From 92a070430a2d45edff787499b4c6a1d1c1b052eb Mon Sep 17 00:00:00 2001
From: Robbert van Waveren <robbert.van.waveren@philips.com>
Date: Thu, 13 Oct 2016 12:03:48 +0200
Subject: [PATCH 1/3] fix resources links being correctly indexed when linking
 eachother as part of a single transaction bundle

---
 .../src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java      | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
index 3ce1acb1c1a..e1ae359e956 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
@@ -1415,6 +1415,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			for (ResourceLink next : links) {
 				myEntityManager.persist(next);
 			}
+			// make sure links are indexed
+			theEntity.setResourceLinks(links);
 
 		} // if thePerformIndexing
 

From b59c24ab7c06cdc3eed462a8c60be29d7d21c717 Mon Sep 17 00:00:00 2001
From: "michael.i.calderero" <michael.i.calderero@accenture.com>
Date: Tue, 17 Jan 2017 20:37:43 -0600
Subject: [PATCH 2/3] return 404 instead of 400 when the FHIR resource/endpoint
 is not recognized/not supported

---
 .../src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java  | 3 ++-
 .../java/ca/uhn/fhir/rest/server/RestfulServerMethodTest.java | 4 ++--
 .../java/ca/uhn/fhir/rest/server/ServerFeaturesDstu2Test.java | 2 +-
 .../interceptor/ResponseHighlightingInterceptorTest.java      | 2 +-
 4 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java
index 215d9c9293e..d673656cd24 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java
+++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java
@@ -75,6 +75,7 @@ import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.NotModifiedException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.interceptor.ExceptionHandlingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
@@ -253,7 +254,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		} else {
 			resourceBinding = myResourceNameToBinding.get(resourceName);
 			if (resourceBinding == null) {
-				throw new InvalidRequestException("Unknown resource type '" + resourceName + "' - Server knows how to handle: " + myResourceNameToBinding.keySet());
+				throw new ResourceNotFoundException("Unknown resource type '" + resourceName + "' - Server knows how to handle: " + myResourceNameToBinding.keySet());
 			}
 		}
 
diff --git a/hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/RestfulServerMethodTest.java b/hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/RestfulServerMethodTest.java
index 7640c06c979..ad9787064b0 100644
--- a/hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/RestfulServerMethodTest.java
+++ b/hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/RestfulServerMethodTest.java
@@ -527,7 +527,7 @@ public class RestfulServerMethodTest {
 	}
 
 	@Test
-	public void testInvalidResourceTriggers400() throws Exception {
+	public void testInvalidResourceTriggers404() throws Exception {
 
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/FooResource?blah=bar");
 		HttpResponse status = ourClient.execute(httpGet);
@@ -537,7 +537,7 @@ public class RestfulServerMethodTest {
 
 		ourLog.info("Response was:\n{}", responseContent);
 
-		assertEquals(400, status.getStatusLine().getStatusCode());
+		assertEquals(404, status.getStatusLine().getStatusCode());
 	}
 
 	@Test
diff --git a/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/ServerFeaturesDstu2Test.java b/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/ServerFeaturesDstu2Test.java
index 78eb1e2fcaa..fa3c5d8bd4d 100644
--- a/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/ServerFeaturesDstu2Test.java
+++ b/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/ServerFeaturesDstu2Test.java
@@ -82,7 +82,7 @@ public class ServerFeaturesDstu2Test {
 		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		ourLog.info(responseContent);
-		assertEquals(400, status.getStatusLine().getStatusCode());
+		assertEquals(404, status.getStatusLine().getStatusCode());
 	}
 
 	/**
diff --git a/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/ResponseHighlightingInterceptorTest.java b/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/ResponseHighlightingInterceptorTest.java
index 0e1dfbfb51a..fc2441a556a 100644
--- a/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/ResponseHighlightingInterceptorTest.java
+++ b/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/ResponseHighlightingInterceptorTest.java
@@ -171,7 +171,7 @@ public class ResponseHighlightingInterceptorTest {
 		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		ourLog.info("Resp: {}", responseContent);
-		assertEquals(400, status.getStatusLine().getStatusCode());
+		assertEquals(404, status.getStatusLine().getStatusCode());
 
 		assertThat(responseContent, not(stringContainsInOrder("<span class='hlTagName'>OperationOutcome</span>", "Unknown resource type 'Foobar' - Server knows how to handle")));
 		assertThat(responseContent, (stringContainsInOrder("Unknown resource type 'Foobar'")));

From dc17157db85a1146ddb79718ab8e63aace105c84 Mon Sep 17 00:00:00 2001
From: James Agnew <jamesagnew@gmail.com>
Date: Fri, 20 Jan 2017 18:49:01 -0500
Subject: [PATCH 3/3] Credit for #539

---
 src/changes/changes.xml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index 213489b85f5..1aed599ba27 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -217,6 +217,11 @@
 				JPA server terminology service was not correctly validating or expanding codes 
 				in SNOMED CT or LOINC code systems. Thanks to David Hay for reporting!
 			</action>
+			<action type="fix" issue="539">
+				Attempting to search for an invalid resource type (e.g. GET base/FooResource) should 
+				return an HTTP 404 and not a 400, per the HTTP spec. Thanks to 
+				GitHub user @CarthageKing for the pull request!
+			</action>
 		</release>
 		<release version="2.1" date="2016-11-11">
 			<action type="add">