Niad-3114: Populate the "no disclosure to patient" label for Laboratory related resources

CHANGELOG.md

@@ -20,10 +20,13 @@ corresponding FHIR resource will now be [appropriately populated][nopat-docs].
     corresponding FHIR resource will now be [appropriately populated][nopat-docs].
 * If a `bloodPressure` record includes a `confidentialityCode`, the `meta.security` field of the
     corresponding FHIR resource will now be [appropriately populated][nopat-docs].
+* If a `Observation`, `Specimen`, `DiagnosticReport` record includes a `confidentialityCode`, the `meta.security` field of the
+  corresponding FHIR resource will now be [appropriately populated][nopat-docs].
 * Addressed a bug in the PS adaptor where immunizations were incorrectly mapped to observations. 
 The adaptor now verifies the Snomed CT ID against both the Concept ID and the Description ID, ensuring 
 that immunizations are correctly identified when a match is found.
 
+
 ### Fixed
 * Resolved issue where the SNOMED import script would reject a password containing a '%' character.
 * Fixed some Test Results being given a duplicated `Observation.category` entries for `Laboratory`.

gp2gp-translator/src/integrationTest/java/uk/nhs/adaptors/pss/translator/mapper/ConditionMapperIT.java

@@ -80,7 +80,6 @@ public static Stream<Arguments> ehrExtractsWithAllergyIntoleranceActualProblemCo
             Arguments.of("linkset-problem-allergy-in-category.xml"),
             Arguments.of("linkset-problem-allergy-flat.xml"),
             Arguments.of("linkset-problem-allergy-in-topic.xml")
-
         );
     }
 

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

@@ -8,6 +8,7 @@
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.DateTimeType;
 import org.hl7.fhir.dstu3.model.Encounter;
+import org.hl7.fhir.dstu3.model.Meta;
 import org.hl7.fhir.dstu3.model.Observation;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.Period;
@@ -18,14 +19,18 @@
 import org.hl7.v3.CR;
 import org.hl7.v3.CV;
 import org.hl7.v3.RCMRMT030101UKAnnotation;
+import org.hl7.v3.RCMRMT030101UKCompoundStatement;
 import org.hl7.v3.RCMRMT030101UKEhrComposition;
 import org.hl7.v3.RCMRMT030101UKEhrExtract;
 import org.hl7.v3.RCMRMT030101UKObservationStatement;
 import org.hl7.v3.RCMRMT030101UKPertinentInformation02;
 import org.hl7.v3.RCMRMT030101UKRequestStatement;
 import org.hl7.v3.RCMRMT030101UKSubject;
+import org.jetbrains.annotations.NotNull;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
+import uk.nhs.adaptors.pss.translator.service.ConfidentialityService;
+import uk.nhs.adaptors.pss.translator.util.CompoundStatementResourceExtractors;
 import uk.nhs.adaptors.pss.translator.util.DatabaseImmunizationChecker;
 import uk.nhs.adaptors.pss.translator.util.DegradedCodeableConcepts;
 
@@ -40,7 +45,6 @@
 import java.util.stream.Stream;
 
 import static org.hl7.fhir.dstu3.model.Observation.ObservationStatus.FINAL;
-
 import static uk.nhs.adaptors.pss.translator.util.CompoundStatementResourceExtractors.extractAllObservationStatementsWithoutAllergiesAndBloodPressures;
 import static uk.nhs.adaptors.pss.translator.util.CompoundStatementResourceExtractors.extractAllRequestStatements;
 import static uk.nhs.adaptors.pss.translator.util.ObservationUtil.getEffective;
@@ -50,7 +54,6 @@
 import static uk.nhs.adaptors.pss.translator.util.ObservationUtil.getValueQuantity;
 import static uk.nhs.adaptors.pss.translator.util.ParticipantReferenceUtil.getParticipantReference;
 import static uk.nhs.adaptors.pss.translator.util.ResourceUtil.buildIdentifier;
-import static uk.nhs.adaptors.pss.translator.util.ResourceUtil.generateMeta;
 import static uk.nhs.adaptors.pss.translator.util.ResourceUtil.addContextToObservation;
 
