Merge remote-tracking branch 'origin/master' into rel_8_3_tracking

Author: dotasek

.gitignore

@@ -124,7 +124,6 @@ local.properties
 .factorypath
 .project
 .settings
-.springBeans
 .sts4-cache
 
 # Code Recommenders

README.md

@@ -51,7 +51,7 @@ HAPI looks in the environment variables for properties in the [application.yaml]
 
 ### Configuration via overridden application.yaml file and using Docker
 
-You can customize HAPI by telling HAPI to look for the configuration file in a different location, eg.:
+You can customize HAPI by telling HAPI to look for the configuration file in a different location, e.g.:
 
 ```
 docker run -p 8090:8080 -v $(pwd)/yourLocalFolder:/configs -e "--spring.config.location=file:///configs/another.application.yaml" hapiproject/hapi:latest
@@ -237,7 +237,7 @@ The Server will then be accessible at http://localhost:8888/fhir and the Capabil
 ```bash
 mvn clean spring-boot:run -Pboot
 ```
-Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to the following:
+Server will then be accessible at http://localhost:8080/ and e.g. http://localhost:8080/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to the following:
 
 ```yaml
     tester:
@@ -253,7 +253,7 @@ Server will then be accessible at http://localhost:8080/ and eg. http://localhos
 ```bash
 mvn clean package spring-boot:repackage -DskipTests=true -Pboot && java -jar target/ROOT.war
 ```
-Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
+Server will then be accessible at http://localhost:8080/ and e.g. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
 
 ```yaml
     tester:
@@ -268,7 +268,7 @@ Server will then be accessible at http://localhost:8080/ and eg. http://localhos
 ```bash
 mvn clean package com.google.cloud.tools:jib-maven-plugin:dockerBuild -Dimage=distroless-hapi && docker run -p 8080:8080 distroless-hapi
 ```
-Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
+Server will then be accessible at http://localhost:8080/ and e.g. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
 
 ```yaml
     tester:
@@ -284,7 +284,7 @@ Server will then be accessible at http://localhost:8080/ and eg. http://localhos
 ```bash
 ./build-docker-image.sh && docker run -p 8080:8080 hapi-fhir/hapi-fhir-jpaserver-starter:latest
 ```
-Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
+Server will then be accessible at http://localhost:8080/ and e.g. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
 
 ```yaml
     tester:
@@ -384,7 +384,7 @@ Several template files that can be customized are found in the following directo
 
 Using the Maven-Embedded Jetty method above is convenient, but it is not a good solution if you want to leave the server running in the background.
 
-Most people who are using HAPI FHIR JPA as a server that is accessible to other people (whether internally on your network or publically hosted) will do so using an Application Server, such as [Apache Tomcat](http://tomcat.apache.org/) or [Jetty](https://www.eclipse.org/jetty/). Note that any Servlet 3.0+ compatible Web Container will work (e.g Wildfly, Websphere, etc.).
+Most people who are using HAPI FHIR JPA as a server that is accessible to other people (whether internally on your network or publicly hosted) will do so using an Application Server, such as [Apache Tomcat](http://tomcat.apache.org/) or [Jetty](https://www.eclipse.org/jetty/). Note that any Servlet 3.0+ compatible Web Container will work (e.g. Wildfly, Websphere, etc.).
 
 Tomcat is very popular, so it is a good choice simply because you will be able to find many tutorials online. Jetty is a great alternative due to its fast startup time and good overall performance.
 
@@ -402,7 +402,7 @@ Again, browse to the following link to use the server (note that the port 8080 m
 
 You will then be able to access the JPA server e.g. using http://localhost:8080/fhir/metadata.
 
-If you would like it to be hosted at eg. hapi-fhir-jpaserver, eg. http://localhost:8080/hapi-fhir-jpaserver/ or http://localhost:8080/hapi-fhir-jpaserver/fhir/metadata - then rename the WAR file to ```hapi-fhir-jpaserver.war``` and adjust the overlay configuration accordingly e.g.
+If you would like it to be hosted at e.g. hapi-fhir-jpaserver, e.g. http://localhost:8080/hapi-fhir-jpaserver/ or http://localhost:8080/hapi-fhir-jpaserver/fhir/metadata - then rename the WAR file to ```hapi-fhir-jpaserver.war``` and adjust the overlay configuration accordingly e.g.
 
