Fix #69

hapi-fhir-base/.classpath

@@ -28,9 +28,9 @@
 			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
 		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="owner.project.facets" value="java"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>

hapi-fhir-base/.settings/org.eclipse.jdt.core.prefs

@@ -7,9 +7,9 @@ org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nul
 org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.compliance=1.8
 org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
@@ -97,4 +97,4 @@ org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
 org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=warning
 org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
 org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
-org.eclipse.jdt.core.compiler.source=1.6
+org.eclipse.jdt.core.compiler.source=1.8

hapi-fhir-base/.settings/org.eclipse.wst.common.project.facet.core.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <faceted-project>
   <installed facet="jst.utility" version="1.0"/>
-  <installed facet="java" version="1.6"/>
+  <installed facet="java" version="1.8"/>
 </faceted-project>

hapi-fhir-base/pom.xml

@@ -203,6 +203,11 @@
 					<artifactId>hapi-fhir-structures-dstu</artifactId>
 					<version>0.9-SNAPSHOT</version>
 				</dependency>
+				<dependency>
+					<groupId>org.slf4j</groupId>
+					<artifactId>slf4j-android</artifactId>
+					<version>${slf4j_version}</version>
+				</dependency>
 			</dependencies>
 			<build>
 				<plugins>
@@ -225,10 +230,13 @@
 											<include>javax.json:javax.json-api</include>
 											-->
 											<include>ca.uhn.hapi.fhir:hapi-fhir-structures-dstu</include>
+											<include>ca.uhn.hapi.fhir:hapi-fhir-structures-dstu</include>
 											<include>org.glassfish:javax.json</include>
 											<include>org.codehaus.woodstox:woodstox-core-asl</include>
 											<include>javax.xml.stream:stax-api</include>
 											<include>org.codehaus.woodstox:stax2-api</include>
+											<include>org.slf4j:slf4j*</include>
+											<include>org.apache.commons:*</include>
 										</includes>
 									</artifactSet>
 									<relocations>

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BundleEntry.java

@@ -210,10 +210,21 @@ public class BundleEntry extends BaseBundle {
 		return myTitle;
 	}
 
+	/**
+	 * @deprecated <b>DSTU2 Note:</b> As of DSTU2, bundle entries no longer have an updated time (this bit of metadata has been moved
+	 * to the resource &lt;meta/&gt; element so it is redundant here). In preparation for DSTU2, it is recommended that you
+	 * migrate code away from using this method and over to using resource metadata instead. 
+	 */
 	public InstantDt getUpdated() {
 		if (myUpdated == null) {
 			myUpdated = new InstantDt();
 		}
+		if (myUpdated.isEmpty() && myResource != null) {
+			InstantDt resourceUpdated = ResourceMetadataKeyEnum.UPDATED.get(myResource);
+			if (resourceUpdated!=null && !resourceUpdated.isEmpty()) {
+				return resourceUpdated;
+			}
+		}
 		return myUpdated;
 	}
 
@@ -279,6 +290,11 @@ public class BundleEntry extends BaseBundle {
 		myStatus = theStatus;
 	}
 
+	/**
+	 * @deprecated <b>DSTU2 Note:</b> As of DSTU2, bundle entries no longer have an updated time (this bit of metadata has been moved
+	 * to the resource &lt;meta/&gt; element so it is redundant here). In preparation for DSTU2, it is recommended that you
+	 * migrate code away from using this method and over to using resource metadata instead. 
+	 */
 	public void setUpdated(InstantDt theUpdated) {
 		Validate.notNull(theUpdated, "Updated may not be null");
 		myUpdated = theUpdated;

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseMethodBinding.java

@@ -34,7 +34,9 @@ import java.util.Set;
 import java.util.TreeSet;
 
 import ca.uhn.fhir.rest.annotation.*;
+
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.instance.model.IBaseResource;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
@@ -435,7 +437,7 @@ public abstract class BaseMethodBinding<T> implements IClientResponseHandler<T>
 		if (theReturnType == null) {
 			return false;
 		}
-		if (!IResource.class.isAssignableFrom(theReturnType)) {
+		if (!IBaseResource.class.isAssignableFrom(theReturnType)) {
 			return false;
 		}
 		return true;

