Merge branch 'main' into NIAD-3393

Author: ORybak5

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * Prevent duplicate processing: after a medication request is processed, the system no longer pulls a subsequent non‑consultation item based on the same request.
 
 ### Added
+* The GP2GP Adaptor now validates references inside condition objects to test whether they actually exist. Otherwise, the bundle is rejected.
 * The GP2GP Adaptor now adds the EhrComposition / confidentialityCode field when Encounter.meta.security contains NOPAT security entry
 * The GP2GP Adaptor now populates the ObservationStatement / confidentialityCode field when the .meta.security field of an Uncategorized Data Observation contains NOPAT
 * When List.meta.security field contains NOPAT, the GP2GP Adaptor will now populate the CompoundStatement.confidentialityCode

e2e-tests/build.gradle

@@ -1,6 +1,6 @@
 plugins {
     id 'java'
-    id "io.freefair.lombok" version "8.14"
+    id "io.freefair.lombok" version "8.14.2"
 }
 
 apply plugin: 'java'
@@ -13,18 +13,18 @@ repositories {
 }
 
 dependencies {
-    implementation 'org.apache.qpid:qpid-jms-client:2.7.0'
+    implementation 'org.apache.qpid:qpid-jms-client:2.9.0'
     implementation "org.apache.geronimo.specs:geronimo-jms_1.1_spec:1.1.1"
     implementation 'org.mongodb:mongo-java-driver:3.12.14'
     testImplementation(platform('org.junit:junit-bom:5.13.4'))
     testImplementation 'org.junit.jupiter:junit-jupiter'
-    testImplementation 'com.fasterxml.jackson.core:jackson-databind:2.19.2'
-    testImplementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.19.2'
+    testImplementation 'com.fasterxml.jackson.core:jackson-databind:2.20.0'
+    testImplementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.20.0'
     testImplementation 'commons-io:commons-io:2.20.0'
     testImplementation 'org.awaitility:awaitility:4.3.0'
-    testImplementation "org.assertj:assertj-core:3.27.4"
+    testImplementation "org.assertj:assertj-core:3.27.5"
     testImplementation 'ch.qos.logback:logback-classic:1.5.18'
-    testImplementation 'org.xmlunit:xmlunit-assertj3:2.10.3'
+    testImplementation 'org.xmlunit:xmlunit-assertj3:2.10.4'
     testImplementation 'org.apache.httpcomponents.client5:httpclient5:5.5'
 
     testRuntimeOnly 'org.junit.platform:junit-platform-launcher'

mock-mhs-adaptor/build.gradle

@@ -1,8 +1,8 @@
 plugins {
-	id 'org.springframework.boot' version '3.5.4'
+	id 'org.springframework.boot' version '3.5.6'
 	id 'io.spring.dependency-management' version '1.1.7'
 	id 'java'
-	id "io.freefair.lombok" version "8.14"
+	id "io.freefair.lombok" version "8.14.2"
 }
 
 apply plugin: 'java'
@@ -19,7 +19,7 @@ dependencies {
 	implementation 'org.springframework.boot:spring-boot-starter-actuator'
 	implementation 'org.springframework.boot:spring-boot-starter-web'
 	implementation 'org.springframework:spring-jms'
-	implementation 'org.apache.qpid:qpid-jms-client:2.7.0'
+	implementation 'org.apache.qpid:qpid-jms-client:2.8.0'
 	implementation 'org.apache.commons:commons-lang3:3.18.0'
 	testImplementation 'org.springframework.boot:spring-boot-starter-test'
 }

service/build.gradle

@@ -3,8 +3,8 @@ plugins {
 	id 'io.spring.dependency-management' version '1.1.7'
 	id 'java'
 	id "checkstyle"
-	id "com.github.spotbugs" version "6.1.13"
-	id "io.freefair.lombok" version "8.14"
+	id "com.github.spotbugs" version "6.4.2"
+	id "io.freefair.lombok" version "8.14.2"
 	id 'jacoco'
 	id 'org.sonarqube' version '6.2.0.5505'
 
@@ -13,16 +13,27 @@ plugins {
 	id 'com.arcmutate.github' version '2.2.3'
 }
 
+spotbugs {
+    toolVersion = '4.9.5'
+}
+
 apply plugin: 'java'
 apply plugin: 'org.springframework.boot'
 apply plugin: 'checkstyle'
 apply plugin: "com.github.spotbugs"
 apply plugin: 'application'
 
