Add support for Binary X-Security-Context header in server

hapi-deployable-pom/pom.xml

@@ -118,6 +118,7 @@
 					</ignoredDependencies>
 					<ignoredResources>
 						<ignoredResource>changelog.txt</ignoredResource>
+						<ignoredResource>javac.bat</ignoredResource>
 					</ignoredResources>
 				</configuration>
 			</plugin>

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirVersionEnum.java

@@ -78,6 +78,10 @@ public enum FhirVersionEnum {
 		return myVersionImplementation;
 	}
 
+	public boolean isEqualOrNewerThan(FhirVersionEnum theVersion) {
+		return ordinal() >= theVersion.ordinal();
+	}
+
 	public boolean isEquivalentTo(FhirVersionEnum theVersion) {
 		if (this.equals(theVersion)) {
 			return true;

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java

@@ -19,19 +19,6 @@ package ca.uhn.fhir.parser;
  * limitations under the License.
  * #L%
  */
-import static org.apache.commons.lang3.StringUtils.*;
-
-import java.io.*;
-import java.math.BigDecimal;
-import java.util.*;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.Validate;
-import org.apache.commons.lang3.text.WordUtils;
-import org.hl7.fhir.instance.model.api.*;
-
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
 
 import ca.uhn.fhir.context.*;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
@@ -46,10 +33,27 @@ import ca.uhn.fhir.parser.json.*;
 import ca.uhn.fhir.parser.json.JsonLikeValue.ScalarType;
 import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType;
 import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.util.BinaryUtil;
 import ca.uhn.fhir.util.ElementUtil;
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.text.WordUtils;
+import org.hl7.fhir.instance.model.api.*;
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Writer;
+import java.math.BigDecimal;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Set;
+
 import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.ID_DATATYPE;
 import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_DATATYPE;
-import java.lang.reflect.Method;
+import static org.apache.commons.lang3.StringUtils.*;
 
 /**
  * This class is the FHIR JSON parser/encoder. Users should not interact with this class directly, but should use
@@ -140,12 +144,6 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		return retVal;
 	}
 
-	@Override
-	protected void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException {
-		JsonLikeWriter eventWriter = createJsonWriter(theWriter);
-		doEncodeResourceToJsonLikeWriter(theResource, eventWriter);
-	}
-
 	public void doEncodeResourceToJsonLikeWriter(IBaseResource theResource, JsonLikeWriter theEventWriter) throws IOException {
 		if (myPrettyPrint) {
 			theEventWriter.setPrettyPrint(myPrettyPrint);
@@ -157,6 +155,12 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		theEventWriter.flush();
 	}
 
+	@Override
+	protected void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException {
+		JsonLikeWriter eventWriter = createJsonWriter(theWriter);
+		doEncodeResourceToJsonLikeWriter(theResource, eventWriter);
+	}
+
 	@Override
 	public <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) {
 		JsonLikeStructure jsonStructure = new GsonStructure();
@@ -452,15 +456,15 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					if (nextChild.getMax() > 1 || nextChild.getMax() == Child.MAX_UNLIMITED) {
 						beginArray(theEventWriter, childName);
 						inArray = true;
-						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, theSubResource,nextChildElem, force);
+						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, theSubResource, nextChildElem, force);
 					} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
 						// suppress narratives from contained resources
 					} else {
-						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theContainedResource, theSubResource,nextChildElem, false);
+						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theContainedResource, theSubResource, nextChildElem, false);
 					}
 					currentChildName = childName;
 				} else {
-					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource,theSubResource, nextChildElem, force);
+					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, theSubResource, nextChildElem, force);
 				}
 
 				valueIdx++;
@@ -696,34 +700,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			}
 		}
 
