Resolve some compile errors

pom.xml

@@ -20,6 +20,10 @@
         <maven>3.5.0</maven>
     </prerequisites>
 
+    <packaging>war</packaging>
+
+    <name>HAPI FHIR JPA Server - Starter Project</name>
+
     <repositories>
         <repository>
             <id>oss-snapshots</id>
@@ -270,22 +274,17 @@
             <version>4.0.0-rc1</version>
             <scope>test</scope>
         </dependency>
+
+        <!-- TODO: remove this and migrate to JU5 -->
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.12</version>
+            <scope>test</scope>
+        </dependency>
+
     </dependencies>
 
-    <packaging>war</packaging>
-
-    <name>HAPI FHIR JPA Server - Starter Project</name>
-
-    <repositories>
-        <repository>
-            <id>oss-snapshots</id>
-            <snapshots>
-                <enabled>false</enabled>
-            </snapshots>
-            <url>https://oss.sonatype.org/content/repositories/snapshots/</url>
-        </repository>
-    </repositories>
-
     <build>
 
         <!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver.war -->
@@ -441,6 +440,7 @@
                     <ignoredResourcePatterns>
                         <ignoredResourcePattern>.*\.txt$</ignoredResourcePattern>
                         <ignoredResourcePattern>.*\.html$</ignoredResourcePattern>
+                        <ignoredResourcePattern>config/favicon.ico</ignoredResourcePattern>
                     </ignoredResourcePatterns>
                 </configuration>
             </plugin>

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

@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -47,8 +48,9 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
         return retVal;
     }
 
-    @Bean()
-    public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+  @Bean
+  @Primary
+  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
         JpaTransactionManager retVal = new JpaTransactionManager();
         retVal.setEntityManagerFactory(entityManagerFactory);
         return retVal;

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java

@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -32,7 +33,7 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
     }
 
     @Override
-    @Bean()
+    @Bean
     public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
         LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
         retVal.setPersistenceUnitName("HAPI_PU");
@@ -47,8 +48,9 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
         return retVal;
     }
 
-    @Bean()
-    public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+    @Bean
+    @Primary
+    public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
         JpaTransactionManager retVal = new JpaTransactionManager();
         retVal.setEntityManagerFactory(entityManagerFactory);
         return retVal;

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java

@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -47,8 +48,9 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
         return retVal;
     }
 
-    @Bean()
-    public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+  @Bean
+  @Primary
+  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
         JpaTransactionManager retVal = new JpaTransactionManager();
         retVal.setEntityManagerFactory(entityManagerFactory);
         return retVal;

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java

@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -47,8 +48,9 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
         return retVal;
     }
 
-    @Bean()
-    public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+  @Bean
+  @Primary
+  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
         JpaTransactionManager retVal = new JpaTransactionManager();
         retVal.setEntityManagerFactory(entityManagerFactory);
         return retVal;

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

@@ -8,7 +8,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
-import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
+import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
@@ -312,7 +312,7 @@ public class JpaRestfulServer extends RestfulServer {
         BundleType type = BundleType.valueOf(o);
         allowedBundleTypes.add(type.toCode());
       });
-      DaoConfig config = (DaoConfig) daoConfig;
+      DaoConfig config = daoConfig;
       config.setBundleTypesAllowedForStorage(
         Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
     }