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NIAD-1573: New reference validation for condition references. (#1335)
* Added method for testing if references exist and fixed tests. * Fixed Checkstyle warnings. * Updated the changelog with the latest changes. * Added Logging for reference checking
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‎CHANGELOG.md‎

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@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [Unreleased]
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### Added
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* The GP2GP Adaptor now validates references inside condition objects to test whether they actually exist. Otherwise, the bundle is rejected.
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* The GP2GP Adaptor now adds the EhrComposition / confidentialityCode field when Encounter.meta.security contains NOPAT security entry
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* The GP2GP Adaptor now populates the ObservationStatement / confidentialityCode field when the .meta.security field of an Uncategorized Data Observation contains NOPAT
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* When List.meta.security field contains NOPAT, the GP2GP Adaptor will now populate the CompoundStatement.confidentialityCode

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

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@@ -65,6 +65,8 @@ public String mapConditionToLinkSet(Condition condition, boolean isNested) {
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.isNested(isNested)
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.linkSetId(idMapper.getOrNew(ResourceType.Condition, condition.getIdElement()));
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testForValidReferences(condition);
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buildEffectiveTimeLow(condition).ifPresent(builder::effectiveTimeLow);
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buildEffectiveTimeHigh(condition).ifPresent(builder::effectiveTimeHigh);
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buildAvailabilityTime(condition).ifPresent(builder::availabilityTime);
@@ -104,6 +106,21 @@ public String mapConditionToLinkSet(Condition condition, boolean isNested) {
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return TemplateUtils.fillTemplate(OBSERVATION_STATEMENT_TEMPLATE, builder.build());
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}
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public void testForValidReferences(Condition condition) {
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for (Extension extension : condition.getExtension()) {
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if (!(extension.getValue() instanceof Reference)) {
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return;
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}
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IdType idType = (IdType) ((Reference) extension.getValue()).getReferenceElement();
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try {
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messageContext.getInputBundleHolder().getResource(idType);
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} catch (Exception e) {
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LOGGER.warn("Bundle mapping aborted. Reason: " + e.getMessage());
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throw e;
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}
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}
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}
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private void setQualifierProperties(ConditionLinkSetMapperParameters.ConditionLinkSetMapperParametersBuilder builder,
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String qualifier) {
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builder.qualifierDisplay(qualifier);

