diff --git a/CHANGELOG.md b/CHANGELOG.md
index 87e0d3eb1..3dd6b24df 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
## [Unreleased]
+* Fixed issue with coding text being set from incorrect place when mapping allergy intolerances.
+
### Added
* Documented database requirements in [OPERATING.md](/OPERATING.md#database-requirements)
diff --git a/gp2gp-translator/src/integrationTest/java/uk/nhs/adaptors/pss/translator/EhrExtractHandlingIT.java b/gp2gp-translator/src/integrationTest/java/uk/nhs/adaptors/pss/translator/EhrExtractHandlingIT.java
index e5e06528f..dda9e9d78 100644
--- a/gp2gp-translator/src/integrationTest/java/uk/nhs/adaptors/pss/translator/EhrExtractHandlingIT.java
+++ b/gp2gp-translator/src/integrationTest/java/uk/nhs/adaptors/pss/translator/EhrExtractHandlingIT.java
@@ -77,7 +77,9 @@ public class EhrExtractHandlingIT {
"entry[59].resource.id",
"entry[59].resource.identifier[0].value",
"entry[60].resource.id",
- "entry[60].resource.identifier[0].value"
+ "entry[60].resource.identifier[0].value",
+ "entry[502].resource.id",
+ "entry[502].resource.identifier[0].value"
);
@Autowired
diff --git a/gp2gp-translator/src/integrationTest/resources/json/expectedBundle.json b/gp2gp-translator/src/integrationTest/resources/json/expectedBundle.json
index c6dd267ab..7cda85827 100644
--- a/gp2gp-translator/src/integrationTest/resources/json/expectedBundle.json
+++ b/gp2gp-translator/src/integrationTest/resources/json/expectedBundle.json
@@ -30538,27 +30538,17 @@
"code": {
"coding": [
{
- "extension": [
- {
- "url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-coding-sctdescid",
- "extension": [
- {
- "url": "descriptionId",
- "valueId": "250208012"
- },
- {
- "url": "descriptionDisplay",
- "valueString": "Civil state unknown"
- }
- ]
- }
- ],
"system": "http://snomed.info/sct",
- "code": "160504008",
- "display": "Marital state unknown"
+ "code": "41891011000001106",
+ "display": "Azelaic acid 20% cream"
+ },
+ {
+ "system": "2.16.840.1.113883.2.1.6.4",
+ "code": "00254001",
+ "display": "Azelaic acid 20% cream"
}
],
- "text": "Adverse reaction to Mebeverine Hydrochloride"
+ "text": "Azelaic acid 20% cream"
},
"patient": {
"reference": "Patient/e2cf4cc1-08da-4971-845f-35b8447cabdd"
@@ -30573,7 +30563,10 @@
},
"note": [
{
- "text": "Status: Active"
+ "text": "Skin Allergy"
+ },
+ {
+ "text": "Allergy Code: Allergy to drug"
}
]
}
diff --git a/gp2gp-translator/src/integrationTest/resources/xml/RCMR_IN030000UK06/payload_part.xml b/gp2gp-translator/src/integrationTest/resources/xml/RCMR_IN030000UK06/payload_part.xml
index 2dc5e2d98..92a421d4e 100644
--- a/gp2gp-translator/src/integrationTest/resources/xml/RCMR_IN030000UK06/payload_part.xml
+++ b/gp2gp-translator/src/integrationTest/resources/xml/RCMR_IN030000UK06/payload_part.xml
@@ -18051,34 +18051,27 @@
-
-
-
- Adverse reaction to Mebeverine Hydrochloride
+
+
+
+ H/O: drug allergy
+
+
-
-
-
+
-
+
+
+
+
- Status: Active
+ Skin Allergy
-
-
-
-
-
-
-
-
-
-
diff --git a/gp2gp-translator/src/integrationTest/resources/xml/RCMR_IN030000UK07/payload_part_with_confidentiality_code.xml b/gp2gp-translator/src/integrationTest/resources/xml/RCMR_IN030000UK07/payload_part_with_confidentiality_code.xml
index db3d391c7..0a1574bb8 100644
--- a/gp2gp-translator/src/integrationTest/resources/xml/RCMR_IN030000UK07/payload_part_with_confidentiality_code.xml
+++ b/gp2gp-translator/src/integrationTest/resources/xml/RCMR_IN030000UK07/payload_part_with_confidentiality_code.xml
@@ -18062,34 +18062,27 @@
-
-
-
