Merge branch 'main' into update-changelog

MartinWheelerMT · web-flow · commit 7eff5517ce59 · 2025-03-24T15:58:16.000Z
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,22 +6,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [2.3.0] - 2025-03-24
+
 ### Fixed
 
-* When mapping to `<code nullFlavor="UNK">` XML elements from an existing `CodeableConcept` the element will now contain
-the original text value from the DisplayExtension, if a separate text field is not provided. 
-In the case that neither of these are present, the existing behavior of using the `code.display` element is used. 
+* When mapping to `<code nullFlavor="UNK">` XML elements from an existing `CodeableConcept` the element will now contain the original text value from the DisplayExtension, if a separate text field is not provided. In the case that neither of these are present, the existing behavior of using the `code.display` element is used.
 
 ### Added
 
+* Legacy codes are preserved as translations within the XML when mapping `CodeableConcepts`, when a SNOMEDCT code is provided along with additional codings for Egton, READ (v2 or v3), or EMIS drug codes. For other unknown code systems, these will not be preserved.
 * GP2GP Adaptor now populates the PlanStatement / confidentialityCode field when the ProcedureRequest.meta.security field contains NOPAT
+
 * When the ReferralRequest.meta.security field contains NOPAT, the GP2GP Adaptor will now populate the RequestStatement / confidentialityCode field accordingly.
 * The GP2GP Adaptor now populates the CompoundStatement / confidentialityCode field when Observation.meta.security field contains NOPAT
 * When mapping from JSON FHIR `codaeableConcept` to HL7 XML `<code>`, if both a legacy code and system (i.e., ReadV2, 
   Egton) and a `SNOMEDCT` code are provided, then the legacy code will be preserved and presented as a nested
  `<translation>` element. The provided `coding.system` will be converted from url to OID format for known codes systems.
 
-
 ## [2.2.2] - 2025-02-07
 
 ### Fixed
diff --git a/e2e-tests/build.gradle b/e2e-tests/build.gradle
@@ -22,7 +22,7 @@ dependencies {
     testImplementation 'org.awaitility:awaitility:4.3.0'
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.11.4'
     testImplementation "org.assertj:assertj-core:3.27.3"
-    testImplementation 'ch.qos.logback:logback-classic:1.5.17'
+    testImplementation 'ch.qos.logback:logback-classic:1.5.18'
     testImplementation 'org.xmlunit:xmlunit-assertj3:2.10.0'
     testImplementation 'org.apache.httpcomponents.client5:httpclient5:5.4.2'
 
diff --git a/mock-mhs-adaptor/build.gradle b/mock-mhs-adaptor/build.gradle
@@ -1,8 +1,8 @@
 plugins {
-	id 'org.springframework.boot' version '3.4.3'
+	id 'org.springframework.boot' version '3.4.4'
 	id 'io.spring.dependency-management' version '1.1.7'
 	id 'java'
-	id "io.freefair.lombok" version "8.12.2.1"
+	id "io.freefair.lombok" version "8.13"
 }
 
 apply plugin: 'java'
diff --git a/service/build.gradle b/service/build.gradle
@@ -10,7 +10,7 @@ plugins {
 
 	// Mutation testing
 	id 'info.solidsoft.pitest' version '1.15.0'
-	id 'com.arcmutate.github' version '2.0.0'
+	id 'com.arcmutate.github' version '2.1.0'
 }
 
 apply plugin: 'java'
@@ -50,8 +50,8 @@ dependencies {
 	implementation 'org.springframework.boot:spring-boot-starter-logging'
 
 	// Infrastructure
-	implementation 'software.amazon.awssdk:s3:2.30.31'
-	implementation ('com.azure:azure-storage-blob:12.29.1')
+	implementation 'software.amazon.awssdk:s3:2.31.6'
+	implementation ('com.azure:azure-storage-blob:12.30.0')
 	implementation 'org.apache.qpid:qpid-jms-client:2.6.1'
 
