Merge branch 'master' of github.com:jamesagnew/hapi-fhir

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

@@ -35,7 +35,7 @@ public interface ITermConceptParentChildLinkDao extends JpaRepository<TermConcep
 	@Modifying
 	void deleteByCodeSystemVersion(@Param("cs_pid") Long thePid);
 
-	@Query("SELECT t FROM TermConceptParentChildLink t WHERE t.myChildPid = :child_pid")
-	Collection<TermConceptParentChildLink> findAllWithChild(@Param("child_pid") Long theConceptPid);
+	@Query("SELECT t.myParentPid FROM TermConceptParentChildLink t WHERE t.myChildPid = :child_pid")
+	Collection<Long> findAllWithChild(@Param("child_pid") Long theConceptPid);
 	
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvc.java

@@ -357,13 +357,14 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 				if (parents.contains(-1L)) {
 					return;
 				} else if (parents.isEmpty()) {
-					Collection<TermConceptParentChildLink> parentLinks = myConceptParentChildLinkDao.findAllWithChild(theConceptPid);
+					ourLog.info("Loading parent concepts of concept {}", theConceptPid);
+					Collection<Long> parentLinks = myConceptParentChildLinkDao.findAllWithChild(theConceptPid);
 					if (parentLinks.isEmpty()) {
 						myChildToParentPidCache.put(theConceptPid, -1L);
 						return;
 					} else {
-						for (TermConceptParentChildLink next : parentLinks) {
-							myChildToParentPidCache.put(theConceptPid, next.getParentPid());
+						for (Long next : parentLinks) {
+							myChildToParentPidCache.put(theConceptPid, next);
 						}
 					}
 				}
@@ -382,6 +383,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 				int maxResult = 1000;
 				Page<TermConcept> concepts = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
 				if (concepts.hasContent() == false) {
+					ourLog.info("Clearing parent concept cache");
 					myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
 					myChildToParentPidCache = null;
 					return;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderInterceptorDstu3Test.java

@@ -79,6 +79,7 @@ public class ResourceProviderInterceptorDstu3Test extends BaseResourceProviderDs
 
 	private void resetServerInterceptor() throws ServletException, IOException {
 		reset(myServerInterceptor);
+		reset(myDaoInterceptor);
 		when(myServerInterceptor.handleException(any(RequestDetails.class), any(BaseServerResponseException.class), any(HttpServletRequest.class), any(HttpServletResponse.class))).thenReturn(true);
 		when(myServerInterceptor.incomingRequestPostProcessed(any(RequestDetails.class), any(HttpServletRequest.class), any(HttpServletResponse.class))).thenReturn(true);
 		when(myServerInterceptor.incomingRequestPreProcessed(any(HttpServletRequest.class), any(HttpServletResponse.class))).thenReturn(true);
@@ -95,6 +96,7 @@ public class ResourceProviderInterceptorDstu3Test extends BaseResourceProviderDs
 		String resource = myFhirCtx.newXmlParser().encodeResourceToString(pt);
 
 		verify(myServerInterceptor, never()).incomingRequestPreHandled(any(RestOperationTypeEnum.class), any(ActionRequestDetails.class));
+		verify(myDaoInterceptor, never()).incomingRequestPreHandled(any(RestOperationTypeEnum.class), any(ActionRequestDetails.class));
 
 		HttpPost post = new HttpPost(ourServerBase + "/Patient");
 		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java

@@ -3,6 +3,8 @@ package ca.uhn.fhir.jpa.demo;
 
 import java.util.Collection;
 import java.util.List;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.servlet.ServletException;
 

hapi-fhir-jpaserver-uhnfhirtest/derby_maintenance.txt

@@ -11,6 +11,7 @@ curl -H "Authorization: Bearer " "http://fhirtest.uhn.ca/baseDstu3/\$mark-all-re
 # Delete all errored resources
 update hfj_res_ver set forced_id_pid = null where res_id in (select res_id from hfj_resource where sp_index_status = 2);
 update hfj_resource set forced_id_pid = null where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_history_tag where res_id in (select res_id from hfj_resource where sp_index_status = 2);
 delete from hfj_res_ver where res_id in (select res_id from hfj_resource where sp_index_status = 2);
 delete from hfj_forced_id where resource_pid in (select res_id from hfj_resource where sp_index_status = 2);
 delete from hfj_res_link where src_resource_id in (select res_id from hfj_resource where sp_index_status = 2);

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/ResponseHighlighterInterceptor.java

