NIAD-2935: Remove EhrExtract / availabilityTime as a fallback (#465)

This time field would always be the current (as of the GP2GP transfer being started) time, which would never be an appropriate value to use for an entry within the medical record.


---------

Co-authored-by: Steven McCullagh <[email protected]>

CHANGELOG.md

@@ -5,6 +5,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+### Changed
+* `AllergyIntoleranceMapper` - Changed `assertedDate` field fallback value from `EhrExtract.AvailiabiltyTime` to `EhrComposition.Author.Time`
+* `BloodPressureMapper` - Removed `issued` field fallback value of `EhrExtract.AvailiabiltyTime`
+* `ConditionMapper` - Removed `assertedDate` field fallback value of `EhrExtract.AvailiabiltyTime`
+* `ConsultationListMapper` - Removed `date` field fallback value of `EhrExtract.AvailiabiltyTime`
+* `DiagnosticReportMapper` - Removed `issued` field fallback value of `EhrExtract.AvailiabiltyTime`
+* `MedicationRequestMapper` - Changed `authoredOn` field fallback value from `EhrExtract.AvailiabiltyTime` to `EhrComposition.Author.Time`
+* `ObservationCommentMapper` - Removed `issued` field fallback value of `EhrExtract.AvailiabiltyTime`
+* `ObservationMapper` - Removed `issued` field fallback value of `EhrExtract.AvailiabiltyTime`
+* `SpecimenBatteryMapper` - Removed `issued` field fallback value of `EhrExtract.AvailiabiltyTime`
+* `TemplateMapper` - Removed `issued` field fallback value of `EhrExtract.AvailiabiltyTime`
+
 ### Fixed
 * Fixed an issue where Plan Statements (Recalls) used a fixed value for Status instead of taking a provided text value into account.
 

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

@@ -92,7 +92,7 @@ private AllergyIntolerance mapAllergyIntolerance(RCMRMT030101UKEhrExtract ehrExt
 
         allergyIntolerance
             .addCategory(getCategory(compoundStatement))
-            .setAssertedDateElement(getAssertedDateElement(compoundStatement.getAvailabilityTime(), ehrExtract, ehrComposition))
+            .setAssertedDateElement(getAssertedDateElement(compoundStatement.getAvailabilityTime(), ehrComposition))
             .setPatient(new Reference(patient))
             .setClinicalStatus(ACTIVE)
             .setVerificationStatus(UNCONFIRMED)
@@ -239,16 +239,18 @@ private void buildOnset(RCMRMT030101UKCompoundStatement compoundStatement, Aller
         }
     }
 
-    private DateTimeType getAssertedDateElement(TS availabilityTime, RCMRMT030101UKEhrExtract ehrExtract,
+    private DateTimeType getAssertedDateElement(TS availabilityTime,
         RCMRMT030101UKEhrComposition ehrComposition) {
 
         if (availabilityTime != null && availabilityTime.hasValue()) {
             return parseToDateTimeType(availabilityTime.getValue());
         } else {
             if (ehrComposition.getAvailabilityTime() != null && ehrComposition.getAvailabilityTime().hasValue()) {
                 return parseToDateTimeType(ehrComposition.getAvailabilityTime().getValue());
-            } else if (ehrExtract.getAvailabilityTime() != null && ehrExtract.getAvailabilityTime().hasValue()) {
-                return parseToDateTimeType(ehrExtract.getAvailabilityTime().getValue());
+            } else if (ehrComposition.getAuthor() != null
+                    && ehrComposition.getAuthor().getTime() != null
+                    && ehrComposition.getAuthor().getTime().hasValue()) {
+                return parseToDateTimeType(ehrComposition.getAuthor().getTime().getValue());
             }
         }
 

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

@@ -84,7 +84,6 @@ private Observation mapObservation(RCMRMT030101UKEhrExtract ehrExtract, RCMRMT03
                 getComment(observationStatements, getNarrativeStatementsFromCompoundStatement(compoundStatement)))
             .setSubject(new Reference(patient))
             .setIssuedElement(getIssued(
-                ehrExtract,
                 ehrComposition))
             .addPerformer(getParticipantReference(
                 compoundStatement.getParticipant(),

