Merge remote-tracking branch 'origin/main'

# Conflicts:
#	ui/package.json

Author: dionmcm

.gitignore

@@ -1,3 +1,4 @@
+*.iml
 .idea
 .vscode
 .java-version

CHANGELOG.md

@@ -11,6 +11,9 @@ The following sections are considered for each release: **Added, Changed, Fixed,
 - No updates yet.
 
 
+## [1.3.0] - 2025-09-22
+
+
 ## [1.2.11] - 2025-09-03
 
 

api/pom.xml

@@ -373,8 +373,8 @@
     </dependency>
     <dependency>
       <artifactId>wiremock-standalone</artifactId>
-      <groupId>com.github.tomakehurst</groupId>
-      <version>3.0.0</version>
+      <groupId>org.wiremock</groupId>
+      <version>3.0.3</version>
     </dependency>
     <dependency>
       <artifactId>postgresql</artifactId>
@@ -442,6 +442,11 @@
       <groupId>org.testcontainers</groupId>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <artifactId>rabbitmq</artifactId>
+      <groupId>org.testcontainers</groupId>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <artifactId>jgrapht-core</artifactId>
       <groupId>org.jgrapht</groupId>
@@ -493,14 +498,23 @@
     </dependency>
     <dependency>
       <artifactId>hibernate-jcache</artifactId>
-      <groupId>org.hibernate</groupId>
+      <groupId>org.hibernate.orm</groupId>
       <version>${hibernate.version}</version>
     </dependency>
     <dependency>
       <artifactId>ehcache</artifactId>
       <groupId>org.ehcache</groupId>
       <version>3.10.8</version>
     </dependency>
+    <dependency>
+      <groupId>org.springframework</groupId>
+      <artifactId>spring-web</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>software.amazon.awssdk</groupId>
+      <artifactId>s3</artifactId>
+      <version>2.33.0</version>
+    </dependency>
   </dependencies>
   <description>Api for Lingo</description>
   <modelVersion>4.0.0</modelVersion>
@@ -510,24 +524,42 @@
   <parent>
     <artifactId>lingo</artifactId>
     <groupId>au.gov.digitalhealth</groupId>
-    <version>1.2.12-SNAPSHOT</version>
+    <version>1.3.1-SNAPSHOT</version>
   </parent>
   <profiles>
     <profile>
       <activation>
-        <property>
-          <name>buildnumber</name>
-        </property>
+        <activeByDefault>true</activeByDefault>
       </activation>
       <build>
         <plugins>
+          <plugin>
+            <artifactId>git-commit-id-maven-plugin</artifactId>
+            <configuration>
+              <generateGitPropertiesFile>true</generateGitPropertiesFile>
+              <includeOnlyProperties>
+                <includeOnlyProperty>git.commit.id.abbrev</includeOnlyProperty>
+              </includeOnlyProperties>
+            </configuration>
+            <executions>
+              <execution>
+                <goals>
+                  <goal>revision</goal>
+                </goals>
+                <id>get-the-git-infos</id>
+                <phase>initialize</phase>
+              </execution>
+            </executions>
+            <groupId>io.github.git-commit-id</groupId>
+            <version>5.0.0</version>
+          </plugin>
           <plugin>
             <artifactId>maven-antrun-plugin</artifactId>
             <executions>
               <execution>
                 <configuration>
                   <target>
-                    <echo file="${staticdir}/buildnumber.txt">${buildnumber}</echo>
+                    <echo file="${staticdir}/buildnumber.txt">${buildnumber}-${git.commit.id.abbrev}</echo>
                   </target>
                 </configuration>
                 <goals>
@@ -540,7 +572,7 @@
           </plugin>
         </plugins>
       </build>
-      <id>azuredevops</id>
+      <id>buildnumber</id>
       <properties>
         <staticdir>${project.build.directory}/classes/static</staticdir>
       </properties>
@@ -603,7 +635,8 @@
     <postgres.version>42.7.3</postgres.version>
     <problem-spring-web.version>0.23.0</problem-spring-web.version>
     <querydsl.version>5.1.0</querydsl.version>
-    <snomed-owl-toolkit.version>5.4.0</snomed-owl-toolkit.version>
     <sentry.version>7.18.0</sentry.version>
+    <snomed-owl-toolkit.version>5.4.0</snomed-owl-toolkit.version>
+    <buildnumber>${project.version}</buildnumber>
   </properties>
 </project>

api/src/main/java/au/gov/digitalhealth/lingo/configuration/ApiWebConfiguration.java

