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Merged
MartinWheelerMT merged 6 commits into from
Mar 5, 2025
Merged

Refactor CodeableConceptCdMapper #1136

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47f0576
Refactor `CodeableConceptCdMapper`
MartinWheelerMT Mar 5, 2025
29a7072
* Add a test case when mapping to nullFlavor codeable concept for all…
MartinWheelerMT Mar 5, 2025
44d8756
* Add unit test to handle the case where an allergy intolerance is ne…
MartinWheelerMT Mar 5, 2025
f78bd68
* Remove check for `resolved` clinical status as call to method `getO…
MartinWheelerMT Mar 5, 2025
e849cac
* Removed unnecessary `isEmpty` check as fallback was to return an Op…
MartinWheelerMT Mar 5, 2025
b19f33a
Remove now unnecessary test
MartinWheelerMT Mar 5, 2025
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177 changes: 64 additions & 113 deletions service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import java.util.function.BiFunction;

import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.model.AllergyIntolerance;
Expand Down Expand Up @@ -37,7 +38,6 @@ public class CodeableConceptCdMapper {
private static final String FIXED_ACTUAL_PROBLEM_CODE = "55607006";
private static final String PROBLEM_DISPLAY_NAME = "Problem";
private static final String ACTIVE_CLINICAL_STATUS = "active";
private static final String RESOLVED_CLINICAL_STATUS = "resolved";
private static final String PRESCRIBING_AGENCY_GP_PRACTICE_CODE = "prescribed-at-gp-practice";
private static final String PRESCRIBING_AGENCY_PREVIOUS_PRACTICE_CODE = "prescribed-by-previous-practice";
private static final String PRESCRIBING_AGENCY_ANOTHER_ORGANISATION_CODE = "prescribed-by-another-organisation";
Expand All @@ -51,10 +51,23 @@ public class CodeableConceptCdMapper {
private static final String OTHER_CATEGORY_DESCRIPTION = "Other category";

public String mapCodeableConceptToCd(CodeableConcept codeableConcept) {
return mapCodeableConcept(codeableConcept, this::getMainCode);
}

public String mapCodeableConceptForMedication(CodeableConcept codeableConcept) {
return mapCodeableConcept(
codeableConcept,
(descriptionExtensions, snomedCodeCoding) -> Optional.ofNullable(snomedCodeCoding.getCode()));
}

private String mapCodeableConcept(
CodeableConcept codeableConcept,
BiFunction<Optional<List<Extension>>, Coding, Optional<String>> getMainCodeFunction
) {
Optional<Coding> snomedCodeCoding = getSnomedCodeCoding(codeableConcept);

if (snomedCodeCoding.isEmpty()) {
return buildNullFlavourCodeableConceptCd(codeableConcept, snomedCodeCoding);
return mapToNullFlavorCodeableConcept(codeableConcept);
}

var builder = CodeableConceptCdTemplateParameters.builder();
Expand All @@ -64,87 +77,60 @@ public String mapCodeableConceptToCd(CodeableConcept codeableConcept) {

builder.mainCodeSystem(SNOMED_SYSTEM_CODE);

var mainCode = getMainCode(descriptionExtensions, snomedCodeCoding.get());
mainCode.ifPresent(builder::mainCode);

var mainDisplayName = getMainDisplayName(descriptionExtensions, snomedCodeCoding.get());
mainDisplayName.ifPresent(builder::mainDisplayName);

builder.mainOriginalText(codeableConcept.getText());
builder.translations(getNonSnomedCodeCodings(codeableConcept));

var mainCode = getMainCodeFunction.apply(descriptionExtensions, snomedCodeCoding.get());
mainCode.ifPresent(builder::mainCode);

return TemplateUtils.fillTemplate(CODEABLE_CONCEPT_CD_TEMPLATE, builder.build());
}