 	// Utils
@@ -66,15 +66,15 @@ dependencies {
 	// Test
 	testImplementation 'org.springframework.boot:spring-boot-starter-test'
 	testImplementation "org.assertj:assertj-core:3.27.3"
-	testImplementation 'org.testcontainers:testcontainers:1.20.5'
+	testImplementation 'org.testcontainers:testcontainers:1.20.6'
 	testImplementation 'org.awaitility:awaitility:4.2.2'
 	testImplementation 'org.wiremock:wiremock-standalone:3.12.1'
 	testImplementation 'com.squareup.okhttp3:okhttp:4.12.0'
 	testImplementation 'com.squareup.okhttp3:mockwebserver:4.12.0'
 	testImplementation 'io.findify:s3mock_2.13:0.2.6'
 
 	pitest 'com.arcmutate:base:1.3.2'
-	pitest 'com.arcmutate:pitest-git-plugin:2.0.0'
+	pitest 'com.arcmutate:pitest-git-plugin:2.1.0'
 }
 
 test {
diff --git a/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/BloodPressureMapper.java b/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/BloodPressureMapper.java
@@ -62,14 +62,11 @@ public class BloodPressureMapper {
 
     public String mapBloodPressure(Observation observation, boolean isNested) {
 
-        var confidentialityCode = confidentialityService.generateConfidentialityCode(observation);
-
         BloodPressureParametersBuilder builder = BloodPressureParameters.builder()
             .isNested(isNested)
             .id(messageContext.getIdMapper().getOrNew(ResourceType.Observation, observation.getIdElement()))
             .effectiveTime(prepareEffectiveTimeForObservation(observation))
             .availabilityTime(prepareAvailabilityTimeForObservation(observation))
-            .confidentialityCode(confidentialityCode.orElse(null))
             .compoundStatementCode(buildBloodPressureCode(observation));
 
         extractBloodPressureComponent(observation, SYSTOLIC_CODE).ifPresent(observationComponent -> {
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
@@ -1,5 +1,6 @@
 package uk.nhs.adaptors.gp2gp.ehr.mapper;
 
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
@@ -316,12 +317,16 @@ private List<Coding> getNonSnomedCodeCodings(CodeableConcept codeableConcept) {
             .filter(coding -> !isSnomed(coding))
             .toList();
 
+        List<Coding> nonSnomedCodings = new ArrayList<>();
+
         for (Coding coding : nonSnomedCodeCodings) {
             var hl7CodeSystem = CodeSystemsUtil.getHl7code(coding.getSystem());
-            coding.setSystem(hl7CodeSystem);
+            if (!hl7CodeSystem.isEmpty()) {
+                nonSnomedCodings.add(new Coding(hl7CodeSystem, coding.getCode(), coding.getDisplay()));
+            }
         }
 
-        return nonSnomedCodeCodings;
+        return nonSnomedCodings;
     }
 
     private Optional<String> findOriginalText(CodeableConcept codeableConcept, Optional<Coding> coding) {
diff --git a/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/RequestStatementMapper.java b/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/RequestStatementMapper.java
@@ -103,14 +103,11 @@ private String map() {
                 processAgent(agentRef, onBehalfOf);
             }
 
-            var confidentialityCode = confidentialityService.generateConfidentialityCode(referralRequest);
-
             final IdMapper idMapper = messageContext.getIdMapper();
             templateParameters
                 .requestStatementId(idMapper.getOrNew(ResourceType.ReferralRequest, referralRequest.getIdElement()))
                 .isNested(isNested)
                 .availabilityTime(StatementTimeMappingUtils.prepareAvailabilityTime(referralRequest.getAuthoredOnElement()))
-                .confidentialityCode(confidentialityCode.orElse(null))
                 .text(buildTextDescription())
                 .priorityCode(buildPriorityCode())
                 .code(buildCode());
diff --git a/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/parameters/BloodPressureParameters.java b/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/parameters/BloodPressureParameters.java
@@ -23,5 +23,4 @@ public class BloodPressureParameters {
     private String systolicCode;
     private String diastolicCode;
     private String participant;
-    private String confidentialityCode;
 }
diff --git a/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/parameters/RequestStatementTemplateParameters.java b/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/parameters/RequestStatementTemplateParameters.java
@@ -17,5 +17,4 @@ public class RequestStatementTemplateParameters {
     private String participant;
     private String responsibleParty;
     private String text;
-    private String confidentialityCode;
 }
diff --git a/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/utils/CodeSystemsUtil.java b/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/utils/CodeSystemsUtil.java
@@ -12,10 +12,11 @@ public final class CodeSystemsUtil {
         "http://snomed.info/sct", "2.16.840.1.113883.2.1.3.2.4.15",
         "https://fhir.hl7.org.uk/Id/egton-codes", "2.16.840.1.113883.2.1.6.3",
         "http://read.info/readv2", "2.16.840.1.113883.2.1.6.2",
-        "http://read.info/ctv3", "2.16.840.1.113883.2.1.3.2.4.14"
+        "http://read.info/ctv3", "2.16.840.1.113883.2.1.3.2.4.14",
+        "https://fhir.hl7.org.uk/Id/emis-drug-codes", "2.16.840.1.113883.2.1.6.9"
     );
 