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

@@ -5,7 +5,6 @@
 
 import static uk.nhs.adaptors.pss.translator.mapper.medication.MedicationMapperUtils.getMedicationStatements;
 import static uk.nhs.adaptors.pss.translator.util.CompoundStatementResourceExtractors.extractAllLinkSets;
-import static uk.nhs.adaptors.pss.translator.util.DateFormatUtil.parseToDateTimeType;
 import static uk.nhs.adaptors.pss.translator.util.ResourceUtil.buildIdentifier;
 import static uk.nhs.adaptors.pss.translator.util.ResourceUtil.buildReferenceExtension;
 import static uk.nhs.adaptors.pss.translator.util.ResourceUtil.generateMeta;
@@ -133,9 +132,7 @@ private Condition getCondition(RCMRMT030101UKEhrExtract ehrExtract, Patient pati
         buildOnsetDateTimeType(linkSet).ifPresent(condition::setOnset);
         buildAbatementDateTimeType(linkSet.getEffectiveTime()).ifPresent(condition::setAbatement);
 
-        buildAssertedDateTimeType(composition).ifPresentOrElse(
-            condition::setAssertedDateElement,
-            () -> condition.setAssertedDateElement(parseToDateTimeType(ehrExtract.getAvailabilityTime().getValue())));
+        buildAssertedDateTimeType(composition).ifPresent(condition::setAssertedDateElement);
 
         composition.getParticipant2()
             .stream()

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

@@ -50,7 +50,7 @@ public ListResource mapToConsultation(RCMRMT030101UK04EhrExtract ehrExtract, Enc
             .setTitle(getConsultationTitle(encounter.getType()))
             .setCode(CodeableConceptUtils.createCodeableConcept(CONSULTATION_CODE_CODE, LIST_CODE_SYSTEM, CONSULTATION_CODE_DISPLAY, null))
             .setSubject(encounter.getSubject())
-            .setDateElement(getConsultationDate(encounter.getPeriod(), ehrExtract))
+            .setDateElement(getConsultationDate(encounter.getPeriod()))
             .setOrderedBy(CodeableConceptUtils.createCodeableConcept(LIST_ORDERED_BY_CODE, LIST_ORDERED_BY_SYSTEM,
                 LIST_ORDERED_BY_DISPLAY, null))
             .setEncounter(new Reference(encounter))
@@ -77,12 +77,12 @@ private String getConsultationTitle(List<CodeableConcept> codeableConceptList) {
         return null;
     }
 
-    private DateTimeType getConsultationDate(Period period, RCMRMT030101UK04EhrExtract ehrExtract) {
+    private DateTimeType getConsultationDate(Period period) {
         if (period != null && period.hasStart()) {
             return period.getStartElement();
-        } else {
-            return DateFormatUtil.parseToDateTimeType(ehrExtract.getAvailabilityTime().getValue());
         }
+
+        return null;
     }
 
     public ListResource mapToTopic(ListResource consultation, RCMRMT030101UKCompoundStatement compoundStatement) {

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

@@ -59,7 +59,7 @@ private Observation mapObservation(RCMRMT030101UKEhrExtract ehrExtract, RCMRMT03
         observation.setMeta(generateMeta(META_URL));
         observation.setStatus(FINAL);
         observation.setSubject(new Reference(patient));
-        observation.setIssuedElement(createIssued(ehrExtract, ehrComposition));
+        observation.setIssuedElement(createIssued(ehrComposition));
         observation.setCode(createCodeableConcept());
         observation.addPerformer(createPerformer(ehrComposition, narrativeStatement));
         observation.addIdentifier(buildIdentifier(narrativeStatementId.getRoot(), practiseCode));
@@ -83,13 +83,13 @@ private void setObservationComment(Observation observation, String text) {
         }
     }
 
-    private InstantType createIssued(RCMRMT030101UKEhrExtract ehrExtract, RCMRMT030101UKEhrComposition composition) {
+    private InstantType createIssued(RCMRMT030101UKEhrComposition composition) {
 
         if (!composition.getAuthor().getTime().hasNullFlavor()) {
             return DateFormatUtil.parseToInstantType(composition.getAuthor().getTime().getValue());
         }
 
-        return DateFormatUtil.parseToInstantType(ehrExtract.getAvailabilityTime().getValue());
+        return null;
     }
 
     private Reference createPerformer(RCMRMT030101UKEhrComposition composition, RCMRMT030101UKNarrativeStatement narrativeStatement) {