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

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@@ -40,6 +40,7 @@
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.Mockito.lenient;
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import static org.mockito.Mockito.when;
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import static org.mockito.Mockito.spy;
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import static uk.nhs.adaptors.gp2gp.utils.ConfidentialityCodeUtility.NOPAT;
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import static uk.nhs.adaptors.gp2gp.utils.ConfidentialityCodeUtility.NOPAT_HL7_CONFIDENTIALITY_CODE;
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import static uk.nhs.adaptors.gp2gp.utils.ConfidentialityCodeUtility.NOSCRUB;
@@ -126,6 +127,8 @@ class ConditionLinkSetMapperTest {
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private ArgumentCaptor<Condition> conditionArgumentCaptor;
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private InputBundle inputBundle;
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private ConditionLinkSetMapper conditionLinkSetMapperSpy;
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private ConditionLinkSetMapper conditionLinkSetMapper;
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@BeforeEach
@@ -155,6 +158,10 @@ void setUp() {
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conditionLinkSetMapper = new ConditionLinkSetMapper(messageContext, randomIdGeneratorService, codeableConceptCdMapper,
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new ParticipantMapper(), confidentialityService);
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conditionLinkSetMapperSpy = spy(conditionLinkSetMapper);
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lenient().doNothing().when(conditionLinkSetMapperSpy).testForValidReferences(any());
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}
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@AfterEach
@@ -170,15 +177,15 @@ void When_MappingParsedConditionWithoutMappedAgent_Expect_EhrMapperException() {
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when(agentDirectory.getAgentId(any(Reference.class)))
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.thenThrow(propagatedException);
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assertThatThrownBy(() -> conditionLinkSetMapper.mapConditionToLinkSet(condition, false))
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assertThatThrownBy(() -> conditionLinkSetMapperSpy.mapConditionToLinkSet(condition, false))
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.isSameAs(propagatedException);
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}
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@Test
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void When_MappingParsedConditionWithAsserterNotPractitioner_Expect_EhrMapperException() {
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final Condition condition = getConditionResourceFromJson(INPUT_JSON_ASSERTER_NOT_PRACTITIONER);
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181-
assertThatThrownBy(() -> conditionLinkSetMapper.mapConditionToLinkSet(condition, false))
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assertThatThrownBy(() -> conditionLinkSetMapperSpy.mapConditionToLinkSet(condition, false))
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.isExactlyInstanceOf(EhrMapperException.class)
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.hasMessage("Condition.asserter must be a Practitioner");
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}
@@ -189,7 +196,7 @@ void When_MappingParsedCondition_With_RealProblem_Expect_LinkSetXml(String condi
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final Condition condition = getConditionResourceFromJson(conditionJson);
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final String expectedXml = getXmlStringFromFile(outputXml);
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final String actualXml = conditionLinkSetMapper.mapConditionToLinkSet(condition, isNested);
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final String actualXml = conditionLinkSetMapperSpy.mapConditionToLinkSet(condition, isNested);
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assertThat(actualXml).isEqualTo(expectedXml);
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}
@@ -201,7 +208,7 @@ void When_MappingParsedCondition_With_ActualProblemContentAndIsObservation_Expec
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final Condition condition = getConditionResourceFromJson(conditionJson);
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final String expectedXml = getXmlStringFromFile(outputXml);
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204-
final String actualXml = conditionLinkSetMapper.mapConditionToLinkSet(condition, isNested);
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final String actualXml = conditionLinkSetMapperSpy.mapConditionToLinkSet(condition, isNested);
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assertThat(actualXml).isEqualTo(expectedXml);
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}
@@ -211,7 +218,7 @@ void When_MappingParsedCondition_With_NoRelatedClinicalContent_Expect_LinkSetXml
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final Condition condition = getConditionResourceFromJson(INPUT_JSON_NO_RELATED_CLINICAL_CONTENT);
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final String expectedXml = getXmlStringFromFile(OUTPUT_XML_WITH_NO_RELATED_CLINICAL_CONTENT);
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final String actualXml = conditionLinkSetMapper.mapConditionToLinkSet(condition, false);
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final String actualXml = conditionLinkSetMapperSpy.mapConditionToLinkSet(condition, false);
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assertThat(actualXml).isEqualTo(expectedXml);
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}
@@ -223,7 +230,7 @@ void When_MappingParsedCondition_With_NonExistentReferenceInRelatedClinicalConte
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when(messageContext.getInputBundleHolder()).thenReturn(inputBundle);
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// TODO: workaround for NIAD-1409 should throw an exception but demonstrator include invalid references
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assumeThatThrownBy(() -> conditionLinkSetMapper.mapConditionToLinkSet(parsedObservation, false))
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assumeThatThrownBy(() -> conditionLinkSetMapperSpy.mapConditionToLinkSet(parsedObservation, false))
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.isExactlyInstanceOf(EhrMapperException.class)
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.hasMessage("Could not resolve Condition Related Medical Content reference");
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}
@@ -232,7 +239,7 @@ void When_MappingParsedCondition_With_NonExistentReferenceInRelatedClinicalConte
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void When_MappingParsedConditionCodeIsMissing_Expect_MapperException() {
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final Condition condition = getConditionResourceFromJson(INPUT_JSON_MISSING_CONDITION_CODE);
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assertThatThrownBy(() -> conditionLinkSetMapper.mapConditionToLinkSet(condition, false))
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assertThatThrownBy(() -> conditionLinkSetMapperSpy.mapConditionToLinkSet(condition, false))
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.isExactlyInstanceOf(EhrMapperException.class)
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.hasMessage("Condition code not present");
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}
@@ -242,7 +249,7 @@ void When_MappingCondition_With_SuppressedMedReqAsRelatedClinicalContent_Expect_
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final Condition condition = getConditionResourceFromJson(INPUT_JSON_SUPPRESSED_RELATED_MEDICATION_REQUEST);
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final String expectedXml = getXmlStringFromFile(OUTPUT_XML_SUPPRESSED_RELATED_MEDICATION_REQUEST);
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final String actualXml = conditionLinkSetMapper.mapConditionToLinkSet(condition, false);
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final String actualXml = conditionLinkSetMapperSpy.mapConditionToLinkSet(condition, false);
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XMLAssert.assertXMLEqual(expectedXml, actualXml);
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}
@@ -258,7 +265,7 @@ void When_MappingCondition_With_NopatMetaSecurity_Expect_ConfidentialityCodeInBo
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when(confidentialityService.generateConfidentialityCode(conditionArgumentCaptor.capture()))
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.thenReturn(Optional.of(NOPAT_HL7_CONFIDENTIALITY_CODE));
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261-
final String actualXml = wrapXmlInRootElement(conditionLinkSetMapper
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final String actualXml = wrapXmlInRootElement(conditionLinkSetMapperSpy
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.mapConditionToLinkSet(condition, false));
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final String conditionSecurityCode = ConfidentialityCodeUtility
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.getSecurityCodeFromResource(conditionArgumentCaptor.getValue());
@@ -278,7 +285,7 @@ void When_MappingCondition_With_NoscrubMetaSecurity_Expect_ConfidentialityCodeNo
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when(confidentialityService.generateConfidentialityCode(conditionArgumentCaptor.capture()))
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.thenReturn(Optional.empty());
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281-
final String actualXml = conditionLinkSetMapper.mapConditionToLinkSet(condition, false);
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final String actualXml = conditionLinkSetMapperSpy.mapConditionToLinkSet(condition, false);
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final String conditionSecurityCode = ConfidentialityCodeUtility
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.getSecurityCodeFromResource(conditionArgumentCaptor.getValue());
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‎service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/EncounterComponentsMapperTest.java‎