-		if (theResource instanceof IBaseBinary) {
-			IBaseBinary bin = (IBaseBinary) theResource;
-			String contentType = bin.getContentType();
-			if (isNotBlank(contentType)) {
-				write(theEventWriter, "contentType", contentType);
-			}
-			String contentAsBase64 = bin.getContentAsBase64();
-			if (isNotBlank(contentAsBase64)) {
-				write(theEventWriter, "content", contentAsBase64);
-			}
-                        try {
-                            Method getSC = bin.getClass().getMethod("getSecurityContext");
-                            Object securityContext = getSC.invoke(bin);
-                            if (securityContext != null) {
-                                Method getRef = securityContext.getClass().getMethod("getReference");
-                                String securityContextRef = (String) getRef.invoke(securityContext);
-                                if (securityContextRef != null) {
-                                    beginObject(theEventWriter, "securityContext");
-                                    writeOptionalTagWithTextNode(theEventWriter, "reference", securityContextRef);
-                                    theEventWriter.endObject();
-                                }
-                            }
-                        } catch (Exception e) {
-                            e.printStackTrace();
-                        }
-		} else {
 		encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
-		}
 
 		theEventWriter.endObject();
 	}
@@ -1344,6 +1321,28 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			return url1.compareTo(url2);
 		}
 
+		private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName) throws IOException {
+			if (def.getChildType().equals(ID_DATATYPE) || def.getChildType().equals(PRIMITIVE_DATATYPE)) {
+				final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
+				final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
+				// Undeclared extensions
+				extractUndeclaredExtensions(theValue, extensions, modifierExtensions, myParent, null);
+				// Declared extensions
+				if (def != null) {
+					extractDeclaredExtensions(theValue, def, extensions, modifierExtensions, myParent);
+				}
+				boolean haveContent = false;
+				if (!extensions.isEmpty() || !modifierExtensions.isEmpty()) {
+					haveContent = true;
+				}
+				if (haveContent) {
+					beginObject(theEventWriter, '_' + childName);
+					writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
+					theEventWriter.endObject();
+				}
+			}
+		}
+
 		public void write(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter) throws IOException {
 			if (myUndeclaredExtension != null) {
 				writeUndeclaredExtension(theResDef, theResource, theEventWriter, myUndeclaredExtension);
@@ -1445,27 +1444,5 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 
 			theEventWriter.endObject();
 		}
-    
-    private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName) throws IOException {
-      if (def.getChildType().equals(ID_DATATYPE) || def.getChildType().equals(PRIMITIVE_DATATYPE)) {
-        final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
-        final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
-        // Undeclared extensions
-        extractUndeclaredExtensions(theValue, extensions, modifierExtensions, myParent, null);
-        // Declared extensions
-        if (def != null) {
-          extractDeclaredExtensions(theValue, def, extensions, modifierExtensions, myParent);
-        }
-        boolean haveContent = false;
-        if (!extensions.isEmpty() || !modifierExtensions.isEmpty()) {
-          haveContent = true;
-        }
-        if (haveContent) {
-          beginObject(theEventWriter, '_' + childName);
-          writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
-          theEventWriter.endObject();
-        }
-      }
-    }    
 	}
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

@@ -187,6 +187,7 @@ public class Constants {
 	public static final String OO_INFOSTATUS_PROCESSING = "processing";
 	public static final String PARAM_GRAPHQL_QUERY = "query";
 	public static final String HEADER_X_CACHE = "X-Cache";
+	public static final String HEADER_X_SECURITY_CONTEXT = "X-Security-Context";
 
 	static {
 		CHARSET_UTF8 = Charset.forName(CHARSET_NAME_UTF8);

