Merge remote-tracking branch 'origin/main' into NIAD-3217

Author: adrianclay

.github/workflows/build_workflow.yml

@@ -94,7 +94,9 @@ jobs:
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v4
-
+        with:
+          # Disabling shallow clone is recommended for improving relevancy of Sonar reporting
+          fetch-depth: 0
       - name: Setup Java 21 LTS
         uses: actions/setup-java@v4
         with:
@@ -105,8 +107,10 @@ jobs:
         uses: gradle/actions/setup-gradle@v4
 
       - name: Execute Unit Tests
-        run: ./gradlew test --parallel --build-cache
+        run: ./gradlew test jacocoTestReport sonar --parallel --build-cache
         working-directory: ./service
+        env:
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
       - name: Collect Artifacts
         if: always()

CHANGELOG.md

@@ -6,13 +6,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## Fixed
-
-* When mapping an `Observation` related to a diagnostic report which does not contain a `code` element, the adaptor will
-  now throw an error reporting that an observation requires a code element and provide the affected resource ID.
-* When mapping a `valueQuantity` contained in an `Observation`, the produced XML `<value>` element now correctly escapes
-  any contained XML characters.
-
 ## Added
 
 * When mapping a `DocumentReference` which contains a `NOPAT` `meta.security` or `NOPAT` `securityLabel` tag the resultant XML for that resource
@@ -32,8 +25,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * When mapping `Immunizations` which contain a `NOPAT` `meta.security` tag, the resultant XML for that resource
   will contain a `NOPAT` `confidentialityCode` element.
 
-### Fixed
-* Removed the 20 MB data processing limit to enable the GP2GP Adaptor to handle larger documents.
+## [2.1.4] - 2014-11-07
+
+## Fixed
+
+* When mapping an `Observation` related to a diagnostic report which does not contain a `code` element, the adaptor will
+  now throw an error reporting that an observation requires a code element and provide the affected resource ID.
+  Previously the adaptor was generating an invalid GP2GP payload which was being rejected by the requesting system with
+  a vague error code.
+* When mapping a `valueQuantity` contained in an `Observation`, the generated XML element now correctly escapes any
+  contained XML characters.
+* Removed a 20 MB data processing limit which was causing large document transfers to fail.
 
 ## [2.1.3] - 2014-10-25
 

e2e-tests/build.gradle

@@ -18,7 +18,7 @@ dependencies {
     implementation 'org.mongodb:mongo-java-driver:3.12.14'
     testImplementation 'com.fasterxml.jackson.core:jackson-databind:2.17.2'
     testImplementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.17.2'
-    testImplementation 'commons-io:commons-io:2.16.1'
+    testImplementation 'commons-io:commons-io:2.17.0'
     testImplementation 'org.awaitility:awaitility:4.2.2'
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.11.0'
     testImplementation "org.assertj:assertj-core:3.26.3"

service/build.gradle

@@ -6,6 +6,7 @@ plugins {
 	id "com.github.spotbugs" version "6.0.25"
 	id "io.freefair.lombok" version "8.10.2"
 	id 'jacoco'
+	id 'org.sonarqube' version '5.1.0.4882'
 
 	// Mutation testing
 	id 'info.solidsoft.pitest' version '1.15.0'
@@ -128,7 +129,6 @@ tasks.withType(Test) {
 }
 
 check.dependsOn integrationTest
-jacocoTestReport.dependsOn integrationTest
 
 spotbugsTest.enabled = false
 spotbugsIntegrationTest.enabled = false
@@ -164,6 +164,14 @@ pitestGithub {
 	deleteOldSummaries = true
 }
 
+sonar {
+	properties {
+		property("sonar.host.url", "https://sonarcloud.io")
+		property("sonar.projectKey", "NHSDigital_integration-adaptor-gp2gp")
+		property("sonar.organization", "nhsdigital")
+	}
+}
+
 bootJar {
 	exclude("**/TransformJsonToXml*")
 }

