Added profiles

pom.xml

@@ -3,7 +3,6 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
-    <!-- mvn clean package spring-boot:repackage && java -jar target/hapi-fhir-jpaserver.war -->
     <!--
     Note: HAPI projects use the "hapi-fhir" POM as their base to provide easy management.
     You do not need to use this in your own projects, so the "parent" tag and it's
@@ -19,10 +18,8 @@
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
 
     <properties>
-        <java.version>11</java.version>
+        <java.version>8</java.version>
-        <maven.compiler.source>${java.version}</maven.compiler.source>
+        <spring.boot>2.3.3.RELEASE</spring.boot>
-        <maven.compiler.target>${java.version}</maven.compiler.target>
-        <jetty_version>9.4.31.v20200723</jetty_version>
     </properties>
 
     <prerequisites>
@@ -77,12 +74,6 @@
                 </exclusion>
             </exclusions>
         </dependency>
-        <!--
-        <dependency>
-            <groupId>javax.mail</groupId>
-            <artifactId>javax.mail-api</artifactId>
-        </dependency>
-        -->
 
         <!-- This dependency includes the core HAPI-FHIR classes -->
         <dependency>
@@ -248,18 +239,7 @@
             <artifactId>jetty-webapp</artifactId>
             <scope>test</scope>
         </dependency>
-        <!--
+
-        <dependency>
-            <groupId>com.helger</groupId>
-            <artifactId>ph-schematron</artifactId>
-            <exclusions>
-                <exclusion>
-                    <artifactId>Saxon-HE</artifactId>
-                    <groupId>net.sf.saxon</groupId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-			-->
 
         <!--
         For some reason JavaDoc crashed during site generation unless we have this dependency
@@ -284,35 +264,10 @@
             <scope>test</scope>
         </dependency>
 
-        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-web</artifactId>
-            <version>2.3.3.RELEASE</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>org.springframework.boot</groupId>
-                    <artifactId>spring-boot-starter-tomcat</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-jetty</artifactId>
-            <version>2.3.3.RELEASE</version>
-        </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-autoconfigure</artifactId>
-            <version>2.3.3.RELEASE</version>
+            <version>${spring.boot}</version>
-        </dependency>
-
-
-        <!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-logging -->
-        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-logging</artifactId>
-            <version>2.3.3.RELEASE</version>
-            <scope>test</scope>
         </dependency>
 
 
@@ -347,6 +302,7 @@
                 </executions>
             </plugin>
             <!-- The following is not required for the application to build, but allows you to test it by issuing "mvn package jetty:run -Dspring.batch.job.enabled=false" from the command line. -->
+            <!--
             <plugin>
                 <groupId>org.eclipse.jetty</groupId>
                 <artifactId>jetty-maven-plugin</artifactId>
@@ -358,6 +314,7 @@
                     </webApp>
                 </configuration>
             </plugin>
+            -->
 
             <!-- Tell Maven which Java source version you want to use -->
             <plugin>
@@ -365,7 +322,7 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.8.1</version>
                 <configuration>
-                    <release>11</release>
+                    <release>8</release>
                 </configuration>
             </plugin>
 
@@ -385,10 +342,7 @@
                             <artifactId>hapi-fhir-testpage-overlay</artifactId>
                         </overlay>
                     </overlays>
-
-
                     <failOnMissingWebXml>false</failOnMissingWebXml>
-
                 </configuration>
             </plugin>
 
@@ -503,9 +457,49 @@
                     </ignoredResourcePatterns>
                 </configuration>
             </plugin>
-
-
         </plugins>
     </build>
 
+    <profiles>
+        <!-- Package the war for your preference. Use the boot profile if you prefer a single jar/war
+        that can be started with and embedded application server. Default is jetty as it is assumed
+        that the main users of this project already have an app server.
+        Different profiles are needed as packing it for spring boot, makes the resulting war undeployable
+        due to a class shading issue between tomcat and jetty.
+        (the error is 'java.util.ServiceConfigurationError: org.apache.juli.logging.Log: org.eclipse.jetty.apache.jsp.JuliLog not a subtype')
+
+         -->
+
+        <!-- example of how to start the server using spring boot-->
+        <!-- mvn clean package spring-boot:repackage -Pboot && java -jar target/hapi-fhir-jpaserver.war -->
+        <profile>
+            <id>boot</id>
+            <dependencies>
+                <dependency>
+                    <groupId>org.springframework.boot</groupId>
+                    <artifactId>spring-boot-starter-web</artifactId>
+                    <version>2.3.3.RELEASE</version>
+                </dependency>
+            </dependencies>
+        </profile>
+        <!-- examples of how to start the server using the default profile-->
+        <!-- mvn clean package jetty:run -Dspring.batch.job.enabled=false -->
+        <!-- java -jar -Dspring.batch.job.enabled=false jetty-runner.jar target/hapi-fhir-jpaserver.war -->
+        <profile>
+            <id>jetty</id>
+            <dependencies>
+                <dependency>
+                    <groupId>org.springframework.boot</groupId>
+                    <artifactId>spring-boot-starter-web</artifactId>
+                    <version>2.3.3.RELEASE</version>
+                    <exclusions>
+                        <exclusion>
+                            <groupId>org.springframework.boot</groupId>
+                            <artifactId>spring-boot-starter-tomcat</artifactId>
+                        </exclusion>
+                    </exclusions>
+                </dependency>
+            </dependencies>
+        </profile>
+    </profiles>
 </project>

