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‎CHANGELOG.md‎

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@@ -25,6 +25,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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* When mapping `Immunizations` which contain a `NOPAT` `meta.security` tag, the resultant XML for that resource
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will contain a `NOPAT` `confidentialityCode` element.
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### Fixed
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* Fix a malformed XML GP2GP message created when mapping a `MedicationRequest` with `intent` of `plan` and is stopped,
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but no free text reason for the discontinuation was provided.
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## [2.1.2] - 2014-10-21
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### Fixed

‎service/build.gradle‎

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@@ -57,7 +57,7 @@ dependencies {
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implementation 'org.apache.commons:commons-lang3:3.17.0'
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implementation 'javax.xml.soap:javax.xml.soap-api:1.4.0'
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implementation 'com.github.spullara.mustache.java:compiler:0.9.14'
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implementation 'org.apache.tika:tika-core:2.9.2'
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implementation 'org.apache.tika:tika-core:3.0.0'
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// Fhir
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implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:7.4.3'
@@ -73,7 +73,7 @@ dependencies {
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testImplementation 'com.squareup.okhttp3:mockwebserver:4.12.0'
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pitest 'com.arcmutate:base:1.3.1'
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pitest 'com.arcmutate:pitest-git-plugin:1.3.2'
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pitest 'com.arcmutate:pitest-git-plugin:1.3.3'
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}
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test {

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

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This file was deleted.

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

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@@ -1,7 +1,6 @@
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package uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport;
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import static uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.DiagnosticReportMapper.DUMMY_OBSERVATION_ID_PREFIX;
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import static uk.nhs.adaptors.gp2gp.ehr.utils.CodeableConceptMappingUtils.hasCode;
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import java.util.List;
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import java.util.Objects;
@@ -30,6 +29,7 @@
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import lombok.RequiredArgsConstructor;
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import lombok.extern.slf4j.Slf4j;
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import uk.nhs.adaptors.gp2gp.common.service.ConfidentialityService;
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import uk.nhs.adaptors.gp2gp.common.service.RandomIdGeneratorService;
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import uk.nhs.adaptors.gp2gp.ehr.exception.EhrMapperException;
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import uk.nhs.adaptors.gp2gp.ehr.mapper.CodeableConceptCdMapper;
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import uk.nhs.adaptors.gp2gp.ehr.mapper.CommentType;
@@ -73,8 +73,6 @@ public class ObservationMapper {
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private static final String RANGE_LOW_PREFIX = "Low: ";
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private static final String RANGE_HIGH_PREFIX = "High: ";
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76-
private static final String COMMENT_NOTE_CODE = "37331000000100";
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private static final String HL7_UNKNOWN_VALUE = "UNK";
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private static final String HAS_MEMBER_TYPE = "HASMEMBER";
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@@ -87,12 +85,11 @@ public class ObservationMapper {
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private final StructuredObservationValueMapper structuredObservationValueMapper;
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private final CodeableConceptCdMapper codeableConceptCdMapper;
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private final ParticipantMapper participantMapper;
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private final MultiStatementObservationHolderFactory multiStatementObservationHolderFactory;
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private final RandomIdGeneratorService randomIdGeneratorService;
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private final ConfidentialityService confidentialityService;
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public String mapObservationToCompoundStatement(Observation observationAssociatedWithSpecimen) {
94-
var holder = multiStatementObservationHolderFactory.newInstance(observationAssociatedWithSpecimen);
95-
return mapAndVerify(holder);
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return mapAndVerify(createHolder(observationAssociatedWithSpecimen));
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}
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private String mapAndVerify(MultiStatementObservationHolder observationAssociatedWithSpecimen) {
@@ -178,7 +175,7 @@ private List<MultiStatementObservationHolder> getRelatedObservations(
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.map(referenceElement -> messageContext.getInputBundleHolder().getResource(referenceElement))
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.flatMap(Optional::stream)
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.map(Observation.class::cast)
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.map(multiStatementObservationHolderFactory::newInstance)
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.map(observation -> createHolder(observation))
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.collect(Collectors.toList());
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}
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@@ -364,7 +361,7 @@ private Optional<String> prepareNarrativeStatementForRelatedObservationComments(
364361
}
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private CommentType prepareCommentType(Observation observation) {
367-
return hasCode(observation.getCode(), List.of(COMMENT_NOTE_CODE))
364+
return DiagnosticReportMapper.isFilingComment(observation)
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? CommentType.USER_COMMENT : CommentType.AGGREGATE_COMMENT_SET;
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}
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@@ -483,7 +480,7 @@ private DateTimeType resolveEffectiveDateTimeType(Observation observation) {
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}
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private boolean observationHasNonCommentNoteCode(Observation observation) {
486-
return observation.hasCode() && !hasCode(observation.getCode(), List.of(COMMENT_NOTE_CODE));
483+
return observation.hasCode() && !DiagnosticReportMapper.isFilingComment(observation);
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}
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private String prepareCodeElement(Observation observation) {
@@ -546,6 +543,10 @@ private boolean hasValidType(Observation.ObservationRelatedComponent observation
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}
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private boolean hasValidComment(Observation observation) {
549-
return observation.hasComment() && hasCode(observation.getCode(), List.of(COMMENT_NOTE_CODE));
546+
return observation.hasComment() && DiagnosticReportMapper.isFilingComment(observation);
547+
}
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private MultiStatementObservationHolder createHolder(Observation observationAssociatedWithSpecimen) {
550+
return new MultiStatementObservationHolder(observationAssociatedWithSpecimen, messageContext, randomIdGeneratorService);
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}
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}

