Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)

* Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT.  This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api).

* Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors.

* Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none.   Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true

* Set allow-bean-definition-overriding: true on test application.yaml as well.

* Remove lines in ExampleServerR4BIT that causes an implementation guide version error.

* Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding.  Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2.

* Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors.  Also, remove explici logger disabling code in Application.java.

* Restore Application.java as well as both application.yaml files to the same as master.

pom.xml

@@ -14,7 +14,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <version>6.2.2</version>
+        <version>6.3.6-SNAPSHOT</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -44,12 +44,12 @@
     <dependencies>
         <dependency>
             <groupId>org.eclipse.jetty.websocket</groupId>
-            <artifactId>websocket-api</artifactId>
+            <artifactId>websocket-jetty-api</artifactId>
             <version>${jetty_version}</version>
         </dependency>
         <dependency>
             <groupId>org.eclipse.jetty.websocket</groupId>
-            <artifactId>websocket-client</artifactId>
+            <artifactId>websocket-jetty-client</artifactId>
             <version>${jetty_version}</version>
         </dependency>
         <dependency>
@@ -150,8 +150,20 @@
         <dependency>
             <groupId>ch.qos.logback</groupId>
             <artifactId>logback-classic</artifactId>
+            <!-- Please note that in the process of upgrading from hapi-fhir 6.22 to 6.3.4-SNAPSHOT logback was upgraded from 1.2.10. to 1.4.4.  This included the removal of the StaticLoggerBinder class. -->
+            <!-- In order to resolve this error, the only solution we found was to explicitly use version 1.2.10.  However, this exposes a Spring dependency issue with the hapi-fhir-jpaserver-base module and JpaConfig method memberMatcherR4Helper(). -->
+            <version>1.2.10</version>
         </dependency>
 
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-core</artifactId>
+            <!-- Please note that in the process of upgrading from hapi-fhir 6.22 to 6.3.4-SNAPSHOT logback was upgraded from 1.2.10. to 1.4.4.  This included the removal of the StaticLoggerBinder class. -->
+            <!-- In order to resolve this error, the only solution we found was to explicitly use version 1.2.10.  However, this exposes a Spring dependency issue with the hapi-fhir-jpaserver-base module and JpaConfig method memberMatcherR4Helper(). -->
+            <version>1.2.10</version>
+        </dependency>
+
+
         <!-- Needed for JEE/Servlet support -->
         <dependency>
             <groupId>javax.servlet</groupId>
@@ -246,7 +258,7 @@
         </dependency>
         <dependency>
             <groupId>org.eclipse.jetty.websocket</groupId>
-            <artifactId>websocket-server</artifactId>
+            <artifactId>websocket-jetty-server</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigDstu2.java

@@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.starter.common;
 
 import ca.uhn.fhir.jpa.config.JpaDstu2Config;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU2Condition;
-import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
 import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
 import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
@@ -24,9 +23,4 @@ public class FhirServerConfigDstu2 {
 		return new TermLoaderSvcImpl(theDeferredStorageSvc, theCodeSystemStorageSvc);
 	}
 
-	@Bean
-	public ITermCodeSystemStorageSvc termCodeSystemStorageSvc() {
-		return new TermCodeSystemStorageSvcImpl();
-	}
-
 }

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

@@ -206,16 +206,6 @@ public class StarterJpaConfig {
 		return packageInstallerSvc;
 	}
 
-	@Bean
-	@Primary
-	/*
-		This bean is currently necessary to override from MDM settings
-	 */
-	IMdmLinkDao mdmLinkDao() {
-		return new MdmLinkDaoJpaImpl();
-	}
-
-
 	@Bean
 	@Conditional(OnCorsPresent.class)
 	public CorsInterceptor corsInterceptor(AppProperties appProperties) {

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java

@@ -20,8 +20,6 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 	"hapi.fhir.fhir_version=r4b",
 	"hapi.fhir.subscription.websocket_enabled=false",
 	"hapi.fhir.mdm_enabled=false",
-	"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
-	"hapi.fhir.implementationguides.dk-core.version=1.1.0",
 	// Override is currently required when using MDM as the construction of the MDM
 	// beans are ambiguous as they are constructed multiple places. This is evident
 	// when running in a spring boot environment