     public static String getHl7code(String fhirCodeSystem) {
-        return SYSTEM_CODES.getOrDefault(fhirCodeSystem, fhirCodeSystem);
+        return SYSTEM_CODES.getOrDefault(fhirCodeSystem, "");
     }
 }
diff --git a/service/src/main/resources/templates/codeable_concept_cd_template.mustache b/service/src/main/resources/templates/codeable_concept_cd_template.mustache
@@ -1,8 +1,8 @@
 <code{{#nullFlavor}} nullFlavor="UNK"{{/nullFlavor}}{{^nullFlavor}} code="{{mainCode}}" codeSystem="{{mainCodeSystem}}" displayName="{{mainDisplayName}}"{{/nullFlavor}}>
+    {{#mainOriginalText}}
+        <originalText>{{mainOriginalText}}</originalText>
+    {{/mainOriginalText}}
     {{#translations}}
     <translation code="{{code}}" codeSystem="{{system}}" displayName="{{display}}" />
     {{/translations}}
-    {{#mainOriginalText}}
-    <originalText>{{mainOriginalText}}</originalText>
-    {{/mainOriginalText}}
 </code>
diff --git a/service/src/main/resources/templates/ehr_compound_statement_blood_pressure_template.mustache b/service/src/main/resources/templates/ehr_compound_statement_blood_pressure_template.mustache
@@ -7,9 +7,6 @@
             {{{effectiveTime}}}
         </effectiveTime>
         {{{availabilityTime}}}
-        {{#confidentialityCode}}
-            {{{confidentialityCode}}}
-        {{/confidentialityCode}}
         {{#systolicId}}
         <component typeCode="COMP" contextConductionInd="true">
             <ObservationStatement classCode="OBS" moodCode="EVN">
diff --git a/service/src/main/resources/templates/ehr_request_statement_template.mustache b/service/src/main/resources/templates/ehr_request_statement_template.mustache
@@ -10,9 +10,6 @@
             <center nullFlavor="NI"/>
         </effectiveTime>
         {{{availabilityTime}}}
-        {{#confidentialityCode}}
-            {{{confidentialityCode}}}
-        {{/confidentialityCode}}
         {{#priorityCode}}
         {{{priorityCode}}}
         {{/priorityCode}}
diff --git a/service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/BloodPressureMapperTest.java b/service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/BloodPressureMapperTest.java
@@ -5,6 +5,7 @@
 import org.hl7.fhir.dstu3.model.Observation;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -94,6 +95,7 @@ public void tearDown() {
         messageContext.resetMessageContext();
     }
 
+    @Disabled
     @Test
     public void When_MappingBloodPressureWithNopat_Expect_CompoundStatementWithConfidentialityCode() {
         when(mockCodeableConceptCdMapper.mapCodeableConceptToCdForBloodPressure(any(CodeableConcept.class)))
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
@@ -123,6 +123,36 @@ void When_MappingCodeableConceptWithNonSnomedCodeSystems_Expect_ManifestedXmlCon
         assertThat(outputMessageXml).isEqualToIgnoringWhitespace(expectedOutputXml);
     }
 
+    @Test
+    void When_MappingCodeableConceptWithUnknownNonSnomedCodeSystem_Expect_ManifestedXmlDoesNotContainTranslations() {
+        var inputJson = """
+            {
+                "resourceType" : "Observation",
+                "code": {
+                    "coding": [
+                        {
+                            "system": "http://snomed.info/sct",
+                            "code": "123456",
+                            "display": "Endometriosis of uterus"
+                        },
+                        {
+                            "system": "http://unknown.code/systen",
+                            "code": "UNKNOWN01",
+                            "display": "Unknown Code System Display"
+                        }
+                   ]
+                }
+            }""";
+        var expectedOutputXml = """
+            <code code="123456" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Endometriosis of uterus">
+            </code>""";
+        var codeableConcept = fhirParseService.parseResource(inputJson, Observation.class).getCode();
+
+        var outputMessageXml = codeableConceptCdMapper.mapCodeableConceptToCd(codeableConcept);
+
+        assertThat(outputMessageXml).isEqualToIgnoringWhitespace(expectedOutputXml);
+    }
+
     @Test
     void When_MapToNullFlavorCodeableConceptForAllergyWithoutSnomedCode_Expect_OriginalTextIsNotPresent() {
         var inputJson = """
@@ -351,9 +381,9 @@ void When_WithSnomedCodingAndLegacyCodings_Expect_SnomedCdXmlWithTranslations()
                 }""";
             var expectedOutput = """
                 <code code="852471000000107" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Prothrombin time">
+                    <originalText>Prothrombin time</originalText>
                     <translation code="42Q5.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Observed Prothrombin time" />
                     <translation code="123456" codeSystem="2.16.840.1.113883.2.1.3.2.4.14" displayName="Prothrombin time (observed)" />
-                    <originalText>Prothrombin time</originalText>
                 </code>""";
             var codeableConcept = fhirParseService.parseResource(inputJson, Observation.class).getCode();
 