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

@@ -0,0 +1,46 @@
+package ca.uhn.fhir.util;
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseBinary;
+import org.hl7.fhir.instance.model.api.IBaseReference;
+
+import java.util.List;
+
+public class BinaryUtil {
+
+	private BinaryUtil() {
+		// non instantiable
+	}
+
+	public static IBaseReference getSecurityContext(FhirContext theCtx, IBaseBinary theBinary) {
+		RuntimeResourceDefinition def = theCtx.getResourceDefinition("Binary");
+		BaseRuntimeChildDefinition child = def.getChildByName("securityContext");
+
+		List<IBase> values = child.getAccessor().getValues(theBinary);
+		IBaseReference retVal = null;
+		if (values.size() > 0) {
+			retVal = (IBaseReference) values.get(0);
+		}
+		return retVal;
+	}
+
+	public static IBaseBinary newBinary(FhirContext theCtx) {
+		return (IBaseBinary) theCtx.getResourceDefinition("Binary").newInstance();
+	}
+
+	public static void setSecurityContext(FhirContext theCtx, IBaseBinary theBinary, String theSecurityContext) {
+		RuntimeResourceDefinition def = theCtx.getResourceDefinition("Binary");
+		BaseRuntimeChildDefinition child = def.getChildByName("securityContext");
+
+		BaseRuntimeElementDefinition<?> referenceDef = theCtx.getElementDefinition("reference");
+		IBaseReference reference = (IBaseReference) referenceDef.newInstance();
+		child.getMutator().addValue(theBinary, reference);
+
+		reference.setReference(theSecurityContext);
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/StaleSearchDeletingSvcImpl.java

@@ -20,8 +20,12 @@ package ca.uhn.fhir.jpa.search;
  * #L%
  */
 
-import java.util.Date;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
-
+import ca.uhn.fhir.jpa.dao.data.ISearchDao;
+import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
+import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
+import ca.uhn.fhir.jpa.entity.Search;
+import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.time.DateUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.PageRequest;
@@ -34,11 +38,7 @@ import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import com.google.common.annotations.VisibleForTesting;
+import java.util.Date;
-
-import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.data.*;
-import ca.uhn.fhir.jpa.entity.Search;
 
 /**
  * Deletes old searches
@@ -46,26 +46,21 @@ import ca.uhn.fhir.jpa.entity.Search;
 public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 	public static final long DEFAULT_CUTOFF_SLACK = 10 * DateUtils.MILLIS_PER_SECOND;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StaleSearchDeletingSvcImpl.class);
-
+	private static Long ourNowForUnitTests;
 	/*
 	 * We give a bit of extra leeway just to avoid race conditions where a query result
 	 * is being reused (because a new client request came in with the same params) right before
 	 * the result is to be deleted
 	 */
 	private long myCutoffSlack = DEFAULT_CUTOFF_SLACK;
-
 	@Autowired
 	private DaoConfig myDaoConfig;
-
 	@Autowired
 	private ISearchDao mySearchDao;
-
 	@Autowired
 	private ISearchIncludeDao mySearchIncludeDao;
-
 	@Autowired
 	private ISearchResultDao mySearchResultDao;
-
 	@Autowired
 	private PlatformTransactionManager myTransactionManager;
 
@@ -87,7 +82,7 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 		if (myDaoConfig.getReuseCachedSearchResultsForMillis() != null) {
 			cutoffMillis = Math.max(cutoffMillis, myDaoConfig.getReuseCachedSearchResultsForMillis());
 		}
-		final Date cutoff = new Date((System.currentTimeMillis() - cutoffMillis) - myCutoffSlack);
+		final Date cutoff = new Date((now() - cutoffMillis) - myCutoffSlack);
 
 		ourLog.debug("Searching for searches which are before {}", cutoff);
 
@@ -131,4 +126,19 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 		myCutoffSlack = theCutoffSlack;
 	}
 
+	private static long now() {
+		if (ourNowForUnitTests != null) {
+			return ourNowForUnitTests;
+		}
+		return System.currentTimeMillis();
+	}
+
+	/**
+	 * This is for unit tests only, do not call otherwise
+	 */
+	@VisibleForTesting
+	public static void setNowForUnitTests(Long theNowForUnitTests) {
+		ourNowForUnitTests = theNowForUnitTests;
+	}
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java

