NIAD-3144 - Send over {Lab Results}.meta.security NOPAT field to incumbent (#828)

* [NIAD-3144] Create TestUtility.java and create method to parse a given JSON file into a FHIR resource

* [NIAD-3144] Update TestUtility.java and update DiagnosticReportMapperTest.java, added two boilerplate tests

* [NIAD-3144] Add failing unit test

* [NIAD-3144] Update tests to support confidentialityService, added failing unit tests

* [NIAD-3144] Add more utility methods to TestUtility.java

* [NIAD-3144] Add and remove test resources

* [NIAD-3144] Update production code for DiagnosticReportMapper

* [NIAD-3144] Improve test assertions

* [NIAD-3144] Checkstyle violations fixed, enhance SpecimenMapperTest.java

* [NIAD-3144] Add failing unit test

* [NIAD-3144] Add logic to production code to for confidentialityCode support of specimens

* [NIAD-3144] Test refactors

* [NIAD-3144] TestUtility refactors

* [NIAD-3144] Add test coverage to SpecimenMapperTest.java

* [NIAD-3144] Refactor code to abide to single responsibility principle

* [NIAD-3144] Address failing unit test

* [NIAD-3144] Address failing unit test

Author: martin-nhs

CHANGELOG.md

@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 * When mapping `AllergyIntolerances` which contain a `NOPAT` `meta.security` tag the resultant XML for that resource
 will contain a `NOPAT` `confidentialityCode` element.
+* When mapping a `DiagnosticReport` or `Specimen` which contains a `NOPAT` `meta.security` tag the resultant XML for that resource
+  will contain a `NOPAT` `confidentialityCode` element.
 
 ## [2.0.6] - 2024-07-29
 

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

@@ -31,6 +31,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
+import uk.nhs.adaptors.gp2gp.common.service.ConfidentialityService;
 import uk.nhs.adaptors.gp2gp.common.service.RandomIdGeneratorService;
 import uk.nhs.adaptors.gp2gp.ehr.mapper.CommentType;
 import uk.nhs.adaptors.gp2gp.ehr.mapper.IdMapper;
@@ -69,6 +70,7 @@ public class DiagnosticReportMapper {
     private final SpecimenMapper specimenMapper;
     private final ParticipantMapper participantMapper;
     private final RandomIdGeneratorService randomIdGeneratorService;
+    private final ConfidentialityService confidentialityService;
 
     public String mapDiagnosticReportToCompoundStatement(DiagnosticReport diagnosticReport) {
         List<Specimen> specimens = fetchSpecimens(diagnosticReport);
@@ -87,7 +89,8 @@ public String mapDiagnosticReportToCompoundStatement(DiagnosticReport diagnostic
             .extensionId(fetchExtensionId(diagnosticReport.getIdentifier()))
             .availabilityTimeElement(StatementTimeMappingUtils.prepareAvailabilityTime(diagnosticReport.getIssuedElement()))
             .narrativeStatements(reportLevelNarrativeStatements)
-            .specimens(mappedSpecimens);
+            .specimens(mappedSpecimens)
+            .confidentialityCode(confidentialityService.generateConfidentialityCode(diagnosticReport).orElse(null));
 
         if (diagnosticReport.hasPerformer() && diagnosticReport.getPerformerFirstRep().hasActor()) {
             final String participantReference = messageContext.getAgentDirectory().getAgentId(

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

@@ -28,6 +28,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
+import uk.nhs.adaptors.gp2gp.common.service.ConfidentialityService;
 import uk.nhs.adaptors.gp2gp.common.service.RandomIdGeneratorService;
 import uk.nhs.adaptors.gp2gp.ehr.mapper.CommentType;
 import uk.nhs.adaptors.gp2gp.ehr.mapper.MessageContext;
@@ -61,6 +62,7 @@ public class SpecimenMapper {
     private final MessageContext messageContext;
     private final ObservationMapper observationMapper;
     private final RandomIdGeneratorService randomIdGeneratorService;
+    private final ConfidentialityService confidentialityService;
 
     public String mapSpecimenToCompoundStatement(Specimen specimen, List<Observation> observations, DiagnosticReport diagnosticReport) {
         String availabilityTimeElement = StatementTimeMappingUtils.prepareAvailabilityTime(diagnosticReport.getIssuedElement());
@@ -71,7 +73,8 @@ public String mapSpecimenToCompoundStatement(Specimen specimen, List<Observation
             .availabilityTimeElement(availabilityTimeElement)
             .specimenRoleId(randomIdGeneratorService.createNewId())
             .narrativeStatementId(randomIdGeneratorService.createNewId())
-            .observations(mappedObservations);
+            .observations(mappedObservations)
+            .confidentialityCode(confidentialityService.generateConfidentialityCode(specimen).orElse(null));
 