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

@@ -8,6 +8,7 @@ import ca.uhn.fhir.rest.api.EncodingEnum;
 import java.util.ArrayList;
 import java.util.List;
 
+import com.google.common.collect.ImmutableList;
 import org.hl7.fhir.r4.model.Bundle;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
@@ -51,7 +52,7 @@ public class AppProperties {
   private List<Bundle.BundleType> allowed_bundle_types = null;
 
   private Validation validation = new Validation();
-  private List<Tester> tester = new ArrayList<>();
+  private List<Tester> tester = ImmutableList.of(new Tester());
   private Logger logger = new Logger();
   private Subscription subscription = new Subscription();
   private Cors cors = null;
@@ -353,7 +354,7 @@ public class AppProperties {
 
   public static class Cors {
     private Boolean allow_Credentials = true;
-    private List<String> allowed_origin = new ArrayList<>();//List.of("*");
+    private List<String> allowed_origin = ImmutableList.of("*");
 
     public List<String> getAllowed_origin() {
       return allowed_origin;

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

@@ -6,7 +6,6 @@ import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration;
 import org.springframework.boot.builder.SpringApplicationBuilder;
-import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.boot.web.servlet.ServletComponentScan;
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
 import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
@@ -14,8 +13,6 @@ import org.springframework.context.annotation.Bean;
 import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
 import org.springframework.web.servlet.DispatcherServlet;
 
-import java.util.Arrays;
-
 @ServletComponentScan(basePackageClasses = {JpaRestfulServer.class}, basePackages = "ca.uhn.fhir.jpa.starter")
 @SpringBootApplication(exclude = ElasticsearchRestClientAutoConfiguration.class)
 public class Application extends SpringBootServletInitializer {
@@ -25,8 +22,8 @@ public class Application extends SpringBootServletInitializer {
     System.setProperty("spring.batch.job.enabled", "false");
     SpringApplication.run(Application.class, args);
 
-    //Server is now accessible at eg. http://localhost:8080/fhir/metadata
+    //Server is now accessible at eg. http://localhost:8080/hapi-fhir-jpaserver/fhir/metadata
-    //UI is now accessible at http://localhost:8080/
+    //UI is now accessible at http://localhost:8080/hapi-fhir-jpaserver/
   }
 
   @Override
@@ -35,7 +32,6 @@ public class Application extends SpringBootServletInitializer {
     return builder.sources(Application.class);
   }
 
-
   @Autowired
   AutowireCapableBeanFactory beanFactory;
 
@@ -51,7 +47,7 @@ public class Application extends SpringBootServletInitializer {
   }
 
   @Bean
-  public ServletRegistrationBean servletRegistrationBean() {
+  public ServletRegistrationBean overlayRegistrationBean() {
 
     AnnotationConfigWebApplicationContext annotationConfigWebApplicationContext = new AnnotationConfigWebApplicationContext();
     annotationConfigWebApplicationContext.register(FhirTesterConfig.class);

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

@@ -9,18 +9,12 @@ import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHan
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
 import com.google.common.base.Strings;
-import org.apache.commons.dbcp2.BasicDataSource;
 import org.hl7.fhir.dstu2.model.Subscription;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Lazy;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
-import org.thymeleaf.util.Validate;
 
-import java.lang.reflect.InvocationTargetException;
-import java.sql.Driver;
 import java.util.Optional;
 
 /**
@@ -32,8 +26,6 @@ public class FhirServerConfigCommon {
 
   private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
 
-  @Autowired
-  private ApplicationContext appContext;
 
   public FhirServerConfigCommon(AppProperties appProperties) {
     ourLog.info("Server configured to " + (appProperties.getAllow_contains_searches() ? "allow" : "deny") + " contains searches");

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

@@ -4,7 +4,6 @@ import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnClass;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;

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

@@ -1,12 +1,10 @@
 package ca.uhn.fhir.jpa.starter;
 
-import javax.servlet.ServletException;
-import javax.servlet.annotation.WebServlet;
-
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Import;
 
-//@WebServlet(urlPatterns = {"/hapi-fhir-jpaserver/fhir/*"})
+import javax.servlet.ServletException;
+
 @Import(AppProperties.class)
 public class JpaRestfulServer extends BaseJpaRestfulServer {