‎service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/utils/StatementTimeMappingUtils.java‎

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@@ -137,7 +137,9 @@ public static String prepareEffectiveTimeForMedicationRequest(MedicationRequest
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}
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return String.format(EFFECTIVE_TIME_LOW_TEMPLATE, toHl7Format(startElement));
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}
140-
throw new EhrMapperException("Could not map Effective Time for Medication Request");
140+
throw new EhrMapperException(
141+
"MedicationRequest/{%s} must contain a dispenseRequest.validityPeriod.start".formatted(medicationRequest.getId())
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);
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}
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public static String prepareAvailabilityTimeForMedicationRequest(MedicationRequest medicationRequest) {
@@ -146,7 +148,9 @@ public static String prepareAvailabilityTimeForMedicationRequest(MedicationReque
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return String.format(AVAILABILITY_TIME_VALUE_TEMPLATE, toHl7Format(
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medicationRequest.getDispenseRequest().getValidityPeriod().getStartElement()));
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}
149-
throw new EhrMapperException("Could not map Availability Time for Medication Request");
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throw new EhrMapperException(
152+
"MedicationRequest/{%s} must contain a dispenseRequest.validityPeriod.start".formatted(medicationRequest.getId())
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);
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}
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public static String prepareEffectiveTimeForEhrFolder(EhrFolderEffectiveTime effectiveTime) {

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

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@@ -60,8 +60,8 @@
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</priorMedicationRef>
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</reversalOf>
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<pertinentInformation typeCode="PERT">
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<pertinentSupplyAnnotation classCode="OBS" moodCode="EVN">
64-
{{#ehrSupplyDiscontinueReasonText}}<text>{{{ehrSupplyDiscontinueReasonText}}}</text>{{/ehrSupplyDiscontinueReasonText}}{{^ehrSupplyDiscontinueReasonText}}<code nullFlavor="UNK"><text>Stopped</text></code>{{/ehrSupplyDiscontinueReasonText}}
63+
<pertinentSupplyAnnotation classCode="OBS" moodCode="EVN"{{^ehrSupplyDiscontinueReasonText}} nullFlavor="UNK"{{/ehrSupplyDiscontinueReasonText}}>
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{{#ehrSupplyDiscontinueReasonText}}<text>{{{ehrSupplyDiscontinueReasonText}}}</text>{{/ehrSupplyDiscontinueReasonText}}{{^ehrSupplyDiscontinueReasonText}}<text>Stopped</text>{{/ehrSupplyDiscontinueReasonText}}
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</pertinentSupplyAnnotation>
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</pertinentInformation>
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</ehrSupplyDiscontinue>

