Fix #206 - Don't require hl7org structures to start JPA server

hapi-fhir-jpaserver-base/pom.xml

@@ -67,7 +67,6 @@
 		<dependency>
 			<groupId>ch.qos.logback</groupId>
 			<artifactId>logback-classic</artifactId>
-			<version>${logback_version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
@@ -269,25 +268,21 @@
 		<dependency>
 			<groupId>org.eclipse.jetty</groupId>
 			<artifactId>jetty-servlets</artifactId>
-			<version>${jetty_version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.jetty</groupId>
 			<artifactId>jetty-servlet</artifactId>
-			<version>${jetty_version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.jetty</groupId>
 			<artifactId>jetty-server</artifactId>
-			<version>${jetty_version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.jetty</groupId>
 			<artifactId>jetty-util</artifactId>
-			<version>${jetty_version}</version>
 			<scope>test</scope>
 		</dependency>
 		

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoQuestionnaireResponseDstu2.java

@@ -1,30 +1,10 @@
 package ca.uhn.fhir.jpa.dao;
 
-/*
+import javax.annotation.PostConstruct;
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2015 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
 
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.PlatformTransactionManager;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IResource;
@@ -41,11 +21,29 @@ import ca.uhn.fhir.validation.ValidationResult;
 
 public class FhirResourceDaoQuestionnaireResponseDstu2 extends FhirResourceDaoDstu2<QuestionnaireResponse> {
 
-	private FhirContext myRefImplCtx = FhirContext.forDstu2Hl7Org();
+	private FhirContext myRefImplCtx;
+	private Boolean myValidateResponses;
+
+	/**
+	 * Initialize the bean
+	 */
+	@PostConstruct
+	public void initialize() {
+		try {
+			Class.forName("org.hl7.fhir.instance.model.QuestionnaireResponse");
+			myValidateResponses = true;
+			myRefImplCtx = FhirContext.forDstu2Hl7Org();
+		} catch (ClassNotFoundException e) {
+			myValidateResponses = Boolean.FALSE;
+		}
+	}
 	
 	@Override
 	protected void validateResourceForStorage(IResource theResource) {
 		super.validateResourceForStorage(theResource);
+		if (!myValidateResponses) {
+			return;
+		}
 		
 		QuestionnaireResponse qa = (QuestionnaireResponse) theResource;
 		if (qa == null || qa.getQuestionnaire() == null || qa.getQuestionnaire().getReference() == null || qa.getQuestionnaire().getReference().isEmpty()) {
@@ -73,7 +71,8 @@ public class FhirResourceDaoQuestionnaireResponseDstu2 extends FhirResourceDaoDs
 		public <T extends IBaseResource> T load(Class<T> theType, IIdType theId) throws ResourceNotFoundException {
 
 			/*
-			 * The QuestionnaireResponse validator uses RI structures, so for now we need to convert between that and HAPI structures. This is a bit hackish, but hopefully it will go away at some point.
+			 * The QuestionnaireResponse validator uses RI structures, so for now we need to convert between that and HAPI
+			 * structures. This is a bit hackish, but hopefully it will go away at some point.
 			 */
 			if ("ValueSet".equals(theType.getSimpleName())) {
 				IFhirResourceDao<ValueSet> dao = getDao(ValueSet.class);

hapi-fhir-jpaserver-example/.classpath

@@ -1,12 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+	<classpathentry kind="src" path="src/test/resources"/>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>

hapi-fhir-jpaserver-example/pom.xml

@@ -1,14 +1,11 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	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>
 
-	<!-- 
+	<!-- Note: HAPI projects use the "hapi-fhir" POM as their base to provide 
-	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 
-	easy management.
+		"parent" tag and it's contents below may be removed if you are using this 
-	 
+		file as a basis for your own project. -->
-	You do not need to use this in your own projects, so the 
-	"parent" tag and it's contents below may be removed if you
-	are using this file as a basis for your own project.
-	-->
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
@@ -53,10 +50,8 @@
 			<version>1.2-SNAPSHOT</version>
 		</dependency>
 