diff --git a/service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/RequestStatementMapperTest.java b/service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/RequestStatementMapperTest.java
@@ -18,6 +18,7 @@
 import org.hl7.fhir.dstu3.model.ResourceType;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -359,6 +360,7 @@ public void When_MappingReferralRequestJsonWithNestedTrue_Expect_RequestStatemen
         assertThat(outputMessage).isEqualTo(expectedOutputMessage);
     }
 
+    @Disabled
     @Test
     public void When_MappingReferralRequestWithNoPat_Expect_RequestStatementWithConfidentialityCode() {
         when(confidentialityService.generateConfidentialityCode(any(ReferralRequest.class)))
diff --git a/service/src/test/java/uk/nhs/adaptors/gp2gp/utils/CodeSystemUtilTest.java b/service/src/test/java/uk/nhs/adaptors/gp2gp/utils/CodeSystemUtilTest.java
@@ -10,14 +10,14 @@
 
 import java.util.stream.Stream;
 
-public class CodeSystemUtilTest {
-
+class CodeSystemUtilTest {
     private static Stream<Arguments> knownCodeSystems() {
         return Stream.of(
             Arguments.of("http://snomed.info/sct", "2.16.840.1.113883.2.1.3.2.4.15"),
             Arguments.of("https://fhir.hl7.org.uk/Id/egton-codes", "2.16.840.1.113883.2.1.6.3"),
             Arguments.of("http://read.info/readv2", "2.16.840.1.113883.2.1.6.2"),
-            Arguments.of("http://read.info/ctv3", "2.16.840.1.113883.2.1.3.2.4.14")
+            Arguments.of("http://read.info/ctv3", "2.16.840.1.113883.2.1.3.2.4.14"),
+            Arguments.of("https://fhir.hl7.org.uk/Id/emis-drug-codes", "2.16.840.1.113883.2.1.6.9")
         );
     }
 
@@ -30,9 +30,9 @@ void When_FhirCodeSystemIsKnown_Expect_CorrectHl7Code(String fhirCodeSystem, Str
     }
 
     @Test
-    void When_FhirCodeSystemIsUnknown_Expect_FhirCodeSystemIsProvided() {
+    void When_FhirCodeSystemIsUnknown_Expect_EmptyString() {
         var hl7Code = CodeSystemsUtil.getHl7code("https://unknown.code/system");
 
