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NIAD-3134 - Add confidentialityCode support for DocumentReference (…
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…#739)

* [NIAD-3134] Added unit test

* [NIAD-3134] Updated DocumentReferenceMapper.java to support confidentialityCode

* [NIAD-3134] Updated test to use External Document over Narrative Statement.

* [NIAD-3134] Updated production code to use ExternalDocument over NarrativeStatement

* [NIAD-3134] Updated CHANGELOG.md
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@martin-nhs
martin-nhs authored Aug 6, 2024
1 parent dd4777c commit e9e54b9
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Showing 5 changed files with 220 additions and 57 deletions.
2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,8 @@ corresponding FHIR resource will now be [appropriately populated][nopat-docs].
corresponding FHIR resource will now be [appropriately populated][nopat-docs].
* If a `linkset` record includes a `confidentialityCode`, the `meta.security` field of the
corresponding FHIR resource will now be [appropriately populated][nopat-docs].
* If a `documentReference` record includes a `confidentialityCode`, the `meta.security` field of the
corresponding FHIR resource will now be [appropriately populated][nopat-docs].
* If an `immunization` record includes a `confidentialityCode`, the `meta.security` field of the
corresponding FHIR resource will now be [appropriately populated][nopat-docs].

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30 changes: 23 additions & 7 deletions ...anslator/src/main/java/uk/nhs/adaptors/pss/translator/mapper/DocumentReferenceMapper.java
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Expand Up @@ -18,17 +18,20 @@
import org.hl7.fhir.dstu3.model.DocumentReference;
import org.hl7.fhir.dstu3.model.Encounter;
import org.hl7.fhir.dstu3.model.InstantType;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.dstu3.model.Organization;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.v3.RCMRMT030101UKEhrComposition;
import org.hl7.v3.RCMRMT030101UKEhrExtract;
import org.hl7.v3.RCMRMT030101UKExternalDocument;
import org.hl7.v3.RCMRMT030101UKNarrativeStatement;
import org.springframework.stereotype.Service;

import lombok.AllArgsConstructor;
import lombok.extern.slf4j.Slf4j;
import uk.nhs.adaptors.connector.model.PatientAttachmentLog;
import uk.nhs.adaptors.pss.translator.service.ConfidentialityService;
import uk.nhs.adaptors.pss.translator.util.DateFormatUtil;
import uk.nhs.adaptors.pss.translator.util.DegradedCodeableConcepts;
import uk.nhs.adaptors.pss.translator.util.ResourceFilterUtil;
Expand All @@ -40,12 +43,13 @@ public class DocumentReferenceMapper extends AbstractMapper<DocumentReference> {

// TODO: Add file Size using the uncompressed/un-encoded size of the document (NIAD-2030)

private static final String META_PROFILE = "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-DocumentReference-1";
private static final String META_PROFILE = "DocumentReference-1";
private static final String ABSENT_ATTACHMENT = "AbsentAttachment";
private static final String PLACEHOLDER_VALUE = "GP2GP generated placeholder. Original document not available. See notes for details";
private static final String INVALID_CONTENT_TYPE = "Content type was not a valid MIME type";

private CodeableConceptMapper codeableConceptMapper;
private ConfidentialityService confidentialityService;

public List<DocumentReference> mapResources(RCMRMT030101UKEhrExtract ehrExtract, Patient patient,
List<Encounter> encounterList, Organization organization,
Expand Down Expand Up @@ -75,7 +79,7 @@ private DocumentReference mapDocumentReference(RCMRMT030101UKNarrativeStatement
List<Encounter> encounterList,
Organization organization, List<PatientAttachmentLog> attachments) {

DocumentReference documentReference = new DocumentReference();
final DocumentReference documentReference = new DocumentReference();

