Work on CLI

.gitignore

@@ -19,7 +19,7 @@ tmp.txt
 .vagrant
 /vagrant/build
 /vagrant/chef/tmp
-
+jpaserver_derby_files
 
 
 # Created by https://www.gitignore.io

hapi-fhir-cli/pom.xml

@@ -1,8 +1,8 @@
 <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 easy management. You do not need to use this in your own projects, so the "parent" tag 
+	<!-- 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 contents below may be removed 
-		and it's contents below may be removed if you are using this file as a basis for your own project. -->
+		if you are using this file as a basis for your own project. -->
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
@@ -24,6 +24,12 @@
 			<artifactId>hapi-fhir-base</artifactId>
 			<version>1.2-SNAPSHOT</version>
 		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-example</artifactId>
+			<version>1.2-SNAPSHOT</version>
+			<type>war</type>
+		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2</artifactId>
@@ -49,6 +55,11 @@
 			<artifactId>javax.servlet-api</artifactId>
 		</dependency>
 
+		<dependency>
+			<groupId>commons-cli</groupId>
+			<artifactId>commons-cli</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-core</artifactId>
@@ -60,55 +71,58 @@
 			</exclusions>
 		</dependency>
 
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-servlets</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-servlet</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-server</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-util</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-webapp</artifactId>
+		</dependency>
+
 	</dependencies>
 
 	<build>
-
-		<!-- 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 you to test it by issuing "mvn jetty:run" from the command line. -->
-		<pluginManagement>
-			<plugins>
-				<plugin>
-					<groupId>org.eclipse.jetty</groupId>
-					<artifactId>jetty-maven-plugin</artifactId>
-					<version>9.1.1.v20140108</version>
-					<configuration>
-						<webApp>
-							<contextPath>/hapi-fhir-jpaserver-example</contextPath>
-						</webApp>
-					</configuration>
-				</plugin>
-			</plugins>
-		</pluginManagement>
-
 		<plugins>
-			<!-- Tell Maven which Java source version you want to use -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-compiler-plugin</artifactId>
+				<artifactId>maven-dependency-plugin</artifactId>
-				<configuration>
+				<executions>
-					<source>1.6</source>
+					<execution>
-					<target>1.6</target>
+						<id>copy</id>
-				</configuration>
+						<phase>process-resources</phase>
+						<goals>
+							<goal>copy</goal>
+						</goals>
+						<configuration>
+							<artifactItems>
+								<artifactItem>
+									<groupId>ca.uhn.hapi.fhir</groupId>
+									<artifactId>hapi-fhir-jpaserver-example</artifactId>
+									<version>1.2-SNAPSHOT</version>
+									<type>war</type>
+									<overWrite>true</overWrite>
+									<outputDirectory>target/classes</outputDirectory>
+									<destFileName>hapi-fhir-jpaserver-example.war</destFileName>
+								</artifactItem>
+							</artifactItems>
+							<!-- other configurations here -->
+						</configuration>
+					</execution>
+				</executions>
 			</plugin>
-
-			<!-- The configuration here tells the WAR plugin to include the FHIR Tester overlay. You can omit it if you are not using that feature. -->
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-war-plugin</artifactId>
-				<configuration>
-					<overlays>
-						<overlay>
-							<groupId>ca.uhn.hapi.fhir</groupId>
-							<artifactId>hapi-fhir-testpage-overlay</artifactId>
-						</overlay>
-					</overlays>
-				</configuration>
-			</plugin>
-
-			<!-- This plugin is just a part of the HAPI internal build process, you do not need to incude it in your own projects -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-deploy-plugin</artifactId>
@@ -116,7 +130,38 @@
 					<skip>true</skip>
 				</configuration>
 			</plugin>
-
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-shade-plugin</artifactId>
+				<version>2.4.1</version>
+				<executions>
+					<execution>
+						<phase>package</phase>
+						<goals>
+							<goal>shade</goal>
+						</goals>
+						<configuration>
+							<finalName>hapi-fhir-cli</finalName>
+							<artifactSet>
+							</artifactSet>
+							<transformers>
+								<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+									<mainClass>ca.uhn.fhir.cli.App</mainClass>
+								</transformer>
+							</transformers>
+							<filters>
+								<filter>
+									<artifact>*</artifact>
+									<excludes>
+										<exclude>**/*.SF</exclude>
+										<exclude>**/*.RSA</exclude>
+									</excludes>
+								</filter>
+							</filters>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
 		</plugins>
 	</build>
 