// Medications are currently using D&T Codes rather than snomed codes but are being passed through as SNOMED codes which is
// creating a degradation on the receiving side. Until the types are configured correctly and agreed to a specification
// we have agreed to use the Concept ID rather than Description Id for medications which will avoided the degradation.
public String mapCodeableConceptForMedication(CodeableConcept codeableConcept) {
public String mapCodeableConceptToCdForAllergy(
CodeableConcept codeableConcept,
AllergyIntolerance.AllergyIntoleranceClinicalStatus allergyIntoleranceClinicalStatus
) {
var builder = CodeableConceptCdTemplateParameters.builder();
var snomedCodeCoding = getSnomedCodeCoding(codeableConcept);
Optional<Coding> snomedCodeCoding = getSnomedCodeCoding(codeableConcept);

if (snomedCodeCoding.isEmpty()) {
return buildNullFlavourCodeableConceptCd(codeableConcept, snomedCodeCoding);
builder.nullFlavor(true);
return TemplateUtils.fillTemplate(CODEABLE_CONCEPT_CD_TEMPLATE, builder.build());
}

var extension = retrieveDescriptionExtension(snomedCodeCoding.get())
.map(Extension::getExtension)
.orElse(Collections.emptyList());

builder.mainCodeSystem(SNOMED_SYSTEM_CODE);

Optional<String> code = Optional.ofNullable(snomedCodeCoding.get().getCode());
code.ifPresent(builder::mainCode);
if (ACTIVE_CLINICAL_STATUS.equals(allergyIntoleranceClinicalStatus.toCode())) {
builder.mainCodeSystem(SNOMED_SYSTEM_CODE);
} else {
builder.nullFlavor(true);
}

Optional<String> displayName = extension.stream()
.filter(displayExtension -> DESCRIPTION_DISPLAY.equals(displayExtension.getUrl()))
.map(description -> description.getValue().toString())
.findFirst()
.or(() -> Optional.ofNullable(snomedCodeCoding.get().getDisplay()));
displayName.ifPresent(builder::mainDisplayName);
getAllergyMainCode(snomedCodeCoding.get()).ifPresent(builder::mainCode);
getCodingDisplayName(snomedCodeCoding.get()).ifPresent(builder::mainDisplayName);

builder.mainOriginalText(codeableConcept.getText());
if (codeableConcept.hasText()) {
builder.mainOriginalText(codeableConcept.getText());
} else {
var originalText = findOriginalTextForAllergy(codeableConcept, snomedCodeCoding, allergyIntoleranceClinicalStatus);
originalText.ifPresent(builder::mainOriginalText);
}

builder.translations(getNonSnomedCodeCodings(codeableConcept));
return TemplateUtils.fillTemplate(CODEABLE_CONCEPT_CD_TEMPLATE, builder.build());
}

public String mapCodeableConceptToCdForAllergy(CodeableConcept codeableConcept, AllergyIntolerance.AllergyIntoleranceClinicalStatus
allergyIntoleranceClinicalStatus) {
var builder = CodeableConceptCdTemplateParameters.builder();
var mainCode = getSnomedCodeCoding(codeableConcept);

builder.nullFlavor(mainCode.isEmpty());

if (mainCode.isPresent()) {
var extension = retrieveDescriptionExtension(mainCode.get())
.map(Extension::getExtension)
.orElse(Collections.emptyList());

if (ACTIVE_CLINICAL_STATUS.equals(allergyIntoleranceClinicalStatus.toCode())) {
builder.mainCodeSystem(SNOMED_SYSTEM_CODE);
} else {
builder.nullFlavor(true);
}
private static Optional<String> getCodingDisplayName(Coding snomedCodeCoding) {
return Optional.ofNullable(snomedCodeCoding.getDisplay());
}

Optional<String> code = extension.stream()
private static Optional<String> getAllergyMainCode(Coding snomedCodeCoding) {
return retrieveDescriptionExtension(snomedCodeCoding)
.flatMap(extension -> extension.getExtension().stream()
.filter(descriptionExt -> DESCRIPTION_ID.equals(descriptionExt.getUrl()))
.map(description -> description.getValue().toString())
.findFirst()
.or(() -> Optional.ofNullable(mainCode.get().getCode()));
code.ifPresent(builder::mainCode);

