Merge branch 'master' into hapi3_refactor

hapi-fhir-jpaserver-base/pom.xml

@@ -632,6 +632,9 @@
 						<artifactId>maven-surefire-plugin</artifactId>
 						<configuration>
 							<forkCount>1</forkCount>
+							<excludes>
+								<exclude>**/stresstest/*</exclude>
+							</excludes>
 						</configuration>
 					</plugin>
 				</plugins>
@@ -647,6 +650,9 @@
 						<configuration>
 							<forkCount>2</forkCount>
 							<reuseForks>true</reuseForks>
+							<excludes>
+								<exclude>**/stresstest/*</exclude>
+							</excludes>
 						</configuration>
 					</plugin>
 				</plugins>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaValidationSupportDstu2.java

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.jpa.dao;
 
+import javax.transaction.Transactional;
+import javax.transaction.Transactional.TxType;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -31,6 +34,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 
+@Transactional(value=TxType.REQUIRED)
 public class JpaValidationSupportDstu2 implements IJpaValidationSupportDstu2 {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JpaValidationSupportDstu2.class);
@@ -52,11 +56,13 @@ public class JpaValidationSupportDstu2 implements IJpaValidationSupportDstu2 {
 	private FhirContext myDstu2Ctx;
 
 	@Override
+	@Transactional(value=TxType.SUPPORTS)
 	public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
 		return null;
 	}
 
 	@Override
+	@Transactional(value=TxType.SUPPORTS)
 	public ValueSet fetchCodeSystem(FhirContext theCtx, String theSystem) {
 		return null;
 	}
@@ -95,11 +101,13 @@ public class JpaValidationSupportDstu2 implements IJpaValidationSupportDstu2 {
 	}
 
 	@Override
+	@Transactional(value=TxType.SUPPORTS)
 	public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
 		return false;
 	}
 
 	@Override
+	@Transactional(value=TxType.SUPPORTS)
 	public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
 		return null;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/JpaValidationSupportDstu3.java

@@ -3,11 +3,10 @@ package ca.uhn.fhir.jpa.dao.dstu3;
 import java.util.Collections;
 import java.util.List;
 
-import org.hl7.fhir.dstu3.model.CodeSystem;
+import javax.transaction.Transactional;
-import org.hl7.fhir.dstu3.model.IdType;
+import javax.transaction.Transactional.TxType;
-import org.hl7.fhir.dstu3.model.Questionnaire;
+
-import org.hl7.fhir.dstu3.model.StructureDefinition;
+import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
 import org.hl7.fhir.instance.model.api.IAnyResource;
@@ -43,6 +42,7 @@ import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 
+@Transactional(value=TxType.REQUIRED)
 public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3 {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JpaValidationSupportDstu3.class);
@@ -72,6 +72,7 @@ public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3 {
 	
 	
 	@Override
+	@Transactional(value=TxType.SUPPORTS)
 	public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
 		return null;
 	}
@@ -81,6 +82,7 @@ public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3 {
 		return fetchResource(theCtx, CodeSystem.class, theSystem);
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
 		IdType id = new IdType(theUri);
@@ -143,11 +145,13 @@ public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3 {
 	}
 
 	@Override
+	@Transactional(value=TxType.SUPPORTS)
 	public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
 		return false;
 	}
 
 	@Override
+	@Transactional(value=TxType.SUPPORTS)
 	public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
 		return null;
 	}
@@ -160,6 +164,7 @@ public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3 {
 
 
 	@Override
+	@Transactional(value=TxType.SUPPORTS)
 	public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
 		return Collections.emptyList();
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java

@@ -37,6 +37,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		retVal.setUrl("jdbc:derby:memory:myUnitTestDB;create=true");
 		retVal.setUsername("");
 		retVal.setPassword("");
+		retVal.setMaxTotal(4);
 
 		DataSource dataSource = ProxyDataSourceBuilder
 				.create(retVal)

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/BaseResourceProviderDstu3Test.java

@@ -31,6 +31,7 @@ import ca.uhn.fhir.jpa.config.dstu3.WebsocketDstu3Config;
 import ca.uhn.fhir.jpa.config.dstu3.WebsocketDstu3DispatcherConfig;
 import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
+import ca.uhn.fhir.jpa.dao.dstu3.SearchParamRegistryDstu3;
 import ca.uhn.fhir.jpa.interceptor.RestHookSubscriptionDstu3Interceptor;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
@@ -47,7 +48,7 @@ import ca.uhn.fhir.util.TestUtil;
 