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@@ -64,6 +64,7 @@ class EncounterComponentsMapperTest {
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private static final String INPUT_BUNDLE_WITH_RESOURCES_NOT_IN_BUNDLE = TEST_DIRECTORY + "input-bundle-7.json";
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private static final String INPUT_BUNDLE_WITH_NON_TOPIC_CONSULTATION_LIST_ENTRY = TEST_DIRECTORY + "input-bundle-8.json";
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private static final String INPUT_BUNDLE_WITH_UNSUPPORTED_RESOURCES = TEST_DIRECTORY + "input-bundle-9-unsupported-resource.json";
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private static final String INPUT_BUNDLE_WITH_INVALID_REFERENCE = TEST_DIRECTORY + "input-bundle-9-missing-reference.json";
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private static final String INPUT_BUNDLE_WITH_IGNORED_RESOURCE = TEST_DIRECTORY + "input-bundle-10-ignored-resource.json";
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private static final String INPUT_BUNDLE_WITH_META_SECURITY = TEST_DIRECTORY + "input-bundle-10-with-meta.json";
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private static final String INPUT_BUNDLE_WITH_NON_CATEGORY_TOPIC_LIST_ENTRY = TEST_DIRECTORY
@@ -315,6 +316,16 @@ void When_MappingEncounterUnsupportedResource_Expect_ExceptionThrown() {
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.isInstanceOf(EhrMapperException.class);
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}
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@Test
320+
void When_MappingEncounterInvalidReference_Expect_ExceptionThrown() {
321+
var bundle = initializeMessageContext(INPUT_BUNDLE_WITH_INVALID_REFERENCE);
322+
var encounter = extractEncounter(bundle);
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324+
assertThatThrownBy(() -> encounterComponentsMapper.mapComponents(encounter))
325+
.hasMessageContaining("Resource not found: Observation/7E277DF1-6F1C-47CD-84F7-E9B7BF4105DB")
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.isInstanceOf(EhrMapperException.class);
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}
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@Test
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void When_MappingConsultation_WithNonTopicList_Expect_ExceptionThrown() {
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var bundle = initializeMessageContext(INPUT_BUNDLE_WITH_NON_TOPIC_CONSULTATION_LIST_ENTRY);

‎service/src/test/resources/ehr/mapper/encountercomponents/input-bundle-1.json‎

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@@ -823,7 +823,7 @@
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{
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"url": "https://fhir.hl7.org.uk/STU3/StructureDefinition/Extension-CareConnect-ActualProblem-1",
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"valueReference": {
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"reference": "Observation/7E277DF1-6F1C-47CD-84F7-E9B7BF4105DB"
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"reference": "Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2"
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}
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},
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{

‎service/src/test/resources/ehr/mapper/encountercomponents/input-bundle-10-ignored-resource.json‎

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@@ -833,7 +833,7 @@
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{
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"url": "https://fhir.hl7.org.uk/STU3/StructureDefinition/Extension-CareConnect-ActualProblem-1",
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"valueReference": {
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"reference": "Observation/7E277DF1-6F1C-47CD-84F7-E9B7BF4105DB"
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"reference": "Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2"
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}
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},
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{

‎service/src/test/resources/ehr/mapper/encountercomponents/input-bundle-10-with-meta.json‎

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@@ -838,7 +838,7 @@
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{
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"url": "https://fhir.hl7.org.uk/STU3/StructureDefinition/Extension-CareConnect-ActualProblem-1",
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"valueReference": {
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"reference": "Observation/7E277DF1-6F1C-47CD-84F7-E9B7BF4105DB"
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"reference": "Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2"
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}
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},
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{

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