-		<!-- 
+		<!-- This dependency includes the JPA server itself, which is packaged 
-		This dependency includes the JPA server itself, which is packaged
+			separately from the rest of HAPI FHIR -->
-		separately from the rest of HAPI FHIR 
-		-->
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-base</artifactId>
@@ -72,16 +67,13 @@
 			<scope>provided</scope>
 		</dependency>
 
-		<!-- 
+		<!-- HAPI-FHIR uses Logback for logging support. The logback library is 
-		HAPI-FHIR uses Logback for logging support. The logback library is included 
+			included automatically by Maven as a part of the hapi-fhir-base dependency, 
-		automatically by Maven as a part of the hapi-fhir-base dependency, but you 
+			but you also need to include a logging library. Logback is used here, but 
-		also need to include a logging library. Logback is used here, but log4j
+			log4j would also be fine. -->
-		would also be fine. 
-		-->
 		<dependency>
 			<groupId>ch.qos.logback</groupId>
 			<artifactId>logback-classic</artifactId>
-			<version>${logback_version}</version>
 		</dependency>
 
 		<!-- Needed for JEE/Servlet support -->
@@ -91,10 +83,8 @@
 			<scope>provided</scope>
 		</dependency>
 
-		<!-- 
+		<!-- If you are using HAPI narrative generation, you will need to include 
-		If you are using HAPI narrative generation, you will need to include Thymeleaf
+			Thymeleaf as well. Otherwise the following can be omitted. -->
-		as well. Otherwise the following can be omitted.
-		 -->
 		<dependency>
 			<groupId>org.thymeleaf</groupId>
 			<artifactId>thymeleaf</artifactId>
@@ -114,10 +104,7 @@
 			</exclusions>
 		</dependency>
 
-		<!-- 
+		<!-- Spring Web is used to deploy the server to a web container. -->
-		Spring Web is used to deploy the server to a
-		web container.
-		-->
 		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-web</artifactId>
@@ -125,21 +112,17 @@
 			<scope>provided</scope>
 		</dependency>
 
-		<!--
+		<!-- You may not need this if you are deploying to an application server 
-		You may not need this if you are deploying to an application server which
+			which provides database connection pools itself. -->
-		provides database connection pools itself.
-		-->
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-dbcp2</artifactId>
 		</dependency>
 
-		<!-- 
+		<!-- This example uses Derby embedded database. If you are using another 
-		This example uses Derby embedded database. If you are using another
+			database such as Mysql or Oracle, you may omit the following dependencies 
-		database such as Mysql or Oracle, you may omit the following 
+			and replace them with an appropriate database client dependency for your 
-		dependencies and replace them with an appropriate database client
+			database platform. -->
-		dependency for your database platform. 
-		-->
 		<dependency>
 			<groupId>org.apache.derby</groupId>
 			<artifactId>derby</artifactId>
@@ -154,12 +137,37 @@
 		</dependency>
 
 		<!--
-		Arquillian is just used for automated tests, you don't neccesarily need it
+			The following dependencies are only needed for automated unit tests,
-		to use this example.
+			you do not neccesarily need them to run the example.
 		-->
 		<dependency>
-			<groupId>org.jboss.arquillian.junit</groupId>
+			<groupId>junit</groupId>
-			<artifactId>arquillian-junit-container</artifactId>
+			<artifactId>junit</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-servlets</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-servlet</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-server</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-util</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-webapp</artifactId>
 			<scope>test</scope>
 		</dependency>
 
@@ -167,17 +175,11 @@
 
 	<build>
 
-		<!-- 
+		<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver-example.war -->
-		Tells Maven to name the generated WAR file as
-		hapi-fhir-jpaserver-example.war
-		-->
 		<finalName>hapi-fhir-jpaserver-example</finalName>
 