 ```yaml
     tester:
@@ -525,7 +525,7 @@ Set `hapi.fhir.store_resource_in_lucene_index_enabled` in the [application.yaml]
 
 ## 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](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/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 milliseconds by default.
 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)

charts/hapi-fhir-jpaserver/Chart.yaml

@@ -14,7 +14,7 @@ dependencies:
     repository: oci://registry-1.docker.io/bitnamicharts
     version: 2.31.3
 appVersion: 8.2.0
-version: 0.20.0
+version: 0.20.1
 annotations:
   artifacthub.io/license: Apache-2.0
   artifacthub.io/containsSecurityUpdates: "false"
@@ -27,14 +27,4 @@ annotations:
     # When using the list of objects option the valid supported kinds are
     # added, changed, deprecated, removed, fixed, and security.
     - kind: changed
-      description: "updated postgresql sub-chart to 16.7.11"
-    - kind: changed
-      description: "updated common sub-chart to 2.31.3"
-    - kind: changed
-      description: "updated curlimages/curl to 8.14.1"
-    - kind: changed
-      description: "updated hapiproject/hapi to v8.2.0-1"
-    - kind: changed
-      description: "use ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect dialect"
-    - kind: changed
-      description: "made the init container waiting for the database to be ready configurable"
+      description: "fixed typo in README.md"

charts/hapi-fhir-jpaserver/README.md

@@ -1,6 +1,6 @@
 # HAPI FHIR JPA Server Starter Helm Chart
 
-![Version: 0.20.0](https://img.shields.io/badge/Version-0.20.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 8.2.0](https://img.shields.io/badge/AppVersion-8.2.0-informational?style=flat-square)
+![Version: 0.20.1](https://img.shields.io/badge/Version-0.20.1-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 8.2.0](https://img.shields.io/badge/AppVersion-8.2.0-informational?style=flat-square)
 
 This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
 
@@ -98,7 +98,7 @@ INFO[2021-11-20T12:38:04Z] Found Chart directories [charts/hapi-fhir-jpaserver]
 INFO[2021-11-20T12:38:04Z] Generating README Documentation for chart /usr/src/app/charts/hapi-fhir-jpaserver
 ```
 
-## Enable Distributed Tracing based on the OpenTelemtry Java Agent
+## Enable Distributed Tracing based on the OpenTelemetry Java Agent
 
 The container image includes the [OpenTelemetry Java agent JAR](https://github.com/open-telemetry/opentelemetry-java-instrumentation)
 which can be used to enable distributed tracing. It can be configured entirely using environment variables,

charts/hapi-fhir-jpaserver/README.md.gotmpl

@@ -27,7 +27,7 @@ INFO[2021-11-20T12:38:04Z] Found Chart directories [charts/hapi-fhir-jpaserver]
 INFO[2021-11-20T12:38:04Z] Generating README Documentation for chart /usr/src/app/charts/hapi-fhir-jpaserver
 ```
 
-## Enable Distributed Tracing based on the OpenTelemtry Java Agent
+## Enable Distributed Tracing based on the OpenTelemetry Java Agent
 
 The container image includes the [OpenTelemetry Java agent JAR](https://github.com/open-telemetry/opentelemetry-java-instrumentation)
 which can be used to enable distributed tracing. It can be configured entirely using environment variables,

pom.xml

@@ -6,7 +6,7 @@
     <properties>
         <java.version>17</java.version>
         <hapi.fhir.jpa.server.starter.revision>1</hapi.fhir.jpa.server.starter.revision>
-        <clinical-reasoning.version>3.23.0</clinical-reasoning.version>
+        <clinical-reasoning.version>3.24.0</clinical-reasoning.version>
     </properties>
 
     <!-- one-liner to take you to the cloud with settings form the application.yaml file: -->
@@ -195,7 +195,7 @@
             <scope>provided</scope>
         </dependency>
 
-        <!-- If you are using HAPI narrative generation, you will need to include Thymeleaf as well. Otherwise the following can be omitted. -->
+        <!-- If you are using HAPI narrative generation, you will need to include Thymeleaf as well. Otherwise, the following can be omitted. -->
         <dependency>
             <groupId>org.thymeleaf</groupId>
             <artifactId>thymeleaf</artifactId>

