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NIAD-3304: Add functionality for medication codeable concepts to include non-SNOMEDCT codes #1134

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Merged
MartinWheelerMT merged 2 commits into from
Mar 5, 2025
Merged

NIAD-3304: Add functionality for medication codeable concepts to include non-SNOMEDCT codes #1134

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NIAD-3304: Add functionality for medication codeable concepts to incl…
MartinWheelerMT Mar 3, 2025
c9ded0b
* Remove unnecessary ifPresent check when populating parameters builder
MartinWheelerMT Mar 3, 2025
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40 changes: 19 additions & 21 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 @@ -81,35 +81,33 @@
// we have agreed to use the Concept ID rather than Description Id for medications which will avoided the degradation.
public String mapCodeableConceptForMedication(CodeableConcept codeableConcept) {
var builder = CodeableConceptCdTemplateParameters.builder();
var mainCode = getSnomedCodeCoding(codeableConcept);
var snomedCodeCoding = getSnomedCodeCoding(codeableConcept);

builder.nullFlavor(mainCode.isEmpty());
if (snomedCodeCoding.isEmpty()) {
return buildNullFlavourCodeableConceptCd(codeableConcept, snomedCodeCoding);
}

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

builder.mainCodeSystem(SNOMED_SYSTEM_CODE);
builder.mainCodeSystem(SNOMED_SYSTEM_CODE);

Optional<String> code = Optional.ofNullable(mainCode.get().getCode());
code.ifPresent(builder::mainCode);
Optional<String> code = Optional.ofNullable(snomedCodeCoding.get().getCode());
code.ifPresent(builder::mainCode);

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

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A change can be made to a lambda on line 100 without causing a test to fail 

replaced boolean return with false for 1st lambda in mapCodeableConceptForMedication (covered by 1 tests BooleanFalseReturnValsMutator)
.map(description -> description.getValue().toString())

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replaced return value with "" for 2nd lambda in mapCodeableConceptForMedication (no tests cover this line EmptyObjectReturnValsMutator)
.findFirst()
.or(() -> Optional.ofNullable(snomedCodeCoding.get().getDisplay()));
displayName.ifPresent(builder::mainDisplayName);

if (codeableConcept.hasText()) {
builder.mainOriginalText(codeableConcept.getText());
}
} else {
var originalText = findOriginalText(codeableConcept, mainCode);
originalText.ifPresent(builder::mainOriginalText);
if (codeableConcept.hasText()) {

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2 different changes can be made to line 106 without causing a test to fail 

removed conditional - replaced equality check with true (covered by 47 tests RemoveConditionalMutator_EQUAL_IF)
removed conditional - replaced equality check with false (covered by 47 tests RemoveConditionalMutator_EQUAL_ELSE)
builder.mainOriginalText(codeableConcept.getText());

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removed call to mainOriginalText (no tests cover this line RemoveChainedCallsMutator)
}

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

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4 changes: 3 additions & 1 deletion service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/MedicationStatementMapperTest.java
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Expand Up @@ -131,7 +131,9 @@ private static Stream<Arguments> resourceFileParams() {
Arguments.of("mr-with-extension-status-reason-with-text.json", "medication-statement-with-status-reason-text.xml"),
Arguments.of("mr-with-no-recorder-reference.json", "medication-statement-with-no-participant.xml"),
Arguments.of("mr-with-invalid-recorder-resource-type.json", "medication-statement-with-no-participant.xml"),
Arguments.of("medication-request-special-character-in-code.json", "medication-statement-with-xml-escaped-text-values.xml")
Arguments.of("medication-request-special-character-in-code.json", "medication-statement-with-xml-escaped-text-values.xml"),
Arguments.of("mr-referencing-medication-with-non-snomed-codes.json", "ms-with-material-coding-containing-translations.xml"),
Arguments.of("mr-referencing-medication-with-no-snomed-code.json", "ms-with-material-coding-containing-null-flavor-code.xml")
);
}

