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MartinWheelerMTMartinWheelerMT
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Testing PR (Do not merge)
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‎service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapper.java‎

Lines changed: 14 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,6 @@
1818
import lombok.RequiredArgsConstructor;
1919
import lombok.extern.slf4j.Slf4j;
2020
import uk.nhs.adaptors.gp2gp.ehr.mapper.parameters.CodeableConceptCdTemplateParameters;
21-
import uk.nhs.adaptors.gp2gp.ehr.utils.CodeSystemsUtil;
2221
import uk.nhs.adaptors.gp2gp.ehr.utils.CodeableConceptMappingUtils;
2322
import uk.nhs.adaptors.gp2gp.ehr.utils.TemplateUtils;
2423

@@ -311,17 +310,20 @@ private Optional<Coding> getSnomedCodeCoding(CodeableConcept codeableConcept) {
311310
}
312311

313312
private List<Coding> getNonSnomedCodeCodings(CodeableConcept codeableConcept) {
314-
var nonSnomedCodeCodings = codeableConcept.getCoding()
315-
.stream()
316-
.filter(coding -> !isSnomed(coding))
317-
.toList();
318-
319-
for (Coding coding : nonSnomedCodeCodings) {
320-
var hl7CodeSystem = CodeSystemsUtil.getHl7code(coding.getSystem());
321-
coding.setSystem(hl7CodeSystem);
322-
}
323-
324-
return nonSnomedCodeCodings;
313+
return List.of();
314+
//
315+
// var nonSnomedCodeCodings = codeableConcept.getCoding()
316+
// .stream()
317+
// .filter(coding -> !isSnomed(coding))
318+
// .filter(coding -> !CodeSystemsUtil.getHl7code(coding.getSystem()).isEmpty())
319+
// .toList();
320+
//
321+
// for (Coding coding : nonSnomedCodeCodings) {
322+
// var hl7CodeSystem = CodeSystemsUtil.getHl7code(coding.getSystem());
323+
// coding.setSystem(hl7CodeSystem);
324+
// }
325+
//
326+
// return nonSnomedCodeCodings;
325327
}
326328

327329
private Optional<String> findOriginalText(CodeableConcept codeableConcept, Optional<Coding> coding) {

‎service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/BloodPressureMapperTest.java‎

Lines changed: 19 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -170,25 +170,25 @@ private static Stream<Arguments> testArguments() {
170170
);
171171
}
172172

173-
@Test
174-
public void When_MappingBloodPressureWithCodeableConcepts_Expect_CompoundStatementXmlReturned() {
175-
when(randomIdGeneratorService.createNewOrUseExistingUUID(any()))
176-
.thenReturn("5E496953-065B-41F2-9577-BE8F2FBD0757");
177-
178-
var jsonInput = ResourceTestFileUtils.getFileContent(BLOOD_PRESSURE_FILE_LOCATION + INPUT_BLOOD_PRESSURE_WITH_CODEABLE_CONCEPTS);
179-
var expectedOutput = ResourceTestFileUtils.getFileContent(
180-
BLOOD_PRESSURE_FILE_LOCATION + EXPECTED_BLOOD_PRESSURE_WITH_CODEABLE_CONCEPTS);
181-
182-
CodeableConceptCdMapper codeableConceptCdMapper = new CodeableConceptCdMapper();
183-
bloodPressureMapper = new BloodPressureMapper(
184-
messageContext, randomIdGeneratorService, new StructuredObservationValueMapper(),
185-
codeableConceptCdMapper, new ParticipantMapper(), confidentialityService);
186-
187-
Observation observation = new FhirParseService().parseResource(jsonInput, Observation.class);
188-
var outputMessage = bloodPressureMapper.mapBloodPressure(observation, true);
189-
190-
assertThat(outputMessage).isEqualToIgnoringWhitespace(expectedOutput);
191-
}
173+
// @Test
174+
// public void When_MappingBloodPressureWithCodeableConcepts_Expect_CompoundStatementXmlReturned() {
175+
// when(randomIdGeneratorService.createNewOrUseExistingUUID(any()))
176+
// .thenReturn("5E496953-065B-41F2-9577-BE8F2FBD0757");
177+
//
178+
// var jsonInput = ResourceTestFileUtils.getFileContent(BLOOD_PRESSURE_FILE_LOCATION + INPUT_BLOOD_PRESSURE_WITH_CODEABLE_CONCEPTS);
179+
// var expectedOutput = ResourceTestFileUtils.getFileContent(
180+
// BLOOD_PRESSURE_FILE_LOCATION + EXPECTED_BLOOD_PRESSURE_WITH_CODEABLE_CONCEPTS);
181+
//
182+
// CodeableConceptCdMapper codeableConceptCdMapper = new CodeableConceptCdMapper();
183+
// bloodPressureMapper = new BloodPressureMapper(
184+
// messageContext, randomIdGeneratorService, new StructuredObservationValueMapper(),
185+
// codeableConceptCdMapper, new ParticipantMapper(), confidentialityService);
186+
//
187+
// Observation observation = new FhirParseService().parseResource(jsonInput, Observation.class);
188+
// var outputMessage = bloodPressureMapper.mapBloodPressure(observation, true);
189+
//
190+
// assertThat(outputMessage).isEqualToIgnoringWhitespace(expectedOutput);
191+
// }
192192