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

@@ -45,7 +45,7 @@ public static void main(String[] args) {
 
 		SpringApplication.run(Application.class, args);
 
-		// Server is now accessible at eg. http://localhost:8080/fhir/metadata
+		// Server is now accessible at e.g. http://localhost:8080/fhir/metadata
 		// UI is now accessible at http://localhost:8080/
 	}
 

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksServlet.java

@@ -22,13 +22,16 @@
 import org.springframework.beans.factory.annotation.Qualifier;
 
 import java.io.IOException;
+import java.io.Serial;
 import java.util.stream.Collectors;
 
 import static org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;
 
 @Configurable
 public class CdsHooksServlet extends HttpServlet {
 	private static final Logger logger = LoggerFactory.getLogger(CdsHooksServlet.class);
+
+	@Serial
 	private static final long serialVersionUID = 1L;
 
 	@Autowired

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/ModuleConfigurationPrefetchSvc.java

@@ -179,9 +179,8 @@ private boolean resourceExists(IBaseResource resource) {
 			return true;
 		}
 		if (resource instanceof IBaseBundle) {
-			return BundleUtil.toListOfEntries(fhirContext, (IBaseBundle) resource)
-							.size()
-					> 0;
+			return !BundleUtil.toListOfEntries(fhirContext, (IBaseBundle) resource)
+					.isEmpty();
 		}
 		return false;
 	}

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

@@ -41,37 +41,43 @@ public class FhirServerConfigCommon {
 	private static final Logger ourLog = LoggerFactory.getLogger(FhirServerConfigCommon.class);
 
 	public FhirServerConfigCommon(AppProperties appProperties) {
-		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");
+				"Server configured to {} contains searches",
+				appProperties.getAllow_contains_searches() ? "allow" : "deny");
 		ourLog.info(
-				"Server configured to " + (appProperties.getAllow_override_default_search_params() ? "allow" : "deny")
-						+ " overriding default search params");
-		ourLog.info("Server configured to "
-				+ (appProperties.getAuto_create_placeholder_reference_targets() ? "allow" : "disable")
-				+ " auto-creating placeholder references");
+				"Server configured to {} multiple deletes",
+				appProperties.getAllow_multiple_delete() ? "allow" : "deny");
+		ourLog.info(
+				"Server configured to {} external references",
+				appProperties.getAllow_external_references() ? "allow" : "deny");
+		ourLog.info(
+				"Server configured to {} DAO scheduling",
+				appProperties.getDao_scheduling_enabled() ? "enable" : "disable");
+		ourLog.info(
+				"Server configured to {} delete expunges",
+				appProperties.getDelete_expunge_enabled() ? "enable" : "disable");
+		ourLog.info("Server configured to {} expunges", appProperties.getExpunge_enabled() ? "enable" : "disable");
+		ourLog.info(
+				"Server configured to {} overriding default search params",
+				appProperties.getAllow_override_default_search_params() ? "allow" : "deny");
+		ourLog.info(
+				"Server configured to {} auto-creating placeholder references",
+				appProperties.getAuto_create_placeholder_reference_targets() ? "allow" : "disable");
 		ourLog.info(
 				"Server configured to auto-version references at paths {}",
 				appProperties.getAuto_version_reference_at_paths());
 
 		if (appProperties.getSubscription().getEmail() != null) {
 			AppProperties.Subscription.Email email =
 					appProperties.getSubscription().getEmail();
-			ourLog.info("Server is configured to enable email with host '" + email.getHost() + "' and port "
-					+ email.getPort());
-			ourLog.info("Server will use '" + email.getFrom() + "' as the from email address");
+			ourLog.info(
+					"Server is configured to enable email with host '{}' and port {}",
+					email.getHost(),
+					email.getPort());
+			ourLog.info("Server will use '{}' as the from email address", email.getFrom());
 
 			if (!Strings.isNullOrEmpty(email.getUsername())) {
-				ourLog.info("Server is configured to use username '" + email.getUsername() + "' for email");
+				ourLog.info("Server is configured to use username '{}' for email", email.getUsername());
 			}
 
 			if (!Strings.isNullOrEmpty(email.getPassword())) {
@@ -91,17 +97,19 @@ public FhirServerConfigCommon(AppProperties appProperties) {
 			ourLog.info("Indexed on contained resource enabled");
 		}
 