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/App.java

@@ -0,0 +1,55 @@
+package ca.uhn.fhir.cli;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+public class App {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(App.class);
+	private static List<BaseCommand> ourCommands;
+
+	static {
+		ourCommands = new ArrayList<BaseCommand>();
+		ourCommands.add(new RunServerCommand());
+	}
+
+	public static void main(String[] theArgs) {
+		if (theArgs.length == 0) {
+			logUsage();
+			return;
+		}
+
+		BaseCommand command = null;
+		for (BaseCommand nextCommand : ourCommands) {
+			if (nextCommand.getCommandName().equals(theArgs[0])) {
+				command = nextCommand;
+				break;
+			}
+		}
+
+		Options options = command.getOptions();
+		DefaultParser parser = new DefaultParser();
+		CommandLine parsedOptions;
+		try {
+			String[] args = Arrays.asList(theArgs).subList(1, theArgs.length).toArray(new String[theArgs.length - 1]);
+			parsedOptions = parser.parse(options, args, true);
+			command.run(parsedOptions);
+		} catch (ParseException e) {
+			ourLog.error("Invalid command options for command: " + command.getCommandName());
+			ourLog.error(e.getMessage());
+			ourLog.error("Aborting!");
+			return;
+		}
+
+	}
+
+	private static void logUsage() {
+		
+	}
+
+}

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/BaseCommand.java

@@ -1,5 +1,9 @@
 package ca.uhn.fhir.cli;
 
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.client.IGenericClient;
 
@@ -14,4 +18,18 @@ public class BaseCommand {
 		return fhirClient;
 	}
 
+	public Options getOptions() {
+		return null;
+	}
+
+	public String getCommandName() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public void run(CommandLine theCommandLine) throws ParseException {
+		// TODO Auto-generated method stub
+		
+	}
+
 }

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java

@@ -0,0 +1,102 @@
+package ca.uhn.fhir.cli;
+
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.webapp.WebAppContext;
+
+public class RunServerCommand extends BaseCommand {
+
+	private static final int DEFAULT_PORT = 8080;
+	private static final String OPTION_P = "p";
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RunServerCommand.class);
+	private int myPort;
+
+	private Server myServer;
+
+	@Override
+	public String getCommandName() {
+		return "run-server";
+	}
+
+	@Override
+	public Options getOptions() {
+		Options options = new Options();
+		options.addOption(OPTION_P, "port", true, "The port to listen on (default is " + DEFAULT_PORT + ")");
+		return options;
+	}
+
+	private int parseOptionInteger(CommandLine theCommandLine, String opt, int defaultPort) throws ParseException {
+		try {
+			return Integer.parseInt(theCommandLine.getOptionValue(opt, Integer.toString(defaultPort)));
+		} catch (NumberFormatException e) {
+			throw new ParseException("Invalid value '" + theCommandLine.getOptionValue(opt) + " (must be numeric)");
+		}
+	}
+
+	@Override
+	public void run(CommandLine theCommandLine) throws ParseException {
+		myPort = parseOptionInteger(theCommandLine, OPTION_P, DEFAULT_PORT);
+
+		ourLog.info("Preparing HAPI FHIR JPA server");
+		File tempWarFile;
+		try {
+			tempWarFile = File.createTempFile("hapi-fhir", ".war");
+			tempWarFile.deleteOnExit();
+			
+			InputStream inStream = RunServerCommand.class.getResourceAsStream("/hapi-fhir-jpaserver-example.war");
+			OutputStream outStream = new BufferedOutputStream(new FileOutputStream(tempWarFile, false));
+			IOUtils.copy(inStream, outStream);
+		} catch (IOException e) {
+			ourLog.error("Failed to create temporary file", e);
+			return;
+		}
+
+		ourLog.info("Starting HAPI FHIR JPA server");
+		WebAppContext root = new WebAppContext();
+		root.setAllowDuplicateFragmentNames(true);
+		root.setWar(tempWarFile.getAbsolutePath());
+		root.setContextPath("/");
+		
+		myServer = new Server(myPort);
+		myServer.setHandler(root);
+		try {
+			myServer.start();
+		} catch (Exception e) {
+			ourLog.error("Server failed to start", e);
+			return;
+		}
+
+		ourLog.info("Server started on port {}", myPort);
+		ourLog.info("Web Testing UI : http://localhost:{}/", myPort);
+		ourLog.info("Server Base URL: http://localhost:{}/baseDstu2/", myPort);
+	}
+
+	public void run(String[] theArgs) {
+
+		getOptions();
+
+		// myServer = new Server(myPort);
+		//
+		// WebAppContext webAppContext = new WebAppContext();
+		// webAppContext.setContextPath("/");
+		// webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
+		// webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-example");
+		// webAppContext.setParentLoaderPriority(true);
+		//
+		// myServer.setHandler(webAppContext);
+		// myServer.start();
+
+	}
+
+}