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

@@ -77,6 +77,7 @@ class DiagnosticReportMapperTest {
     private static final String INPUT_JSON_MULTIPLE_CODED_DIAGNOSIS = "diagnostic-report-with-multiple-coded-diagnosis.json";
     private static final String INPUT_JSON_EXTENSION_ID = "diagnostic-report-with-extension-id.json";
     private static final String INPUT_JSON_URN_OID_EXTENSION_ID = "diagnostic-report-with-urn-oid-extension-id.json";
+    private static final String INPUT_JSON_UNRELATED_TEST_RESULT = "diagnostic-report-with-one-specimen-and-one-unrelated-observation.json";
 
     private static final String OUTPUT_XML_REQUIRED_DATA = "diagnostic-report-with-required-data.xml";
     private static final String OUTPUT_XML_STATUS_NARRATIVE = "diagnostic-report-with-status-narrative.xml";
@@ -88,6 +89,7 @@ class DiagnosticReportMapperTest {
     private static final String OUTPUT_XML_MULTIPLE_CODED_DIAGNOSIS = "diagnostic-report-with-multiple-coded-diagnosis.xml";
     private static final String OUTPUT_XML_EXTENSION_ID = "diagnostic-report-with-extension-id.xml";
     private static final String OUTPUT_XML_MULTIPLE_RESULTS = "diagnostic-report-with-multiple-results.xml";
+    private static final String OUTPUT_XML_UNRELATED_TEST_RESULT = "diagnostic-report-with-one-specimen-and-one-unrelated-observation.xml";
     private static final String REGEXP_UUID = "[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}";
     private static final String MOCKED_SPECIMEN_PREFIX = "Mapped Specimen with id";
     private static final String MOCKED_SPECIMEN_LINKED_OBSERVATION = "with linked Observations";
@@ -141,7 +143,7 @@ void When_MappingDiagnosticReportJson_Expect_CompoundStatementXmlOutput(String i
 
         final String outputMessage = mapper.mapDiagnosticReportToCompoundStatement(diagnosticReport);
 
-        assertThat(removeLineEndings(outputMessage)).isEqualToIgnoringWhitespace(removeLineEndings(expectedOutputMessage.toString()));
+        assertThat(outputMessage).isEqualToIgnoringWhitespace(expectedOutputMessage.toString());
     }
 
     @Test
@@ -305,7 +307,7 @@ void When_DiagnosticReport_Has_SpecimenAndUnlinkedTestResult_Expect_ADummySpecim
         final DiagnosticReport diagnosticReport = getDiagnosticReportResourceFromJson(diagnosticReportFileName);
         final Bundle bundle = getBundleResourceFromJson(INPUT_JSON_BUNDLE);
         final InputBundle inputBundle = new InputBundle(bundle);
-        final String expectObservation = "Observation/AD373CA7-3940-4249-85A2-D3A22E9F17C7";
+        final String expectObservation = "Observation/TestResult-WithoutSpecimenReference";
         final String dummyNamePrefix = DiagnosticReportMapper.DUMMY_SPECIMEN_ID_PREFIX;
 
         when(messageContext.getInputBundleHolder()).thenReturn(inputBundle);
@@ -360,10 +362,6 @@ private DiagnosticReport getDiagnosticReportResourceFromJson(String filename) {
         return FileParsingUtility.parseResourceFromJsonFile(filePath, DiagnosticReport.class);
     }
 
-    private String removeLineEndings(String input) {
-        return input.replace("\n", "").replace("\r", "");
-    }
-
     private static Stream<Arguments> resourceFileParams() {
         return Stream.of(
             Arguments.of(INPUT_JSON_REQUIRED_DATA, OUTPUT_XML_STATUS_NARRATIVE),
@@ -379,7 +377,8 @@ private static Stream<Arguments> resourceFileParams() {
             Arguments.of(INPUT_JSON_CODED_DIAGNOSIS, OUTPUT_XML_CODED_DIAGNOSIS),
             Arguments.of(INPUT_JSON_MULTIPLE_CODED_DIAGNOSIS, OUTPUT_XML_MULTIPLE_CODED_DIAGNOSIS),
             Arguments.of(INPUT_JSON_EXTENSION_ID, OUTPUT_XML_EXTENSION_ID),
-            Arguments.of(INPUT_JSON_URN_OID_EXTENSION_ID, OUTPUT_XML_EXTENSION_ID)
+            Arguments.of(INPUT_JSON_URN_OID_EXTENSION_ID, OUTPUT_XML_EXTENSION_ID),
+            Arguments.of(INPUT_JSON_UNRELATED_TEST_RESULT, OUTPUT_XML_UNRELATED_TEST_RESULT)
         );
     }
 

service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-one-specimen-and-one-unrelated-observation.json