// document references actually use the narrative statement id rather than the referenceDocument root id in EMIS data
// if EMIS is incorrect, replace the id below with the following...
Expand All @@ -84,7 +88,7 @@ private DocumentReference mapDocumentReference(RCMRMT030101UKNarrativeStatement

documentReference.addIdentifier(buildIdentifier(id, organization.getIdentifierFirstRep().getValue()));
documentReference.setId(id);
documentReference.getMeta().addProfile(META_PROFILE);
documentReference.setMeta(generateMeta(narrativeStatement));
documentReference.setStatus(DocumentReferenceStatus.CURRENT);
documentReference.setType(getType(narrativeStatement));
documentReference.setSubject(new Reference(patient));
Expand All @@ -111,6 +115,18 @@ private DocumentReference mapDocumentReference(RCMRMT030101UKNarrativeStatement
return documentReference;
}

private Meta generateMeta(RCMRMT030101UKNarrativeStatement narrativeStatement) {
final RCMRMT030101UKExternalDocument externalDocument = narrativeStatement
.getReference()
.getFirst()
.getReferredToExternalDocument();

return confidentialityService.createMetaAndAddSecurityIfConfidentialityCodesPresent(
META_PROFILE,
externalDocument.getConfidentialityCode()
);
}

private DateTimeType getCreatedTime(RCMRMT030101UKEhrComposition ehrComposition) {
if (ehrComposition.hasAvailabilityTime() && ehrComposition.getAvailabilityTime().hasValue()) {
return DateFormatUtil.parseToDateTimeType(ehrComposition.getAvailabilityTime().getValue());
Expand All @@ -128,7 +144,7 @@ private InstantType getIndexed(RCMRMT030101UKEhrComposition ehrComposition) {

private CodeableConcept getType(RCMRMT030101UKNarrativeStatement narrativeStatement) {

var referenceToExternalDocument = narrativeStatement.getReference().get(0).getReferredToExternalDocument();
var referenceToExternalDocument = narrativeStatement.getReference().getFirst().getReferredToExternalDocument();
CodeableConcept codeableConcept = null;
if (referenceToExternalDocument != null && referenceToExternalDocument.hasCode()) {
if (!referenceToExternalDocument.getCode().hasOriginalText() && referenceToExternalDocument.getCode().hasDisplayName()) {
Expand Down Expand Up @@ -163,21 +179,21 @@ private String buildDescription(RCMRMT030101UKNarrativeStatement narrativeStatem
if (isAbsentAttachment(narrativeStatement)) {
return PLACEHOLDER_VALUE;
} else {
return buildFileName(narrativeStatement.getReference().get(0)
return buildFileName(narrativeStatement.getReference().getFirst()
.getReferredToExternalDocument().getText().getReference().getValue());
}
}

private boolean isAbsentAttachment(RCMRMT030101UKNarrativeStatement narrativeStatement) {

return narrativeStatement.getReference().get(0)
return narrativeStatement.getReference().getFirst()
.getReferredToExternalDocument().getText().getReference().getValue().contains(ABSENT_ATTACHMENT);
}

private void setContentAttachments(DocumentReference documentReference, RCMRMT030101UKNarrativeStatement narrativeStatement,
List<PatientAttachmentLog> patientAttachmentLogs) {

var referenceToExternalDocument = narrativeStatement.getReference().get(0).getReferredToExternalDocument();
var referenceToExternalDocument = narrativeStatement.getReference().getFirst().getReferredToExternalDocument();
var attachment = new Attachment();
if (referenceToExternalDocument.hasText()) {
var mediaType = referenceToExternalDocument.getText().getMediaType();
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8 changes: 8 additions & 0 deletions gp2gp-translator/src/test/java/uk/nhs/adaptors/pss/translator/TestUtility.java
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Expand Up @@ -27,4 +27,12 @@ public static CV createCv(String code, String codeSystem, String displayName) {
public static CV createCv(String code) {
return createCv(code, "", "");
}

public static class NoConfidentialityCodePresentException extends RuntimeException {
private static final String EXCEPTION_MESSAGE = "No confidentiality code is present within the test file.";

public NoConfidentialityCodePresentException() {
super(EXCEPTION_MESSAGE);
}
}
}
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