Merge branch 'master' into feature-userRequestRetryVersionConflictsIn…

…terceptor

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

@@ -80,6 +80,7 @@ public class AppProperties {
   private Subscription subscription = new Subscription();
   private Cors cors = null;
   private Partitioning partitioning = null;
+  private Boolean validate_resource_status_for_package_upload = true;
   private Boolean install_transitive_ig_dependencies = true;
   private Map<String, PackageInstallationSpec> implementationGuides = null;
 
@@ -107,6 +108,8 @@ public class AppProperties {
 
 	private boolean userRequestRetryVersionConflictsInterceptorEnabled = false;
 
+	private List<Integer> search_prefetch_thresholds = new ArrayList<>();
+
 	public List<String> getCustomInterceptorClasses() {
     return custom_interceptor_classes;
   }
@@ -588,6 +591,14 @@ public void setInstall_transitive_ig_dependencies(boolean install_transitive_ig_
 		this.install_transitive_ig_dependencies = install_transitive_ig_dependencies;
 	}
 
+  public Boolean getValidate_resource_status_for_package_upload() {
+		return validate_resource_status_for_package_upload;
+	}
+
+	public void setValidate_resource_status_for_package_upload(Boolean validate_resource_status_for_package_upload) {
+		this.validate_resource_status_for_package_upload = validate_resource_status_for_package_upload;
+	}
+
 	public Integer getBundle_batch_pool_size() {
 		return this.bundle_batch_pool_size;
 	}
@@ -645,6 +656,14 @@ public void setLanguage_search_parameter_enabled(Boolean language_search_paramet
 		this.language_search_parameter_enabled = language_search_parameter_enabled;
 	}
 
+	public List<Integer> getSearch_prefetch_thresholds() {
+		return this.search_prefetch_thresholds;
+	}
+
+	public void  setSearch_prefetch_thresholds(List<Integer> thePrefetchThresholds) {
+		this.search_prefetch_thresholds = thePrefetchThresholds;
+	}
+
 	public boolean getUpliftedRefchains_enabled() {
 		return upliftedRefchains_enabled;
 	}
@@ -790,6 +809,7 @@ public static class Partitioning {
 
     private Boolean partitioning_include_in_search_hashes = false;
     private Boolean allow_references_across_partitions = false;
+    private Boolean conditional_create_duplicate_identifiers_enabled = false;
 
     public Boolean getPartitioning_include_in_search_hashes() {
       return partitioning_include_in_search_hashes;
@@ -805,6 +825,14 @@ public Boolean getAllow_references_across_partitions() {
     public void setAllow_references_across_partitions(Boolean allow_references_across_partitions) {
       this.allow_references_across_partitions = allow_references_across_partitions;
     }
+
+    public Boolean getConditional_create_duplicate_identifiers_enabled() {
+      return conditional_create_duplicate_identifiers_enabled;
+    }
+
+    public void setConditional_create_duplicate_identifiers_enabled(Boolean conditional_create_duplicate_identifiers_enabled) {
+      this.conditional_create_duplicate_identifiers_enabled = conditional_create_duplicate_identifiers_enabled;
+    }
   }
 
   public static class Subscription {

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

@@ -149,8 +149,12 @@ public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
 		jpaStorageSettings.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
 		jpaStorageSettings.setExpungeEnabled(appProperties.getExpunge_enabled());
 		jpaStorageSettings.setLanguageSearchParameterEnabled(appProperties.getLanguage_search_parameter_enabled());
+		jpaStorageSettings.setValidateResourceStatusForPackageUpload(appProperties.getValidate_resource_status_for_package_upload());
 		jpaStorageSettings.setIndexOnUpliftedRefchains(appProperties.getUpliftedRefchains_enabled());
 
+		if (!appProperties.getSearch_prefetch_thresholds().isEmpty()) {
+			jpaStorageSettings.setSearchPreFetchThresholds(appProperties.getSearch_prefetch_thresholds());
+		}
 