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

@@ -101,7 +101,7 @@ private Observation mapObservation(RCMRMT030101UKEhrExtract ehrExtract, RCMRMT03
             .setStatus(FINAL)
             .addIdentifier(buildIdentifier(id, practiseCode))
             .setCode(getCode(observationStatement.getCode()))
-            .setIssuedElement(getIssued(ehrExtract, ehrComposition))
+            .setIssuedElement(getIssued(ehrComposition))
             .addPerformer(getParticipantReference(observationStatement.getParticipant(), ehrComposition))
             .setInterpretation(getInterpretation(observationStatement.getInterpretationCode()))
             .setComment(getComment(
@@ -137,7 +137,7 @@ private Observation mapObservationFromRequestStatement(RCMRMT030101UKEhrExtract
                 .setStatus(FINAL)
                 .addIdentifier(buildIdentifier(id, practiseCode))
                 .setCode(getCode(requestStatement.getCode()))
-                .setIssuedElement(getIssued(ehrExtract, ehrComposition))
+                .setIssuedElement(getIssued(ehrComposition))
                 .addPerformer(getParticipantReference(requestStatement.getParticipant(), ehrComposition))
                 .setComment(SELF_REFERRAL)
                 .setSubject(new Reference(patient))

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

@@ -142,7 +142,7 @@ private Observation createParentObservation(RCMRMT030101UKCompoundStatement comp
 
         parentObservation
             .setSubject(new Reference(patient))
-            .setIssuedElement(getIssued(ehrComposition, ehrExtract))
+            .setIssuedElement(getIssued(ehrComposition))
             .addPerformer(getParticipantReference(compoundStatement.getParticipant(), ehrComposition))
             .setCode(codeableConcept)
             .setStatus(FINAL)
@@ -165,12 +165,12 @@ private void addEffective(Observation observation, Object effective) {
         }
     }
 
-    private InstantType getIssued(RCMRMT030101UKEhrComposition ehrComposition, RCMRMT030101UKEhrExtract ehrExtract) {
+    private InstantType getIssued(RCMRMT030101UKEhrComposition ehrComposition) {
         if (ehrComposition.getAuthor().getTime().hasValue()) {
 
             return parseToInstantType(ehrComposition.getAuthor().getTime().getValue());
         }
-        return parseToInstantType(ehrExtract.getAvailabilityTime().getValue());
+        return null;
     }
 
     private List<RCMRMT030101UKCompoundStatement> getCompoundStatementsByIds(RCMRMT030101UK04EhrExtract ehrExtract, List<String> ids) {

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

@@ -70,7 +70,7 @@ public List<DiagnosticReport> mapResources(RCMRMT030101UKEhrExtract ehrExtract,
                     DiagnosticReport diagnosticReport = createDiagnosticReport(
                         compoundStatement, patient, composition, encounters, practiseCode
                     );
-                    getIssued(ehrExtract, compoundStatement, composition).ifPresent(diagnosticReport::setIssuedElement);
+                    getIssued(compoundStatement, composition).ifPresent(diagnosticReport::setIssuedElement);
                     return diagnosticReport;
                 }
                 )).toList();
@@ -195,8 +195,8 @@ private Optional<Reference> buildContext(RCMRMT030101UKEhrComposition ehrComposi
             .map(Reference::new);
     }
 
-    private Optional<InstantType> getIssued(RCMRMT030101UKEhrExtract ehrExtract,
-        RCMRMT030101UKCompoundStatement compoundStatement, RCMRMT030101UKEhrComposition ehrComposition) {
+    private Optional<InstantType> getIssued(RCMRMT030101UKCompoundStatement compoundStatement,
+                                            RCMRMT030101UKEhrComposition ehrComposition) {
 
         if (compoundStatementHasValidAvailabilityTime(compoundStatement)) {
             return Optional.of(parseToInstantType(compoundStatement.getAvailabilityTime().getValue()));
@@ -206,10 +206,6 @@ private Optional<InstantType> getIssued(RCMRMT030101UKEhrExtract ehrExtract,
             return Optional.of(parseToInstantType(ehrComposition.getAuthor().getTime().getValue()));
         }
 
