NIAD-3304: Add non-snomed code mapping to translations when mapping CodeableConcepts

MartinWheelerMT · MartinWheelerMT · commit 93bfb696fd1d · 2025-03-03T11:36:03.000Z
* Remove unnecessary non-snomed code systems from test files as the functionality has changed and are testing in a separate test
* Update `CodeableConceptCdTemplateParameters` to include a property for translations.
* Update `codeable_concept_cd_template.mustache` to handle translations.
* Add test to ensure that non-snomed codes are populated as translations in the produced XML when a SNOMEDCT code is present.
* Add functionality to `CodeableConceptCdMapper` to populate translations in the XML when non-SNOMEDCT codes have been provided alongside the SNOMEDCT Code.
diff --git a/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapper.java b/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapper.java
@@ -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;
 
@@ -63,18 +64,17 @@ 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());
-            }
+        if (codeableConcept.hasText()) {
+            builder.mainOriginalText(codeableConcept.getText());
         }
 
+        addNonSnomedCodeTranslationsToTemplateParametersBuilder(codeableConcept, builder);
         return TemplateUtils.fillTemplate(CODEABLE_CONCEPT_CD_TEMPLATE, builder.build());
     }
 
@@ -329,6 +329,20 @@ 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()) {
@@ -457,30 +471,43 @@ 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());
     }
 
+    private void addNonSnomedCodeTranslationsToTemplateParametersBuilder(
+        CodeableConcept codeableConcept,
+        CodeableConceptCdTemplateParameters.CodeableConceptCdTemplateParametersBuilder builder
+    ) {
+        var nonSnomedCodeCodings = getNonSnomedCodeCodings(codeableConcept);
+        if (!nonSnomedCodeCodings.isEmpty()) {
+            builder.translations(nonSnomedCodeCodings);
+        }
+    }
 }
diff --git a/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/parameters/CodeableConceptCdTemplateParameters.java b/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/parameters/CodeableConceptCdTemplateParameters.java
@@ -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
@@ -12,5 +15,6 @@ public class CodeableConceptCdTemplateParameters {
     private String mainCodeSystem;
     private String mainDisplayName;
     private String mainOriginalText;
+    private List<Coding> translations;
     private boolean nullFlavor;
 }
diff --git a/service/src/main/resources/templates/codeable_concept_cd_template.mustache b/service/src/main/resources/templates/codeable_concept_cd_template.mustache
@@ -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}}
diff --git a/service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapperTest.java b/service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapperTest.java
@@ -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)
diff --git a/service/src/test/resources/ehr/mapper/codeableconcept/codeable_concept_snomed_with_description.json b/service/src/test/resources/ehr/mapper/codeableconcept/codeable_concept_snomed_with_description.json
@@ -2,12 +2,6 @@
     "resourceType" : "Observation",
     "code": {
         "coding": [
-            {
-                "system": "http://blah.info/blahsomecodesystem",
-                "code": "X%^^%",
-                "display": "Display for invalid code/system",
-                "userSelected": true
-            },
             {
                 "extension": [
                     {
diff --git a/service/src/test/resources/ehr/mapper/codeableconcept/codeable_concept_snomed_with_no_description.json b/service/src/test/resources/ehr/mapper/codeableconcept/codeable_concept_snomed_with_no_description.json
@@ -2,12 +2,6 @@
     "resourceType" : "Observation",
     "code": {
         "coding": [
-            {
-                "system": "http://blah.info/blahsomecodesystem",
-                "code": "X%^^%",
-                "display": "Display for invalid code/system",
-                "userSelected": true
-            },
             {
                 "extension": [
                     {
diff --git a/service/src/test/resources/ehr/mapper/codeableconcept/codeable_concept_with_text.json b/service/src/test/resources/ehr/mapper/codeableconcept/codeable_concept_with_text.json
@@ -2,12 +2,6 @@
     "resourceType" : "Observation",
     "code": {
         "coding": [
-            {
-                "system": "http://blah.info/blahsomecodesystem",
-                "code": "X%^^%",
-                "display": "Display for invalid code/system",
-                "userSelected": true
-            },
             {
                 "extension": [
                     {
diff --git a/service/src/test/resources/ehr/mapper/codeableconcept/codeable_concept_without_text.json b/service/src/test/resources/ehr/mapper/codeableconcept/codeable_concept_without_text.json
@@ -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",

Original file line number	Diff line number	Diff line change
`@@ -2,12 +2,6 @@`
`2`	`2`	`"resourceType" : "Observation",`
`3`	`3`	`"code": {`
`4`	`4`	`"coding": [`
`5`		`- {`
`6`		`- "system": "http://blah.info/blahsomecodesystem",`
`7`		`- "code": "X%^^%",`
`8`		`- "display": "Display for invalid code/system",`
`9`		`- "userSelected": true`
`10`		`- },`
`11`	`5`	`{`
`12`	`6`	`"extension": [`
`13`	`7`	`{`