@@ -37,7 +37,7 @@
   "issued": "2010-02-25T15:41:00+00:00",
   "result": [
     {
-      "reference": "Observation/AD373CA7-3940-4249-85A2-D3A22E9F17C7"
+      "reference": "Observation/TestResult-WithoutSpecimenReference"
     }
   ],
   "specimen":[

service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-one-specimen-and-one-unrelated-observation.xml

@@ -20,7 +20,7 @@ Status: unknown</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
+        <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 with linked Observations: Observation/TestResult-WithoutSpecimenReference-->
         <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-0 -->
-        <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 -->
     </CompoundStatement>
 </component>

service/src/test/resources/ehr/mapper/diagnosticreport/fhir_bundle.json

@@ -398,6 +398,73 @@
         ]
       }
     },
+
+    {
+      "resource":{
+        "resourceType":"Observation",
+        "id":"TestResult-WithoutSpecimenReference",
+        "meta":{
+          "profile":[
+            "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-Observation-1"
+          ]
+        },
+        "identifier":[
+          {
+            "system":"https://EMISWeb/A82038",
+            "value":"AD373CA7-3940-4249-85A2-D3A22E9F17C7"
+          }
+        ],
+        "status":"unknown",
+        "category":[
+          {
+            "coding":[
+              {
+                "system":"http://hl7.org/fhir/observation-category",
+                "code":"laboratory",
+                "display":"Laboratory"
+              }
+            ]
+          }
+        ],
+        "code":{
+          "coding":[
+            {
+              "system":"http://read.info/readv2",
+              "code":"4483.00",
+              "display":"Serum ACTH",
+              "userSelected":true
+            },
+            {
+              "extension":[
+                {
+                  "url":"https://fhir.nhs.uk/STU3/StructureDefinition/Extension-coding-sctdescid",
+                  "extension":[
+                    {
+                      "url":"descriptionId",
+                      "valueId":"2563401000000119"
+                    }
+                  ]
+                }
+              ],
+              "system":"http://snomed.info/sct",
+              "code":"997201000000100",
+              "display":"Normal levels detected"
+            }
+          ]
+        },
+        "subject":{
+          "reference":"Patient/DAED5527-1985-45D9-993E-C5FF51F36828"
+        },
+        "effectiveDateTime":"2010-02-23",
+        "issued":"2010-02-25T15:41:00+00:00",
+        "performer":[
+          {
+            "reference":"Practitioner/C8FD0E2C-3124-4C72-AC8D-ABEA65537D1B"
+          }
+        ],
+        "comment":"This is a test result without a specimen."
+      }
+    },
     {
       "resource":{
         "resourceType":"Observation",

wiremock/README.md

@@ -105,10 +105,10 @@ To change the patient record returned to have 100 3.5MB = 350MB total attachment
 curl --request PUT --data '{"state": "350MB Attachments"}' http://localhost:8110/__admin/scenarios/migrateStructuredRecord/state
 ```
 
-To change the patient record returned to have a 10MB attachment (useful for testing fragments) [10MBDocument](stubs/__files/correctPatientStructuredRecordResponse10MBAttachment.json):
+To change the patient record returned to have a 30MB attachment (useful for testing fragments) [30MBDocument](stubs/__files/correctPatientStructuredRecordResponse30MBAttachment.json):
 
 ```shell
-curl --request PUT --data '{"state": "10MB Attachment"}' http://localhost:8110/__admin/scenarios/migrateStructuredRecord/state
+curl --request PUT --data '{"state": "30MB Attachment"}' http://localhost:8110/__admin/scenarios/migrateStructuredRecord/state
 ```
 
 To change the patient record returned to be NOT FOUND:

…__files/correct10MBDocumentResponse.json …__files/correct30MBDocumentResponse.jsonwiremock/stubs/__files/correct10MBDocumentResponse.json renamed to wiremock/stubs/__files/correct30MBDocumentResponse.json wiremock/stubs/__files/correct10MBDocumentResponse.json renamed to wiremock/stubs/__files/correct30MBDocumentResponse.json

@@ -2,5 +2,5 @@
   "resourceType": "Binary",
   "id": "2cb1f113-3b15-41e8-b6b1-21e761838b19",
   "contentType": "text/plain",
-  "content": "{{#base64}}{{randomValue length=10485760 type='ALPHANUMERIC'}}{{/base64}}"
+  "content": "{{#base64}}{{randomValue length=31457280 type='ALPHANUMERIC'}}{{/base64}}"
 }