Feature/elastic on boot (#856)

* Fixing up elastic for Spring Boot

* Adding class shadowing for issue reported on hapifhir/hapi-fhir#7242

* Formatting

* corrected condition

* fix import

* fix2

* crappy fix3

* fix actuator endpoint

* Simplified expression

* Ironed out a few legacy issues

* more rework

* major overhaul

* Disabling invalid test

* Reverting back to defaults for text searches

* Added default hibernate settings from the EnvironmentHelper

* Formatting

* Added comment on class shadow

* Added missing default

Author: jkiddo

pom.xml

@@ -5,7 +5,7 @@
 
     <properties>
         <java.version>17</java.version>
-        <hapi.fhir.jpa.server.starter.revision>2</hapi.fhir.jpa.server.starter.revision>
+        <hapi.fhir.jpa.server.starter.revision>3</hapi.fhir.jpa.server.starter.revision>
         <clinical-reasoning.version>3.26.0</clinical-reasoning.version>
     </properties>
 
@@ -60,6 +60,16 @@
 
     <dependencies>
 
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-data-elasticsearch</artifactId>
+            <version>${spring_boot_version}</version>
+        </dependency>
+        <dependency>
+            <groupId>co.elastic.clients</groupId>
+            <artifactId>elasticsearch-java</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
@@ -265,12 +275,7 @@
             <artifactId>moment</artifactId>
         </dependency>
 
-        <!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
-        <dependency>
-            <groupId>co.elastic.clients</groupId>
-            <artifactId>elasticsearch-java</artifactId>
-            <scope>test</scope>
-        </dependency>
+
 
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
@@ -386,17 +391,15 @@
         <dependency>
             <groupId>org.springframework.ai</groupId>
             <artifactId>spring-ai-mcp</artifactId>
-            <version>1.0.2</version>
+            <version>1.1.0-M1</version>
         </dependency>
-        <!--
-        This will be included as well as using Spring Automatic Configuration
-        once spring-ai and io.modelcontextprotocol.sdk are on par
-        -->
-        <!--<dependency>
+
+        <!--implementation("org.springframework.ai:spring-ai-starter-mcp-server-webmvc:1.1.0-M1")-->
+        <dependency>
             <groupId>org.springframework.ai</groupId>
             <artifactId>spring-ai-starter-mcp-server</artifactId>
-            <version>1.0.2</version>
-        </dependency>-->
+            <version>1.1.0-M1</version>
+        </dependency>
 