- Adverse reaction to Mebeverine Hydrochloride
+
+
+
+ H/O: drug allergy
+
+
-
-
-
+
-
+
+
+
+
- Status: Active
+ Skin Allergy
-
-
-
-
-
-
-
-
-
-
diff --git a/gp2gp-translator/src/main/java/uk/nhs/adaptors/pss/translator/mapper/AllergyIntoleranceMapper.java b/gp2gp-translator/src/main/java/uk/nhs/adaptors/pss/translator/mapper/AllergyIntoleranceMapper.java
index 51a50f882..61a284919 100644
--- a/gp2gp-translator/src/main/java/uk/nhs/adaptors/pss/translator/mapper/AllergyIntoleranceMapper.java
+++ b/gp2gp-translator/src/main/java/uk/nhs/adaptors/pss/translator/mapper/AllergyIntoleranceMapper.java
@@ -18,6 +18,7 @@
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.model.AllergyIntolerance;
import org.hl7.fhir.dstu3.model.Annotation;
+import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.DateTimeType;
import org.hl7.fhir.dstu3.model.Encounter;
import org.hl7.fhir.dstu3.model.Extension;
@@ -42,10 +43,10 @@
public class AllergyIntoleranceMapper extends AbstractMapper {
private static final String DRUG_ALLERGY_CODE = "14L..00";
private static final String NON_DRUG_ALLERGY_CODE = "SN53.00";
- // the meta profile is pre processed with the url so only the final section is required here
+ // the meta profile is pre-processed with the url so only the final section is required here
private static final String META_PROFILE = "AllergyIntolerance-1";
private static final String ENCOUNTER_URL = "http://hl7.org/fhir/StructureDefinition/encounter-associatedEncounter";
- private static final String CODE_SYSTEM = "2.16.840.1.113883.2.1.6.3";
+ private static final String EGTON_CODE_SYSTEM = "2.16.840.1.113883.2.1.6.3";
private static final String ALLERGY_TERM_TEXT = "H/O: drug allergy";
private static final String ALLERGY_NOTE = "Allergy Code: %s";
@@ -111,9 +112,34 @@ private AllergyIntolerance.AllergyIntoleranceCategory getCategory(RCMRMT030101UK
return compoundStatement.getCode().getCode().equals(DRUG_ALLERGY_CODE) ? MEDICATION : ENVIRONMENT;
}
+ private Annotation getAllergyNote(CodeableConcept codeableConceptFromCode, CodeableConcept codeableConceptFromValue) {
+ var codeDisplayName = codeableConceptFromCode.getCodingFirstRep().getDisplay();
+ if (codeDisplayName != null
+ && !ALLERGY_TERM_TEXT.equals(codeDisplayName)
+ && !codeDisplayName.equals(codeableConceptFromValue.getCodingFirstRep().getDisplay())) {
+
+ return new Annotation().setText(ALLERGY_NOTE.formatted(codeDisplayName));
+ }
+ return null;
+ }
+
+ private CodeableConcept getCodeableConceptFromNonEgtonCodeValue(RCMRMT030101UK04ObservationStatement observationStatement) {
+ if (observationStatement.hasValue()
+ && observationStatement.getValue() instanceof CD value
+ && !EGTON_CODE_SYSTEM.equals(value.getCodeSystem())) {
+
+ return codeableConceptMapper.mapToCodeableConcept(value);
+ }
+ return null;
+ }
+
private void buildCode(AllergyIntolerance allergyIntolerance, RCMRMT030101UK04CompoundStatement compoundStatement) {
- var observationStatement =
- compoundStatement.getComponent().stream().map(RCMRMT030101UK04Component02::getObservationStatement).findFirst().get();
+ var observationStatement = compoundStatement.getComponent()
+ .stream()
+ .map(RCMRMT030101UK04Component02::getObservationStatement)
+ .findFirst()
+ .get();
+
var codeableConceptFromCode = codeableConceptMapper.mapToCodeableConcept(observationStatement.getCode());
var compoundCode = compoundStatement.getCode().getCode();
@@ -124,39 +150,43 @@ private void buildCode(AllergyIntolerance allergyIntolerance, RCMRMT030101UK04Co
return;
}