hapi-fhir-jpaserver-base/pom.xml

@@ -258,8 +258,6 @@
 			<scope>test</scope>
 		</dependency>
 		
-		
-		
 	</dependencies>
 
 

hapi-fhir-jpaserver-example/pom.xml

@@ -10,7 +10,6 @@
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
-	<groupId>ca.uhn.hapi.example</groupId>
 	<artifactId>hapi-fhir-jpaserver-example</artifactId>
 	<packaging>war</packaging>
 

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

@@ -12,7 +12,7 @@
 	<bean class="ca.uhn.fhir.to.TesterConfig">
 		<property name="servers">
 			<list>
-				<value>home     , DSTU2 , Local Server                 , ${serverBase}/base</value>
+				<value>home     , DSTU2 , Local Server                 , ${serverBase}/baseDstu2</value>
 			</list>
 		</property>
 	</bean>

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

@@ -49,7 +49,7 @@
 
 	<servlet-mapping>
 		<servlet-name>fhirServlet</servlet-name>
-		<url-pattern>/base/*</url-pattern>
+		<url-pattern>/baseDstu2/*</url-pattern>
 	</servlet-mapping>
 
 	<servlet-mapping>

pom.xml

@@ -185,7 +185,7 @@
 		<developer>
 			<id>SingingTree</id>
 			<name>Bryce Van Dyk</name>
-		</developer>	
+		</developer>
 	</developers>
 