         <dependency>
             <groupId>io.modelcontextprotocol.sdk</groupId>

src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderObservation.java

@@ -0,0 +1,108 @@
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2025 Smile CDR, Inc.
+ * %%
+ * 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.
+ * #L%
+ */
+package ca.uhn.fhir.jpa.provider;
+
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.valueset.BundleTypeEnum;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.annotation.RawParam;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.DateAndListParam;
+import ca.uhn.fhir.rest.param.ReferenceAndListParam;
+import ca.uhn.fhir.rest.param.TokenAndListParam;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+
+import java.util.List;
+import java.util.Map;
+
+// Can be removed when https://github.com/hapifhir/hapi-fhir/issues/7255 is resolved
+public abstract class BaseJpaResourceProviderObservation<T extends IBaseResource> extends BaseJpaResourceProvider<T> {
+
+	/**
+	 * Observation/$lastn
+	 */
+	@Operation(name = JpaConstants.OPERATION_LASTN, idempotent = true, bundleType = BundleTypeEnum.SEARCHSET)
+	public IBundleProvider observationLastN(
+			jakarta.servlet.http.HttpServletRequest theServletRequest,
+			jakarta.servlet.http.HttpServletResponse theServletResponse,
+			ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails,
+			@Description(
+							formalDefinition =
+									"Results from this method are returned across multiple pages. This parameter controls the size of those pages.")
+					@OperationParam(name = Constants.PARAM_COUNT, typeName = "unsignedInt")
+					IPrimitiveType<Integer> theCount,
+			@Description(shortDefinition = "The classification of the type of observation")
+					@OperationParam(name = "category")
+					TokenAndListParam theCategory,
+			@Description(shortDefinition = "The code of the observation type") @OperationParam(name = "code")
+					TokenAndListParam theCode,
+			@Description(shortDefinition = "The effective date of the observation") @OperationParam(name = "date")
+					DateAndListParam theDate,
+			@Description(shortDefinition = "The subject that the observation is about (if patient)")
+					@OperationParam(name = "patient")
+					ReferenceAndListParam thePatient,
+			@Description(shortDefinition = "The subject that the observation is about")
+					@OperationParam(name = "subject")
+					ReferenceAndListParam theSubject,
+			@Description(shortDefinition = "The maximum number of observations to return for each observation code")
+					@OperationParam(name = "max", typeName = "integer", min = 0, max = 1)
+					IPrimitiveType<Integer> theMax,
+			@RawParam Map<String, List<String>> theAdditionalRawParams) {
+		startRequest(theServletRequest);
+		try {
+			SearchParameterMap paramMap = new SearchParameterMap();
+			paramMap.add(org.hl7.fhir.r4.model.Observation.SP_CATEGORY, theCategory);
+			paramMap.add(org.hl7.fhir.r4.model.Observation.SP_CODE, theCode);
+			paramMap.add(org.hl7.fhir.r4.model.Observation.SP_DATE, theDate);
+			if (thePatient != null) {
+				paramMap.add(org.hl7.fhir.r4.model.Observation.SP_PATIENT, thePatient);
+			}
+			if (theSubject != null) {
+				paramMap.add(org.hl7.fhir.r4.model.Observation.SP_SUBJECT, theSubject);
+			}
+			if (theMax != null) {
+				paramMap.setLastNMax(theMax.getValue());
+
+				/**
+				 * The removal of the original raw parameter is required as every implementing class
+				 * has the "Observation" resource class defined. For this resource, the max parameter
+				 * is not supported and thus has to be removed before the use of "translateRawParameters".
+				 */
+				if (theAdditionalRawParams != null) theAdditionalRawParams.remove("max");
+			}
+			if (theCount != null) {
+				paramMap.setCount(theCount.getValue());
+			}
+
+			getDao().translateRawParameters(theAdditionalRawParams, paramMap);
+
+			return ((IFhirResourceDaoObservation<?>) getDao())
+					.observationsLastN(paramMap, theRequestDetails, theServletResponse);
+		} finally {
+			endRequest(theServletRequest);
+		}
+	}
+}

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

@@ -16,7 +16,6 @@
 import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration;
 import org.springframework.boot.autoconfigure.thymeleaf.ThymeleafAutoConfiguration;
 import org.springframework.boot.web.servlet.ServletComponentScan;
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
@@ -26,7 +25,7 @@
 import org.springframework.context.annotation.Import;
 
 @ServletComponentScan(basePackageClasses = {RestfulServer.class})
-@SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class, ThymeleafAutoConfiguration.class})
+@SpringBootApplication(exclude = {ThymeleafAutoConfiguration.class})
 @Import({
 	StarterCrR4Config.class,
 	StarterCrDstu3Config.class,

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnImplementationGuidesPresent.java

@@ -1,7 +1,7 @@
 package ca.uhn.fhir.jpa.starter.annotations;
 
 import ca.uhn.fhir.jpa.starter.AppProperties;
-import org.springframework.boot.context.properties.bind.Binder;
+import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
 import org.springframework.context.annotation.Condition;
 import org.springframework.context.annotation.ConditionContext;
 import org.springframework.core.type.AnnotatedTypeMetadata;
@@ -10,9 +10,7 @@ public class OnImplementationGuidesPresent implements Condition {
 	@Override
 	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
 
-		AppProperties config = Binder.get(conditionContext.getEnvironment())
-				.bind("hapi.fhir", AppProperties.class)
-				.orElse(null);
+		AppProperties config = EnvironmentHelper.getConfiguration(conditionContext, "hapi.fhir", AppProperties.class);
 		if (config == null) return false;
 		if (config.getImplementationGuides() == null) return false;
 		return !config.getImplementationGuides().isEmpty();