-		ourLog.info("Server configured to " + (appProperties.getPre_expand_value_sets() ? "enable" : "disable")
-				+ " value set pre-expansion");
 		ourLog.info(
-				"Server configured to " + (appProperties.getEnable_task_pre_expand_value_sets() ? "enable" : "disable")
-						+ " value set pre-expansion task");
-		ourLog.info("Server configured for pre-expand value set default count of "
-				+ (appProperties.getPre_expand_value_sets_default_count().toString()));
-		ourLog.info("Server configured for pre-expand value set max count of "
-				+ (appProperties.getPre_expand_value_sets_max_count().toString()));
-		ourLog.info("Server configured for maximum expansion size of "
-				+ (appProperties.getMaximum_expansion_size().toString()));
+				"Server configured to {} value set pre-expansion",
+				appProperties.getPre_expand_value_sets() ? "enable" : "disable");
+		ourLog.info(
+				"Server configured to {} value set pre-expansion task",
+				appProperties.getEnable_task_pre_expand_value_sets() ? "enable" : "disable");
+		ourLog.info(
+				"Server configured for pre-expand value set default count of {}",
+				appProperties.getPre_expand_value_sets_default_count());
+		ourLog.info(
+				"Server configured for pre-expand value set max count of {}",
+				appProperties.getPre_expand_value_sets_max_count());
+		ourLog.info("Server configured for maximum expansion size of {}", appProperties.getMaximum_expansion_size());
 	}
 
 	@Bean
@@ -194,8 +202,9 @@ public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
 
 		Integer maxFetchSize = appProperties.getMax_page_size();
 		jpaStorageSettings.setFetchSizeDefaultMaximum(maxFetchSize);
-		ourLog.info("Server configured to have a maximum fetch size of "
-				+ (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
+		ourLog.info(
+				"Server configured to have a maximum fetch size of {}",
+				maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize);
 
 		Long reuseCachedSearchResultsMillis = appProperties.getReuse_cached_search_results_millis();
 		jpaStorageSettings.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
@@ -237,19 +246,21 @@ public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
 		// Set and/or recommend default Server ID Strategy of UUID when using the ANY Client ID Strategy
 		if (appProperties.getClient_id_strategy() == JpaStorageSettings.ClientIdStrategyEnum.ANY) {
 			if (appProperties.getServer_id_strategy() == null) {
-				ourLog.info("Defaulting server to use '" + JpaStorageSettings.IdStrategyEnum.UUID
-						+ "' Server ID Strategy when using the '" + JpaStorageSettings.ClientIdStrategyEnum.ANY
-						+ "' Client ID Strategy");
+				ourLog.info(
+						"Defaulting server to use '{}' Server ID Strategy when using the '{}' Client ID Strategy",
+						JpaStorageSettings.IdStrategyEnum.UUID,
+						JpaStorageSettings.ClientIdStrategyEnum.ANY);
 				appProperties.setServer_id_strategy(JpaStorageSettings.IdStrategyEnum.UUID);
 			} else if (appProperties.getServer_id_strategy() != JpaStorageSettings.IdStrategyEnum.UUID) {
-				ourLog.warn("WARNING: '" + JpaStorageSettings.IdStrategyEnum.UUID
-						+ "' Server ID Strategy is highly recommended when using the '"
-						+ JpaStorageSettings.ClientIdStrategyEnum.ANY + "' Client ID Strategy");
+				ourLog.warn(
+						"WARNING: '{}' Server ID Strategy is highly recommended when using the '{}' Client ID Strategy",
+						JpaStorageSettings.IdStrategyEnum.UUID,
+						JpaStorageSettings.ClientIdStrategyEnum.ANY);
 			}
 		}
 		if (appProperties.getServer_id_strategy() != null) {
 			jpaStorageSettings.setResourceServerIdStrategy(appProperties.getServer_id_strategy());
-			ourLog.info("Server configured to use '" + appProperties.getServer_id_strategy() + "' Server ID Strategy");
+			ourLog.info("Server configured to use '{}' Server ID Strategy", appProperties.getServer_id_strategy());
 		}
 
 		// to Disable the Resource History