Add configuration flag to enable storing of resources in lucene index (#304)

* Add configuration flag to enable storing of resources in lucene index

* Fix build issue

* Fix code review suggestions

Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com>

README.md

@@ -354,10 +354,14 @@ elasticsearch.schema_management_strategy=CREATE
 
 Set `hapi.fhir.lastn_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable the $lastn operation on this server.  Note that the $lastn operation relies on Elasticsearch, so for $lastn to work, indexing must be enabled using Elasticsearch.
 
+## Enabling Resource to be stored in Lucene Index
+
+Set `hapi.fhir.store_resource_in_lucene_index_enabled` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable storing of resource json along with Lucene/Elasticsearch index mappings.
+
 ## Changing cached search results time
 
-It is possible to change the cached search results time. The option `reuse_cached_search_results_millis` in the [application.yaml] is 6000 miliseconds by default.
+It is possible to change the cached search results time. The option `reuse_cached_search_results_millis` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) is 6000 miliseconds by default.
-Set `reuse_cached_search_results_millis: -1` in the [application.yaml] file to ignore the cache time every search. 
+Set `reuse_cached_search_results_millis: -1` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to ignore the cache time every search. 
 
 ## Build the distroless variant of the image (for lower footprint and improved security)
 

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

@@ -66,6 +66,7 @@ public class AppProperties {
   private Map<String, ImplementationGuide> implementationGuides = null;
 
   private Boolean lastn_enabled = false;
+  private boolean store_resource_in_lucene_index_enabled = false;
   private NormalizedQuantitySearchLevel normalized_quantity_search_level = NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED;
 
   private Integer search_coord_core_pool_size = 20;
@@ -469,7 +470,15 @@ public class AppProperties {
     this.lastn_enabled = lastn_enabled;
   }
 
-  public NormalizedQuantitySearchLevel getNormalized_quantity_search_level() {
+	public boolean getStore_resource_in_lucene_index_enabled() {
+		return store_resource_in_lucene_index_enabled;
+	}
+
+	public void setStore_resource_in_lucene_index_enabled(Boolean store_resource_in_lucene_index_enabled) {
+		this.store_resource_in_lucene_index_enabled = store_resource_in_lucene_index_enabled;
+	}
+
+	public NormalizedQuantitySearchLevel getNormalized_quantity_search_level() {
 	return this.normalized_quantity_search_level;
   }
 

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

@@ -407,8 +407,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
       daoConfig.setLastNEnabled(true);
     }
 
+	 daoConfig.setStoreResourceInLuceneIndex(appProperties.getStore_resource_in_lucene_index_enabled());
     daoConfig.getModelConfig().setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
-
+	 daoConfig.getModelConfig().setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
-		daoConfig.getModelConfig().setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
   }
 }

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

@@ -11,6 +11,7 @@ import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHan
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
 import ca.uhn.fhir.rest.server.mail.MailConfig;
+import ca.uhn.fhir.rest.server.mail.MailSvc;
 import com.google.common.base.Strings;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.dstu2.model.Subscription;
@@ -69,7 +70,7 @@ public class FhirServerConfigCommon {
     if (appProperties.getSubscription().getEmail() != null) {
       ourLog.info("Email subscriptions enabled");
     }
-    
+
     if (appProperties.getEnable_index_contained_resource() == Boolean.TRUE) {
         ourLog.info("Indexed on contained resource enabled");
       }
@@ -145,7 +146,7 @@ public class FhirServerConfigCommon {
       if(appProperties.getPartitioning().getAllow_references_across_partitions()) {
         retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.ALLOWED_UNQUALIFIED);
       } else {
-        retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.NOT_ALLOWED); 
+        retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.NOT_ALLOWED);
       }
     }
 
@@ -178,7 +179,7 @@ public class FhirServerConfigCommon {
     }
 
     modelConfig.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
-    
+
     modelConfig.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
     return modelConfig;
   }
@@ -225,10 +226,9 @@ public class FhirServerConfigCommon {
       mailConfig.setSmtpPassword(email.getPassword());
       mailConfig.setSmtpUseStartTLS(email.getStartTlsEnable());
 
-		 IEmailSender emailSender = new EmailSenderImpl(mailConfig);
+		IEmailSender emailSender = new EmailSenderImpl(new MailSvc(mailConfig));
 
-      if(subscriptionDeliveryHandlerFactory.isPresent())
+		subscriptionDeliveryHandlerFactory.ifPresent(theSubscriptionDeliveryHandlerFactory -> theSubscriptionDeliveryHandlerFactory.setEmailSender(emailSender));
-       subscriptionDeliveryHandlerFactory.get().setEmailSender(emailSender);
 
       return emailSender;
     }

src/main/resources/application.yaml

@@ -154,6 +154,7 @@ hapi:
 #        startTlsRequired:
 #        quitWait:
 #    lastn_enabled: true
+#    store_resource_in_lucene_index_enabled: true
 ###  This is configuration for normalized quantity serach level default is 0
 ###   0: NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED - default
 ###   1: NORMALIZED_QUANTITY_STORAGE_SUPPORTED

src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java

@@ -42,6 +42,7 @@ import org.testcontainers.elasticsearch.ElasticsearchContainer;
     "spring.datasource.url=jdbc:h2:mem:dbr4",
     "hapi.fhir.fhir_version=r4",
     "hapi.fhir.lastn_enabled=true",
+	 "hapi.fhir.store_resource_in_lucene_index_enabled=true",
     "elasticsearch.enabled=true",
     // Because the port is set randomly, we will set the rest_url using the Initializer.
     // "elasticsearch.rest_url='http://localhost:9200'",