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

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2020-08-13"
+codename: "Manticore"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/changes.yaml

@@ -0,0 +1,8 @@
+---
+- item:
+    type: "add"
+    title: "The version of a few dependencies have been bumped to the latest versions
+    (dependent HAPI modules listed in brackets):
+    <ul>
+        <li>Flyway (JPA): 6.4.1-&gt; 6.5.4</li>
+    </ul>"

hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IDao.java

@@ -34,8 +34,9 @@ import java.util.Collection;
  * time to time, even within minor point releases.
  */
 public interface IDao {
+	String RESOURCE_PID_KEY = "RESOURCE_PID";
 
-	MetadataKeyResourcePid RESOURCE_PID = new MetadataKeyResourcePid("RESOURCE_PID");
+	MetadataKeyResourcePid RESOURCE_PID = new MetadataKeyResourcePid(RESOURCE_PID_KEY);
 
 	MetadataKeyCurrentlyReindexing CURRENTLY_REINDEXING = new MetadataKeyCurrentlyReindexing("CURRENTLY_REINDEXING");
 

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

@@ -79,7 +79,6 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@@ -114,10 +113,8 @@ import org.springframework.context.ApplicationContext;
 import org.springframework.context.ApplicationContextAware;
 import org.springframework.stereotype.Repository;
 import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionSynchronizationAdapter;
 import org.springframework.transaction.support.TransactionSynchronizationManager;
-import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.PostConstruct;
 import javax.persistence.EntityManager;
@@ -636,7 +633,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		ResourceMetadataKeyEnum.VERSION.put(res, Long.toString(theEntity.getVersion()));
 		ResourceMetadataKeyEnum.PUBLISHED.put(res, theEntity.getPublished());
 		ResourceMetadataKeyEnum.UPDATED.put(res, theEntity.getUpdated());
-		IDao.RESOURCE_PID.put(res, theEntity.getId());
+		IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
 
 		Collection<? extends BaseTag> tags = theTagList;
 		if (theEntity.isHasTags()) {
@@ -708,7 +705,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		res.setId(res.getIdElement().withVersion(theVersion.toString()));
 
 		res.getMeta().setLastUpdated(theEntity.getUpdatedDate());
-		IDao.RESOURCE_PID.put(res, theEntity.getId());
+		IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
 
 		Collection<? extends BaseTag> tags = theTagList;
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/HookInterceptorR4Test.java

@@ -1,13 +1,25 @@
 package ca.uhn.fhir.jpa.provider.r4;
 
 import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.dao.IDao;
+import ca.uhn.fhir.jpa.dao.index.IdHelperService;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.Patient;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 
+import java.util.Collections;
 import java.util.concurrent.atomic.AtomicLong;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -15,16 +27,24 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class HookInterceptorR4Test extends BaseResourceProviderR4Test {
+	private static final Logger ourLog = LoggerFactory.getLogger(HookInterceptorR4Test.class);
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(HookInterceptorR4Test.class);
+	@Autowired
+	IdHelperService myIdHelperService;
 
-//	@Override
+	@BeforeEach
-//	@AfterEach
+	public void before() throws Exception {
-//	public void after( ) throws Exception {
+		super.before();
-//		super.after();
+
-//
+		myDaoConfig.setExpungeEnabled(true);
-//		myInterceptorRegistry.unregisterAllInterceptors();
+	}
-//	}
+
+	@AfterEach
+	public void after() throws Exception {
+		myDaoConfig.setExpungeEnabled(new DaoConfig().isExpungeEnabled());
+
+		super.after();
+	}
 