         buildAccessionIdentifier(specimen).ifPresent(specimenCompoundStatementTemplateParameters::accessionIdentifier);
         buildEffectiveTimeForSpecimen(specimen).ifPresent(specimenCompoundStatementTemplateParameters::effectiveTime);
@@ -151,7 +154,7 @@ private String mapObservationsAssociatedWithSpecimen(Specimen specimen, List<Obs
 
     private boolean dummySpecimenOrObservationExists(Specimen specimen, List<Observation> observations) {
         return specimen.getIdElement().getIdPart().contains(DUMMY_SPECIMEN_ID_PREFIX)
-            || (!observations.isEmpty() && observations.get(0).getIdElement().getIdPart().contains(DUMMY_OBSERVATION_ID_PREFIX));
+            || (!observations.isEmpty() && observations.getFirst().getIdElement().getIdPart().contains(DUMMY_OBSERVATION_ID_PREFIX));
     }
 
     private Optional<String> buildSpecimenNarrativeStatement(Specimen specimen, String availabilityTimeElement,

service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/parameters/diagnosticreport/DiagnosticReportCompoundStatementTemplateParameters.java

@@ -14,4 +14,5 @@ public class DiagnosticReportCompoundStatementTemplateParameters {
     private String narrativeStatements;
     private String specimens;
     private String participant;
+    private String confidentialityCode;
 }

service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/parameters/diagnosticreport/SpecimenCompoundStatementTemplateParameters.java

@@ -18,4 +18,5 @@ public class SpecimenCompoundStatementTemplateParameters {
     private String narrativeStatementId;
     private String participant;
     private String observations;
+    private String confidentialityCode;
 }

service/src/main/resources/templates/diagnostic_report_compound_statement_template.mustache

@@ -12,6 +12,9 @@
             <center nullFlavor="NI"/>
         </effectiveTime>
         {{{availabilityTimeElement}}}
+        {{#confidentialityCode}}
+            {{{confidentialityCode}}}
+        {{/confidentialityCode}}
         {{#narrativeStatements}}
             {{{.}}}
         {{/narrativeStatements}}

service/src/main/resources/templates/specimen_compound_statement_template.mustache

@@ -7,6 +7,9 @@
             <center nullFlavor="NI"/>
         </effectiveTime>
         {{{availabilityTimeElement}}}
+        {{#confidentialityCode}}
+            {{{confidentialityCode}}}
+        {{/confidentialityCode}}
         <specimen typeCode="SPC">
             <specimenRole classCode="SPEC">
                 <id root="{{specimenRoleId}}"/>

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

@@ -153,7 +153,8 @@ public void setUp() {
         ObservationMapper specimenObservationMapper = new ObservationMapper(
             messageContext, structuredObservationValueMapper, codeableConceptCdMapper,
             participantMapper, multiStatementObservationHolderFactory);
-        SpecimenMapper specimenMapper = new SpecimenMapper(messageContext, specimenObservationMapper, randomIdGeneratorService);
+        SpecimenMapper specimenMapper = new SpecimenMapper(messageContext, specimenObservationMapper,
+            randomIdGeneratorService, confidentialityService);
         DocumentReferenceToNarrativeStatementMapper documentReferenceToNarrativeStatementMapper
             = new DocumentReferenceToNarrativeStatementMapper(
                 messageContext, new SupportedContentTypes(), timestampService, participantMapper);
@@ -180,7 +181,7 @@ codeableConceptCdMapper, new ParticipantMapper()),
             ),
             new RequestStatementMapper(messageContext, codeableConceptCdMapper, participantMapper),
             new DiagnosticReportMapper(
-                messageContext, specimenMapper, participantMapper, randomIdGeneratorService
+                messageContext, specimenMapper, participantMapper, randomIdGeneratorService, confidentialityService
             ),
             new BloodPressureValidator(),
             codeableConceptCdMapper