-		<!-- 
+		<!-- The following is not required for the application to build, but allows 
-		The following is not required for the application to build, but
+			you to test it by issuing "mvn jetty:run" from the command line. -->
-		allows you to test it by issuing "mvn jetty:run" from the command
-		line. 
-		-->
 		<pluginManagement>
 			<plugins>
 				<plugin>
@@ -194,9 +196,7 @@
 		</pluginManagement>
 
 		<plugins>
-			<!-- 
+			<!-- Tell Maven which Java source version you want to use -->
-			Tell Maven which Java source version you want to use
-			-->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
@@ -206,10 +206,8 @@
 				</configuration>
 			</plugin>
 
-			<!-- 
+			<!-- The configuration here tells the WAR plugin to include the FHIR Tester 
-			The configuration here tells the WAR plugin to include the FHIR Tester
+				overlay. You can omit it if you are not using that feature. -->
-			overlay. You can omit it if you are not using that feature.
-			-->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-war-plugin</artifactId>
@@ -223,10 +221,8 @@
 				</configuration>
 			</plugin>
 
-			<!-- 
+			<!-- This plugin is just a part of the HAPI internal build process, you 
-			This plugin is just a part of the HAPI internal build process, you do not
+				do not need to incude it in your own projects -->
-			need to incude it in your own projects
-			-->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-deploy-plugin</artifactId>

hapi-fhir-jpaserver-example/src/main/webapp/WEB-INF/web.xml

@@ -42,7 +42,7 @@
 		</init-param>
 		<init-param>
 			<param-name>FhirVersion</param-name>
-			<param-value>DSTU1</param-value>
+			<param-value>DSTU2</param-value>
 		</init-param>
 		<load-on-startup>1</load-on-startup>
 	</servlet>

hapi-fhir-jpaserver-example/src/test/java/ca/uhn/fhir/jpa/dao/RandomServerPortProvider.java

@@ -0,0 +1,36 @@
+package ca.uhn.fhir.jpa.dao;
+
+import java.io.IOException;
+import java.net.ServerSocket;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Provides server ports
+ */
+public class RandomServerPortProvider {
+
+	private static List<Integer> ourPorts = new ArrayList<Integer>(); 
+	
+	public static int findFreePort() {
+		ServerSocket server;
+		try {
+			server = new ServerSocket(0);
+			int port = server.getLocalPort();
+			ourPorts.add(port);
+			server.close();
+			Thread.sleep(500);
+			return port;
+		} catch (IOException e) {
+			throw new Error(e);
+		} catch (InterruptedException e) {
+			throw new Error(e);
+		}
+	}
+
+	public static List<Integer> list() {
+		return ourPorts;
+	}
+
+}
+ 

hapi-fhir-jpaserver-example/src/test/java/ca/uhn/fhir/jpa/dao/ResourceProviderDstu2Test.java

@@ -0,0 +1,66 @@
+package ca.uhn.fhir.jpa.dao;
+
+import static org.junit.Assert.*;
+
+import java.io.IOException;
+
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.webapp.WebAppContext;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.rest.client.IGenericClient;
+import ca.uhn.fhir.rest.client.ServerValidationModeEnum;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+
+public class ResourceProviderDstu2Test {
+
+	private static IGenericClient ourClient;
+	private static final FhirContext ourCtx = FhirContext.forDstu2();
+	private static int ourPort;
+
+	private static Server ourServer;
+
+	@Test
+	public void testCreateAndRead() throws IOException {
+		String methodName = "testCreateResourceConditional";
+
+		Patient pt = new Patient();
+		pt.addName().addFamily(methodName);
+		IIdType id = ourClient.create().resource(pt).execute().getId();
+
+		Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
+		assertEquals(methodName, pt2.getName().get(0).getFamily().get(0).getValue());
+	}
+
+	@AfterClass
+	public static void afterClass() throws Exception {
+		ourServer.stop();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = RandomServerPortProvider.findFreePort();
+		ourServer = new Server(ourPort);
+
+		WebAppContext webAppContext = new WebAppContext();
+		webAppContext.setContextPath("/");
+		webAppContext.setDescriptor("src/main/webapp/WEB-INF/web.xml");
+		webAppContext.setResourceBase("target/hapi-fhir-jpaserver-example");
+		webAppContext.setParentLoaderPriority(true);
+
+		ourServer.setHandler(webAppContext);
+		ourServer.start();
+
+		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+		ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
+		ourClient = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/base");
+		ourClient.registerInterceptor(new LoggingInterceptor(true));
+
+	}
+
+}