 	@Test
 	public void testOP_PRESTORAGE_RESOURCE_CREATED_ModifyResource() {
@@ -69,7 +89,7 @@ public class HookInterceptorR4Test extends BaseResourceProviderR4Test {
 		AtomicLong pid = new AtomicLong();
 		myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED, (thePointcut, t) -> {
 			IAnyResource resource = (IAnyResource) t.get(IBaseResource.class, 0);
-			Long resourcePid = (Long) resource.getUserData("RESOURCE_PID");
+			Long resourcePid = (Long) resource.getUserData(IDao.RESOURCE_PID_KEY);
 			assertNotNull(resourcePid, "Expecting RESOURCE_PID to be set on resource user data.");
 			pid.set(resourcePid);
 		});
@@ -77,6 +97,72 @@ public class HookInterceptorR4Test extends BaseResourceProviderR4Test {
 		assertTrue(pid.get() > 0);
 	}
 
+
+	@Test
+	public void testSTORAGE_PRECOMMIT_RESOURCE_CREATED_hasCorrectPid() {
+		AtomicLong pid = new AtomicLong();
+		myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED, (thePointcut, t) -> {
+			IAnyResource resource = (IAnyResource) t.get(IBaseResource.class, 0);
+			Long resourcePid = (Long) resource.getUserData(IDao.RESOURCE_PID_KEY);
+			assertNotNull(resourcePid, "Expecting RESOURCE_PID to be set on resource user data.");
+			pid.set(resourcePid);
+		});
+		IIdType savedPatientId = myClient.create().resource(new Patient()).execute().getId();
+		Long savedPatientPid = myIdHelperService.resolveResourcePersistentIdsWithCache(null, Collections.singletonList(savedPatientId)).get(0).getIdAsLong();
+		assertEquals(savedPatientPid.longValue(), pid.get());
+	}
+
+	@Test
+	public void testSTORAGE_PRESTORAGE_EXPUNGE_RESOURCE_hasCorrectPid() {
+		AtomicLong pid = new AtomicLong();
+		myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE, (thePointcut, t) -> {
+			IAnyResource resource = (IAnyResource) t.get(IBaseResource.class, 0);
+			Long resourcePid = (Long) resource.getUserData(IDao.RESOURCE_PID_KEY);
+			assertNotNull(resourcePid, "Expecting RESOURCE_PID to be set on resource user data.");
+			pid.set(resourcePid);
+		});
+		IIdType savedPatientId = myClient.create().resource(new Patient()).execute().getId();
+		Long savedPatientPid = myIdHelperService.resolveResourcePersistentIdsWithCache(null, Collections.singletonList(savedPatientId)).get(0).getIdAsLong();
+
+		myClient.delete().resourceById(savedPatientId).execute();
+		Parameters parameters = new Parameters();
+
+		parameters.addParameter().setName(JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_DELETED_RESOURCES).setValue(new BooleanType(true));
+		myClient
+			.operation()
+			.onInstance(savedPatientId)
+			.named(JpaConstants.OPERATION_EXPUNGE)
+			.withParameters(parameters)
+			.execute();
+
+		assertEquals(savedPatientPid.longValue(), pid.get());
+	}
+
+
+	@Test
+	public void testSTORAGE_PRECOMMIT_RESOURCE_UPDATED_hasCorrectPid() {
+		AtomicLong pidOld = new AtomicLong();
+		AtomicLong pidNew = new AtomicLong();
+		Patient patient = new Patient();
+		IIdType savedPatientId = myClient.create().resource(patient).execute().getId();
+		patient.setId(savedPatientId);
+		myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, (thePointcut, t) -> {
+			IAnyResource resourceOld = (IAnyResource) t.get(IBaseResource.class, 0);
+			IAnyResource resourceNew = (IAnyResource) t.get(IBaseResource.class, 1);
+			Long resourceOldPid = (Long) resourceOld.getUserData(IDao.RESOURCE_PID_KEY);
+			Long resourceNewPid = (Long) resourceNew.getUserData(IDao.RESOURCE_PID_KEY);
+			assertNotNull(resourceOldPid, "Expecting RESOURCE_PID to be set on resource user data.");
+			assertNotNull(resourceNewPid, "Expecting RESOURCE_PID to be set on resource user data.");
+			pidOld.set(resourceOldPid);
+			pidNew.set(resourceNewPid);
+		});
+		patient.setActive(true);
+		myClient.update().resource(patient).execute();
+		Long savedPatientPid = myIdHelperService.resolveResourcePersistentIdsWithCache(null, Collections.singletonList(savedPatientId)).get(0).getIdAsLong();
+		assertEquals(savedPatientPid.longValue(), pidOld.get());
+		assertEquals(savedPatientPid.longValue(), pidNew.get());
+	}
+
 	@Test
 	public void testSTORAGE_PRECOMMIT_RESOURCE_UPDATED_hasPid() {
 		AtomicLong oldPid = new AtomicLong();
@@ -84,12 +170,12 @@ public class HookInterceptorR4Test extends BaseResourceProviderR4Test {
 		myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, (thePointcut, t) -> {
 