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

@@ -19,6 +19,7 @@
 import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.Reference;
 import org.hl7.fhir.dstu3.model.ResourceType;
+import org.jetbrains.annotations.NotNull;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -154,12 +155,7 @@ public void setUp() {
             = new MedicationStatementMapper(messageContext, codeableConceptCdMapper, participantMapper, randomIdGeneratorService);
         ObservationToNarrativeStatementMapper observationToNarrativeStatementMapper =
             new ObservationToNarrativeStatementMapper(messageContext, participantMapper);
-        MultiStatementObservationHolderFactory multiStatementObservationHolderFactory =
-            new MultiStatementObservationHolderFactory(messageContext, randomIdGeneratorService);
-        ObservationMapper specimenObservationMapper = new ObservationMapper(
-            messageContext, structuredObservationValueMapper, codeableConceptCdMapper, participantMapper,
-            multiStatementObservationHolderFactory);
-        SpecimenMapper specimenMapper = new SpecimenMapper(messageContext, specimenObservationMapper, randomIdGeneratorService);
+        SpecimenMapper specimenMapper = getSpecimenMapper(structuredObservationValueMapper, participantMapper);
 
         ObservationStatementMapper observationStatementMapper = new ObservationStatementMapper(
             messageContext,
@@ -172,7 +168,7 @@ public void setUp() {
         RequestStatementMapper requestStatementMapper
             = new RequestStatementMapper(messageContext, codeableConceptCdMapper, participantMapper);
         DiagnosticReportMapper diagnosticReportMapper = new DiagnosticReportMapper(
-            messageContext, specimenMapper, participantMapper, randomIdGeneratorService
+            messageContext, specimenMapper, participantMapper, randomIdGeneratorService, confidentialityService
         );
 
         encounterComponentsMapper = new EncounterComponentsMapper(
@@ -193,6 +189,16 @@ public void setUp() {
         );
     }
 
+    private @NotNull SpecimenMapper getSpecimenMapper(StructuredObservationValueMapper structuredObservationValueMapper,
+                                                      ParticipantMapper participantMapper) {
+        MultiStatementObservationHolderFactory multiStatementObservationHolderFactory =
+            new MultiStatementObservationHolderFactory(messageContext, randomIdGeneratorService);
+        ObservationMapper specimenObservationMapper = new ObservationMapper(
+            messageContext, structuredObservationValueMapper, codeableConceptCdMapper, participantMapper,
+            multiStatementObservationHolderFactory);
+        return new SpecimenMapper(messageContext, specimenObservationMapper, randomIdGeneratorService, confidentialityService);
+    }
+
     @AfterEach
     public void tearDown() {
         messageContext.resetMessageContext();

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

@@ -1,10 +1,12 @@
 package uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport;
 
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.junit.jupiter.api.Assertions.assertAll;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.when;
 
 import java.io.IOException;
+import java.util.Optional;
 import java.util.stream.Stream;
 
 import org.hl7.fhir.dstu3.model.Bundle;
@@ -14,6 +16,7 @@
 import org.hl7.fhir.dstu3.model.Reference;
 import org.hl7.fhir.dstu3.model.ResourceType;
 import org.hl7.fhir.dstu3.model.Specimen;
+import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -26,6 +29,9 @@
 import org.mockito.quality.Strictness;
 import org.mockito.stubbing.Answer;
 
+import uk.nhs.adaptors.gp2gp.utils.ConfidentialityCodeUtility;
+import uk.nhs.adaptors.gp2gp.utils.FileParsingUtility;
+import uk.nhs.adaptors.gp2gp.common.service.ConfidentialityService;
 import uk.nhs.adaptors.gp2gp.common.service.FhirParseService;
 import uk.nhs.adaptors.gp2gp.common.service.RandomIdGeneratorService;
 import uk.nhs.adaptors.gp2gp.ehr.mapper.AgentDirectory;
@@ -41,7 +47,7 @@
 
 @ExtendWith(MockitoExtension.class)
 @MockitoSettings(strictness = Strictness.LENIENT)
-public class DiagnosticReportMapperTest {
+class DiagnosticReportMapperTest {
     private static final String TEST_FILE_DIRECTORY = "/ehr/mapper/diagnosticreport/";
 
     private static final String INPUT_JSON_BUNDLE = "fhir_bundle.json";
@@ -74,13 +80,17 @@ public class DiagnosticReportMapperTest {
     private static final String OUTPUT_XML_EXTENSION_ID = "diagnostic-report-with-extension-id.xml";
     private static final String OUTPUT_XML_MULTIPLE_RESULTS = "diagnostic-report-with-multiple-results.xml";
 