 @Service
@@ -66,6 +69,7 @@ public class ObservationMapper extends AbstractMapper<Observation> {
 
     private final CodeableConceptMapper codeableConceptMapper;
     private final DatabaseImmunizationChecker immunizationChecker;
+    private final ConfidentialityService confidentialityService;
 
     public List<Observation> mapResources(RCMRMT030101UKEhrExtract ehrExtract, Patient patient, List<Encounter> encounters,
                                           String practiseCode) {
@@ -93,45 +97,75 @@ public List<Observation> mapResources(RCMRMT030101UKEhrExtract ehrExtract, Patie
     }
 
     private Observation mapObservation(RCMRMT030101UKEhrComposition ehrComposition,
-                                       RCMRMT030101UKObservationStatement observationStatement, Patient patient, List<Encounter> encounters,
+                                       RCMRMT030101UKObservationStatement observationStatement,
+                                       Patient patient,
+                                       List<Encounter> encounters,
                                        String practiseCode) {
 
+        var compoundStatement = ehrComposition
+            .getComponent()
+            .stream()
+            .flatMap(CompoundStatementResourceExtractors::extractAllCompoundStatements)
+            .filter(Objects::nonNull)
+            .findFirst().orElseGet(RCMRMT030101UKCompoundStatement::new);
+
         var id = observationStatement.getId().getRoot();
+        var meta = confidentialityService.createMetaAndAddSecurityIfConfidentialityCodesPresent(
+            META_PROFILE,
+            ehrComposition.getConfidentialityCode(),
+            observationStatement.getConfidentialityCode(),
+            compoundStatement.getConfidentialityCode());
 
-        Observation observation = new Observation()
+        var observation = buildBaseObservation(ehrComposition, observationStatement, patient, practiseCode, id, meta);
+
+        addContextToObservation(observation, encounters, ehrComposition);
+        addValue(observation, getValueQuantity(observationStatement.getValue(), observationStatement.getUncertaintyCode()),
+            getValueString(observationStatement.getValue()));
+        addEffective(observation,
+            getEffective(observationStatement.getEffectiveTime(), observationStatement.getAvailabilityTime()));
+
+        return observation;
+    }
+
+    private @NotNull Observation buildBaseObservation(RCMRMT030101UKEhrComposition ehrComposition,
+                                                RCMRMT030101UKObservationStatement observationStatement,
+                                                Patient patient,
+                                                String practiseCode,
+                                                String id,
+                                                Meta meta) {
+        var observation = new Observation()
             .setStatus(FINAL)
             .addIdentifier(buildIdentifier(id, practiseCode))
             .setCode(getCode(observationStatement.getCode()))
             .setIssuedElement(getIssued(ehrComposition))
             .addPerformer(getParticipantReference(observationStatement.getParticipant(), ehrComposition))
             .setInterpretation(getInterpretation(observationStatement.getInterpretationCode()))
             .setComment(getComment(
-                    observationStatement.getPertinentInformation(),
-                    observationStatement.getSubject(),
-                    observationStatement.getCode(),
-                    Optional.of(Optional.ofNullable(observationStatement.getCode())
+                observationStatement.getPertinentInformation(),
+                observationStatement.getSubject(),
+                observationStatement.getCode(),
+                Optional.of(Optional.ofNullable(observationStatement.getCode())
                             .map(CD::getQualifier)
                             .orElse(Collections.emptyList()))
             ))
             .setReferenceRange(getReferenceRange(observationStatement.getReferenceRange()))
-            .setSubject(new Reference(patient));
-        observation.setId(id);
-        observation.setMeta(generateMeta(META_PROFILE));
+            .setSubject(new Reference(patient))
+            .setMeta(meta)
+            .setId(id);
 
