Merge branch 'master' into rel_6_0_0_mergeback

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

@@ -25,12 +25,14 @@ public class AppProperties {
   private Boolean openapi_enabled = false;
   private Boolean mdm_enabled = false;
   private boolean advanced_lucene_indexing = false;
+  private boolean enable_index_of_type = false;
   private Boolean allow_cascading_deletes = false;
   private Boolean allow_contains_searches = true;
   private Boolean allow_external_references = false;
   private Boolean allow_multiple_delete = false;
   private Boolean allow_override_default_search_params = true;
   private Boolean auto_create_placeholder_reference_targets = false;
+  private Boolean dao_scheduling_enabled = true;
   private Boolean delete_expunge_enabled = false;
   private Boolean enable_index_missing_fields = false;
   private Boolean enable_index_contained_resource = false;
@@ -286,6 +288,14 @@ public class AppProperties {
     this.default_page_size = default_page_size;
   }
 
+  public Boolean getDao_scheduling_enabled() {
+    return dao_scheduling_enabled;
+  }
+
+  public void setDao_scheduling_enabled(Boolean dao_scheduling_enabled) {
+    this.dao_scheduling_enabled = dao_scheduling_enabled;
+  }
+
   public Boolean getDelete_expunge_enabled() {
     return delete_expunge_enabled;
   }
@@ -807,4 +817,12 @@ public class AppProperties {
       private Boolean quitWait = false;
     }
   }
+
+  public boolean getEnable_index_of_type() {
+    return enable_index_of_type;
+  }
+
+  public void setEnable_index_of_type(boolean enable_index_of_type) {
+    this.enable_index_of_type = enable_index_of_type;
+  }
 }

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

@@ -28,6 +28,7 @@ import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
 import ca.uhn.fhir.rest.server.*;
 import ca.uhn.fhir.rest.server.interceptor.*;
 import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
+import ca.uhn.fhir.rest.server.provider.ReindexProvider;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
@@ -80,6 +81,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
   @Autowired
   ValueSetOperationProvider valueSetOperationProvider;
   @Autowired
+  ReindexProvider reindexProvider;
+  @Autowired
   BinaryStorageInterceptor binaryStorageInterceptor;
   @Autowired
   IPackageInstallerSvc packageInstallerSvc;
@@ -113,8 +116,10 @@ public class BaseJpaRestfulServer extends RestfulServer {
     // Customize supported resource types
     List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
 
-    if (!supportedResourceTypes.isEmpty() && !supportedResourceTypes.contains("SearchParameter")) {
-      supportedResourceTypes.add("SearchParameter");
+    if (!supportedResourceTypes.isEmpty()) {
+      if (!supportedResourceTypes.contains("SearchParameter")) {
+        supportedResourceTypes.add("SearchParameter");
+      }
       daoRegistry.setSupportedResourceTypes(supportedResourceTypes);
     }
 
@@ -358,6 +363,9 @@ public class BaseJpaRestfulServer extends RestfulServer {
     // valueSet Operations i.e $expand
     registerProvider(valueSetOperationProvider);
 
+	 //reindex Provider $reindex
+	 registerProvider(reindexProvider);
+
     // Partitioning
     if (appProperties.getPartitioning() != null) {
       registerInterceptor(new RequestTenantPartitionInterceptor());

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

@@ -40,6 +40,7 @@ public class FhirServerConfigCommon {
     ourLog.info("Server configured to " + (appProperties.getAllow_contains_searches() ? "allow" : "deny") + " contains searches");
     ourLog.info("Server configured to " + (appProperties.getAllow_multiple_delete() ? "allow" : "deny") + " multiple deletes");
     ourLog.info("Server configured to " + (appProperties.getAllow_external_references() ? "allow" : "deny") + " external references");
+    ourLog.info("Server configured to " + (appProperties.getDao_scheduling_enabled() ? "enable" : "disable") + " DAO scheduling");
     ourLog.info("Server configured to " + (appProperties.getDelete_expunge_enabled() ? "enable" : "disable") + " delete expunges");
     ourLog.info("Server configured to " + (appProperties.getExpunge_enabled() ? "enable" : "disable") + " expunges");
     ourLog.info("Server configured to " + (appProperties.getAllow_override_default_search_params() ? "allow" : "deny") + " overriding default search params");
@@ -86,6 +87,7 @@ public class FhirServerConfigCommon {
     retVal.setAllowContainsSearches(appProperties.getAllow_contains_searches());
     retVal.setAllowMultipleDelete(appProperties.getAllow_multiple_delete());
     retVal.setAllowExternalReferences(appProperties.getAllow_external_references());
+    retVal.setSchedulingDisabled(!appProperties.getDao_scheduling_enabled());
     retVal.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
     retVal.setExpungeEnabled(appProperties.getExpunge_enabled());
     if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
@@ -177,6 +179,7 @@ public class FhirServerConfigCommon {
     modelConfig.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
 
     modelConfig.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
+    modelConfig.setIndexIdentifierOfType(appProperties.getEnable_index_of_type());
     return modelConfig;
   }
 

src/main/resources/application.yaml

@@ -1,6 +1,14 @@
+#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:
+  endpoints:
+    web:
+      exposure:
+        include: "health,prometheus"
 spring:
   main:
     allow-circular-references: true
+    #allow-bean-definition-overriding: true
   flyway:
     enabled: false
     check-location: false
@@ -83,9 +91,13 @@ hapi:
     #    delete_expunge_enabled: true
     #    enable_repository_validating_interceptor: false
     #    enable_index_missing_fields: false
+    #    enable_index_of_type: true
     #    enable_index_contained_resource: false
-    # This is an experimental feature, and does not fully support _total and other FHIR features.
+    ###  !!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
     advanced_lucene_indexing: false
+    #    enforce_referential_integrity_on_delete: false
+    # This is an experimental feature, and does not fully support _total and other FHIR features.
 #    enforce_referential_integrity_on_delete: false
     #    enforce_referential_integrity_on_write: false
     #    etag_support_enabled: true