+    private static final String NOPAT_CONFIDENTIALITY_CODE = ConfidentialityCodeUtility.getNopatHl7v3ConfidentialityCode();
+
     @Mock
     private CodeableConceptCdMapper codeableConceptCdMapper;
     @Mock
     private SpecimenMapper specimenMapper;
     @Mock
     private MessageContext messageContext;
     @Mock
+    private ConfidentialityService confidentialityService;
+    @Mock
     private IdMapper idMapper;
     @Mock
     private AgentDirectory agentDirectory;
@@ -108,7 +118,8 @@ public void setUp() throws IOException {
 
         when(randomIdGeneratorService.createNewId()).thenReturn(TEST_ID);
 
-        mapper = new DiagnosticReportMapper(messageContext, specimenMapper, new ParticipantMapper(), randomIdGeneratorService);
+        mapper = new DiagnosticReportMapper(
+            messageContext, specimenMapper, new ParticipantMapper(), randomIdGeneratorService, confidentialityService);
     }
 
     @AfterEach
@@ -118,15 +129,52 @@ public void tearDown() {
 
     @ParameterizedTest
     @MethodSource("resourceFileParams")
-    public void When_MappingDiagnosticReportJson_Expect_CompoundStatementXmlOutput(String inputJson, String outputXml) {
+    void When_MappingDiagnosticReportJson_Expect_CompoundStatementXmlOutput(String inputJson, String outputXml) {
         final CharSequence expectedOutputMessage = ResourceTestFileUtils.getFileContent(TEST_FILE_DIRECTORY + outputXml);
-        final String jsonInput = ResourceTestFileUtils.getFileContent(TEST_FILE_DIRECTORY + inputJson);
-        final DiagnosticReport diagnosticReport = new FhirParseService().parseResource(jsonInput, DiagnosticReport.class);
+        final DiagnosticReport diagnosticReport = getDiagnosticReportResourceFromJson(inputJson);
 
         final String outputMessage = mapper.mapDiagnosticReportToCompoundStatement(diagnosticReport);
+
         assertThat(removeLineEndings(outputMessage)).isEqualTo(removeLineEndings(expectedOutputMessage.toString()));
     }
 
+    @Test
+    void When_DiagnosticReport_With_NopatMetaSecurity_Expect_ConfidentialityCodeWithinCompoundStatement() {
+        final String testFile = "diagnostic-report-with-multi-specimens-nopat.json";
+        final DiagnosticReport diagnosticReport = getDiagnosticReportResourceFromJson(testFile);
+
+        when(confidentialityService.generateConfidentialityCode(diagnosticReport))
+            .thenReturn(Optional.of(NOPAT_CONFIDENTIALITY_CODE));
+
+        final String result = mapper.mapDiagnosticReportToCompoundStatement(diagnosticReport);
+
+        assertAll(
+            () -> assertThat(result).contains(NOPAT_CONFIDENTIALITY_CODE),
+            () -> assertThat(ConfidentialityCodeUtility.getSecurityCodeFromResource(diagnosticReport)).isEqualTo("NOPAT")
+        );
+    }
+
+    @Test
+    void When_DiagnosticReport_With_NoscrubMetaSecurity_Expect_ConfidentialityCodeNotWithinCompoundStatement() {
+        final String testFile = "diagnostic-report-with-multi-specimens-noscrub.json";
+        final DiagnosticReport diagnosticReport = getDiagnosticReportResourceFromJson(testFile);
+
+        when(confidentialityService.generateConfidentialityCode(diagnosticReport))
+            .thenReturn(Optional.empty());
+
+        final String result = mapper.mapDiagnosticReportToCompoundStatement(diagnosticReport);
+
+        assertAll(
+            () -> assertThat(result).doesNotContain(NOPAT_CONFIDENTIALITY_CODE),
+            () -> assertThat(ConfidentialityCodeUtility.getSecurityCodeFromResource(diagnosticReport)).isEqualTo("NOSCRUB")
+        );
+    }
+
+    private DiagnosticReport getDiagnosticReportResourceFromJson(String filename) {
+        final String filePath = TEST_FILE_DIRECTORY + filename;
+        return FileParsingUtility.parseResourceFromJsonFile(filePath, DiagnosticReport.class);
+    }
+
     private String removeLineEndings(String input) {
         return input.replace("\n", "").replace("\r", "");
     }
@@ -171,5 +219,4 @@ private Answer<String> mockSpecimenMapping() {
             return String.format("<!-- Mapped Specimen with id: %s -->", specimen.getId());
         };
     }
-
-}
+}