193193
@Test
194194
public void When_MappingBloodPressureWithNoCodeableConcepts_Expect_Exception() {

‎service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapperTest.java‎

Lines changed: 87 additions & 87 deletions
Original file line numberDiff line numberDiff line change
@@ -86,42 +86,42 @@ public void When_MappingStubbedCodeableConcept_Expect_HL7CdObjectXml(String inpu
8686
.isEqualToIgnoringWhitespace(expectedOutput);
8787
}
8888

89-
@Test
90-
void When_MappingCodeableConceptWithNonSnomedCodeSystems_Expect_ManifestedXmlContainsTranslationsForThoseCodes() {
91-
var inputJson = """
92-
{
93-
"resourceType" : "Observation",
94-
"code": {
95-
"coding": [
96-
{
97-
"system": "http://snomed.info/sct",
98-
"code": "123456",
99-
"display": "Endometriosis of uterus"
100-
},
101-
{
102-
"system": "http://read.info/readv2",
103-
"code": "READ0",
104-
"display": "Read V2 Code Display"
105-
},
106-
{
107-
"system": "http://read.info/ctv3",
108-
"code": "READ1",
109-
"display": "Read CTV3 Code Display"
110-
}
111-
]
112-
}
113-
}""";
114-
var expectedOutputXml = """
115-
<code code="123456" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Endometriosis of uterus">
116-
<translation code="READ0" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Read V2 Code Display" />
117-
<translation code="READ1" codeSystem="2.16.840.1.113883.2.1.3.2.4.14" displayName="Read CTV3 Code Display" />
118-
</code>""";
119-
var codeableConcept = fhirParseService.parseResource(inputJson, Observation.class).getCode();
120-
121-
var outputMessageXml = codeableConceptCdMapper.mapCodeableConceptToCd(codeableConcept);
122-
123-
assertThat(outputMessageXml).isEqualToIgnoringWhitespace(expectedOutputXml);
124-
}
89+
// @Test
90+
// void When_MappingCodeableConceptWithNonSnomedCodeSystems_Expect_ManifestedXmlContainsTranslationsForThoseCodes() {
91+
// var inputJson = """
92+
// {
93+
// "resourceType" : "Observation",
94+
// "code": {
95+
// "coding": [
96+
// {
97+
// "system": "http://snomed.info/sct",
98+
// "code": "123456",
99+
// "display": "Endometriosis of uterus"
100+
// },
101+
// {
102+
// "system": "http://read.info/readv2",
103+
// "code": "READ0",
104+
// "display": "Read V2 Code Display"
105+
// },
106+
// {
107+
// "system": "http://read.info/ctv3",
108+
// "code": "READ1",
109+
// "display": "Read CTV3 Code Display"
110+
// }
111+
// ]
112+
// }
113+
// }""";
114+
// var expectedOutputXml = """
115+
// <code code="123456" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Endometriosis of uterus">
116+
// <translation code="READ0" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Read V2 Code Display" />
117+
// <translation code="READ1" codeSystem="2.16.840.1.113883.2.1.3.2.4.14" displayName="Read CTV3 Code Display" />
118+
// </code>""";
119+
// var codeableConcept = fhirParseService.parseResource(inputJson, Observation.class).getCode();
120+
//
121+
// var outputMessageXml = codeableConceptCdMapper.mapCodeableConceptToCd(codeableConcept);
122+
//
123+
// assertThat(outputMessageXml).isEqualToIgnoringWhitespace(expectedOutputXml);
124+
// }
125125

126126
@Test
127127
void When_MapToNullFlavorCodeableConceptForAllergyWithoutSnomedCode_Expect_OriginalTextIsNotPresent() {
@@ -194,20 +194,20 @@ void When_MappingStubbedCodeableConceptAsResolvedAllergy_Expect_HL7CdObjectXml(S
194194
.isEqualToIgnoringWhitespace(expectedOutput);
195195
}
196196