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

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@@ -19,7 +19,6 @@
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import uk.nhs.adaptors.gp2gp.common.service.RandomIdGeneratorService;
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import uk.nhs.adaptors.gp2gp.common.service.TimestampService;
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import uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.DiagnosticReportMapper;
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import uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.MultiStatementObservationHolderFactory;
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import uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.ObservationMapper;
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import uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.SpecimenMapper;
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import uk.nhs.adaptors.gp2gp.ehr.mapper.parameters.EhrExtractTemplateParameters;
@@ -148,11 +147,9 @@ public void setUp() {
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ParticipantMapper participantMapper = new ParticipantMapper();
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StructuredObservationValueMapper structuredObservationValueMapper = new StructuredObservationValueMapper();
151-
MultiStatementObservationHolderFactory multiStatementObservationHolderFactory =
152-
new MultiStatementObservationHolderFactory(messageContext, randomIdGeneratorService);
153150
ObservationMapper specimenObservationMapper = new ObservationMapper(
154151
messageContext, structuredObservationValueMapper, codeableConceptCdMapper,
155-
participantMapper, multiStatementObservationHolderFactory, confidentialityService);
152+
participantMapper, randomIdGeneratorService, confidentialityService);
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SpecimenMapper specimenMapper = new SpecimenMapper(messageContext, specimenObservationMapper,
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randomIdGeneratorService, confidentialityService);
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DocumentReferenceToNarrativeStatementMapper documentReferenceToNarrativeStatementMapper

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

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@@ -24,7 +24,6 @@
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import uk.nhs.adaptors.gp2gp.common.service.TimestampService;
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import uk.nhs.adaptors.gp2gp.ehr.exception.EhrMapperException;
2626
import uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.DiagnosticReportMapper;
27-
import uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.MultiStatementObservationHolderFactory;
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import uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.ObservationMapper;
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import uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.SpecimenMapper;
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import uk.nhs.adaptors.gp2gp.ehr.utils.BloodPressureValidator;
@@ -207,11 +206,9 @@ public void setUp() {
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private @NotNull SpecimenMapper getSpecimenMapper(StructuredObservationValueMapper structuredObservationValueMapper,
209208
ParticipantMapper participantMapper) {
210-
MultiStatementObservationHolderFactory multiStatementObservationHolderFactory =
211-
new MultiStatementObservationHolderFactory(messageContext, randomIdGeneratorService);
212209
ObservationMapper specimenObservationMapper = new ObservationMapper(
213210
messageContext, structuredObservationValueMapper, codeableConceptCdMapper, participantMapper,
214-
multiStatementObservationHolderFactory, confidentialityService);
211+
randomIdGeneratorService, confidentialityService);
215212
return new SpecimenMapper(messageContext, specimenObservationMapper, randomIdGeneratorService, confidentialityService);
216213
}
217214

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

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@@ -275,7 +275,7 @@ void When_DiagnosticReport_With_NoReferencedSpecimenAndFilingCommentWithNoCommen
275275
new StructuredObservationValueMapper(),
276276
codeableConceptCdMapper,
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new ParticipantMapper(),
278-
new MultiStatementObservationHolderFactory(messageContext, randomIdGeneratorService),
278+
randomIdGeneratorService,
279279
confidentialityService
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),
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randomIdGeneratorService,

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

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@@ -159,15 +159,12 @@ void setUp() {
159159
when(idMapper.getOrNew(any(ResourceType.class), any(IdType.class)))
160160
.thenAnswer(params -> "Mapped-From-" + ((IdType) params.getArgument(1)).getValue());
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162-
MultiStatementObservationHolderFactory multiStatementObservationHolderFactory =
163-
new MultiStatementObservationHolderFactory(messageContext, randomIdGeneratorService);
164-
165162
observationMapper = new ObservationMapper(
166163
messageContext,
167164
new StructuredObservationValueMapper(),
168165
new CodeableConceptCdMapper(),
169166
new ParticipantMapper(),
170-
multiStatementObservationHolderFactory,
167+
randomIdGeneratorService,
171168
confidentialityService
172169
);
173170
}

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