-        addContextToObservation(observation, encounters, ehrComposition);
-        addValue(observation, getValueQuantity(observationStatement.getValue(), observationStatement.getUncertaintyCode()),
-            getValueString(observationStatement.getValue()));
-        addEffective(observation,
-            getEffective(observationStatement.getEffectiveTime(), observationStatement.getAvailabilityTime()));
-
-        return observation;
+        return (Observation) observation;
     }
 
     private Observation mapObservationFromRequestStatement(RCMRMT030101UKEhrComposition ehrComposition,
                                                            RCMRMT030101UKRequestStatement requestStatement, Patient patient,
                                                            List<Encounter> encounters, String practiseCode) {
 
         var id = requestStatement.getId().get(0).getRoot();
+        var meta = confidentialityService.createMetaAndAddSecurityIfConfidentialityCodesPresent(
+            META_PROFILE,
+            ehrComposition.getConfidentialityCode(),
+            requestStatement.getConfidentialityCode());
+
 
         Observation observation = new Observation()
                 .setStatus(FINAL)
@@ -144,7 +178,7 @@ private Observation mapObservationFromRequestStatement(RCMRMT030101UKEhrComposit
                 .setComponent(createComponentList(requestStatement));
 
         observation.setId(id);
-        observation.setMeta(generateMeta(META_PROFILE));
+        observation.setMeta(meta);
 
         addContextToObservation(observation, encounters, ehrComposition);
         addEffective(observation,

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

@@ -6,7 +6,6 @@
 import static uk.nhs.adaptors.pss.translator.util.CompoundStatementResourceExtractors.extractAllCompoundStatements;
 import static uk.nhs.adaptors.pss.translator.util.DateFormatUtil.parseToInstantType;
 import static uk.nhs.adaptors.pss.translator.util.ResourceUtil.buildIdentifier;
-import static uk.nhs.adaptors.pss.translator.util.ResourceUtil.generateMeta;
 import static uk.nhs.adaptors.pss.translator.util.TextUtil.extractPmipComment;
 
 import java.util.ArrayList;
@@ -41,6 +40,7 @@
 import org.springframework.stereotype.Service;
 
 import uk.nhs.adaptors.pss.translator.mapper.AbstractMapper;
+import uk.nhs.adaptors.pss.translator.service.ConfidentialityService;
 import uk.nhs.adaptors.pss.translator.service.IdGeneratorService;
 import uk.nhs.adaptors.pss.translator.util.CompoundStatementResourceExtractors;
 import uk.nhs.adaptors.pss.translator.util.ResourceFilterUtil;
@@ -61,6 +61,7 @@ public class DiagnosticReportMapper extends AbstractMapper<DiagnosticReport> {
     public static final String USER_COMMENT_COMMENT_TYPE = "CommentType:USER COMMENT";
 
     private final IdGeneratorService idGeneratorService;
+    private final ConfidentialityService confidentialityService;
 
     public static void addResultToDiagnosticReport(Observation observation, DiagnosticReport diagnosticReport) {
         if (!containsReference(diagnosticReport.getResult(), observation.getId())) {
@@ -126,7 +127,12 @@ private DiagnosticReport createDiagnosticReport(RCMRMT030101UKCompoundStatement
         final DiagnosticReport diagnosticReport = new DiagnosticReport();
         final String id = compoundStatement.getId().get(0).getRoot();
 
-        diagnosticReport.setMeta(generateMeta(META_PROFILE_URL_SUFFIX));
+        var meta = confidentialityService.createMetaAndAddSecurityIfConfidentialityCodesPresent(
+            META_PROFILE_URL_SUFFIX,
+            composition.getConfidentialityCode(),
+            compoundStatement.getConfidentialityCode());
+
+        diagnosticReport.setMeta(meta);
         diagnosticReport.setId(id);
         diagnosticReport.addIdentifier(buildIdentifier(id, practiceCode));
         diagnosticReport.setCode(createCode());