@@ -130,4 +130,19 @@ public class TestUtil {
 		}
 	}
 
+	public static void sleepAtLeast(int theMillis) {
+		long start = System.currentTimeMillis();
+		while (System.currentTimeMillis() <= start + theMillis) {
+			try {
+				long timeSinceStarted = System.currentTimeMillis() - start;
+				long timeToSleep = Math.max(0, theMillis - timeSinceStarted);
+				ourLog.info("Sleeping for {}ms", timeToSleep);
+				Thread.sleep(timeToSleep);
+			} catch (InterruptedException theE) {
+				theE.printStackTrace();
+			}
+		}
+	}
+
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchPageExpiryTest.java

@@ -1,12 +1,16 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
+import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.junit.Assert.*;
 
+import ca.uhn.fhir.jpa.util.StopWatch;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.test.util.AopTestUtils;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@@ -18,15 +22,13 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.StringParam;
 
 public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
-	@Before
+	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoDstu3SearchPageExpiryTest.class);
-	public void beforeDisableResultReuse() {
-		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
-	}
 
 	@After()
 	public void after() {
 		StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
 		staleSearchDeletingSvc.setCutoffSlackForUnitTest(StaleSearchDeletingSvcImpl.DEFAULT_CUTOFF_SLACK);
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(null);
 	}
 
 	@Before
@@ -35,48 +37,9 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
 		staleSearchDeletingSvc.setCutoffSlackForUnitTest(0);
 	}
 
-	@Test
+	@Before
-	public void testExpirePagesAfterSingleUse() throws Exception {
+	public void beforeDisableResultReuse() {
-		IIdType pid1;
+		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
-		IIdType pid2;
-		{
-			Patient patient = new Patient();
-			patient.addName().setFamily("EXPIRE");
-			pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
-		}
-		Thread.sleep(10);
-		{
-			Patient patient = new Patient();
-			patient.addName().setFamily("EXPIRE");
-			pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
-		}
-		Thread.sleep(10);
-
-		SearchParameterMap params;
-		params = new SearchParameterMap();
-		params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
-		final IBundleProvider bundleProvider = myPatientDao.search(params);
-		assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
-		assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
-
-		myDaoConfig.setExpireSearchResultsAfterMillis(500);
-		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
-		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
-		txTemplate.execute(new TransactionCallbackWithoutResult() {
-			@Override
-			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
-				assertNotNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
-			}
-		});
-
-		Thread.sleep(750);
-		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
-		txTemplate.execute(new TransactionCallbackWithoutResult() {
-			@Override
-			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
-				assertNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
-			}
-		});
 	}
 
 	@Test
@@ -98,6 +61,7 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
 
 		myDaoConfig.setExpireSearchResultsAfterMillis(1000L);
 		myDaoConfig.setReuseCachedSearchResultsForMillis(500L);
+		long start = System.currentTimeMillis();
 
 		final String searchUuid1;
 		{
@@ -109,7 +73,7 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
 			Validate.notBlank(searchUuid1);
 		}
 
-		Thread.sleep(250);
+		sleepAtLeast(250);
 
 		String searchUuid2;
 		{
@@ -122,7 +86,7 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
 		}
 		assertEquals(searchUuid1, searchUuid2);
 
-		Thread.sleep(500);
+		sleepAtLeast(500);
 
 		// We're now past 500ms so we shouldn't reuse the search
 
@@ -139,18 +103,31 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
 
 		// Search just got used so it shouldn't be deleted
 
-		Thread.sleep(750);
+		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
+		newTxTemplate().execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				assertNotNull(mySearchEntityDao.findByUuid(searchUuid3));
+			}
+		});
+
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 1400);
 
 		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
 		newTxTemplate().execute(new TransactionCallbackWithoutResult() {
 			@Override
 			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
-				assertNull(mySearchEntityDao.findByUuid(searchUuid1));
 				assertNotNull(mySearchEntityDao.findByUuid(searchUuid3));
 			}
 		});
+		newTxTemplate().execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				assertNull(mySearchEntityDao.findByUuid(searchUuid1));
+			}
+		});
 
-		Thread.sleep(300);
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 2200);
 
 		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
 		newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@@ -162,4 +139,63 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
 		});
 