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseResourceReturningMethodBinding.java

@@ -34,6 +34,8 @@ import java.util.Set;
 
 import javax.servlet.http.HttpServletResponse;
 
+import org.hl7.fhir.instance.model.IBaseResource;
+
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
@@ -90,7 +92,7 @@ abstract class BaseResourceReturningMethodBinding extends BaseMethodBinding<Obje
 			}
 			myResourceListCollectionType = collectionType;
 
-		} else if (IResource.class.isAssignableFrom(methodReturnType)) {
+		} else if (IBaseResource.class.isAssignableFrom(methodReturnType)) {
 			myMethodReturnType = MethodReturnTypeEnum.RESOURCE;
 		} else if (Bundle.class.isAssignableFrom(methodReturnType)) {
 			myMethodReturnType = MethodReturnTypeEnum.BUNDLE;

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/ConformanceMethodBinding.java

@@ -42,7 +42,7 @@ public class ConformanceMethodBinding extends BaseResourceReturningMethodBinding
 //		if (Modifier.isAbstract(theMethod.getReturnType().getModifiers())) {
 //			throw new ConfigurationException("Conformance resource provider method '" + theMethod.getName() + "' must not be abstract");
 //		}
-		if (getMethodReturnType() != MethodReturnTypeEnum.RESOURCE || !BaseConformance.class.isAssignableFrom(theMethod.getReturnType())) {
+		if (getMethodReturnType() != MethodReturnTypeEnum.RESOURCE || !BaseConformance.class.isAssignableFrom((Class<?>) theMethod.getGenericReturnType())) {
 			throw new ConfigurationException("Conformance resource provider method '" + theMethod.getName() + "' should return a Conformance resource class, returns: " + theMethod.getReturnType());
 		}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/ReadMethodBinding.java

@@ -222,7 +222,7 @@ public class ReadMethodBinding extends BaseResourceReturningMethodBinding implem
 	}
 
 	public static HttpGetClientInvocation createAbsoluteReadInvocation(IdDt theId) {
-		return new HttpGetClientInvocation(theId.getValue());
+		return new HttpGetClientInvocation(theId.toVersionless().getValue());
 	}
 
 	public static HttpGetClientInvocation createAbsoluteVReadInvocation(IdDt theId) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java

@@ -41,6 +41,7 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.NotModifiedException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.util.ReflectionUtil;
 import ca.uhn.fhir.util.VersionUtil;
 
 import org.apache.commons.lang3.StringUtils;
@@ -196,7 +197,7 @@ public class RestfulServer extends HttpServlet {
 	private int findResourceMethods(Object theProvider, Class<?> clazz) throws ConfigurationException {
 		int count = 0;
 
-		for (Method m : clazz.getDeclaredMethods()) {
+		for (Method m : ReflectionUtil.getDeclaredMethods(clazz)) {
 			BaseMethodBinding<?> foundMethodBinding = BaseMethodBinding.bindMethod(m, myFhirContext, theProvider);
 			if (foundMethodBinding == null) {
 				continue;
@@ -263,7 +264,7 @@ public class RestfulServer extends HttpServlet {
 			findSystemMethods(theSystemProvider, supertype);
 		}
 
-		for (Method m : clazz.getDeclaredMethods()) {
+		for (Method m : ReflectionUtil.getDeclaredMethods(clazz)) {
 			if (Modifier.isPublic(m.getModifiers())) {
 				ourLog.debug("Scanning public method: {}#{}", theSystemProvider.getClass(), m.getName());
 
