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NIAD-3304: Allow non-SNOMEDCT codes to be preserved when mapping CodeableConcepts #1133

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Merged
MartinWheelerMT merged 4 commits into from
Mar 3, 2025
Merged

NIAD-3304: Allow non-SNOMEDCT codes to be preserved when mapping CodeableConcepts #1133

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1079b76
NIAD-3304: Add non-snomed code mapping to translations when mapping `…
MartinWheelerMT Mar 3, 2025
03ee4a4
* Update ObservationMapperTest XML files to reflect that Read V2 code…
MartinWheelerMT Mar 3, 2025
e1dac86
* Remove unnecessary null checks when populating builder parameters.
MartinWheelerMT Mar 3, 2025
1fcce06
* SonarCube recommended fix: Remove useless assignment to local varia…
MartinWheelerMT Mar 3, 2025
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63 changes: 39 additions & 24 deletions service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapper.java
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Expand Up @@ -17,6 +17,7 @@
import lombok.RequiredArgsConstructor;
import lombok.extern.slf4j.Slf4j;
import uk.nhs.adaptors.gp2gp.ehr.mapper.parameters.CodeableConceptCdTemplateParameters;
import uk.nhs.adaptors.gp2gp.ehr.utils.CodeSystemsUtil;
import uk.nhs.adaptors.gp2gp.ehr.utils.CodeableConceptMappingUtils;
import uk.nhs.adaptors.gp2gp.ehr.utils.TemplateUtils;

Expand Down Expand Up @@ -63,17 +64,14 @@ public String mapCodeableConceptToCd(CodeableConcept codeableConcept) {

builder.mainCodeSystem(SNOMED_SYSTEM_CODE);

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

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

if (codeableConcept.hasText()) {
builder.mainOriginalText(codeableConcept.getText());
}
}
builder.mainOriginalText(codeableConcept.getText());
builder.translations(getNonSnomedCodeCodings(codeableConcept));

return TemplateUtils.fillTemplate(CODEABLE_CONCEPT_CD_TEMPLATE, builder.build());
}
Expand Down Expand Up @@ -329,6 +327,20 @@ private Optional<Coding> getSnomedCodeCoding(CodeableConcept codeableConcept) {
.findFirst();
}

private List<Coding> getNonSnomedCodeCodings(CodeableConcept codeableConcept) {
var nonSnomedCodeCodings = codeableConcept.getCoding()
.stream()
.filter(coding -> !isSnomed(coding))
.toList();

for (Coding coding : nonSnomedCodeCodings) {
var hl7CodeSystem = CodeSystemsUtil.getHl7code(coding.getSystem());
coding.setSystem(hl7CodeSystem);
}

return nonSnomedCodeCodings;
}

private Optional<String> findOriginalText(CodeableConcept codeableConcept, Optional<Coding> coding) {
if (coding.isPresent()) {
if (codeableConcept.hasText()) {
Expand Down Expand Up @@ -457,30 +469,33 @@ private String buildNullFlavourCodeableConceptCd(CodeableConcept codeableConcept
return TemplateUtils.fillTemplate(CODEABLE_CONCEPT_CD_TEMPLATE, builder.build());
}

private Optional<String> getMainCode(List<Extension> descriptionExtensions, Coding snomedCodeCoding) {
var descriptionCode = descriptionExtensions.stream()
.filter(descriptionExt -> DESCRIPTION_ID.equals(descriptionExt.getUrl()))
.map(description -> description.getValue().toString())
.findFirst();
private Optional<String> getMainCode(Optional<List<Extension>> descriptionExtensions, Coding snomedCodeCoding) {
if (descriptionExtensions.isPresent()) {
var descriptionCode = descriptionExtensions.get().stream()
.filter(descriptionExt -> DESCRIPTION_ID.equals(descriptionExt.getUrl()))
.map(description -> description.getValue().toString())
.findFirst();

if (descriptionCode.isPresent()) {
return descriptionCode;
if (descriptionCode.isPresent()) {
return descriptionCode;
}
}