-        if (availabilityTimeHasValue(ehrExtract.getAvailabilityTime())) {
-            return Optional.of(parseToInstantType(ehrExtract.getAvailabilityTime().getValue()));
-        }
-
         return Optional.empty();
     }
 

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

@@ -68,7 +68,6 @@ public class SpecimenBatteryMapper {
     public Observation mapBatteryObservation(SpecimenBatteryParameters batteryParameters) {
         final var batteryCompoundStatement = batteryParameters.getBatteryCompoundStatement();
         final var ehrComposition = batteryParameters.getEhrComposition();
-        final var ehrExtract = batteryParameters.getEhrExtract();
 
         final Observation observation = new Observation();
         final String id = batteryParameters.getBatteryCompoundStatement().getId().get(0).getRoot();
@@ -84,7 +83,7 @@ public Observation mapBatteryObservation(SpecimenBatteryParameters batteryParame
             batteryParameters.getBatteryCompoundStatement(), batteryParameters.getObservationComments()));
         getContext(batteryParameters.getEncounters(), ehrComposition).ifPresent(observation::setContext);
         addEffective(batteryCompoundStatement, observation);
-        getIssued(ehrExtract, ehrComposition).ifPresent(observation::setIssuedElement);
+        getIssued(ehrComposition).ifPresent(observation::setIssuedElement);
         getPerformer(batteryCompoundStatement, ehrComposition).ifPresent(observation::addPerformer);
         getRelated(batteryCompoundStatement).forEach(observation::addRelated);
         handleDirectChildNarrativeStatementUserComments(batteryCompoundStatement, observation, batteryParameters.getObservationComments());
@@ -210,16 +209,12 @@ private Reference createSpecimenReference(RCMRMT030101UKCompoundStatement specim
         return new Reference(new IdType(Specimen.name(), specimenCompoundStatement.getId().get(0).getRoot()));
     }
 
-    private Optional<InstantType> getIssued(RCMRMT030101UKEhrExtract ehrExtract, RCMRMT030101UKEhrComposition ehrComposition) {
+    private Optional<InstantType> getIssued(RCMRMT030101UKEhrComposition ehrComposition) {
 
         if (hasValidTimeValue(ehrComposition.getAuthor())) {
             return Optional.of(parseToInstantType(ehrComposition.getAuthor().getTime().getValue()));
         }
 
-        if (availabilityTimeHasValue(ehrExtract.getAvailabilityTime())) {
-            return Optional.of(parseToInstantType(ehrExtract.getAvailabilityTime().getValue()));
-        }
-
         return Optional.empty();
     }
 

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

@@ -61,7 +61,7 @@ private Stream<DomainResource> mapMedicationStatement(RCMRMT030101UKEhrExtract e
 
         var context = encounters.stream()
             .filter(encounter1 -> encounter1.getId().equals(ehrComposition.getId().getRoot())).findFirst();
-        var authoredOn = getAuthoredOn(medicationStatement.getAvailabilityTime(), ehrExtract, ehrComposition);
+        var authoredOn = getAuthoredOn(medicationStatement.getAvailabilityTime(), ehrComposition);
         var dateAsserted = extractDateAsserted(ehrComposition, ehrExtract);
         var requester = extractRequester(ehrComposition, medicationStatement);
         var recorder = extractRecorder(ehrComposition, medicationStatement);
@@ -98,16 +98,17 @@ private DomainResource setCommonFields(DomainResource resource, Optional<Referen
         return resource;
     }
 
-    private DateTimeType getAuthoredOn(TS availabilityTime, RCMRMT030101UKEhrExtract ehrExtract,
-                                       RCMRMT030101UKEhrComposition ehrComposition) {
 
+    private DateTimeType getAuthoredOn(TS availabilityTime,
+                                       RCMRMT030101UKEhrComposition ehrComposition) {
         if (availabilityTime != null && availabilityTime.hasValue()) {
             return DateFormatUtil.parseToDateTimeType(availabilityTime.getValue());
         } else {
             if (ehrComposition.getAvailabilityTime() != null && ehrComposition.getAvailabilityTime().hasValue()) {
                 return DateFormatUtil.parseToDateTimeType(ehrComposition.getAvailabilityTime().getValue());
-            } else if (ehrExtract.getAvailabilityTime() != null && ehrExtract.getAvailabilityTime().hasValue()) {
-                return DateFormatUtil.parseToDateTimeType(ehrExtract.getAvailabilityTime().getValue());
+            }
+            if (ehrComposition.hasAuthor() && ehrComposition.getAuthor().hasTime() && ehrComposition.getAuthor().getTime().hasValue()) {
+                return DateFormatUtil.parseToDateTimeType(ehrComposition.getAuthor().getTime().getValue());
             }
         }
 