@@ -351,6 +351,7 @@ public class ResponseHighlighterInterceptor extends InterceptorAdapter {
 	 * 
 	 * @return Returns a reference to this for easy method chaining
 	 */
+	@SuppressWarnings("UnusedReturnValue")
 	public ResponseHighlighterInterceptor setShowRequestHeaders(boolean theShowRequestHeaders) {
 		myShowRequestHeaders = theShowRequestHeaders;
 		return this;
@@ -362,6 +363,7 @@ public class ResponseHighlighterInterceptor extends InterceptorAdapter {
 	 * 
 	 * @return Returns a reference to this for easy method chaining
 	 */
+	@SuppressWarnings("UnusedReturnValue")
 	public ResponseHighlighterInterceptor setShowResponseHeaders(boolean theShowResponseHeaders) {
 		myShowResponseHeaders = theShowResponseHeaders;
 		return this;
@@ -415,7 +417,7 @@ public class ResponseHighlighterInterceptor extends InterceptorAdapter {
 			}
 		}
 		if (prettyPrintResponse) {
-			p.setPrettyPrint(prettyPrintResponse);
+			p.setPrettyPrint(true);
 		}
 
 		EncodingEnum encoding = p.getEncoding();
@@ -558,18 +560,16 @@ public class ResponseHighlighterInterceptor extends InterceptorAdapter {
 			b.append("\n");
 			b.append("\n");
 
-			if (true) {
-				try {
-					if (isShowRequestHeaders()) {
-						streamRequestHeaders(theServletRequest, b);
-					}
-					if (isShowResponseHeaders()) {
-						streamResponseHeaders(theRequestDetails, theServletResponse, b);
-					}
-				} catch (Throwable t) {
-					// ignore (this will hit if we're running in a servlet 2.5 environment)
-				}
-			}
+			try {
+            if (isShowRequestHeaders()) {
+               streamRequestHeaders(theServletRequest, b);
+            }
+            if (isShowResponseHeaders()) {
+               streamResponseHeaders(theRequestDetails, theServletResponse, b);
+            }
+         } catch (Throwable t) {
+            // ignore (this will hit if we're running in a servlet 2.5 environment)
+         }
 
 			StringBuilder target = new StringBuilder();
 			int linesCount = format(encoded, target, encoding);

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/ResponseHighlightingInterceptorTest.java

@@ -761,6 +761,7 @@ public class ResponseHighlightingInterceptorTest {
 	@BeforeClass
 	public static void beforeClass() throws Exception {
 		ourPort = PortUtil.findFreePort();
+		ourLog.info("Using port: {}", ourPort);
 		ourServer = new Server(ourPort);
 
 		DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/ServerActionInterceptorTest.java

@@ -1,33 +1,5 @@
 package ca.uhn.fhir.rest.server.interceptor;
 
-import static org.junit.Assert.assertEquals;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.eq;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.reset;
-import static org.mockito.Mockito.verify;
-import static org.mockito.Mockito.when;
-
-import java.util.Collections;
-import java.util.List;
-import java.util.concurrent.TimeUnit;
-
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.http.client.methods.CloseableHttpResponse;
-import org.apache.http.client.methods.HttpGet;
-import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.impl.client.HttpClientBuilder;
-import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
-import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.servlet.ServletHandler;
-import org.eclipse.jetty.servlet.ServletHolder;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.junit.*;
-import org.mockito.ArgumentCaptor;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.api.BundleInclusionRule;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
@@ -44,6 +16,32 @@ import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.util.PortUtil;
 import ca.uhn.fhir.util.TestUtil;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.mockito.ArgumentCaptor;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.util.Collections;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import static org.junit.Assert.*;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.eq;
+import static org.mockito.Mockito.*;
 
 public class ServerActionInterceptorTest {
 

pom.xml

@@ -358,6 +358,10 @@
 			<id>InfiniteLoop90</id>
 			<name>Clayton Bodendein</name>
 		</developer>
+		<developer>
+			<id>rhausam</id>
+			<name>Rob Hausam</name>
+		</developer>
 	</developers>
 
 	<licenses>

src/changes/changes.xml

@@ -328,6 +328,10 @@
 				specified, regardless of whether the source event was a create or an
 				update
 			</action>
+			<action type="add" issue="712">
+				Add appropriate import statements for logging to JPA demo code. Thanks to
+				Rob Hausam for the pull request!
+			</action>
 		</release>
 		<release version="2.5" date="2017-06-08">
 			<action type="fix">