return Optional.ofNullable(snomedCodeCoding.getCode());
}

private Optional<String> getMainDisplayName(List<Extension> descriptionExtensions, Coding snomedCodeCoding) {
var descriptionDisplayName = descriptionExtensions.stream()
.filter(descriptionExt -> DESCRIPTION_DISPLAY.equals(descriptionExt.getUrl()))
.map(description -> description.getValue().toString())
.findFirst();
private Optional<String> getMainDisplayName(Optional<List<Extension>> descriptionExtensions, Coding snomedCodeCoding) {
if (descriptionExtensions.isPresent()) {
var descriptionDisplayName = descriptionExtensions.get().stream()
.filter(descriptionExt -> DESCRIPTION_DISPLAY.equals(descriptionExt.getUrl()))
.map(description -> description.getValue().toString())
.findFirst();

if (descriptionDisplayName.isPresent()) {
return descriptionDisplayName;
if (descriptionDisplayName.isPresent()) {
return descriptionDisplayName;
}
}

return Optional.ofNullable(snomedCodeCoding.getDisplay());
}

}
4 changes: 4 additions & 0 deletions ...java/uk/nhs/adaptors/gp2gp/ehr/mapper/parameters/CodeableConceptCdTemplateParameters.java
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Expand Up @@ -3,6 +3,9 @@
import lombok.Builder;
import lombok.Getter;
import lombok.Setter;
import org.hl7.fhir.dstu3.model.Coding;

import java.util.List;

@Getter
@Setter
Expand All @@ -12,5 +15,6 @@ public class CodeableConceptCdTemplateParameters {
private String mainCodeSystem;
private String mainDisplayName;
private String mainOriginalText;
private List<Coding> translations;
private boolean nullFlavor;
}
3 changes: 3 additions & 0 deletions service/src/main/resources/templates/codeable_concept_cd_template.mustache
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@@ -1,4 +1,7 @@
<code{{#nullFlavor}} nullFlavor="UNK"{{/nullFlavor}}{{^nullFlavor}} code="{{mainCode}}" codeSystem="{{mainCodeSystem}}" displayName="{{mainDisplayName}}"{{/nullFlavor}}>
{{#translations}}
<translation code="{{code}}" codeSystem="{{system}}" displayName="{{display}}" />
{{/translations}}
{{#mainOriginalText}}
<originalText>{{mainOriginalText}}</originalText>
{{/mainOriginalText}}
Expand Down
37 changes: 37 additions & 0 deletions service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapperTest.java
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Expand Up @@ -85,6 +85,43 @@ public void When_MappingStubbedCodeableConcept_Expect_HL7CdObjectXml(String inpu
.isEqualToIgnoringWhitespace(expectedOutput);
}

@Test
void When_MappingCodeableConceptWithNonSnomedCodeSystems_Expect_ManifestedXmlContainsTranslationsForThoseCodes() {
var inputJson = """
{
"resourceType" : "Observation",
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "123456",
"display": "Endometriosis of uterus"
},
{
"system": "http://read.info/readv2",
"code": "READ0",
"display": "Read V2 Code Display"
},
{
"system": "http://read.info/ctv3",
"code": "READ1",
"display": "Read CTV3 Code Display"
}
]
}
}""";
var expectedOutputXml = """
<code code="123456" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Endometriosis of uterus">
<translation code="READ0" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Read V2 Code Display" />
<translation code="READ1" codeSystem="2.16.840.1.113883.2.1.3.2.4.14" displayName="Read CTV3 Code Display" />
</code>""";
var codeableConcept = fhirParseService.parseResource(inputJson, Observation.class).getCode();

var outputMessageXml = codeableConceptCdMapper.mapCodeableConceptToCd(codeableConcept);