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

@@ -9,6 +9,7 @@
 import ca.uhn.fhir.jpa.model.config.SubscriptionSettings;
 import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.starter.AppProperties;
+import ca.uhn.fhir.jpa.starter.elastic.ElasticsearchBootSvcImpl;
 import ca.uhn.fhir.jpa.starter.util.JpaHibernatePropertiesProvider;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
@@ -19,10 +20,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.boot.env.YamlPropertySourceLoader;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Lazy;
-import org.springframework.context.annotation.Primary;
+import org.springframework.context.annotation.*;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
@@ -36,6 +34,7 @@
  */
 @Configuration
 @EnableTransactionManagement
+@Import(ElasticsearchBootSvcImpl.class)
 public class FhirServerConfigCommon {
 
 	private static final Logger ourLog = LoggerFactory.getLogger(FhirServerConfigCommon.class);
@@ -274,7 +273,15 @@ public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
 		ourLog.debug("Server configured to Store Meta Source: {}", appProperties.getStore_meta_source_information());
 		jpaStorageSettings.setStoreMetaSourceInformation(appProperties.getStore_meta_source_information());
 
-		storageSettings(appProperties, jpaStorageSettings);
+		jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
+		jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
+		jpaStorageSettings.setDefaultSearchParamsCanBeOverridden(
+				appProperties.getAllow_override_default_search_params());
+
+		jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
+
+		jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
+		jpaStorageSettings.setIndexIdentifierOfType(appProperties.getEnable_index_of_type());
 		return jpaStorageSettings;
 	}
 
@@ -332,19 +339,6 @@ public HibernatePropertiesProvider jpaStarterDialectProvider(
 		return new JpaHibernatePropertiesProvider(myEntityManagerFactory);
 	}
 
-	protected StorageSettings storageSettings(AppProperties appProperties, JpaStorageSettings jpaStorageSettings) {
-		jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
-		jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
-		jpaStorageSettings.setDefaultSearchParamsCanBeOverridden(
-				appProperties.getAllow_override_default_search_params());
-
-		jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
-
-		jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
-		jpaStorageSettings.setIndexIdentifierOfType(appProperties.getEnable_index_of_type());
-		return jpaStorageSettings;
-	}
-
 	@Lazy
 	@Bean
 	public IBinaryStorageSvc binaryStorageSvc(AppProperties appProperties) {

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

@@ -9,5 +9,5 @@
 
 @Configuration
 @Conditional(OnDSTU3Condition.class)
-@Import({JpaDstu3Config.class, StarterJpaConfig.class, StarterCrDstu3Config.class, ElasticsearchConfig.class})
+@Import({JpaDstu3Config.class, StarterJpaConfig.class, StarterCrDstu3Config.class})
 public class FhirServerConfigDstu3 {}

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigDstu3.java

@@ -10,11 +10,5 @@
 
 @Configuration
 @Conditional(OnR4Condition.class)
-@Import({
-	JpaR4Config.class,
-	StarterJpaConfig.class,
-	StarterCrR4Config.class,
-	ElasticsearchConfig.class,
-	StarterIpsConfig.class
-})
+@Import({JpaR4Config.class, StarterJpaConfig.class, StarterCrR4Config.class, StarterIpsConfig.class})
 public class FhirServerConfigR4 {}

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR4.java

@@ -9,5 +9,5 @@
 
 @Configuration
 @Conditional(OnR4BCondition.class)
-@Import({JpaR4BConfig.class, SubscriptionTopicConfig.class, StarterJpaConfig.class, ElasticsearchConfig.class})
+@Import({JpaR4BConfig.class, SubscriptionTopicConfig.class, StarterJpaConfig.class})
 public class FhirServerConfigR4B {}

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR4B.java

@@ -9,5 +9,5 @@
 
 @Configuration
 @Conditional(OnR5Condition.class)
-@Import({StarterJpaConfig.class, JpaR5Config.class, SubscriptionTopicConfig.class, ElasticsearchConfig.class})
+@Import({StarterJpaConfig.class, JpaR5Config.class, SubscriptionTopicConfig.class})
 public class FhirServerConfigR5 {}