-mainClassName = ' uk.nhs.adaptors.gp2gp.Gp2gpApplication'
+application {
+    mainClassName = 'uk.nhs.adaptors.gp2gp.Gp2gpApplication'
+}
 
 group = 'uk.nhs.adaptors'
-sourceCompatibility = '21'
+
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(21)
+    }
+}
 
 checkstyle {
 	toolVersion '10.18.2'
@@ -50,9 +61,9 @@ dependencies {
 	implementation 'org.springframework.boot:spring-boot-starter-logging'
 
 	// Infrastructure
-	implementation 'software.amazon.awssdk:s3:2.32.14'
+	implementation 'software.amazon.awssdk:s3:2.33.9'
 	implementation ('com.azure:azure-storage-blob:12.30.0')
-	implementation 'org.apache.qpid:qpid-jms-client:2.7.0'
+	implementation 'org.apache.qpid:qpid-jms-client:2.8.0'
 
 	// Utils
 	implementation 'org.apache.commons:commons-lang3:3.18.0'
@@ -75,8 +86,11 @@ dependencies {
 	testImplementation 'com.squareup.okhttp3:mockwebserver3:5.1.0'
 	testImplementation 'com.adobe.testing:s3mock-testcontainers:4.7.0'
 
-   pitest 'com.arcmutate:base:1.3.2'
-   pitest 'com.arcmutate:pitest-git-plugin:2.1.0'
+  spotbugs 'com.github.spotbugs:spotbugs:4.9.5'
+  spotbugs 'com.github.spotbugs:spotbugs-annotations:4.9.5'
+
+  pitest 'com.arcmutate:base:1.3.2'
+  pitest 'com.arcmutate:pitest-git-plugin:2.1.0'
 }
 
 test {
@@ -104,9 +118,10 @@ sourceSets {
 	}
 }
 
-task(interoperabilityTestingToolJsonToXml, dependsOn: 'classes', type: JavaExec) {
-	mainClass.set('uk.nhs.adaptors.gp2gp.transformjsontoxmltool.TransformJsonToXml')
-	classpath = sourceSets.main.runtimeClasspath
+tasks.register('interoperabilityTestingToolJsonToXml', JavaExec) {
+    dependsOn 'classes'
+    mainClass.set('uk.nhs.adaptors.gp2gp.transformjsontoxmltool.TransformJsonToXml')
+    classpath = sourceSets.main.runtimeClasspath
 }
 
 configurations {
@@ -116,21 +131,21 @@ configurations {
 	integrationTestAnnotationProcessor.extendsFrom testAnnotationProcessor
 }
 
-task integrationTest(type: Test) {
-	useJUnitPlatform() {
-		description = 'Runs integration tests.'
-		group = 'verification'
+tasks.register('integrationTest', Test) {
+    useJUnitPlatform() {
+        description = 'Runs integration tests.'
+        group = 'verification'
 
-		testClassesDirs = sourceSets.integrationTest.output.classesDirs
-		classpath = sourceSets.integrationTest.runtimeClasspath
-		shouldRunAfter test
-	}
+        testClassesDirs = sourceSets.integrationTest.output.classesDirs
+        classpath = sourceSets.integrationTest.runtimeClasspath
+        shouldRunAfter test
+    }
 }
 
-tasks.withType(Test) {
-	testLogging {
-		events "passed", "skipped", "failed"
-	}
+tasks.withType(Test).configureEach {
+    testLogging {
+        events "passed", "skipped", "failed"
+    }
 }
 
 check.dependsOn integrationTest
@@ -140,13 +155,13 @@ spotbugsIntegrationTest.enabled = false
 spotbugsMain {
 	reports {
 		html {
-			enabled = true
+			enabled(true)
 		}
 		xml {
-			enabled = true
+			enabled(true)
 		}
-		excludeFilter.set(file("spotbugs/exclude.xml"))
 	}
+    excludeFilter.set(file("spotbugs/exclude.xml"))
 }
 
 pitest {

service/src/main/java/uk/nhs/adaptors/gp2gp/common/configuration/CustomTrustStore.java

@@ -57,7 +57,6 @@ private X509TrustManager getDefaultTrustManager() {
     }
 
     @SneakyThrows
-    @SuppressFBWarnings("RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE")
     protected X509TrustManager getCustomDbTrustManager(S3Uri s3Uri, String trustStorePassword) {
         TrustManagerFactory trustManagerFactory = TrustManagerFactory.getInstance(TrustManagerFactory.getDefaultAlgorithm());
         trustManagerFactory.init((KeyStore) null);

service/src/main/java/uk/nhs/adaptors/gp2gp/common/mongo/ttl/CosmosTtlCreator.java

