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

Add unit tests for mapping allergy codeable concepts #1135

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d61949d
Add unit tests for mapping allergy codeable concepts
MartinWheelerMT Mar 4, 2025
1a7c71d
* Remove public modifier for new tests.
MartinWheelerMT Mar 4, 2025
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32 changes: 26 additions & 6 deletions service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapperTest.java
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Expand Up @@ -24,7 +24,8 @@ public class CodeableConceptCdMapperTest {
private static final String TEST_FILE_DIRECTORY = "/ehr/mapper/codeableconcept/";
private static final String TEST_FILE_DIRECTORY_NULL_FLAVOR = "/ehr/mapper/codeableconcept/nullFlavor/";
private static final String TEST_FILE_DIRECTORY_ACTUAL_PROBLEM = "/ehr/mapper/codeableconcept/actualProblem/";
private static final String TEST_FILE_DIRECTORY_ALLERGY_CLINICAL_STATUS = "/ehr/mapper/codeableconcept/allergyClinicalStatus/";
private static final String TEST_FILE_DIRECTORY_ALLERGY_RESOLVED = "/ehr/mapper/codeableconcept/allergyResolved/";
private static final String TEST_FILE_DIRECTORY_ALLERGY_ACTIVE = "/ehr/mapper/codeableconcept/allergyActive/";
private static final String TEST_FILE_DIRECTORY_MEDICATION = "/ehr/mapper/codeableconcept/medication/";

private static final String TEST_FILE_TOPIC_RELATED_CONDITION = TEST_FILE_DIRECTORY
Expand Down Expand Up @@ -54,8 +55,12 @@ private static Stream<Arguments> getTestArgumentsActualProblem() {
return TestArgumentsLoaderUtil.readTestCases(TEST_FILE_DIRECTORY_ACTUAL_PROBLEM);
}

private static Stream<Arguments> getTestArgumentsAllergyClinicalStatus() {
return TestArgumentsLoaderUtil.readTestCases(TEST_FILE_DIRECTORY_ALLERGY_CLINICAL_STATUS);
private static Stream<Arguments> getTestArgumentsAllergyResolved() {
return TestArgumentsLoaderUtil.readTestCases(TEST_FILE_DIRECTORY_ALLERGY_RESOLVED);
}

private static Stream<Arguments> getTestArgumentsAllergyActive() {
return TestArgumentsLoaderUtil.readTestCases(TEST_FILE_DIRECTORY_ALLERGY_ACTIVE);
}

private static Stream<Arguments> getTestArgumentsMedication() {
Expand Down Expand Up @@ -151,15 +156,30 @@ public void When_MappingStubbedCodeableConceptAsNullFlavor_Expect_HL7CdObjectXml
}

@ParameterizedTest
@MethodSource("getTestArgumentsAllergyClinicalStatus")
public void When_MappingStubbedCodeableConceptAsAllergy_Expect_HL7CdObjectXml(String inputJson, String outputXml)
throws IOException {
@MethodSource("getTestArgumentsAllergyResolved")
void When_MappingStubbedCodeableConceptAsResolvedAllergy_Expect_HL7CdObjectXml(String inputJson, String outputXml) {
var allergyCodeableConcept = ResourceTestFileUtils.getFileContent(inputJson);
var expectedOutput = ResourceTestFileUtils.getFileContent(outputXml);
var codeableConcept = fhirParseService.parseResource(allergyCodeableConcept, AllergyIntolerance.class).getCode();

var outputMessage = codeableConceptCdMapper.mapCodeableConceptToCdForAllergy(codeableConcept,
AllergyIntolerance.AllergyIntoleranceClinicalStatus.RESOLVED);

assertThat(outputMessage)
.describedAs(TestArgumentsLoaderUtil.FAIL_MESSAGE, inputJson, outputXml)
.isEqualToIgnoringWhitespace(expectedOutput);
}