@@ -797,7 +798,7 @@ public class RestfulServer extends HttpServlet {
 	}
 
 	private void invokeDestroy(Object theProvider, Class<?> clazz) {
-		for (Method m : clazz.getDeclaredMethods()) {
+		for (Method m : ReflectionUtil.getDeclaredMethods(clazz)) {
 			Destroy destroy = m.getAnnotation(Destroy.class);
 			if (destroy != null) {
 				try {
@@ -1392,7 +1393,7 @@ public class RestfulServer extends HttpServlet {
 
 		if (theServer.getETagSupport() == ETagSupportEnum.ENABLED) {
 			if (theResource.getId().hasVersionIdPart()) {
-				theHttpResponse.addHeader(Constants.HEADER_ETAG, '"' + theResource.getId().getVersionIdPart() + '"');
+				theHttpResponse.addHeader(Constants.HEADER_ETAG, "W/\"" + theResource.getId().getVersionIdPart() + '"');
 			}
 		}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ReflectionUtil.java

@@ -26,6 +26,8 @@ import java.lang.reflect.ParameterizedType;
 import java.lang.reflect.Type;
 import java.lang.reflect.TypeVariable;
 import java.lang.reflect.WildcardType;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
 
 public class ReflectionUtil {
 
@@ -83,4 +85,19 @@ public class ReflectionUtil {
 		return type;
 	}
 
+	public static LinkedHashSet<Method> getDeclaredMethods(Class<?> theClazz) {
+		LinkedHashSet<Method> retVal = new LinkedHashSet<Method>();
+		for (Method next : theClazz.getDeclaredMethods()) {
+			try {
+				Method method = theClazz.getMethod(next.getName(), next.getParameterTypes());
+				retVal.add(method);
+			} catch (NoSuchMethodException e) {
+				retVal.add(next);
+			} catch (SecurityException e) {
+				retVal.add(next);
+			}
+		}
+		return retVal;
+	}
+
 }

hapi-fhir-structures-dev/src/test/java/ca/uhn/fhir/rest/server/ETagServerTest.java

@@ -69,7 +69,7 @@ public class ETagServerTest {
 
 		Header cl = status.getFirstHeader(Constants.HEADER_ETAG_LC);
 		assertNotNull(cl);
-		assertEquals("\"222\"", cl.getValue());
+		assertEquals("W/\"222\"", cl.getValue());
 	}
 
 	

hapi-fhir-structures-dstu/.settings/org.eclipse.wst.common.project.facet.core.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <faceted-project>
   <installed facet="jst.utility" version="1.0"/>
-  <installed facet="java" version="1.6"/>
+  <installed facet="java" version="1.8"/>
 </faceted-project>

hapi-fhir-structures-dstu/src/main/java/ca/uhn/fhir/rest/server/provider/ServerConformanceProvider.java

@@ -97,6 +97,7 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 	 * 
 	 * See the class documentation for an important note if you are extending this class
 	 */
+	@Override
 	@Metadata
 	public Conformance getServerConformance(HttpServletRequest theRequest) {
 		if (myConformance != null && myCache) {

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/exceptions/ExceptionTest.java

@@ -15,6 +15,7 @@ import com.google.common.reflect.ClassPath.ClassInfo;
 public class ExceptionTest {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExceptionTest.class);
 
+	@SuppressWarnings("deprecation")
 	@Test
 	public void testExceptionsAreGood() throws Exception {
 		ImmutableSet<ClassInfo> classes = ClassPath.from(Thread.currentThread().getContextClassLoader()).getTopLevelClasses(BaseServerResponseException.class.getPackage().getName());
@@ -35,8 +36,12 @@ public class ExceptionTest {
 			if (next == UnclassifiedServerFailureException.class) {
 				continue;
 			}
+			if (next == ResourceVersionNotSpecifiedException.class) {
+				// This one is deprocated
+				continue;
+			}
 			
