Merge branch 'master' into expose-search-prefetch-thresholds

pom.xml

@@ -43,14 +43,6 @@
     <dependencyManagement>
        <dependencies>
 
-            <!-- Temporarily override CR depedencies for debugging -->
-<!--            <dependency>-->
-<!--                <groupId>org.opencds.cqf.fhir</groupId>-->
-<!--                <artifactId>cqf-fhir-bom</artifactId>-->
-<!--                <version>3.4.0</version>-->
-<!--                <type>pom</type>-->
-<!--                <scope>import</scope>-->
-<!--            </dependency>-->
             <dependency>
                <groupId>org.glassfish.jaxb</groupId>
                <artifactId>jaxb-runtime</artifactId>
@@ -364,6 +356,14 @@
             <version>1.13.3</version>
         </dependency>
 
+        <!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-registry-prometheus-simpleclient -->
+        <dependency>
+            <groupId>io.micrometer</groupId>
+            <artifactId>micrometer-registry-prometheus-simpleclient</artifactId>
+            <version>1.13.3</version>
+        </dependency>
+
+
         <dependency>
             <groupId>com.zaxxer</groupId>
             <artifactId>HikariCP</artifactId>

src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java

@@ -103,6 +103,7 @@ public class AppProperties {
   private final List<String> custom_interceptor_classes = new ArrayList<>();
 
 	private final List<String> custom_provider_classes = new ArrayList<>();
+	private Boolean upliftedRefchains_enabled = false;
 
 	private List<Integer> search_prefetch_thresholds = new ArrayList<>();
 
@@ -653,6 +654,13 @@ public Cors getCors() {
 		this.search_prefetch_thresholds = thePrefetchThresholds;
 	}
 
+	public boolean getUpliftedRefchains_enabled() {
+		return upliftedRefchains_enabled;
+	}
+
+	public void setUpliftedRefchains_enabled(boolean upliftedRefchains_enabled) {
+		this.upliftedRefchains_enabled = upliftedRefchains_enabled;
+	}
 
 	public static class Cors {
     private Boolean allow_Credentials = true;

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java

@@ -149,6 +149,7 @@ public class FhirServerConfigCommon {
 		jpaStorageSettings.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
 		jpaStorageSettings.setExpungeEnabled(appProperties.getExpunge_enabled());
 		jpaStorageSettings.setLanguageSearchParameterEnabled(appProperties.getLanguage_search_parameter_enabled());
+		jpaStorageSettings.setIndexOnUpliftedRefchains(appProperties.getUpliftedRefchains_enabled());
 
 
 		if (!appProperties.getSearch_prefetch_thresholds().isEmpty()) {

src/main/resources/application.yaml

@@ -1,31 +1,37 @@
 #Uncomment the "servlet" and "context-path" lines below to make the fhir endpoint available at /example/path/fhir instead of the default value of /fhir
 server:
-#  servlet:
+  #  servlet:
-#    context-path: /example/path
+  #    context-path: /example/path
   port: 8080
 #Adds the option to go to eg. http://localhost:8080/actuator/health for seeing the running configuration
 #see https://docs.spring.io/spring-boot/docs/current/reference/html/actuator.html#actuator.endpoints
 management:
-  endpoint:
+  #The following configuration will enable the actuator endpoints at /actuator/health, /actuator/info, /actuator/prometheus, /actuator/metrics. For security purposes, only /actuator/health is enabled by default.
   endpoints:
     enabled-by-default: false
     web:
       exposure:
-          include: health,prometheus
+        include: 'health' # or e.g. 'info,health,prometheus,metrics' or '*' for all'
+  endpoint:
+    info:
+      enabled: true
+    metrics:
+      enabled: true
     health:
       enabled: true
       probes:
         enabled: true
-      livenessState:
+      group:
-        enabled: true
+        liveness:
-      readinessState:
+          include:
-        enabled: true
+            - livenessState
+            - readinessState
     prometheus:
       enabled: true
+  prometheus:
     metrics:
       export:
         enabled: true
-
 spring:
   main:
     allow-circular-references: true
@@ -184,6 +190,7 @@ hapi:
     #    enable_index_missing_fields: false
     #    enable_index_of_type: true
     #    enable_index_contained_resource: false
+    #    upliftedRefchains_enabled: true
     #    resource_dbhistory_enabled: false
     ###  !!Extended Lucene/Elasticsearch Indexing is still a experimental feature, expect some features (e.g. _total=accurate) to not work as expected!!
     ###  more information here: https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html

src/main/resources/cds.application.yaml

@@ -6,10 +6,32 @@ server:
 #Adds the option to go to eg. http://localhost:8080/actuator/health for seeing the running configuration
 #see https://docs.spring.io/spring-boot/docs/current/reference/html/actuator.html#actuator.endpoints
 management:
+  #The following configuration will enable the actuator endpoints at /actuator/health, /actuator/info, /actuator/prometheus, /actuator/metrics. For security purposes, only /actuator/health is enabled by default.
   endpoints:
+    enabled-by-default: false
     web:
       exposure:
-        include: "health,prometheus"
+        include: 'health' # or e.g. 'info,health,prometheus,metrics' or '*' for all'
+  endpoint:
+    info:
+      enabled: true
+    metrics:
+      enabled: true
+    health:
+      enabled: true
+      probes:
+        enabled: true
+      group:
+        liveness:
+          include:
+            - livenessState
+            - readinessState
+    prometheus:
+      enabled: true
+  prometheus:
+    metrics:
+      export:
+        enabled: true
 spring:
   main:
     allow-circular-references: true

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java

@@ -13,6 +13,10 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import jakarta.websocket.ContainerProvider;
 import jakarta.websocket.Session;
 import jakarta.websocket.WebSocketContainer;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
@@ -29,6 +33,8 @@ import org.hl7.fhir.r4.model.Subscription;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Order;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.ValueSource;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.web.server.LocalServerPort;
@@ -306,6 +312,17 @@ class ExampleServerR4IT implements IServerSupport {
 			.size();
 	}
 
+	@ParameterizedTest
+	@ValueSource(strings = {"prometheus", "health", "metrics", "info"})
+	void testActuatorEndpointExists(String endpoint) throws IOException {
+
+		CloseableHttpClient httpclient = HttpClients.createDefault();
+		CloseableHttpResponse response = httpclient.execute(new HttpGet("http://localhost:" + port + "/actuator/" + endpoint));
+		int statusCode = response.getStatusLine().getStatusCode();
+		assertEquals(200, statusCode);
+
+	}
+
 	@BeforeEach
 	void beforeEach() {
 

src/test/resources/application.yaml

@@ -1,3 +1,30 @@
+management:
+  #The following configuration will enable the actuator endpoints at /actuator/health, /actuator/info, /actuator/prometheus
+  endpoints:
+    enabled-by-default: false
+    web:
+      exposure:
+        include: 'info,health,prometheus,metrics' # or '*' for all'
+  endpoint:
+    info:
+      enabled: true
+    metrics:
+      enabled: true
+    health:
+      enabled: true
+      probes:
+        enabled: true
+      group:
+        liveness:
+          include:
+            - livenessState
+            - readinessState
+    prometheus:
+      enabled: true
+  prometheus:
+    metrics:
+      export:
+        enabled: true
 spring:
   main:
     allow-circular-references: true