@ParameterizedTest
@MethodSource("getTestArgumentsAllergyActive")
void When_MappingStubbedCodeableConceptAsActiveAllergy_Expect_HL7CdObjectXml(String inputJson, String outputXml) {
var allergyCodeableConcept = ResourceTestFileUtils.getFileContent(inputJson);
var expectedOutput = ResourceTestFileUtils.getFileContent(outputXml);
var codeableConcept = fhirParseService.parseResource(allergyCodeableConcept, AllergyIntolerance.class).getCode();

var outputMessage = codeableConceptCdMapper.mapCodeableConceptToCdForAllergy(codeableConcept,
AllergyIntolerance.AllergyIntoleranceClinicalStatus.ACTIVE);

assertThat(outputMessage)
.describedAs(TestArgumentsLoaderUtil.FAIL_MESSAGE, inputJson, outputXml)
.isEqualToIgnoringWhitespace(expectedOutput);
Expand Down
16 changes: 7 additions & 9 deletions ...Status/codeable_concept_with_allergy.json → ..._both_description_extensions_no_text.json
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Expand Up @@ -19,27 +19,25 @@
],
"code": {
"coding": [
{
"system": "http://read.info/readv2",
"code": "TJ00800",
"display": "Adverse reaction to pivampicillin rt",
"userSelected": true
},
{
"extension": [
{
"url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-coding-sctdescid",
"extension": [
{
"url": "descriptionId",
"valueId": "2164497013"
"valueId": "442108015"
},
{
"url": "descriptionDisplay",
"valueString": "Chocolate allergy"
}
]
}
],
"system": "http://snomed.info/sct",
"code": "292971006",
"display": "Pivampicillin adverse reaction pt"
"code": "300912001",
"display": "Allergy to chocolate"
}
]
},
Expand Down
3 changes: 3 additions & 0 deletions ...mapper/codeableconcept/allergyActive/allergy_with_both_description_extensions_no_text.xml
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@@ -0,0 +1,3 @@
<code code="442108015" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Allergy to chocolate">
<originalText>Chocolate allergy</originalText>
</code>
52 changes: 52 additions & 0 deletions ...pper/codeableconcept/allergyActive/allergy_with_only_descriptionId_extension_no_text.json
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@@ -0,0 +1,52 @@
{
"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"
}
],
"clinicalStatus": "resolved",
"verificationStatus": "unconfirmed",
"category": [
"medication"
],
"code": {
"coding": [
{
"extension": [
{
"url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-coding-sctdescid",
"extension": [
{
"url": "descriptionId",
"valueId": "442108015"
}
]
}
],
"system": "http://snomed.info/sct",
"code": "300912001",
"display": "Allergy to chocolate"
}
]
},
"patient": {
"reference": "Patient/55D2363D-57A2-48F4-9A74-5B2E03F5E93D"
},
"assertedDate": "2019-01-28T13:43:36.107+00:00",
"recorder": {
"reference": "Practitioner/2DB481A3-306A-4133-9491-1558161D6A2B"
},
"note": [
{
"text": "allergy with no date recorded"
}
]
}
2 changes: 2 additions & 0 deletions ...apper/codeableconcept/allergyActive/allergy_with_only_descriptionId_extension_no_text.xml
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@@ -0,0 +1,2 @@
<code code="442108015" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Allergy to chocolate">
</code>
53 changes: 53 additions & 0 deletions ...er/codeableconcept/allergyActive/allergy_with_only_descriptionId_extension_with_text.json
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@@ -0,0 +1,53 @@
{
"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"
}
],
"clinicalStatus": "resolved",
"verificationStatus": "unconfirmed",
"category": [
"medication"
],
"code": {
"coding": [
{
"extension": [
{
"url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-coding-sctdescid",
"extension": [
{
"url": "descriptionId",
"valueId": "442108015"
}
]
}
],
"system": "http://snomed.info/sct",
"code": "300912001",
"display": "Allergy to chocolate"
}
],
"text": "Chocolate Allergy"
},
"patient": {
"reference": "Patient/55D2363D-57A2-48F4-9A74-5B2E03F5E93D"