@@ -25,7 +25,7 @@ public void create(Class<? extends TimeToLive> clazz) {
             String indexName = findTtlIndex().map(IndexInfo::getName).orElseThrow();
             getIndexOperations().dropIndex(indexName);
         }
-        getIndexOperations().ensureIndex(new Index()
+        getIndexOperations().createIndex(new Index()
             .expire(getDuration())
             .on(INDEX_FIELD_KEY, Sort.Direction.ASC)
         );

service/src/main/java/uk/nhs/adaptors/gp2gp/common/mongo/ttl/MongoTtlCreator.java

@@ -25,7 +25,7 @@ public void create(Class<? extends TimeToLive> clazz) {
                 clazz.getSimpleName(), getDuration());
             getIndexOperations().dropIndex(TTL_INDEX_NAME);
         }
-        getIndexOperations().ensureIndex(new Index()
+        getIndexOperations().createIndex(new Index()
             .expire(getDuration())
             .named(TTL_INDEX_NAME)
             .on(FIELD_KEY, Sort.Direction.ASC)

service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/ConditionLinkSetMapper.java

@@ -65,6 +65,8 @@ public String mapConditionToLinkSet(Condition condition, boolean isNested) {
             .isNested(isNested)
             .linkSetId(idMapper.getOrNew(ResourceType.Condition, condition.getIdElement()));
 
+        testForValidReferences(condition);
+
         buildEffectiveTimeLow(condition).ifPresent(builder::effectiveTimeLow);
         buildEffectiveTimeHigh(condition).ifPresent(builder::effectiveTimeHigh);
         buildAvailabilityTime(condition).ifPresent(builder::availabilityTime);
@@ -104,6 +106,21 @@ public String mapConditionToLinkSet(Condition condition, boolean isNested) {
         return TemplateUtils.fillTemplate(OBSERVATION_STATEMENT_TEMPLATE, builder.build());
     }
 
+    public void testForValidReferences(Condition condition) {
+        for (Extension extension : condition.getExtension()) {
+            if (!(extension.getValue() instanceof Reference)) {
+                return;
+            }
+            IdType idType = (IdType) ((Reference) extension.getValue()).getReferenceElement();
+            try {
+                messageContext.getInputBundleHolder().getResource(idType);
+            } catch (Exception e) {
+                LOGGER.warn("Bundle mapping aborted. Reason: " + e.getMessage());
+                throw e;
+            }
+        }
+    }
+
     private void setQualifierProperties(ConditionLinkSetMapperParameters.ConditionLinkSetMapperParametersBuilder builder,
         String qualifier) {
         builder.qualifierDisplay(qualifier);

service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/EncounterMapper.java

@@ -23,7 +23,6 @@
 
 import com.github.mustachejava.Mustache;
 
-import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 import lombok.RequiredArgsConstructor;
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
@@ -171,8 +170,6 @@ private String buildOriginalText(Encounter encounter) {
     }
 
     @SneakyThrows
-    @SuppressFBWarnings(value = "RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE",
-        justification = "https://github.com/spotbugs/spotbugs/issues/1338")
     private static Set<String> getEhrCompositionNameVocabularyCodes() {
         try (InputStream is = EncounterMapper.class.getClassLoader().getResourceAsStream("ehr_composition_name_vocabulary_codes.txt");
              BufferedReader reader = new BufferedReader(new InputStreamReader(is, UTF_8))) {

service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/SupportedContentTypes.java

@@ -12,7 +12,6 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
-import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 import lombok.AllArgsConstructor;
 import lombok.SneakyThrows;
 
@@ -27,8 +26,6 @@ public boolean isContentTypeSupported(String attachmentContentType) {
     }
 
     @SneakyThrows
-    @SuppressFBWarnings(value = "RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE",
-        justification = "https://github.com/spotbugs/spotbugs/issues/1338")
     private static Set<String> loadSupportedContentTypes() {
         try (InputStream is = SupportedContentTypes.class.getClassLoader().getResourceAsStream(SUPPORTED_CONTENT_TYPES_PATH);
              BufferedReader reader = new BufferedReader(new InputStreamReader(is, UTF_8))) {