-			assertTrue(BaseServerResponseException.isExceptionTypeRegistered(next));
+			assertTrue("Type " + next + " is not registered", BaseServerResponseException.isExceptionTypeRegistered(next));
 			
 			if (next == AuthenticationException.class) {
 				continue;

hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/Controller.java

@@ -45,6 +45,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.model.api.BundleEntry;
 import ca.uhn.fhir.model.api.ExtensionDt;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.Include;
@@ -58,6 +59,7 @@ import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.DecimalDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.client.GenericClient;
 import ca.uhn.fhir.rest.client.IClientInterceptor;
@@ -343,7 +345,7 @@ public class Controller {
 			haveSearchParams = extractSearchParamsDstu1(conformance, resourceName, includes, sortParams, queries, haveSearchParams, queryIncludes);
 			break;
 		default:
-			throw new IllegalStateException("Unknown FHIR version: "+theRequest.getFhirVersion(myConfig));
+			throw new IllegalStateException("Unknown FHIR version: " + theRequest.getFhirVersion(myConfig));
 		}
 
 		theModel.put("includes", includes);
@@ -366,7 +368,8 @@ public class Controller {
 		return "resource";
 	}
 
-	private boolean extractSearchParamsDstu1(IResource theConformance, String resourceName, TreeSet<String> includes, TreeSet<String> sortParams, List<RestQuery> queries, boolean haveSearchParams, List<List<String>> queryIncludes) {
+	private boolean extractSearchParamsDstu1(IResource theConformance, String resourceName, TreeSet<String> includes, TreeSet<String> sortParams, List<RestQuery> queries, boolean haveSearchParams,
+			List<List<String>> queryIncludes) {
 		Conformance conformance = (Conformance) theConformance;
 		for (Rest nextRest : conformance.getRest()) {
 			for (RestResource nextRes : nextRest.getResource()) {
@@ -414,8 +417,9 @@ public class Controller {
 		return haveSearchParams;
 	}
 
-	private boolean extractSearchParamsDev(IResource theConformance, String resourceName, TreeSet<String> includes, TreeSet<String> sortParams, List<RestQuery> queries, boolean haveSearchParams, List<List<String>> queryIncludes) {
+	private boolean extractSearchParamsDev(IResource theConformance, String resourceName, TreeSet<String> includes, TreeSet<String> sortParams, List<RestQuery> queries, boolean haveSearchParams,
-		ca.uhn.fhir.model.dev.resource.Conformance conformance = (ca.uhn.fhir.model.dev.resource.Conformance)theConformance;
+			List<List<String>> queryIncludes) {
+		ca.uhn.fhir.model.dev.resource.Conformance conformance = (ca.uhn.fhir.model.dev.resource.Conformance) theConformance;
 		for (ca.uhn.fhir.model.dev.resource.Conformance.Rest nextRest : conformance.getRest()) {
 			for (ca.uhn.fhir.model.dev.resource.Conformance.RestResource nextRes : nextRest.getResource()) {
 				if (nextRes.getTypeElement().getValue().equals(resourceName)) {
@@ -456,7 +460,7 @@ public class Controller {
 		IQuery query;
 		if (isNotBlank(theReq.getParameter("resource"))) {
 			try {
-				query = search.forResource((Class<? extends IResource>)getResourceType(theRequest, theReq).getImplementingClass());
+				query = search.forResource((Class<? extends IResource>) getResourceType(theRequest, theReq).getImplementingClass());
 			} catch (ServletException e) {
 				theModel.put("errorMsg", e.toString());
 				return "resource";
@@ -913,7 +917,7 @@ public class Controller {
 	private FhirContext getContext(HomeRequest theRequest) {
 		FhirVersionEnum version = theRequest.getFhirVersion(myConfig);
 		FhirContext retVal = myContexts.get(version);
-		if (retVal==null) {
+		if (retVal == null) {
 			retVal = new FhirContext(version);
 			myContexts.put(version, retVal);
 		}
@@ -956,13 +960,13 @@ public class Controller {
 		}
 