 public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 
-	private static JpaValidationSupportChainDstu3 myValidationSupport;
+	protected static JpaValidationSupportChainDstu3 myValidationSupport;
 	protected static IGenericClient ourClient;
 	protected static CloseableHttpClient ourHttpClient;
 	protected static int ourPort;
@@ -56,6 +57,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 	protected static String ourServerBase;
 	private static GenericWebApplicationContext ourWebApplicationContext;
 	private TerminologyUploaderProviderDstu3 myTerminologyUploaderProvider;
+	protected static SearchParamRegistryDstu3 ourSearchParamRegistry;
 	protected static DatabaseBackedPagingProvider ourPagingProvider;
 	protected static RestHookSubscriptionDstu3Interceptor ourRestHookSubscriptionInterceptor;
 	protected static ISearchDao mySearchEntityDao;
@@ -150,7 +152,9 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 			mySearchCoordinatorSvc = wac.getBean(ISearchCoordinatorSvc.class);
 			mySearchEntityDao = wac.getBean(ISearchDao.class);
 			ourRestHookSubscriptionInterceptor = wac.getBean(RestHookSubscriptionDstu3Interceptor.class);
+			ourSearchParamRegistry = wac.getBean(SearchParamRegistryDstu3.class);
 
+			myFhirCtx.getRestfulClientFactory().setSocketTimeout(5000000);
 			ourClient = myFhirCtx.newRestfulGenericClient(ourServerBase);
 			if (shouldLogClient()) {
 				ourClient.registerInterceptor(new LoggingInterceptor(true));
@@ -159,6 +163,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 			PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
 			HttpClientBuilder builder = HttpClientBuilder.create();
 			builder.setConnectionManager(connectionManager);
+			builder.setMaxConnPerRoute(99);
 			ourHttpClient = builder.build();
 
 			ourServer = server;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/stresstest/README.txt

@@ -0,0 +1,5 @@
+Note: Tests in this package are not executed by Travis, because travis
+just gets mad that the build is taking too long. So make sure to run them
+locally!
+
+A normal build (mvn install) will run them.

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/stresstest/StressTestDstu3Test.java

@@ -0,0 +1,171 @@
+package ca.uhn.fhir.jpa.stresstest;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import java.util.List;
+import java.util.UUID;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
+import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.Bundle.BundleType;
+import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
+import org.junit.*;
+
+import com.google.common.collect.Lists;
+
+import ca.uhn.fhir.jpa.provider.dstu3.BaseResourceProviderDstu3Test;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.util.TestUtil;
+
+public class StressTestDstu3Test extends BaseResourceProviderDstu3Test {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StressTestDstu3Test.class);
+	private RequestValidatingInterceptor myRequestValidatingInterceptor;
+
+	@Before
+	public void before() throws Exception {
+		super.before();
+		
+		myRequestValidatingInterceptor = new RequestValidatingInterceptor();
+		FhirInstanceValidator module = new FhirInstanceValidator();
+		module.setValidationSupport(myValidationSupport);
+		myRequestValidatingInterceptor.addValidatorModule(module);
+	}
+
+	@After
+	public void after() throws Exception {
+		super.after();
+		
+		ourRestServer.unregisterInterceptor(myRequestValidatingInterceptor);
+	}
+	
+	/**
+	 * This test prevents a deadlock that was detected with a large number of 
+	 * threads creating resources and blocking on the searchparamcache refreshing
+	 * (since this is a synchronized method) while the instance that was actually
+	 * executing was waiting on a DB connection. This was solved by making
+	 * JpaValidationSupportDstuXX be transactional, which it should have been
+	 * anyhow.
+	 */
+	@Test
+	public void testMultithreadedSearchWithValidation() throws Exception {
+		ourRestServer.registerInterceptor(myRequestValidatingInterceptor);
+		
+		Bundle input = new Bundle();
+		input.setType(BundleType.TRANSACTION);
+		for (int i = 0; i < 500; i++) {
+			Patient p = new Patient();
+			p.addIdentifier().setSystem("http://test").setValue("BAR");
+			input.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
+		}
+		ourClient.transaction().withBundle(input).execute();
+		
+		CloseableHttpResponse getMeta = ourHttpClient.execute(new HttpGet(ourServerBase + "/metadata"));
+		try {
+			assertEquals(200, getMeta.getStatusLine().getStatusCode());
+		} finally {
+			IOUtils.closeQuietly(getMeta);
+		}
+
+		List<BaseTask> tasks = Lists.newArrayList();
+		try {
+			for (int threadIndex = 0; threadIndex < 8; threadIndex++) {
+				SearchTask task = new SearchTask();
+				tasks.add(task);
+				task.start();
+			}
+			for (int threadIndex = 0; threadIndex < 8; threadIndex++) {
+				CreateTask task = new CreateTask();
+				tasks.add(task);
+				task.start();
+			}
+		} finally {
+			for (BaseTask next : tasks) {
+				next.join();
+			}
+		}
+
+		int total = 0;
+		for (BaseTask next : tasks) {
+			if (next.getError() != null) {
+				fail(next.getError().toString());
+			}
+			total += next.getTaskCount();
+		}
+		
+		ourLog.info("Loaded {} searches", total);
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	public class BaseTask extends Thread  {
+		protected Throwable myError;
+		protected int myTaskCount = 0;
+		
+		public BaseTask() {
+			setDaemon(true);
+		}
+		
+		public Throwable getError() {
+			return myError;
+		}
+
+		public int getTaskCount() {
+			return myTaskCount;
+		}
+
+	}
+
+	private final class SearchTask extends BaseTask {
+
+		@Override
+		public void run() {
+			CloseableHttpResponse get = null;
+			for (int i = 0; i < 20; i++) {
+				try {
+					get = ourHttpClient.execute(new HttpGet(ourServerBase + "/Patient?identifier=http%3A%2F%2Ftest%7CBAR," + UUID.randomUUID().toString()));
+					try {
+						assertEquals(200, get.getStatusLine().getStatusCode());
+						myTaskCount++;
+					} finally {
+						IOUtils.closeQuietly(get);
+					}
+				} catch (Throwable e) {
+					ourLog.error("Failure during search", e);
+					myError = e;
+					return;
+				}
+			}
+		}
+	}
+
+	private final class CreateTask extends BaseTask {
+
+		@Override
+		public void run() {
+			for (int i = 0; i < 50; i++) {
+				try {
+					Patient p = new Patient();
+					p.addIdentifier().setSystem("http://test").setValue("BAR").setType(new CodeableConcept().addCoding(new Coding().setSystem("http://foo").setCode("bar")));
+					p.setGender(org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender.MALE);
+					ourClient.create().resource(p).execute();
+					
+					ourSearchParamRegistry.forceRefresh();
+					
+				} catch (Throwable e) {
+					ourLog.error("Failure during search", e);
+					myError = e;
+					return;
+				}
+			}
+		}
+	}
+
+}