assertThat(outputMessageXml).isEqualToIgnoringWhitespace(expectedOutputXml);
}

@ParameterizedTest
@MethodSource("getTestArgumentsActualProblem")
public void When_MappingStubbedCodeableConceptForActualProblemHeader_Expect_HL7CdObjectXml(String inputJson, String outputXml)
Expand Down
6 changes: 0 additions & 6 deletions ...c/test/resources/ehr/mapper/codeableconcept/codeable_concept_snomed_with_description.json
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Expand Up @@ -2,12 +2,6 @@
"resourceType" : "Observation",
"code": {
"coding": [
{
"system": "http://blah.info/blahsomecodesystem",
"code": "X%^^%",
"display": "Display for invalid code/system",
"userSelected": true
},
{
"extension": [
{
Expand Down
6 changes: 0 additions & 6 deletions ...est/resources/ehr/mapper/codeableconcept/codeable_concept_snomed_with_no_description.json
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Expand Up @@ -2,12 +2,6 @@
"resourceType" : "Observation",
"code": {
"coding": [
{
"system": "http://blah.info/blahsomecodesystem",
"code": "X%^^%",
"display": "Display for invalid code/system",
"userSelected": true
},
{
"extension": [
{
Expand Down
6 changes: 0 additions & 6 deletions service/src/test/resources/ehr/mapper/codeableconcept/codeable_concept_with_text.json
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Expand Up @@ -2,12 +2,6 @@
"resourceType" : "Observation",
"code": {
"coding": [
{
"system": "http://blah.info/blahsomecodesystem",
"code": "X%^^%",
"display": "Display for invalid code/system",
"userSelected": true
},
{
"extension": [
{
Expand Down
7 changes: 1 addition & 6 deletions service/src/test/resources/ehr/mapper/codeableconcept/codeable_concept_without_text.json
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Expand Up @@ -2,12 +2,7 @@
"resourceType" : "Observation",
"code": {
"coding": [
{
"system": "http://blah.info/blahsomecodesystem",
"code": "F%^^%",
"display": "Happy puppet syndrome",
"userSelected": true
}, {
{
"extension": [
{
"url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-coding-sctdescid",
Expand Down
6 changes: 4 additions & 2 deletions ...st/resources/ehr/mapper/diagnosticreport/observation/observation_compound_statement_1.xml
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Expand Up @@ -2,7 +2,8 @@
<CompoundStatement classCode="CLUSTER" moodCode="EVN">
<id root="Mapped-From-Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2"/>
<code code="2564081000000118" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Urine pregnancy test">
</code>
<translation code="465..00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Urine pregnancy test" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand All @@ -12,7 +13,8 @@
<ObservationStatement classCode="OBS" moodCode="EVN">
<id root="random-unmapped-id"/>
<code code="2564081000000118" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Urine pregnancy test">
</code>
<translation code="465..00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Urine pregnancy test" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand Down
6 changes: 4 additions & 2 deletions ...er/diagnosticreport/observation/observation_compound_statement_1_with_related_comment.xml
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Expand Up @@ -2,7 +2,8 @@
<CompoundStatement classCode="CLUSTER" moodCode="EVN">
<id root="Mapped-From-Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2"/>
<code code="2564081000000118" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Urine pregnancy test">
</code>
<translation code="465..00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Urine pregnancy test" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand All @@ -12,7 +13,8 @@
<ObservationStatement classCode="OBS" moodCode="EVN">
<id root="random-unmapped-id"/>
<code code="2564081000000118" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Urine pregnancy test">
</code>
<translation code="465..00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Urine pregnancy test" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand Down
6 changes: 4 additions & 2 deletions ...st/resources/ehr/mapper/diagnosticreport/observation/observation_compound_statement_2.xml
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Expand Up @@ -2,7 +2,8 @@
<CompoundStatement classCode="CLUSTER" moodCode="EVN">
<id root="Mapped-From-Observation/6E30A9E3-FF9A-4868-8FCD-7DAC26A16E78"/>
<code code="2551971000000110" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Serum oestradiol level">
</code>
<translation code="4465.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Serum oestradiol level" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand All @@ -12,7 +13,8 @@
<ObservationStatement classCode="OBS" moodCode="EVN">
<id root="random-unmapped-id"/>
<code code="2551971000000110" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Serum oestradiol level">
</code>
<translation code="4465.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Serum oestradiol level" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand Down
6 changes: 4 additions & 2 deletions ...st/resources/ehr/mapper/diagnosticreport/observation/observation_compound_statement_3.xml
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Expand Up @@ -2,7 +2,8 @@
<CompoundStatement classCode="CLUSTER" moodCode="EVN">