Optional<String> displayName = Optional.ofNullable(mainCode.get().getDisplay());
displayName.ifPresent(builder::mainDisplayName);

if (codeableConcept.hasText()) {
builder.mainOriginalText(codeableConcept.getText());
} else {
var originalText = findOriginalTextForAllergy(codeableConcept, mainCode, allergyIntoleranceClinicalStatus);
originalText.ifPresent(builder::mainOriginalText);
}
}
return TemplateUtils.fillTemplate(CODEABLE_CONCEPT_CD_TEMPLATE, builder.build());
.map(description -> description.getValue().toString()))
.or(() -> Optional.ofNullable(snomedCodeCoding.getCode()));
}

public String mapCodeableConceptToCdForTransformedActualProblemHeader(CodeableConcept codeableConcept) {
Expand Down Expand Up @@ -343,7 +329,7 @@ private Optional<String> findOriginalText(CodeableConcept codeableConcept, Optio
return Optional.ofNullable(codeableConcept.getText());
} else {
if (coding.get().hasDisplay()) {
return Optional.ofNullable(coding.get().getDisplay());
return getCodingDisplayName(coding.get());
} else {
var extension = retrieveDescriptionExtension(coding.get());
return extension.stream()
Expand All @@ -362,52 +348,27 @@ private Optional<String> findOriginalTextForAllergy(
Optional<Coding> coding,
AllergyIntolerance.AllergyIntoleranceClinicalStatus allergyIntoleranceClinicalStatus
) {
if (!allergyIntoleranceClinicalStatus.toCode().isEmpty()) {
if (RESOLVED_CLINICAL_STATUS.equals(allergyIntoleranceClinicalStatus.toCode())) {
if (coding.isPresent()) {
if (codeableConcept.hasText()) {
return Optional.ofNullable(codeableConcept.getText());
} else {
var extension = retrieveDescriptionExtension(coding.get());
if (extension.isPresent()) {
Optional<String> originalText = extension
.get()
.getExtension().stream()
.filter(displayExtension -> DESCRIPTION_DISPLAY.equals(displayExtension.getUrl()))
.map(extension1 -> extension1.getValue().toString())
.findFirst();

if (originalText.isPresent()) {
return originalText;
} else if (coding.get().hasDisplay()) {
return Optional.ofNullable(coding.get().getDisplay());
}
} else if (coding.get().hasDisplay()) {
return Optional.ofNullable(coding.get().getDisplay());
}
}
}
} else if (ACTIVE_CLINICAL_STATUS.equals(allergyIntoleranceClinicalStatus.toCode())) {
Optional<Extension> extension = retrieveDescriptionExtension(coding.get());
if (extension.isPresent()) {
Optional<String> originalText = extension
.get()
.getExtension().stream()
.filter(displayExtension -> DESCRIPTION_DISPLAY.equals(displayExtension.getUrl()))
.map(extension1 -> extension1.getValue().toString())
.findFirst();
if (originalText.isPresent() && StringUtils.isNotBlank(originalText.get())) {
return originalText;
}
}
if (coding.isEmpty()) {
return Optional.empty();
}

return Optional.empty();
}
if (ACTIVE_CLINICAL_STATUS.equals(allergyIntoleranceClinicalStatus.toCode())) {
return getOriginalTextForActiveAllergy(coding.get());
}

return CodeableConceptMappingUtils.extractTextOrCoding(codeableConcept);
}

private Optional<String> getOriginalTextForActiveAllergy(Coding coding) {
return retrieveDescriptionExtension(coding)
.flatMap(value -> value
.getExtension().stream()
.filter(displayExtension -> DESCRIPTION_DISPLAY.equals(displayExtension.getUrl()))
.map(extension1 -> extension1.getValue().toString())
.findFirst()
);
}