-        assertThat(hl7Code).isEqualTo("https://unknown.code/system");
+        assertThat(hl7Code).isEmpty();
     }
 }
diff --git a/service/src/test/resources/ehr/mapper/blood_pressure/blood-pressure-with-codeable-concepts.xml b/service/src/test/resources/ehr/mapper/blood_pressure/blood-pressure-with-codeable-concepts.xml
@@ -2,8 +2,8 @@
     <CompoundStatement classCode="BATTERY" moodCode="EVN">
         <id root="5E496953-065B-41F2-9577-BE8F2FBD0757"/>
         <code code="852471000000107" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Prothrombin time">
-            <translation code="42Q5.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Prothrombin time" />
             <originalText>Prothrombin time</originalText>
+            <translation code="42Q5.00" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Prothrombin time" />
         </code>
         <statusCode code="COMPLETE"/>
         <effectiveTime>
@@ -14,8 +14,8 @@
             <ObservationStatement classCode="OBS" moodCode="EVN">
                 <id root="5E496953-065B-41F2-9577-BE8F2FBD0757"/>
                 <code code="72313002" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Systolic arterial pressure">
-                    <translation code="2469" codeSystem="2.16.840.1.113883.2.1.6.3" displayName="Systolic arterial pressure" />
                     <originalText>Systolic arterial pressure</originalText>
+                    <translation code="2469" codeSystem="2.16.840.1.113883.2.1.6.3" displayName="Systolic arterial pressure" />
                 </code>
                 <statusCode code="COMPLETE"/>
                 <effectiveTime>
@@ -36,8 +36,8 @@
             <ObservationStatement classCode="OBS" moodCode="EVN">
                 <id root="5E496953-065B-41F2-9577-BE8F2FBD0757"/>
                 <code code="1091811000000102" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Diastolic arterial pressure">
-                    <translation code="246A" codeSystem="2.16.840.1.113883.2.1.6.3" displayName="Diastolic arterial pressure" />
                     <originalText>Diastolic arterial pressure</originalText>
+                    <translation code="246A" codeSystem="2.16.840.1.113883.2.1.6.3" displayName="Diastolic arterial pressure" />
                 </code>
                 <statusCode code="COMPLETE"/>
                 <effectiveTime>
diff --git a/service/src/test/resources/ehr/mapper/codeableconcept/allergyActive/allergy_with_snomed_and_non_snomed_codes_in_coding_with_text.xml b/service/src/test/resources/ehr/mapper/codeableconcept/allergyActive/allergy_with_snomed_and_non_snomed_codes_in_coding_with_text.xml
@@ -1,5 +1,5 @@
 <code code="292971006" codeSystem="2.16.840.1.113883.2.1.3.2.4.15" displayName="Pivampicillin adverse reaction pt">
+    <originalText>Pivampicillin adverse reaction (rt)</originalText>
     <translation code="TJ00800" codeSystem="2.16.840.1.113883.2.1.6.2" displayName="Adverse reaction to pivampicillin pt" />
     <translation code="TJ00800-1" codeSystem="2.16.840.1.113883.2.1.3.2.4.14" displayName="Adverse reaction to pivampicillin" />
-    <originalText>Pivampicillin adverse reaction (rt)</originalText>
 </code>
diff --git a/wiremock/stubs/__files/EMISPatientStructurede2eResponsePWTP3.json b/wiremock/stubs/__files/EMISPatientStructurede2eResponsePWTP3.json
@@ -8817,7 +8817,7 @@
                     "coding": [
                         {
                             "system": "https://fhir.hl7.org.uk/Id/emis-drug-codes",
-                            "code": "CO2 27587NEMIS",
+                            "code": "CO227587NEMIS",
                             "display": "Coloplast Micro-bag two piece ostomy system urostomy bag 14204 40mm (Coloplast Ltd)",
                             "userSelected": true
                         },

Original file line number	Diff line number	Diff line change
`@@ -23,5 +23,4 @@ public class BloodPressureParameters {`
`23`	`23`	`private String systolicCode;`
`24`	`24`	`private String diastolicCode;`
`25`	`25`	`private String participant;`
`26`		`- private String confidentialityCode;`
`27`	`26`	`}`
Original file line number	Diff line number	Diff line change
`@@ -17,5 +17,4 @@ public class RequestStatementTemplateParameters {`
`17`	`17`	`private String participant;`
`18`	`18`	`private String responsibleParty;`
`19`	`19`	`private String text;`
`20`		`- private String confidentialityCode;`
`21`	`20`	`}`
Original file line number	Diff line number	Diff line change
`@@ -12,10 +12,11 @@ public final class CodeSystemsUtil {`
`12`	`12`	`"http://snomed.info/sct", "2.16.840.1.113883.2.1.3.2.4.15",`
`13`	`13`	`"https://fhir.hl7.org.uk/Id/egton-codes", "2.16.840.1.113883.2.1.6.3",`
`14`	`14`	`"http://read.info/readv2", "2.16.840.1.113883.2.1.6.2",`
`15`		`- "http://read.info/ctv3", "2.16.840.1.113883.2.1.3.2.4.14"`
	`15`	`+ "http://read.info/ctv3", "2.16.840.1.113883.2.1.3.2.4.14",`
	`16`	`+ "https://fhir.hl7.org.uk/Id/emis-drug-codes", "2.16.840.1.113883.2.1.6.9"`
`16`	`17`	`);`
`17`	`18`
`18`	`19`	`public static String getHl7code(String fhirCodeSystem) {`
`19`		`- return SYSTEM_CODES.getOrDefault(fhirCodeSystem, fhirCodeSystem);`
	`20`	`+ return SYSTEM_CODES.getOrDefault(fhirCodeSystem, "");`
`20`	`21`	`}`
`21`	`22`	`}`