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45 changes: 45 additions & 0 deletions service/src/test/resources/ehr/mapper/medication_request/fhir-bundle.json
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Expand Up @@ -22,6 +22,51 @@
}
}
},
{
"resource": {
"resourceType": "Medication",
"id": "21",
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "430127000",
"display": "Oral Form Oxycodone (product)"
},
{
"system": "http://read.info/readv2",
"code": "READ0",
"display": "Display for Read V2"
},
{
"system": "http://read.info/ctv3",
"code": "READ1",
"display": "Display for Read CTV3"
}
]
}
}
},
{
"resource": {
"resourceType": "Medication",
"id": "22",
"code": {
"coding": [
{
"system": "http://read.info/readv2",
"code": "READ0",
"display": "Display for Read V2"
},
{
"system": "http://read.info/ctv3",
"code": "READ1",
"display": "Display for Read CTV3"
}
]
}
}
},
{
"resource": {
"resourceType":"MedicationRequest",
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59 changes: 59 additions & 0 deletions ...esources/ehr/mapper/medication_request/mr-referencing-medication-with-no-snomed-code.json
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@@ -0,0 +1,59 @@
{
"resourceType":"MedicationRequest",
"id":"3377543D-5B1B-4C4F-BFF6-9F7BC3A1C3B8",
"meta":{
"profile":[
"https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-MedicationRequest-1"
]
},
"extension":[
{
"url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-MedicationRepeatInformation-1",
"extension": [
{
"url": "numberOfRepeatPrescriptionsAllowed",
"valuePositiveInt": 12
},
{
"url": "numberOfRepeatPrescriptionsIssued",
"valuePositiveInt": 11
}
]
}
],
"identifier":[
{
"system":"https://fhir.nhs.uk/Id/cross-care-setting-identifier",
"value":"f2489066-7082-11eb-bb13-00505692d4aa"
}
],
"status":"active",
"intent":"order",
"medicationReference":{
"reference":"Medication/22"
},
"subject":{
"reference":"Patient/2"
},
"authoredOn":"2017-11-10T00:00:00+00:00",
"recorder":{
"reference":"Practitioner/1"
},
"dosageInstruction":[
{
"text":"1 tablet once a day",
"patientInstruction":"Take in morning"
}
],
"dispenseRequest":{
"validityPeriod":{
"start":"2017-11-10T00:00:00+00:00",
"end":"2018-08-15T00:00:00+01:00"
}
},
"basedOn": [
{
"reference": "MedicationRequest/D66D84C9-C073-4EDF-8C2C-F309A83C3DC7"
}
]
}
59 changes: 59 additions & 0 deletions ...ources/ehr/mapper/medication_request/mr-referencing-medication-with-non-snomed-codes.json
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@@ -0,0 +1,59 @@
{
"resourceType":"MedicationRequest",
"id":"3377543D-5B1B-4C4F-BFF6-9F7BC3A1C3B8",
"meta":{
"profile":[
"https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-MedicationRequest-1"
]
},
"extension":[
{
"url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-MedicationRepeatInformation-1",
"extension": [
{
"url": "numberOfRepeatPrescriptionsAllowed",
"valuePositiveInt": 12
},
{
"url": "numberOfRepeatPrescriptionsIssued",
"valuePositiveInt": 11
}
]
}
],
"identifier":[
{
"system":"https://fhir.nhs.uk/Id/cross-care-setting-identifier",
"value":"f2489066-7082-11eb-bb13-00505692d4aa"
}
],
"status":"active",
"intent":"order",
"medicationReference":{
"reference":"Medication/21"
},
"subject":{
"reference":"Patient/2"
},
"authoredOn":"2017-11-10T00:00:00+00:00",
"recorder":{
"reference":"Practitioner/1"
},
"dosageInstruction":[
{
"text":"1 tablet once a day",
"patientInstruction":"Take in morning"
}
],
"dispenseRequest":{
"validityPeriod":{
"start":"2017-11-10T00:00:00+00:00",
"end":"2018-08-15T00:00:00+01:00"
}
},
"basedOn": [
{
"reference": "MedicationRequest/D66D84C9-C073-4EDF-8C2C-F309A83C3DC7"
}
]
}
52 changes: 52 additions & 0 deletions ...ces/ehr/mapper/medication_request/ms-with-material-coding-containing-null-flavor-code.xml