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

@@ -9,6 +9,7 @@
 	<body>
 		<form action="" method="get" id="outerForm">
 		<input type="hidden" id="serverId" name="serverId" th:value="${serverId}"></input> 
+		<input th:if="${_csrf} != null" type="hidden" th:name="${_csrf.parameterName}" th:value="${_csrf.token}" />
 
 		<div th:replace="tmpl-navbar-top :: top" ></div>
 		

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

@@ -315,8 +315,8 @@
 																	<a th:if="${entry.resource} != null" th:href="${entry.resource.id}" th:text="${entry.resource.idElement.toUnqualified()}" style="font-size: 0.8em"/>
 																</td>
 																<td th:if="${entry.resource} == null or ${entry.resource.meta.lastUpdatedElement.value} == null"></td>
-																<td th:if="${entry.resource.meta.lastUpdatedElement.value} != null and ${entry.resource.meta.lastUpdatedElement.today} == true" th:text="${#dates.format(entry.resource.meta.lastUpdated, 'HH:mm:ss')}"></td>
+																<td th:if="${entry.resource} != null and ${entry.resource.meta.lastUpdatedElement.value} != null and ${entry.resource.meta.lastUpdatedElement.today} == true" th:text="${#dates.format(entry.resource.meta.lastUpdated, 'HH:mm:ss')}"></td>
-																<td th:if="${entry.resource.meta.lastUpdatedElement.value} != null and ${entry.resource.meta.lastUpdatedElement.today} == false" th:text="${#dates.format(entry.resource.meta.lastUpdated, 'yyyy-MM-dd HH:mm:ss')}"></td>
+																<td th:if="${entry.resource} != null and ${entry.resource.meta.lastUpdatedElement.value} != null and ${entry.resource.meta.lastUpdatedElement.today} == false" th:text="${#dates.format(entry.resource.meta.lastUpdated, 'yyyy-MM-dd HH:mm:ss')}"></td>
 															</tr>
 															</tbody>
 														</table>

src/changes/changes.xml

@@ -134,6 +134,17 @@
 				JpaConformanceProvider now has a configuration setting to enable and 
 				disable adding resource counts to the server metadata.
 			</action>
+			<action type="fix">
+				Avoid a deadlock in JPA server when the RequestValidatingInterceptor is being
+				used and a large number of resources are being created by clients at
+				the same time.
+			</action>
+			<action type="fix">
+				Testpage Overlay's transaction method did not work if the response
+				Bundle contained any entries that did not contain a resource (which
+				is often the case in more recent versions of HAPI). Thanks to Sujay R
+				for reporting!
+			</action>
 		</release>
 		<release version="2.5" date="2017-06-08">
 			<action type="fix">