197-
@ParameterizedTest
198-
@MethodSource("getTestArgumentsAllergyActive")
199-
void When_MappingStubbedCodeableConceptAsActiveAllergy_Expect_HL7CdObjectXml(String inputJson, String outputXml) {
200-
var allergyCodeableConcept = ResourceTestFileUtils.getFileContent(inputJson);
201-
var expectedOutput = ResourceTestFileUtils.getFileContent(outputXml);
202-
var codeableConcept = fhirParseService.parseResource(allergyCodeableConcept, AllergyIntolerance.class).getCode();
203-
204-
var outputMessage = codeableConceptCdMapper.mapCodeableConceptToCdForAllergy(codeableConcept,
205-
AllergyIntolerance.AllergyIntoleranceClinicalStatus.ACTIVE);
206-
207-
assertThat(outputMessage)
208-
.describedAs(TestArgumentsLoaderUtil.FAIL_MESSAGE, inputJson, outputXml)
209-
.isEqualToIgnoringWhitespace(expectedOutput);
210-
}
197+
// @ParameterizedTest
198+
// @MethodSource("getTestArgumentsAllergyActive")
199+
// void When_MappingStubbedCodeableConceptAsActiveAllergy_Expect_HL7CdObjectXml(String inputJson, String outputXml) {
200+
// var allergyCodeableConcept = ResourceTestFileUtils.getFileContent(inputJson);
201+
// var expectedOutput = ResourceTestFileUtils.getFileContent(outputXml);
202+
// var codeableConcept = fhirParseService.parseResource(allergyCodeableConcept, AllergyIntolerance.class).getCode();
203+
//
204+
// var outputMessage = codeableConceptCdMapper.mapCodeableConceptToCdForAllergy(codeableConcept,
205+
// AllergyIntolerance.AllergyIntoleranceClinicalStatus.ACTIVE);
206+
//
207+
// assertThat(outputMessage)
208+
// .describedAs(TestArgumentsLoaderUtil.FAIL_MESSAGE, inputJson, outputXml)
209+
// .isEqualToIgnoringWhitespace(expectedOutput);
210+
// }
211211

212212
@Nested
213213
class WhenMappingStubbedCodeableConceptForBloodPressure {
@@ -324,43 +324,43 @@ <originalText>Prothrombin time (observed)</originalText>
324324
assertThat(outputMessage).isEqualToIgnoringWhitespace(expectedOutput);
325325
}
326326

327-
@Test
328-
void When_WithSnomedCodingAndLegacyCodings_Expect_SnomedCdXmlWithTranslations() {
329-
var inputJson = """
330-
{
331-
"resourceType": "Observation",
332-
"code": {
333-
"coding": [
334-
{
335-
"system": "http://snomed.info/sct",
336-
"display": "Prothrombin time",
337-
"code": "852471000000107"
338-
},
339-
{
340-
"system": "http://read.info/readv2",
341-
"code": "42Q5.00",
342-
"display": "Observed Prothrombin time"
343-
},
344-
{
345-
"system": "http://read.info/ctv3",
346-
"code": "123456",
347-
"display": "Prothrombin time (observed)"
348-
}
349-
]
350-
}
351-
}""";
352-
var expectedOutput = """
353-
<code code="852471000000107" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Prothrombin time">
354-
<translation code="42Q5.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Observed Prothrombin time" />
355-
<translation code="123456" codeSystem="2.16.840.1.113883.2.1.3.2.4.14" displayName="Prothrombin time (observed)" />
356-
<originalText>Prothrombin time</originalText>
357-
</code>""";
358-
var codeableConcept = fhirParseService.parseResource(inputJson, Observation.class).getCode();
359-
360-
var outputMessage = codeableConceptCdMapper.mapCodeableConceptToCdForBloodPressure(codeableConcept);
361-
362-
assertThat(outputMessage).isEqualToIgnoringWhitespace(expectedOutput);
363-
}
327+
// @Test
328+
// void When_WithSnomedCodingAndLegacyCodings_Expect_SnomedCdXmlWithTranslations() {
329+
// var inputJson = """
330+
// {
331+
// "resourceType": "Observation",
332+
// "code": {
333+
// "coding": [
334+
// {
335+
// "system": "http://snomed.info/sct",
336+
// "display": "Prothrombin time",
337+
// "code": "852471000000107"
338+
// },
339+
// {
340+
// "system": "http://read.info/readv2",
341+
// "code": "42Q5.00",
342+
// "display": "Observed Prothrombin time"
343+
// },
344+
// {
345+
// "system": "http://read.info/ctv3",
346+
// "code": "123456",
347+
// "display": "Prothrombin time (observed)"
348+
// }
349+
// ]
350+
// }
351+
// }""";
352+
// var expectedOutput = """
353+
// <code code="852471000000107" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Prothrombin time">
354+
// <translation code="42Q5.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Observed Prothrombin time" />
355+
// <translation code="123456" codeSystem="2.16.840.1.113883.2.1.3.2.4.14" displayName="Prothrombin time (observed)" />
356+
// <originalText>Prothrombin time</originalText>
357+
// </code>""";
358+
// var codeableConcept = fhirParseService.parseResource(inputJson, Observation.class).getCode();
359+
//
360+
// var outputMessage = codeableConceptCdMapper.mapCodeableConceptToCdForBloodPressure(codeableConcept);
361+
//
362+
// assertThat(outputMessage).isEqualToIgnoringWhitespace(expectedOutput);
363+
// }
364364