- DegradedCodeableConcepts.addDegradedEntryIfRequired(
- allergyIntolerance.getCode(),
- DegradedCodeableConcepts.DEGRADED_NON_DRUG_ALLERGY);
+ DegradedCodeableConcepts.addDegradedEntryIfRequired(allergyIntolerance.getCode(),
+ DegradedCodeableConcepts.DEGRADED_NON_DRUG_ALLERGY);
}
if (DRUG_ALLERGY_CODE.equals(compoundCode)) {
- if (observationStatement.hasValue() && observationStatement.getValue() instanceof CD value) {
- if (!CODE_SYSTEM.equals(value.getCodeSystem())) {
- var codeableConceptFromValue = codeableConceptMapper.mapToCodeableConcept(value);
- allergyIntolerance.setCode(codeableConceptFromValue);
-
- var codeDisplayName = codeableConceptFromCode.getCodingFirstRep().getDisplay();
- if (codeDisplayName != null && !ALLERGY_TERM_TEXT.equals(codeDisplayName)
- && !codeDisplayName.equals(codeableConceptFromValue.getCodingFirstRep().getDisplay())) {
- allergyIntolerance.getNote().add(new Annotation().setText(ALLERGY_NOTE.formatted(codeDisplayName)));
- }
- } else {
- allergyIntolerance.setCode(codeableConceptFromCode);
- }
- } else {
- allergyIntolerance.setCode(codeableConceptFromCode);
- }
-
- if (allergyIntolerance.getCode() == null) {
+ var codeableConceptFromValue = getCodeableConceptFromNonEgtonCodeValue(observationStatement);
+ if (codeableConceptFromValue == null && codeableConceptFromCode == null) {
return;
}
+ if (codeableConceptFromValue == null) {
+ allergyIntolerance.setCode(codeableConceptFromCode);
- DegradedCodeableConcepts.addDegradedEntryIfRequired(
+ buildAllergyIntoleranceText(observationStatement, allergyIntolerance);
+
+ DegradedCodeableConcepts.addDegradedEntryIfRequired(
allergyIntolerance.getCode(),
DegradedCodeableConcepts.DEGRADED_DRUG_ALLERGY);
+ return;
+ }
+
+ allergyIntolerance.setCode(codeableConceptFromValue);
+
+ var allergyNote = getAllergyNote(codeableConceptFromCode, codeableConceptFromValue);
+ if (allergyNote != null) {
+ allergyIntolerance.getNote().add(allergyNote);
+ }
+ }
+
+ if (allergyIntolerance.getCode() == null) {
+ return;
}
buildAllergyIntoleranceText(observationStatement, allergyIntolerance);
+
+ DegradedCodeableConcepts.addDegradedEntryIfRequired(
+ allergyIntolerance.getCode(),
+ DegradedCodeableConcepts.DEGRADED_DRUG_ALLERGY);
}
private void buildOnset(RCMRMT030101UK04CompoundStatement compoundStatement, AllergyIntolerance allergyIntolerance) {
@@ -190,6 +220,13 @@ private DateTimeType getAssertedDateElement(TS availabilityTime, RCMRMT030101UK0
private void buildAllergyIntoleranceText(RCMRMT030101UK04ObservationStatement observationStatement,
AllergyIntolerance allergyIntolerance) {
if (allergyIntolerance.getCode() != null) {
+ if (observationStatement.hasValue() && observationStatement.getValue() instanceof CD value) {
+ var valueDisplayName = value.getDisplayName();
+ if (!StringUtils.isEmpty(valueDisplayName)) {
+ allergyIntolerance.getCode().setText(valueDisplayName);
+ return;
+ }
+ }
var originalTextFromCode = observationStatement.getCode().getOriginalText();
if (!StringUtils.isEmpty(originalTextFromCode)) {
allergyIntolerance.getCode().setText(originalTextFromCode);
diff --git a/gp2gp-translator/src/test/java/uk/nhs/adaptors/pss/translator/mapper/AllergyIntoleranceMapperTest.java b/gp2gp-translator/src/test/java/uk/nhs/adaptors/pss/translator/mapper/AllergyIntoleranceMapperTest.java
index 362b91bce..397e41d21 100644
--- a/gp2gp-translator/src/test/java/uk/nhs/adaptors/pss/translator/mapper/AllergyIntoleranceMapperTest.java
+++ b/gp2gp-translator/src/test/java/uk/nhs/adaptors/pss/translator/mapper/AllergyIntoleranceMapperTest.java