<id root="Mapped-From-Observation/D0A358C9-4833-4827-B14B-E8515C25CB12"/>
<code code="2563401000000119" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Serum ACTH (adrenocorticotrophic hormone) level">
</code>
<translation code="4483.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Serum ACTH" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand All @@ -12,7 +13,8 @@
<ObservationStatement classCode="OBS" moodCode="EVN">
<id root="random-unmapped-id"/>
<code code="2563401000000119" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Serum ACTH (adrenocorticotrophic hormone) level">
</code>
<translation code="4483.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Serum ACTH" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand Down
6 changes: 4 additions & 2 deletions ...rt/observation/observation_compound_statement_clustered_by_diagnosticreport_reference.xml
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Expand Up @@ -2,7 +2,8 @@
<CompoundStatement classCode="CLUSTER" moodCode="EVN">
<id root="random-unmapped-id"/>
<code code="257472014" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="International normalised ratio">
</code>
<translation code="42QE.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="International normalised ratio" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand All @@ -12,7 +13,8 @@
<ObservationStatement classCode="OBS" moodCode="EVN">
<id root="random-unmapped-id"/>
<code code="257472014" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="International normalised ratio">
</code>
<translation code="42QE.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="International normalised ratio" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand Down
6 changes: 4 additions & 2 deletions ...bservation/observation_compound_statement_with_availabilitytime_and_low_effectivetime.xml
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Expand Up @@ -2,7 +2,8 @@
<CompoundStatement classCode="CLUSTER" moodCode="EVN">
<id root="Mapped-From-Observation/6E30A9E3-FF9A-4868-8FCD-7DAC26A16E78"/>
<code code="2551971000000110" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Serum oestradiol level">
</code>
<translation code="4465.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Serum oestradiol level" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<low value="19971020"/>
Expand All @@ -12,7 +13,8 @@
<ObservationStatement classCode="OBS" moodCode="EVN">
<id root="random-unmapped-id"/>
<code code="2551971000000110" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Serum oestradiol level">
</code>
<translation code="4465.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Serum oestradiol level" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<low value="19971020"/>
Expand Down
3 changes: 3 additions & 0 deletions .../diagnosticreport/observation/observation_compound_statement_with_battery_test_result.xml
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Expand Up @@ -2,6 +2,7 @@
<CompoundStatement classCode="BATTERY" moodCode="EVN">
<id root="Mapped-From-Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2"/>
<code code="2564081000000118" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Urine pregnancy test">
<translation code="465..00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Urine pregnancy test" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
Expand All @@ -12,6 +13,7 @@
<CompoundStatement classCode="CLUSTER" moodCode="EVN">
<id root="random-unmapped-id"/>
<code code="2551971000000110" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Serum oestradiol level">
<translation code="4465.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Serum oestradiol level" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
Expand All @@ -22,6 +24,7 @@
<ObservationStatement classCode="OBS" moodCode="EVN">
<id root="Mapped-From-Observation/TestResult-WithRelatedMember-WhichIsntAFilingComment"/>
<code code="2551971000000110" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Serum oestradiol level">
<translation code="4465.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Serum oestradiol level" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
Expand Down
6 changes: 4 additions & 2 deletions ...ompound_statement_with_data_absent_reason_and_interpretation_and_body_site_and_method.xml
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Expand Up @@ -2,7 +2,8 @@
<CompoundStatement classCode="CLUSTER" moodCode="EVN">
<id root="Mapped-From-Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2"/>
<code code="2564081000000118" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Urine pregnancy test">
</code>
<translation code="465..00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Urine pregnancy test" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand All @@ -12,7 +13,8 @@
<ObservationStatement classCode="OBS" moodCode="EVN">
<id root="random-unmapped-id"/>
<code code="2564081000000118" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Urine pregnancy test">
</code>
<translation code="465..00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Urine pregnancy test" />
</code>
<statusCode code="COMPLETE"/>
<effectiveTime>
<center value="20100223"/>
Expand Down
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