 		List<String> values;
-		boolean addToWhere=true;
+		boolean addToWhere = true;
 		if ("token".equals(nextType)) {
 			if (isBlank(parts.get(2))) {
 				return true;
 			}
 			values = Collections.singletonList(StringUtils.join(parts, ""));
-			addToWhere=false;
+			addToWhere = false;
 			theQuery.where(new TokenClientParam(nextName + nextQualifier).exactly().systemAndCode(parts.get(0), parts.get(2)));
 		} else if ("date".equals(nextType)) {
 			values = new ArrayList<String>();
@@ -997,7 +1001,7 @@ public class Controller {
 		}
 
 		if (StringUtils.isNotBlank(theReq.getParameter("param." + paramIdxString + ".0.name"))) {
-			handleSearchParam(paramIdxString + ".0", theReq, theQuery , theClientCodeJsonWriter);
+			handleSearchParam(paramIdxString + ".0", theReq, theQuery, theClientCodeJsonWriter);
 		}
 
 		return true;
@@ -1010,7 +1014,7 @@ public class Controller {
 		case DSTU1:
 			return loadAndAddConfDstu1(theRequest, theModel);
 		}
-		throw new IllegalStateException("Unknown version: "+theRequest.getFhirVersion(myConfig));
+		throw new IllegalStateException("Unknown version: " + theRequest.getFhirVersion(myConfig));
 	}
 
 	private Conformance loadAndAddConfDstu1(final HomeRequest theRequest, final ModelMap theModel) {
@@ -1018,7 +1022,7 @@ public class Controller {
 
 		Conformance conformance;
 		try {
-			conformance = (Conformance)client.conformance();
+			conformance = (Conformance) client.conformance();
 		} catch (Exception e) {
 			ourLog.warn("Failed to load conformance statement", e);
 			theModel.put("errorMsg", "Failed to load conformance statement, error was: " + e.toString());
@@ -1077,7 +1081,7 @@ public class Controller {
 
 		ca.uhn.fhir.model.dev.resource.Conformance conformance;
 		try {
-			conformance = (ca.uhn.fhir.model.dev.resource.Conformance)client.conformance();
+			conformance = (ca.uhn.fhir.model.dev.resource.Conformance) client.conformance();
 		} catch (Exception e) {
 			ourLog.warn("Failed to load conformance statement", e);
 			theModel.put("errorMsg", "Failed to load conformance statement, error was: " + e.toString());
@@ -1226,6 +1230,22 @@ public class Controller {
 				}
 			}
 
+			/*
+			 * DSTU2 no longer has a title in the bundle format, but it's still
+			 * useful here..
+			 */
+			if (bundle != null) {
+				INarrativeGenerator gen = getContext(theRequest).getNarrativeGenerator();
+				if (gen != null) {
+					for (BundleEntry next : bundle.getEntries()) {
+						if (next.getTitle().isEmpty() && next.getResource() != null) {
+							String title = gen.generateTitle(next.getResource());
+							next.getTitle().setValue(title);
+						}
+					}
+				}
+			}
+
 			resultDescription.append(" (").append(resultBody.length() + " bytes)");
 
 			Header[] requestHeaders = lastRequest != null ? applyHeaderFilters(lastRequest.getAllHeaders()) : new Header[0];

hapi-fhir-testpage-overlay/src/main/webapp/WEB-INF/templates/result.html

@@ -175,7 +175,7 @@
 														<table class="table table-condensed" style="padding-bottom: 0px; margin-bottom: 0px;">
 															<colgroup>
 																<col style="width: 100px;"/>
-																<col style="width: 100px;"/>
+																<col/>
 																<col/>
 																<col style="width: 100px;"/>
 															</colgroup>
@@ -196,7 +196,7 @@
 																	</th:block>
 																</td>
 																<td>
-																	<small th:if="${entry.resource} != null" th:text="${entry.resource.id.toUnqualified()}"/>
+																	<a th:if="${entry.resource} != null" th:href="${entry.resource.id}" th:text="${entry.resource.id.toUnqualified()}" style="font-size: 0.8em"/>
 																</td>
 																<td>
 																	<small th:text="${entry.title}"/>

hapi-fhir-testpage-overlay/src/main/webapp/css/tester.css

@@ -143,6 +143,7 @@ PRE.resultBodyPre {
 	border: none;
 	background-color: transparent;
 	overflow: visible;
+	/*white-space: normal;*/
 }
 
 /*

pom.xml

@@ -176,7 +176,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.1</version>
+					<version>3.2</version>
 					<configuration>
 						<source>1.6</source>
 						<target>1.6</target>