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@@ -0,0 +1,52 @@
<component typeCode="COMP">
<MedicationStatement classCode="SBADM" moodCode="ORD">
<id root="394559384658936"/>
<statusCode code="ACTIVE"/>
<effectiveTime>
<low value="20171110000000"/><high value="20180815000000"/>
</effectiveTime>
<availabilityTime value="20171110000000"/>
<consumable typeCode="CSM">
<manufacturedProduct classCode="MANU">
<manufacturedMaterial determinerCode="KIND" classCode="MMAT">
<code nullFlavor="UNK">
<originalText>Display for Read V2</originalText>
</code>
</manufacturedMaterial>
</manufacturedProduct>
</consumable>
<component typeCode="COMP">
<ehrSupplyPrescribe>
<id root="394559384658936"/>
<code code="394823007" displayName="NHS Prescription" codeSystem="2.16.840.1.113883.2.1.3.2.4.15"/>
<statusCode code="ACTIVE"/>
<availabilityTime value="20171110000000"/>
<quantity value="1" unit="1">
<translation value="1">
<originalText>Unk UoM</originalText>
</translation>
</quantity>
<inFulfillmentOf typeCode="FLFS">
<priorMedicationRef moodCode="INT">
<id root="394559384658936"/>
</priorMedicationRef>
</inFulfillmentOf>
<pertinentInformation typeCode="PERT">
<pertinentSupplyAnnotation>
<text>Patient Instruction: Take in morning</text>
</pertinentSupplyAnnotation>
</pertinentInformation>
</ehrSupplyPrescribe>
</component>
<pertinentInformation typeCode="PERT">
<pertinentMedicationDosage classCode="SBADM" moodCode="RMD">
<text>1 tablet once a day</text>
</pertinentMedicationDosage>
</pertinentInformation>
<Participant typeCode="AUT" contextControlCode="OP">
<agentRef classCode="AGNT">
<id root="394559384658936"/>
</agentRef>
</Participant>
</MedicationStatement>
</component>
53 changes: 53 additions & 0 deletions ...sources/ehr/mapper/medication_request/ms-with-material-coding-containing-translations.xml
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<component typeCode="COMP">
<MedicationStatement classCode="SBADM" moodCode="ORD">
<id root="394559384658936"/>
<statusCode code="ACTIVE"/>
<effectiveTime>
<low value="20171110000000"/><high value="20180815000000"/>
</effectiveTime>
<availabilityTime value="20171110000000"/>
<consumable typeCode="CSM">
<manufacturedProduct classCode="MANU">
<manufacturedMaterial determinerCode="KIND" classCode="MMAT">
<code code="430127000" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Oral Form Oxycodone (product)">
<translation code="READ0" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Display for Read V2" />
<translation code="READ1" codeSystem="2.16.840.1.113883.2.1.3.2.4.14" displayName="Display for Read CTV3" />
</code>
</manufacturedMaterial>
</manufacturedProduct>
</consumable>
<component typeCode="COMP">
<ehrSupplyPrescribe>
<id root="394559384658936"/>
<code code="394823007" displayName="NHS Prescription" codeSystem="2.16.840.1.113883.2.1.3.2.4.15"/>
<statusCode code="ACTIVE"/>
<availabilityTime value="20171110000000"/>
<quantity value="1" unit="1">
<translation value="1">
<originalText>Unk UoM</originalText>
</translation>
</quantity>
<inFulfillmentOf typeCode="FLFS">
<priorMedicationRef moodCode="INT">
<id root="394559384658936"/>
</priorMedicationRef>
</inFulfillmentOf>
<pertinentInformation typeCode="PERT">
<pertinentSupplyAnnotation>
<text>Patient Instruction: Take in morning</text>
</pertinentSupplyAnnotation>
</pertinentInformation>
</ehrSupplyPrescribe>
</component>
<pertinentInformation typeCode="PERT">
<pertinentMedicationDosage classCode="SBADM" moodCode="RMD">
<text>1 tablet once a day</text>
</pertinentMedicationDosage>
</pertinentInformation>
<Participant typeCode="AUT" contextControlCode="OP">
<agentRef classCode="AGNT">
<id root="394559384658936"/>
</agentRef>
</Participant>
</MedicationStatement>
</component>