 	<licenses>
@@ -209,9 +209,8 @@
 		<apache_httpclient_version>4.4</apache_httpclient_version>
 		<apache_httpcore_version>4.4</apache_httpcore_version>
 		<derby_version>10.11.1.1</derby_version>
-		<!-- Note on Hibernate versions: Hibernate 4.3+ uses JPA 2.1, which is too new for a number of platforms including JBoss EAP 6.x and Glassfish 3.0. Upgrade this 
+		<!-- Note on Hibernate versions: Hibernate 4.3+ uses JPA 2.1, which is too new for a number of platforms including JBoss EAP 6.x and Glassfish 3.0. Upgrade this version with caution! Also note that if 
-			version with caution! Also note that if you change this, you may get a failure in hibernate4-maven-plugin. See the note in hapi-fhir-jpaserver-base/pom.xml's configuration 
+			you change this, you may get a failure in hibernate4-maven-plugin. See the note in hapi-fhir-jpaserver-base/pom.xml's configuration for that plugin... <hibernate_version>4.3.7.Final</hibernate_version> -->
-			for that plugin... <hibernate_version>4.3.7.Final</hibernate_version> -->
 		<hibernate_version>4.2.17.Final</hibernate_version>
 		<hibernate_validator_version>5.1.0.Final</hibernate_validator_version>
 		<jetty_version>9.2.6.v20141205</jetty_version>
@@ -263,15 +262,20 @@
 				<version>${phloc_commons_version}</version>
 			</dependency>
 			<dependency>
-				<groupId>commons-io</groupId>
+				<groupId>commons-cli</groupId>
-				<artifactId>commons-io</artifactId>
+				<artifactId>commons-cli</artifactId>
-				<version>2.4</version>
+				<version>1.3.1</version>
 			</dependency>
 			<dependency>
 				<groupId>commons-codec</groupId>
 				<artifactId>commons-codec</artifactId>
 				<version>1.10</version>
 			</dependency>
+			<dependency>
+				<groupId>commons-io</groupId>
+				<artifactId>commons-io</artifactId>
+				<version>2.4</version>
+			</dependency>
 			<dependency>
 				<groupId>javax.el</groupId>
 				<artifactId>javax.el-api</artifactId>
@@ -562,6 +566,11 @@
 						</dependency>
 					</dependencies>
 				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-dependency-plugin</artifactId>
+					<version>2.10</version>
+				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-deploy-plugin</artifactId>
@@ -821,47 +830,43 @@
 						<configuration>
 							<target>
 								<copy todir="target/site/apidocs">
-									<fileset dir="hapi-fhir-base/target/site/apidocs" />
+									<fileset dir="hapi-fhir-base/target/site/apidocs"/>
 								</copy>
 								<copy todir="target/site/apidocs-dstu">
-									<fileset dir="hapi-fhir-structures-dstu/target/site/apidocs" />
+									<fileset dir="hapi-fhir-structures-dstu/target/site/apidocs"/>
 								</copy>
 								<copy todir="target/site/apidocs-hl7org-dstu2">
-									<fileset dir="hapi-fhir-structures-hl7org-dstu2/target/site/apidocs" />
+									<fileset dir="hapi-fhir-structures-hl7org-dstu2/target/site/apidocs"/>
 								</copy>
 								<copy todir="target/site/apidocs-dstu2">
-									<fileset dir="hapi-fhir-structures-dstu2/target/site/apidocs" />
+									<fileset dir="hapi-fhir-structures-dstu2/target/site/apidocs"/>
 								</copy>
 								<copy todir="target/site/apidocs-jpaserver">
-									<fileset dir="hapi-fhir-jpaserver-base/target/site/apidocs" />
+									<fileset dir="hapi-fhir-jpaserver-base/target/site/apidocs"/>
 								</copy>
 								<copy todir="target/site/xref-jpaserver">
-									<fileset dir="hapi-fhir-jpaserver-base/target/site/xref" />
+									<fileset dir="hapi-fhir-jpaserver-base/target/site/xref"/>
 								</copy>
 								<copy todir="target/site/xref-base">
-									<fileset dir="hapi-fhir-base/target/site/xref" />
+									<fileset dir="hapi-fhir-base/target/site/xref"/>
 								</copy>
-								<!--
+								<!-- <copy todir="target/site/cobertura"> <fileset dir="hapi-fhir-cobertura/target/site/cobertura" /> </copy> -->
-								<copy todir="target/site/cobertura">
-									<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">
-									<include name="checkstyle.html" />
+									<include name="checkstyle.html"/>
 									<replacetoken>"../../</replacetoken>
 									<replacevalue>"./</replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken>http://netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/css/bootstrap-responsive.min.css</replacetoken>
 									<replacevalue>./css/bootstrap-responsive.min.css</replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="index.html" />
+									<include name="index.html"/>
 									<replacetoken><![CDATA[<h2 id="Welcome">Welcome</h2>]]></replacetoken>
 									<replacevalue><![CDATA[<div class="jumbotron subhead">
 		<div class="row" id="banner">
@@ -890,33 +895,33 @@
 							<target>
 								<echo>Adding Fontawesome</echo>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken><![CDATA[<a href="download.html" title="Download">Download</a>]]></replacetoken>
 									<replacevalue><![CDATA[<a href="download.html"  title="Download"><i class="fa fa-download"></i> Download</a>]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken><![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project" class="externalLink">GitHub Project</a>]]></replacetoken>
 									<replacevalue><![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project"  class="externalLink"><i class="fa fa-github"></i> GitHub Project</a>]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Test Servers <]]></replacetoken>
 									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-fire"></i>&nbsp;Test Servers&nbsp;<]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Documentation <]]></replacetoken>
 									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-book"></i>&nbsp;Documentation&nbsp;<]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Get Help <]]></replacetoken>
 									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-support"></i>&nbsp;Get Help&nbsp;<]]></replacevalue>
 								</replace>
 								<echo>Changing Breadcrumbs</echo>
 								<replace dir="target/site" summary="true">
-									<include name="doc_*.html" />
+									<include name="doc_*.html"/>
 									<replacetoken><![CDATA[<li class="divider">/</li>]]></replacetoken>
 									<replacevalue><![CDATA[<li  class="divider">/</li>
 			<li><a href="docindex.html" title="Documentation">Documentation</a></li>
@@ -967,8 +972,8 @@
 								<echo>Adding Google analytics in target/site for &lt;body&gt;</echo>
 								<replace dir="target/site" summary="true">
 									<include name="**/*.html"></include>
-									<replacefilter token="#build#" value="${label}" />
+									<replacefilter token="#build#" value="${label}"/>
-									<replacefilter token="#version#" value="${project.version}" />
+									<replacefilter token="#version#" value="${project.version}"/>
 									<replacetoken><![CDATA[</body>]]></replacetoken>
 									<replacevalue><![CDATA[
 <script>
@@ -1106,9 +1111,8 @@
 