 			IAnyResource oldResource = (IAnyResource) t.get(IBaseResource.class, 0);
-			Long oldResourcePid = (Long) oldResource.getUserData("RESOURCE_PID");
+			Long oldResourcePid = (Long) oldResource.getUserData(IDao.RESOURCE_PID_KEY);
 			assertNotNull(oldResourcePid, "Expecting RESOURCE_PID to be set on resource user data.");
 			oldPid.set(oldResourcePid);
 
 			IAnyResource newResource = (IAnyResource) t.get(IBaseResource.class, 1);
-			Long newResourcePid = (Long) newResource.getUserData("RESOURCE_PID");
+			Long newResourcePid = (Long) newResource.getUserData(IDao.RESOURCE_PID_KEY);
 			assertNotNull(newResourcePid, "Expecting RESOURCE_PID to be set on resource user data.");
 			newPid.set(newResourcePid);
 		});

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/ServerExceptionDstu3Test.java

@@ -1,12 +1,14 @@
 package ca.uhn.fhir.rest.server;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.api.HookParams;
+import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
+import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.rest.annotation.Create;
 import ca.uhn.fhir.rest.annotation.ResourceParam;
 import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
-import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.test.utilities.JettyUtil;
@@ -29,11 +31,13 @@ import org.hl7.fhir.dstu3.model.OperationOutcome.IssueType;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
+import java.util.Collections;
 import java.util.List;
 import java.util.concurrent.TimeUnit;
 
@@ -44,11 +48,17 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 public class ServerExceptionDstu3Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerExceptionDstu3Test.class);
-	public static BaseServerResponseException ourException;
+	public static Exception ourException;
 	private static CloseableHttpClient ourClient;
 	private static FhirContext ourCtx = FhirContext.forDstu3();
 	private static int ourPort;
 	private static Server ourServer;
+	private static RestfulServer ourServlet;
+
+	@AfterEach
+	public void after() {
+		ourException = null;
+	}
 
 	@Test
 	public void testAddHeadersNotFound() throws Exception {
@@ -56,8 +66,8 @@ public class ServerExceptionDstu3Test {
 		OperationOutcome operationOutcome = new OperationOutcome();
 		operationOutcome.addIssue().setCode(IssueType.BUSINESSRULE);
 
-		ourException = new ResourceNotFoundException("SOME MESSAGE");
+		ourException = new ResourceNotFoundException("SOME MESSAGE")
-		ourException.addResponseHeader("X-Foo", "BAR BAR");
+			.addResponseHeader("X-Foo", "BAR BAR");
 
 
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient");
@@ -99,6 +109,65 @@ public class ServerExceptionDstu3Test {
 