@@ -59,6 +59,7 @@ public class AllergyIntoleranceMapperTest {
private static final int THREE = 3;
private static final String ORIGINAL_TEXT_IN_CODE = "OriginalText from Code";
+ private static final String DISPLAY_NAME_IN_VALUE = "Value displayName";
private static final String MULTILEX_CODE_SYSTEM = "2.16.840.1.113883.2.1.6.4";
private static final String MULTILEX_COCONUT_OIL = "01142009";
private static final String SNOMED_CODE_SYSTEM = "2.16.840.1.113883.2.1.3.2.4.15";
@@ -159,7 +160,7 @@ public void testMapDegradedDrugAllergy() {
}
@Test
- public void testMapAllergyWithOriginalTextInObservationCode() {
+ public void When_AllergyWithOriginalTextAndNoValue_Expect_MapsCodingTextFromCodeOriginalText() {
when(codeableConceptMapper.mapToCodeableConcept(any(CD.class)))
.thenReturn(defaultCodeableConcept())
.thenReturn(secondaryCodeableConcept());
@@ -270,6 +271,24 @@ public void testMapAllergyWithDrugTermText() {
assertThat(allergyIntolerance.getNote().size()).isOne();
}
+ @Test void When_DrugAllergyWithValueElement_Expect_MapsCodingTextFromValueDescription() {
+ when(codeableConceptMapper.mapToCodeableConcept(any(CD.class)))
+ .thenReturn(defaultCodeableConcept())
+ .thenReturn(secondaryCodeableConcept());
+ var ehrExtract = unmarshallEhrExtract("drug-allergy-with-value.xml");
+ List allergyIntolerances = allergyIntoleranceMapper.mapResources(ehrExtract, getPatient(),
+ getEncounterList(), PRACTISE_CODE);
+
+ assertThat(allergyIntolerances.size()).isEqualTo(1);
+ var allergyIntolerance = allergyIntolerances.get(0);
+
+ assertFixedValues(allergyIntolerance);
+
+ assertExtension(allergyIntolerance);
+
+ assertThat(allergyIntolerance.getCode().getText()).isEqualTo(DISPLAY_NAME_IN_VALUE);
+ }
+
@ParameterizedTest
@MethodSource("allergyStructuresWithTranslations")
public void testTppNamedSchemaInValue(String filename) {
@@ -345,6 +364,7 @@ private CodeableConcept defaultCodeableConcept() {
var codeableConcept = new CodeableConcept();
var coding = new Coding();
coding.setDisplay(CODING_DISPLAY_1);
+ coding.setSystem(SNOMED_CODE_SYSTEM);
codeableConcept.addCoding(coding);
return codeableConcept;
@@ -353,6 +373,7 @@ private CodeableConcept defaultCodeableConcept() {
private CodeableConcept secondaryCodeableConcept() {
var codeableConcept = new CodeableConcept();
var coding = new Coding();
+ coding.setSystem(SNOMED_CODE_SYSTEM);
coding.setDisplay(CODING_DISPLAY_2);
codeableConcept.addCoding(coding);
diff --git a/gp2gp-translator/src/test/resources/xml/AllergyIntolerance/allergy-structure-with-original-text-in-code.xml b/gp2gp-translator/src/test/resources/xml/AllergyIntolerance/allergy-structure-with-original-text-in-code.xml
index da3e008da..ba71320e1 100644
--- a/gp2gp-translator/src/test/resources/xml/AllergyIntolerance/allergy-structure-with-original-text-in-code.xml
+++ b/gp2gp-translator/src/test/resources/xml/AllergyIntolerance/allergy-structure-with-original-text-in-code.xml
@@ -29,9 +29,6 @@
-
-
diff --git a/gp2gp-translator/src/test/resources/xml/AllergyIntolerance/drug-allergy-with-value.xml b/gp2gp-translator/src/test/resources/xml/AllergyIntolerance/drug-allergy-with-value.xml
new file mode 100644
index 000000000..744075a14
--- /dev/null
+++ b/gp2gp-translator/src/test/resources/xml/AllergyIntolerance/drug-allergy-with-value.xml
@@ -0,0 +1,54 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ H/O: drug allergy
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Skin Allergy
+
+
+
+
+
+
+
+
+
+
+