 	<reporting>
 		<plugins>
-			<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-checkstyle-plugin</artifactId> <reportSets> <reportSet> <reports><report>checkstyle-aggregate</report></reports> 
+			<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-checkstyle-plugin</artifactId> <reportSets> <reportSet> <reports><report>checkstyle-aggregate</report></reports> </reportSet> 
-				</reportSet> </reportSets> <configuration> <configLocation>config/sun_checks.xml</configLocation> <includes> hapi-fhir-base/src/main/java/**/*.java </includes> </configuration> 
+				</reportSets> <configuration> <configLocation>config/sun_checks.xml</configLocation> <includes> hapi-fhir-base/src/main/java/**/*.java </includes> </configuration> </plugin> -->
-				</plugin> -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-changes-plugin</artifactId>
@@ -1183,9 +1187,8 @@
 			</modules>
 			<build>
 				<plugins>
-					<!-- <plugin> <artifactId>maven-assembly-plugin</artifactId> <version>${maven_assembly_plugin_version}</version> <executions> <execution> <phase>package</phase> 
+					<!-- <plugin> <artifactId>maven-assembly-plugin</artifactId> <version>${maven_assembly_plugin_version}</version> <executions> <execution> <phase>package</phase> <goals> <goal>single</goal> </goals> 
-						<goals> <goal>single</goal> </goals> <configuration> <attach>false</attach> <descriptors> <descriptor>${project.basedir}/src/assembly/hapi-fhir-sample-projects.xml</descriptor> 
+						<configuration> <attach>false</attach> <descriptors> <descriptor>${project.basedir}/src/assembly/hapi-fhir-sample-projects.xml</descriptor> </descriptors> </configuration> </execution> </executions> </plugin> -->
-						</descriptors> </configuration> </execution> </executions> </plugin> -->
 				</plugins>
 			</build>
 
@@ -1224,9 +1227,7 @@
 				<module>hapi-fhir-structures-dstu2</module>
 				<module>hapi-fhir-structures-hl7org-dstu2</module>
 				<module>hapi-fhir-jpaserver-base</module>
-				<!-- 
+				<!-- <module>hapi-fhir-cobertura</module> -->
-				<module>hapi-fhir-cobertura</module>
-				-->
 				<module>examples</module>
 			</modules>
 			<reporting>