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

@@ -20,7 +20,6 @@
 import org.hl7.v3.PQ;
 import org.hl7.v3.RCMRMT030101UKAuthor;
 import org.hl7.v3.RCMRMT030101UKEhrComposition;
-import org.hl7.v3.RCMRMT030101UKEhrExtract;
 import org.hl7.v3.RCMRMT030101UKInterpretationRange;
 import org.hl7.v3.RCMRMT030101UKReferenceRange;
 import org.hl7.v3.TS;
@@ -110,16 +109,12 @@ public static List<Observation.ObservationReferenceRangeComponent> getReferenceR
         return outputReferenceRanges;
     }
 
-    public static InstantType getIssued(RCMRMT030101UKEhrExtract ehrExtract, RCMRMT030101UKEhrComposition matchingEhrComposition) {
+    public static InstantType getIssued(RCMRMT030101UKEhrComposition matchingEhrComposition) {
 
         if (authorHasValidTimeValue(matchingEhrComposition.getAuthor())) {
             return DateFormatUtil.parseToInstantType(matchingEhrComposition.getAuthor().getTime().getValue());
         }
 
-        if (availabilityTimeHasValue(ehrExtract.getAvailabilityTime())) {
-            return DateFormatUtil.parseToInstantType(ehrExtract.getAvailabilityTime().getValue());
-        }
-
         return null;
     }
 

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

@@ -271,6 +271,21 @@ public void testMapAllergyWithNoOptionalData() {
         assertThat(allergyIntolerance.getNote()).isEmpty();
     }
 
+    @Test
+    public void testMapAllergyAssertedDateFallbackData() {
+        when(codeableConceptMapper.mapToCodeableConcept(any(CD.class))).thenReturn(defaultCodeableConcept());
+        var ehrExtract = unmarshallEhrExtract("allergy-structure-with-asserted-date-fallback.xml");
+        List<AllergyIntolerance> allergyIntolerances = allergyIntoleranceMapper.mapResources(ehrExtract, getPatient(),
+                getEncounterList(), PRACTISE_CODE);
+
+        assertThat(allergyIntolerances.size()).isEqualTo(1);
+        var allergyIntolerance = allergyIntolerances.get(0);
+
+        assertFixedValues(allergyIntolerance);
+
+        assertThat(allergyIntolerance.getAssertedDateElement().asStringValue()).isEqualTo("2010-02-09T12:31:51+00:00");
+    }
+
     @Test
     public void testMapMultipleAllergies() {
         when(codeableConceptMapper.mapToCodeableConcept(any(CD.class))).thenReturn(defaultCodeableConcept());

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

@@ -114,7 +114,7 @@ public void testConditionIsMappedCorrectlyNoReferences() {
 
         assertThat(condition.getOnsetDateTimeType()).isEqualTo(EHR_EXTRACT_AVAILABILITY_DATETIME);
         assertThat(condition.getAbatementDateTimeType()).isEqualTo(EHR_EXTRACT_AVAILABILITY_DATETIME);
-        assertThat(condition.getAssertedDateElement().getValue()).isEqualTo(EHR_EXTRACT_AVAILABILITY_DATETIME.getValue());
+        assertThat(condition.getAssertedDateElement().getValue()).isNull();
 
         assertThat(condition.getNote().size()).isEqualTo(0);
     }
@@ -185,7 +185,7 @@ public void testLinkSetWithNoDatesIsMappedCorrectly() {
         assertThat(conditions.get(0).getClinicalStatus().getDisplay()).isEqualTo("Inactive");
 
         assertThat(conditions.get(0).getAbatementDateTimeType()).isNull();
-        assertThat(conditions.get(0).getAssertedDateElement().getValue()).isEqualTo(EHR_EXTRACT_AVAILABILITY_DATETIME.getValue());
+        assertThat(conditions.get(0).getAssertedDateElement().getValue()).isNull();
     }
 
     @Test