 	}
 
+	@Test
+	public void testMethodThrowsNonHapiUncheckedExceptionHandledCleanly() throws Exception {
+
+		ourException = new NullPointerException("Hello");
+
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_format=json");
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
+			assertEquals(500, status.getStatusLine().getStatusCode());
+			byte[] responseContentBytes = IOUtils.toByteArray(status.getEntity().getContent());
+			String responseContent = new String(responseContentBytes, Charsets.UTF_8);
+			ourLog.info(status.getStatusLine().toString());
+			ourLog.info(responseContent);
+			assertThat(responseContent, containsString("\"diagnostics\":\"Failed to call access method: java.lang.NullPointerException: Hello\""));
+		}
+
+	}
+
+	@Test
+	public void testMethodThrowsNonHapiCheckedExceptionHandledCleanly() throws Exception {
+
+		ourException = new IOException("Hello");
+
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_format=json");
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
+			assertEquals(500, status.getStatusLine().getStatusCode());
+			byte[] responseContentBytes = IOUtils.toByteArray(status.getEntity().getContent());
+			String responseContent = new String(responseContentBytes, Charsets.UTF_8);
+			ourLog.info(status.getStatusLine().toString());
+			ourLog.info(responseContent);
+			assertThat(responseContent, containsString("\"diagnostics\":\"Failed to call access method: java.io.IOException: Hello\""));
+		}
+
+	}
+
+	@Test
+	public void testInterceptorThrowsNonHapiUncheckedExceptionHandledCleanly() throws Exception {
+
+		ourServlet.getInterceptorService().registerAnonymousInterceptor(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED, new IAnonymousInterceptor() {
+			@Override
+			public void invoke(Pointcut thePointcut, HookParams theArgs) {
+				throw new NullPointerException("Hello");
+			}
+		});
+
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_format=json");
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
+			assertEquals(500, status.getStatusLine().getStatusCode());
+			byte[] responseContentBytes = IOUtils.toByteArray(status.getEntity().getContent());
+			String responseContent = new String(responseContentBytes, Charsets.UTF_8);
+			ourLog.info(status.getStatusLine().toString());
+			ourLog.info(responseContent);
+			assertThat(responseContent, containsString("\"diagnostics\":\"Hello\""));
+		}
+
+		ourServlet.getInterceptorService().unregisterAllInterceptors();
+
+	}
+
+
 	@Test
 	public void testPostWithNoBody() throws IOException {
 
@@ -143,7 +212,10 @@ public class ServerExceptionDstu3Test {
 		}
 
 		@Search()
-		public List<Patient> search() {
+		public List<Patient> search() throws Exception {
+			if (ourException == null) {
+				return Collections.emptyList();
+			}
 			throw ourException;
 		}
 
@@ -168,15 +240,15 @@ public class ServerExceptionDstu3Test {
 		DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
 
 		ServletHandler proxyHandler = new ServletHandler();
-		RestfulServer servlet = new RestfulServer(ourCtx);
+		ourServlet = new RestfulServer(ourCtx);
-		servlet.setPagingProvider(new FifoMemoryPagingProvider(10));
+		ourServlet.setPagingProvider(new FifoMemoryPagingProvider(10));
 
-		servlet.setResourceProviders(patientProvider);
+		ourServlet.setResourceProviders(patientProvider);
-		ServletHolder servletHolder = new ServletHolder(servlet);
+		ServletHolder servletHolder = new ServletHolder(ourServlet);
 		proxyHandler.addServletWithMapping(servletHolder, "/*");
 		ourServer.setHandler(proxyHandler);
 		JettyUtil.startServer(ourServer);
-        ourPort = JettyUtil.getPortForStartedServer(ourServer);
+		ourPort = JettyUtil.getPortForStartedServer(ourServer);
 
 		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
 		HttpClientBuilder builder = HttpClientBuilder.create();

pom.xml

@@ -717,7 +717,7 @@
 		<!-- 9.4.17 seems to have issues -->
 		<jetty_version>9.4.30.v20200611</jetty_version>
 		<jsr305_version>3.0.2</jsr305_version>
-		<flyway_version>6.4.1</flyway_version>
+		<flyway_version>6.5.4</flyway_version>
 		<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
 		<hibernate_version>5.4.14.Final</hibernate_version>
 		<!-- Update lucene version when you update hibernate-search version -->