 		Integer maxFetchSize = appProperties.getMax_page_size();
 		jpaStorageSettings.setFetchSizeDefaultMaximum(maxFetchSize);
@@ -243,6 +247,8 @@ public PartitionSettings partitionSettings(AppProperties appProperties) {
 			} else {
 				retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.NOT_ALLOWED);
 			}
+			retVal.setConditionalCreateDuplicateIdentifiersEnabled(
+				appProperties.getPartitioning().getConditional_create_duplicate_identifiers_enabled());
 		}
 
 		return retVal;

src/main/resources/application.yaml

@@ -152,6 +152,8 @@ hapi:
     ### enable to set the Server URL
     #    server_address: http://hapi.fhir.org/baseR4
     #    defer_indexing_for_codesystems_of_size: 101
+    ### Flag is true by default. This flag filters resources during package installation, allowing only those resources with a valid status (e.g. active) to be installed.
+    #    validate_resource_status_for_package_upload: false 
     #    install_transitive_ig_dependencies: true
     #implementationguides:
     ###    example from registry (packages.fhir.org)
@@ -228,6 +230,7 @@ hapi:
     #    partitioning:
     #      allow_references_across_partitions: false
     #      partitioning_include_in_search_hashes: false
+    #      conditional_create_duplicate_identifiers_enabled: false
     cors:
       allow_Credentials: true
       # These are allowed_origin patterns, see: https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/cors/CorsConfiguration.html#setAllowedOriginPatterns-java.util.List-
@@ -238,7 +241,18 @@ hapi:
     search-coord-core-pool-size: 20
     search-coord-max-pool-size: 100
     search-coord-queue-capacity: 200
-
+
+    # Search Prefetch Thresholds.
+
+    # This setting sets the number of search results to prefetch. For example, if this list
+    # is set to [100, 1000, -1] then the server will initially load 100 results and not
+    # attempt to load more. If the user requests subsequent page(s) of results and goes
+    # past 100 results, the system will load the next 900 (up to the following threshold of 1000).
+    # The system will progressively work through these thresholds.
+    # A threshold of -1 means to load all results. Note that if the final threshold is a
+    # number other than -1, the system will never prefetch more than the given number.
+    search_prefetch_thresholds: 13,503,2003,-1
+
     # comma-separated package names, will be @ComponentScan'ed by Spring to allow for creating custom Spring beans
     #custom-bean-packages:
 

src/main/resources/cds.application.yaml

@@ -153,6 +153,8 @@ hapi:
     ### enable to set the Server URL
     #    server_address: http://hapi.fhir.org/baseR4
     #    defer_indexing_for_codesystems_of_size: 101
+    ### Flag is true by default. This flag filters resources during package installation, allowing only those resources with a valid status (e.g. active) to be installed.
+    #    validate_resource_status_for_package_upload: false 
     #    install_transitive_ig_dependencies: true
     #implementationguides:
     ###    example from registry (packages.fhir.org)
@@ -225,6 +227,7 @@ hapi:
     #    partitioning:
     #      allow_references_across_partitions: false
     #      partitioning_include_in_search_hashes: false
+    #      conditional_create_duplicate_identifiers_enabled: false
     cors:
       allow_Credentials: true
       # These are allowed_origin patterns, see: https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/cors/CorsConfiguration.html#setAllowedOriginPatterns-java.util.List-

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

@@ -88,7 +88,14 @@ void beforeEach() {
 
 	private Boolean hasCdsServices() throws IOException {
 		var response = callCdsServicesDiscovery();
-		return response.getEntity().getContentLength() > 21 || response.getEntity().isChunked();
+
+		// NOTE: this is looking for a repsonse that indicates there are CDS services availalble.
+		// And empty response looks like: {"services": []}
+		// Looking at the actual response string consumes the InputStream which has side-effects, making it tricky to compare the actual contents.
+		// Hence the test just looks at the length to make this determination.
+		// The actual response has newlines in it which vary in size on some systems, but a value of 25 seems to work across linux/mac/windows
+		// to ensure the repsonse actually contains CDS services in it
+		return response.getEntity().getContentLength() > 25 || response.getEntity().isChunked();
 	}
 
 	private CloseableHttpResponse callCdsServicesDiscovery() {

src/test/resources/application.yaml

@@ -94,6 +94,8 @@ hapi:
     ### enable to set the Server URL
     #    server_address: http://hapi.fhir.org/baseR4
     #    defer_indexing_for_codesystems_of_size: 101
+    ### Flag is true by default. This flag filters resources during package installation, allowing only those resources with a valid status (e.g. active) to be installed.
+    #    validate_resource_status_for_package_upload: false 
     #    install_transitive_ig_dependencies: true
     #    implementationguides:
     ###    example from registry (packages.fhir.org)
@@ -146,6 +148,7 @@ hapi:
     #    partitioning:
     #      allow_references_across_partitions: false
     #      partitioning_include_in_search_hashes: false
+    #      partitioning_include_in_search_hashes
     #cors:
     #  allow_Credentials: true
       # These are allowed_origin patterns, see: https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/cors/CorsConfiguration.html#setAllowedOriginPatterns-java.util.List-