},
"assertedDate": "2019-01-28T13:43:36.107+00:00",
"recorder": {
"reference": "Practitioner/2DB481A3-306A-4133-9491-1558161D6A2B"
},
"note": [
{
"text": "allergy with no date recorded"
}
]
}
3 changes: 3 additions & 0 deletions ...per/codeableconcept/allergyActive/allergy_with_only_descriptionId_extension_with_text.xml
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@@ -0,0 +1,3 @@
<code code="442108015" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Allergy to chocolate">
<originalText>Chocolate Allergy</originalText>
</code>
41 changes: 41 additions & 0 deletions ...esources/ehr/mapper/codeableconcept/allergyActive/allergy_without_extensions_no_text.json
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@@ -0,0 +1,41 @@
{
"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"
}
],
"clinicalStatus": "resolved",
"verificationStatus": "unconfirmed",
"category": [
"medication"
],
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "292971006",
"display": "Pivampicillin adverse reaction pt"
}
]
},
"patient": {
"reference": "Patient/55D2363D-57A2-48F4-9A74-5B2E03F5E93D"
},
"assertedDate": "2019-01-28T13:43:36.107+00:00",
"recorder": {
"reference": "Practitioner/2DB481A3-306A-4133-9491-1558161D6A2B"
},
"note": [
{
"text": "allergy with no date recorded"
}
]
}
2 changes: 2 additions & 0 deletions ...resources/ehr/mapper/codeableconcept/allergyActive/allergy_without_extensions_no_text.xml
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@@ -0,0 +1,2 @@
<code code="292971006" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Pivampicillin adverse reaction pt">
</code>
42 changes: 42 additions & 0 deletions ...ources/ehr/mapper/codeableconcept/allergyActive/allergy_without_extensions_with_text.json
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@@ -0,0 +1,42 @@
{
"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"
}
],
"clinicalStatus": "resolved",
"verificationStatus": "unconfirmed",
"category": [
"medication"
],
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "292971006",
"display": "Pivampicillin adverse reaction pt"
}
],
"text": "Pivampicillin adverse reaction"
},
"patient": {
"reference": "Patient/55D2363D-57A2-48F4-9A74-5B2E03F5E93D"
},
"assertedDate": "2019-01-28T13:43:36.107+00:00",
"recorder": {
"reference": "Practitioner/2DB481A3-306A-4133-9491-1558161D6A2B"
},
"note": [
{
"text": "allergy with no date recorded"
}
]
}
3 changes: 3 additions & 0 deletions ...sources/ehr/mapper/codeableconcept/allergyActive/allergy_without_extensions_with_text.xml
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@@ -0,0 +1,3 @@
<code code="292971006" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Pivampicillin adverse reaction pt">
<originalText>Pivampicillin adverse reaction</originalText>
</code>
40 changes: 40 additions & 0 deletions ...r/mapper/codeableconcept/allergyActive/allergy_without_snomed_code_in_coding_no_text.json
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@@ -0,0 +1,40 @@
{
"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"
}
],
"clinicalStatus": "resolved",
"verificationStatus": "unconfirmed",
"category": [ "medication" ],
"code": {
"coding": [
{
"system": "http://read.info/readv2",
"code": "TJ00800",
"display": "Adverse reaction to pivampicillin rt",
"userSelected": true
}
]
},
"patient": {
"reference": "Patient/55D2363D-57A2-48F4-9A74-5B2E03F5E93D"
},
"assertedDate": "2019-01-28T13:43:36.107+00:00",
"recorder": {
"reference": "Practitioner/2DB481A3-306A-4133-9491-1558161D6A2B"
},
"note": [
{
"text": "allergy with no date recorded"
}
]
}
2 changes: 2 additions & 0 deletions ...hr/mapper/codeableconcept/allergyActive/allergy_without_snomed_code_in_coding_no_text.xml
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@@ -0,0 +1,2 @@
<code nullFlavor="UNK">
</code>
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