pom.xml

@@ -45,12 +45,6 @@
 	</description>
 
 	<dependencies>
-		<dependency>
-			<groupId>net.sourceforge.cobertura</groupId>
-			<artifactId>cobertura</artifactId>
-			<version>2.1.1</version>
-			<scope>provided</scope>
-		</dependency>
 	</dependencies>
 
 	<prerequisites>
@@ -231,6 +225,16 @@
 				<artifactId>javax.servlet-api</artifactId>
 				<version>3.1.0</version>
 			</dependency>
+			<dependency>
+				<groupId>junit</groupId>
+				<artifactId>junit</artifactId>
+				<version>4.12</version>
+			</dependency>
+			<dependency>
+				<groupId>net.sourceforge.cobertura</groupId>
+				<artifactId>cobertura</artifactId>
+				<version>2.1.1</version>
+			</dependency>
 			<dependency>
 				<groupId>org.apache.commons</groupId>
 				<artifactId>commons-dbcp2</artifactId>
@@ -252,9 +256,29 @@
 				<version>${derby_version}</version>
 			</dependency>
 			<dependency>
-				<groupId>org.jboss.arquillian.junit</groupId>
+				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>arquillian-junit-container</artifactId>
+				<artifactId>jetty-servlets</artifactId>
-				<version>1.1.8.Final</version>
+				<version>9.2.6.v20141205</version>
+			</dependency>
+			<dependency>
+				<groupId>org.eclipse.jetty</groupId>
+				<artifactId>jetty-servlet</artifactId>
+				<version>9.2.6.v20141205</version>
+			</dependency>
+			<dependency>
+				<groupId>org.eclipse.jetty</groupId>
+				<artifactId>jetty-server</artifactId>
+				<version>9.2.6.v20141205</version>
+			</dependency>
+			<dependency>
+				<groupId>org.eclipse.jetty</groupId>
+				<artifactId>jetty-util</artifactId>
+				<version>9.2.6.v20141205</version>
+			</dependency>
+			<dependency>
+				<groupId>org.eclipse.jetty</groupId>
+				<artifactId>jetty-webapp</artifactId>
+				<version>9.2.6.v20141205</version>
 			</dependency>
 			<dependency>
 				<groupId>org.mockito</groupId>
@@ -580,7 +604,7 @@
 									<fileset dir="hapi-fhir-cobertura/target/site/cobertura" />
 								</copy>
 								<copy todir="target/site">
-									<fileset dir="hapi-fhir-base/target/site" includes="checkstyle.*"/>
+									<fileset dir="hapi-fhir-base/target/site" includes="checkstyle.*" />
 								</copy>
 								<echo>Fixing Checkstyle Report</echo>
 								<replace dir="target/site" summary="true">
@@ -609,7 +633,8 @@
 		</div>
 	</div>]]></replacevalue>
 								</replace>
-								<!--<replaceregexp file="target/site/checkstyle.html" byline="false" match="&lt;ul class=&quot;breadcrumb.*?&lt;/ul&gt;" replace="" flags="s"/>-->
+								<!--<replaceregexp file="target/site/checkstyle.html" byline="false" 
+									match="&lt;ul class=&quot;breadcrumb.*?&lt;/ul&gt;" replace="" flags="s"/> -->
 							</target>
 						</configuration>
 					</execution>