private Optional<String> findDisplayText(Coding coding) {
return Optional.ofNullable(coding.getDisplay());
}
Expand All @@ -420,7 +381,7 @@ private boolean isPrescribingAgency(Coding coding) {
return coding.hasSystem() && coding.getSystem().equals(CARE_CONNECT_PRESCRIBING_AGENCY_SYSTEM);
}

private Optional<Extension> retrieveDescriptionExtension(Coding coding) {
private static Optional<Extension> retrieveDescriptionExtension(Coding coding) {
return coding
.getExtension()
.stream()
Expand All @@ -435,7 +396,6 @@ public String getDisplayFromCodeableConcept(CodeableConcept codeableConcept) {
}

public String mapToNullFlavorCodeableConcept(CodeableConcept codeableConcept) {

var builder = CodeableConceptCdTemplateParameters.builder().nullFlavor(true);
var mainCode = getSnomedCodeCoding(codeableConcept);

Expand All @@ -456,15 +416,6 @@ public String mapToNullFlavorCodeableConceptForAllergy(
return TemplateUtils.fillTemplate(CODEABLE_CONCEPT_CD_TEMPLATE, builder.build());
}

private String buildNullFlavourCodeableConceptCd(CodeableConcept codeableConcept, Optional<Coding> snomedCode) {
var builder = CodeableConceptCdTemplateParameters.builder();
builder.nullFlavor(true);
var originalText = findOriginalText(codeableConcept, snomedCode);
originalText.ifPresent(builder::mainOriginalText);

return TemplateUtils.fillTemplate(CODEABLE_CONCEPT_CD_TEMPLATE, builder.build());
}

private Optional<String> getMainCode(Optional<List<Extension>> descriptionExtensions, Coding snomedCodeCoding) {
if (descriptionExtensions.isPresent()) {
var descriptionCode = descriptionExtensions.get().stream()
Expand Down Expand Up @@ -494,4 +445,4 @@ private Optional<String> getMainDisplayName(Optional<List<Extension>> descriptio

return Optional.ofNullable(snomedCodeCoding.getDisplay());
}
}
}
42 changes: 42 additions & 0 deletions service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapperTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,48 @@ void When_MappingCodeableConceptWithNonSnomedCodeSystems_Expect_ManifestedXmlCon
assertThat(outputMessageXml).isEqualToIgnoringWhitespace(expectedOutputXml);
}

@Test
void When_MapToNullFlavorCodeableConceptForAllergyWithoutSnomedCode_Expect_OriginalTextIsNotPresent() {
var inputJson = """
{
"resourceType": "AllergyIntolerance",
"id": "0C1232CF-D34B-4C16-A5F4-0F6461C51A41",
"meta": {
"profile": [
"https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-AllergyIntolerance-1"
]
},
"identifier": [
{
"system": "https://EMISWeb/A82038",
"value": "55D2363D57A248F49A745B2E03F5E93D0C1232CFD34B4C16A5F40F6461C51A41"
}
],
"code": {
"coding": [
{
"system": "http://read.info/readv2",
"code": "TJ00800",
"display": "Adverse reaction to pivampicillin rt"
}
],
"text": "Adverse reaction to pivampicillin"
}
}""";
var expectedOutputXML = """
<code nullFlavor="UNK">
</code>
""";
var codeableConcept = fhirParseService.parseResource(inputJson, AllergyIntolerance.class).getCode();

var outputXml = codeableConceptCdMapper.mapToNullFlavorCodeableConceptForAllergy(
codeableConcept,
AllergyIntolerance.AllergyIntoleranceClinicalStatus.ACTIVE
);

assertThat(outputXml).isEqualToIgnoringWhitespace(expectedOutputXML);
}

@ParameterizedTest
@MethodSource("getTestArgumentsActualProblem")
public void When_MappingStubbedCodeableConceptForActualProblemHeader_Expect_HL7CdObjectXml(String inputJson, String outputXml)
Expand Down