365365
@Test
366366
void When_WithNonSnomedCodingWithText_Expect_NullFlavorUnkCDWithOriginalTextFromText() {

‎service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/MedicationStatementMapperTest.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -132,7 +132,7 @@ private static Stream<Arguments> resourceFileParams() {
132132
Arguments.of("mr-with-no-recorder-reference.json", "medication-statement-with-no-participant.xml"),
133133
Arguments.of("mr-with-invalid-recorder-resource-type.json", "medication-statement-with-no-participant.xml"),
134134
Arguments.of("medication-request-special-character-in-code.json", "medication-statement-with-xml-escaped-text-values.xml"),
135-
Arguments.of("mr-referencing-medication-with-non-snomed-codes.json", "ms-with-material-coding-containing-translations.xml"),
135+
//Arguments.of("mr-referencing-medication-with-non-snomed-codes.json", "ms-with-material-coding-containing-translations.xml"),
136136
Arguments.of("mr-referencing-medication-with-no-snomed-code.json", "ms-with-material-coding-containing-null-flavor-code.xml")
137137
);
138138
}

‎service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/ObservationMapperTest.java‎

Lines changed: 14 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -10,9 +10,7 @@
1010
import org.junit.jupiter.api.BeforeEach;
1111
import org.junit.jupiter.api.Test;
1212
import org.junit.jupiter.api.extension.ExtendWith;
13-
import org.junit.jupiter.params.ParameterizedTest;
1413
import org.junit.jupiter.params.provider.Arguments;
15-
import org.junit.jupiter.params.provider.MethodSource;
1614
import org.mockito.ArgumentCaptor;
1715
import org.mockito.Captor;
1816
import org.mockito.Mock;
@@ -180,20 +178,20 @@ void tearDown() {
180178
messageContext.resetMessageContext();
181179
}
182180

183-
@ParameterizedTest
184-
@MethodSource("resourceFileParams")
185-
void When_MappingObservationJson_Expect_CompoundStatementXmlOutput(String inputJson, String outputXml) {
186-
final Observation observationAssociatedWithSpecimen = getObservationResourceFromJson(inputJson);
187-
final String expectedXml = getXmlStringFromFile(outputXml);
188-
189-
lenient().when(randomIdGeneratorService.createNewId())
190-
.thenReturn("random-unmapped-id");
191-
192-
final String actualXml = observationMapper.mapObservationToCompoundStatement(
193-
observationAssociatedWithSpecimen);
194-
195-
assertThat(actualXml).isEqualToIgnoringWhitespace(expectedXml);
196-
}
181+
// @ParameterizedTest
182+
// @MethodSource("resourceFileParams")
183+
// void When_MappingObservationJson_Expect_CompoundStatementXmlOutput(String inputJson, String outputXml) {
184+
// final Observation observationAssociatedWithSpecimen = getObservationResourceFromJson(inputJson);
185+
// final String expectedXml = getXmlStringFromFile(outputXml);
186+
//
187+
// lenient().when(randomIdGeneratorService.createNewId())
188+
// .thenReturn("random-unmapped-id");
189+
//
190+
// final String actualXml = observationMapper.mapObservationToCompoundStatement(
191+
// observationAssociatedWithSpecimen);
192+
//
193+
// assertThat(actualXml).isEqualToIgnoringWhitespace(expectedXml);
194+
// }
197195

198196
@Test
199197
void When_MappingDefaultObservationJson_Expect_DefaultObservationStatementXmlOutput() {

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