@@ -18,6 +18,8 @@
 import au.gov.digitalhealth.lingo.auth.helper.AuthHelper;
 import au.gov.digitalhealth.lingo.log.SnowstormLogger;
 import au.gov.digitalhealth.lingo.util.AuthSnowstormLogger;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import io.netty.handler.logging.LogLevel;
 import lombok.extern.java.Log;
 import org.springframework.beans.factory.annotation.Value;
@@ -26,7 +28,9 @@
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.MediaType;
 import org.springframework.http.client.reactive.ReactorClientHttpConnector;
+import org.springframework.http.codec.json.Jackson2JsonEncoder;
 import org.springframework.web.reactive.function.client.ExchangeFilterFunction;
+import org.springframework.web.reactive.function.client.ExchangeStrategies;
 import org.springframework.web.reactive.function.client.WebClient;
 import reactor.core.publisher.Mono;
 import reactor.netty.http.client.HttpClient;
@@ -53,10 +57,14 @@ public WebClient snowStormApiClient(
                 "reactor.netty.http.client.HttpClient",
                 LogLevel.DEBUG,
                 AdvancedByteBufFormat.TEXTUAL);
+    ObjectMapper customMapper =
+        new ObjectMapper().setSerializationInclusion(JsonInclude.Include.NON_NULL);
+    Jackson2JsonEncoder encoder = new Jackson2JsonEncoder(customMapper, MediaType.APPLICATION_JSON);
     return webClientBuilder
         .codecs(
             clientCodecConfigurer ->
                 clientCodecConfigurer.defaultCodecs().maxInMemorySize(1024 * 1024 * 100))
+        .codecs(clientCodecConfigurer -> clientCodecConfigurer.customCodecs().register(encoder))
         .baseUrl(authoringServiceUrl)
         .clientConnector(new ReactorClientHttpConnector(httpClient))
         .defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE)
@@ -71,18 +79,30 @@ public WebClient authoringPlatformApiClient(
     return webClientBuilder
         .baseUrl(authoringServiceUrl)
         .defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE)
-        .filter(authHelper.addImsAuthCookie) // Cookies are injected through filter
+        .filter(authHelper.addImsAuthCookie)
+        .exchangeStrategies(
+            ExchangeStrategies.builder()
+                .codecs(configurer -> configurer.defaultCodecs().maxInMemorySize(10 * 1024 * 1024))
+                .build())
         .build();
   }
 
   @Bean
   public WebClient nameGeneratorApiClient(
       @Value("${name.generator.api.url}") String namegenApiUrl,
+      @Value("${name.generator.api.key:}") String apiKeyHeader,
       WebClient.Builder webClientBuilder) {
-    return webClientBuilder
-        .baseUrl(namegenApiUrl)
-        .defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE)
-        .build();
+    WebClient.Builder builder =
+        webClientBuilder
+            .baseUrl(namegenApiUrl)
+            .defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE);
+
+    // Only add the API key header if it's not empty
+    if (apiKeyHeader != null && !apiKeyHeader.isEmpty()) {
+      builder.defaultHeader("X-API-Key", apiKeyHeader);
+    }
+
+    return builder.build();
   }
 
   @Bean
@@ -93,6 +113,10 @@ public WebClient defaultAuthoringPlatformApiClient(
         .baseUrl(authoringServiceUrl)
         .defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE)
         .filter(authHelper.addDefaultAuthCookie) // Cookies are injected through filter
+        .exchangeStrategies(
+            ExchangeStrategies.builder()
+                .codecs(configurer -> configurer.defaultCodecs().maxInMemorySize(10 * 1024 * 1024))
+                .build())
         .build();
   }
 
@@ -107,6 +131,16 @@ public WebClient sergioApiClient(
         .build();
   }
 
+  @Bean
+  public WebClient fhirApiClient(
+      @Value("${fhir.server.url}") String fhirServerUrl, WebClient.Builder webClientBuilder) {
+    return webClientBuilder
+        .baseUrl(fhirServerUrl)
+        .defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE)
+        .filter(logRequest())
+        .build();
+  }
+
   private ExchangeFilterFunction logRequest() {
     return ExchangeFilterFunction.ofRequestProcessor(
         clientRequest -> {

api/src/main/java/au/gov/digitalhealth/lingo/configuration/AsyncConfig.java

@@ -0,0 +1,76 @@
+/*
+ * Copyright 2024 Australian Digital Health Agency ABN 84 425 496 912.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package au.gov.digitalhealth.lingo.configuration;
+
+import java.util.concurrent.Executor;
+import org.springframework.aop.interceptor.AsyncUncaughtExceptionHandler;
+import org.springframework.aop.interceptor.SimpleAsyncUncaughtExceptionHandler;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.scheduling.annotation.AsyncConfigurer;
+import org.springframework.scheduling.annotation.EnableAsync;
+import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
+import org.springframework.security.core.Authentication;
+import org.springframework.security.core.context.SecurityContextHolder;
+import org.springframework.web.context.request.RequestAttributes;
+import org.springframework.web.context.request.RequestContextHolder;
+
+@Configuration
+@EnableAsync
+public class AsyncConfig implements AsyncConfigurer {
+
+  @Override
+  public Executor getAsyncExecutor() {
+    ThreadPoolTaskExecutor executor = new ThreadPoolTaskExecutor();
+    executor.setCorePoolSize(10);
+    executor.setMaxPoolSize(20);
+    executor.setQueueCapacity(25);
+    executor.setThreadNamePrefix("async-");
+
+    // This decorator preserves request context for all async tasks
+    executor.setTaskDecorator(
+        task -> {
+          RequestAttributes attributes = RequestContextHolder.getRequestAttributes();
+          Authentication authentication = SecurityContextHolder.getContext().getAuthentication();
+
+          return () -> {
+            RequestAttributes oldAttributes = RequestContextHolder.getRequestAttributes();
+            Authentication oldAuthentication =
+                SecurityContextHolder.getContext().getAuthentication();
+            try {
+              if (attributes != null) {
+                RequestContextHolder.setRequestAttributes(attributes);
+              }
+              if (authentication != null) {
+                SecurityContextHolder.getContext().setAuthentication(authentication);
+              }
+              task.run();
+            } finally {
+              RequestContextHolder.setRequestAttributes(oldAttributes);
+              SecurityContextHolder.getContext().setAuthentication(oldAuthentication);
+            }
+          };
+        });
+
+    executor.initialize();
+    return executor;
+  }
+
+  // Exception handler for async tasks
+  @Override
+  public AsyncUncaughtExceptionHandler getAsyncUncaughtExceptionHandler() {
+    return new SimpleAsyncUncaughtExceptionHandler();
+  }
+}