClinicalStatus().getDisplay();
+    }
+
+    private String buildTypePertinentInformation(AllergyIntolerance allergyIntolerance) {
+        return allergyIntolerance.hasType()
+            ? TYPE + allergyIntolerance.getType().getDisplay()
+            : StringUtils.EMPTY;
+    }
+
+    private String buildCriticalityPertinentInformation(AllergyIntolerance allergyIntolerance) {
+        return allergyIntolerance.hasCriticality()
+            ? CRITICALITY + allergyIntolerance.getCriticality().getDisplay()
+            : StringUtils.EMPTY;
+    }
+
+    private String buildAsserterPertinentInformation(AllergyIntolerance allergyIntolerance) {
+        if (allergyIntolerance.hasAsserter()) {
+            IIdType reference = allergyIntolerance.getAsserter().getReferenceElement();
+            if (reference.getResourceType().equals(ResourceType.Patient.name())) {
+                return PATIENT_ASSERTER;
+            } else if (reference.getResourceType().equals(ResourceType.RelatedPerson.name())) {
+                return messageContext
+                    .getInputBundleHolder()
+                    .getResource(reference)
+                    .map(RelatedPerson.class::cast)
+                    .filter(RelatedPerson::hasName)
+                    .map(RelatedPerson::getName)
+                    .filter(names -> !names.isEmpty())
+                    .map(List::getFirst)
+                    .map(name -> Optional.ofNullable(name.getText())
+                        .filter(StringUtils::isNotBlank)
+                        .orElseGet(name::getNameAsSingleString))
+                    .filter(StringUtils::isNotBlank)
+                    .map(name -> RELATED_PERSON_ASSERTER + StringUtils.SPACE + name)
+                    .orElse(RELATED_PERSON_ASSERTER);
+            }
+        }
+        return StringUtils.EMPTY;
+    }
+
+    private String buildLastOccurrencePertinentInformation(AllergyIntolerance allergyIntolerance) {
+        if (allergyIntolerance.hasLastOccurrence()) {
+            return LAST_OCCURRENCE + toTextFormat(allergyIntolerance.getLastOccurrenceElement());
+        }
+        return StringUtils.EMPTY;
+    }
+
+    private String buildRecorderPertinentInformation(AllergyIntolerance allergyIntolerance) {
+        if (allergyIntolerance.hasRecorder()) {
+            IIdType reference = allergyIntolerance.getRecorder().getReferenceElement();
+            if (reference.getResourceType().equals(ResourceType.Patient.name())) {
+                return PATIENT_RECORDER;
+            }
+        }
+        return StringUtils.EMPTY;
+    }
+
+    private String buildReactionPertinentInformation(AllergyIntolerance allergyIntolerance) {
+        AtomicInteger reactionCount = new AtomicInteger(1);
+        if (allergyIntolerance.hasReaction()) {
+            return allergyIntolerance.getReaction()
+                .stream()
+                .map(reaction -> extractReaction(reaction, reactionCount))
+                .collect(Collectors.joining(COMMA));
+        }
+        return StringUtils.EMPTY;
+    }
+
+    private String buildNotePertinentInformation(AllergyIntolerance allergyIntolerance) {
+        return Stream.concat(
+                messageContext.getInputBundleHolder().getRelatedConditions(allergyIntolerance.getId())
+                    .stream()
+                    .map(Condition::getNote)
+                    .flatMap(List::stream),
+                allergyIntolerance.hasNote() ? allergyIntolerance.getNote().stream() : Stream.empty()
+            )
+            .map(Annotation::getText)
+            .collect(Collectors.joining(StringUtils.SPACE));
+    }
+
+    private String buildEndDatePertinentInformation(AllergyIntolerance allergyIntolerance) {
+        return filterExtensionByUrl(allergyIntolerance, ALLERGY_INTOLERANCE_END_URL)
+            .map(extension -> AllergyStructureExtractor.extractEndDate(extension, DateFormatUtil::toTextFormat))
+            .filter(StringUtils::isNotBlank)
+            .map(endDate -> END_DATE + endDate)
+            .orElse(StringUtils.EMPTY);
+    }
+}

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

@@ -113,8 +113,6 @@ private static Stream<Arguments> resourceFileParamsWithEnvironmentCategoryAndCon
     void setUp() {
         when(randomIdGeneratorService.createNewId()).thenReturn(TEST_ID);
         when(randomIdGeneratorService.createNewOrUseExistingUUID(anyString())).thenReturn(TEST_ID);
-        when(confidentialityService.generateConfidentialityCode(any()))
-            .thenReturn(Optional.empty());
 
         var bundleInput = ResourceTestFileUtils.getFileContent(INPUT_JSON_BUNDLE);
         Bundle bundle = new FhirParseService().parseResource(bundleInput, Bundle.class);
@@ -128,7 +126,8 @@ void setUp() {
             messageContext,
             codeableConceptCdMapper,
             new ParticipantMapper(),
-            confidentialityService);
+            confidentialityService,
+            new PertinentInformationAllergyMapper(messageContext));
     }
 
     @AfterEach

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

@@ -145,7 +145,9 @@ public void setUp() {
 
         EncounterComponentsMapper encounterComponentsMapper = new EncounterComponentsMapper(
                 messageContext,
-                new AllergyStructureMapper(messageContext, codeableConceptCdMapper, participantMapper, confidentialityService),
+                new AllergyStructureMapper(messageContext, codeableConceptCdMapper, participantMapper,
+                        confidentialityService,
+                        new PertinentInformationAllergyMapper(messageContext)),
                 new BloodPressureMapper(messageContext, randomIdGeneratorService,
                         new StructuredObservationValueMapper(), codeableConceptCdMapper,
                         new ParticipantMapper(), confidentialityService),

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

@@ -147,7 +147,8 @@ public void setUp() {
             messageContext,
             codeableConceptCdMapper,
             participantMapper,
-            confidentialityService
+            confidentialityService,
+            new PertinentInformationAllergyMapper(messageContext)
         );
         BloodPressureMapper bloodPressureMapper = new BloodPressureMapper(
             messageContext,

service/src/test/java/uk/nhs/adaptors/gp2gp/uat/EhrExtractUATTest.java

@@ -40,6 +40,7 @@
 import uk.nhs.adaptors.gp2gp.ehr.mapper.ObservationToNarrativeStatementMapper;
 import uk.nhs.adaptors.gp2gp.ehr.mapper.OutputMessageWrapperMapper;
 import uk.nhs.adaptors.gp2gp.ehr.mapper.ParticipantMapper;
+import uk.nhs.adaptors.gp2gp.ehr.mapper.PertinentInformationAllergyMapper;
 import uk.nhs.adaptors.gp2gp.ehr.mapper.PertinentInformationObservationValueMapper;
 import uk.nhs.adaptors.gp2gp.ehr.mapper.RequestStatementMapper;
 import uk.nhs.adaptors.gp2gp.ehr.mapper.StructuredObservationValueMapper;
@@ -177,7 +178,8 @@ public void setUp() {
 
         return new EncounterComponentsMapper(
             messageContext,
-            new AllergyStructureMapper(messageContext, codeableConceptCdMapper, participantMapper, confidentialityService),
+            new AllergyStructureMapper(messageContext, codeableConceptCdMapper, participantMapper, confidentialityService,
+                new PertinentInformationAllergyMapper(messageContext)),
             new BloodPressureMapper(
                 messageContext, randomIdGeneratorService, new StructuredObservationValueMapper(),
                 codeableConceptCdMapper, new ParticipantMapper(), confidentialityService),