 	}
+
+	@Test
+	public void testExpirePagesAfterSingleUse() throws Exception {
+		IIdType pid1;
+		IIdType pid2;
+		{
+			Patient patient = new Patient();
+			patient.addName().setFamily("EXPIRE");
+			pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		Thread.sleep(10);
+		{
+			Patient patient = new Patient();
+			patient.addName().setFamily("EXPIRE");
+			pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		Thread.sleep(10);
+
+		final StopWatch sw = new StopWatch();
+
+		long start = System.currentTimeMillis();
+
+		SearchParameterMap params;
+		params = new SearchParameterMap();
+		params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
+		final IBundleProvider bundleProvider = myPatientDao.search(params);
+		assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
+		assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
+
+		myDaoConfig.setExpireSearchResultsAfterMillis(500);
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(start);
+
+		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
+		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
+		txTemplate.execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				assertNotNull("Failed after " + sw.toString(), mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
+			}
+		});
+
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 499);
+		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
+		txTemplate.execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				assertNotNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
+			}
+		});
+
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 600);
+		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
+		txTemplate.execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				assertNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
+			}
+		});
+	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchPageExpiryTest.java

@@ -1,33 +1,35 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import static org.hamcrest.Matchers.containsInAnyOrder;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
-import static org.junit.Assert.*;
+import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
-
 import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.StringParam;
 import org.apache.commons.lang3.Validate;
-import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.*;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.test.util.AopTestUtils;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
-import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
+import static org.hamcrest.Matchers.containsInAnyOrder;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import static org.junit.Assert.*;
-import ca.uhn.fhir.rest.param.StringParam;
 
 public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
-	@Before
+	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4SearchPageExpiryTest.class);
-	public void beforeDisableResultReuse() {
-		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
-	}
 
 	@After()
 	public void after() {
 		StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
 		staleSearchDeletingSvc.setCutoffSlackForUnitTest(StaleSearchDeletingSvcImpl.DEFAULT_CUTOFF_SLACK);
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(null);
 	}
 
 	@Before
@@ -36,50 +38,9 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
 		staleSearchDeletingSvc.setCutoffSlackForUnitTest(0);
 	}
 
-	@Test
+	@Before
-	public void testExpirePagesAfterSingleUse() throws Exception {
+	public void beforeDisableResultReuse() {
-		IIdType pid1;
+		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
-		IIdType pid2;
-		{
-			Patient patient = new Patient();
-			patient.addName().setFamily("EXPIRE");
-			pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
-		}
-		Thread.sleep(10);
-		{
-			Patient patient = new Patient();
-			patient.addName().setFamily("EXPIRE");
-			pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
-		}
-		Thread.sleep(10);
-
-		final StopWatch sw = new StopWatch();
-
-		SearchParameterMap params;
-		params = new SearchParameterMap();
-		params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
-		final IBundleProvider bundleProvider = myPatientDao.search(params);
-		assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
-		assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
-
-		myDaoConfig.setExpireSearchResultsAfterMillis(500);
-		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
-		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
-		txTemplate.execute(new TransactionCallbackWithoutResult() {
-			@Override
-			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
-				assertNotNull("Failed after " + sw.toString(), mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
-			}
-		});
-
-		Thread.sleep(750);
-		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
-		txTemplate.execute(new TransactionCallbackWithoutResult() {
-			@Override
-			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
-				assertNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
-			}
-		});
 	}
 
 	@Test
@@ -101,6 +62,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
 
 		myDaoConfig.setExpireSearchResultsAfterMillis(1000L);
 		myDaoConfig.setReuseCachedSearchResultsForMillis(500L);
+		long start = System.currentTimeMillis();
 
 		final String searchUuid1;
 		{
@@ -112,7 +74,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
 			Validate.notBlank(searchUuid1);
 		}
 
-		Thread.sleep(250);
+		sleepAtLeast(250);
 
 		String searchUuid2;
 		{
@@ -125,7 +87,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
 		}
 		assertEquals(searchUuid1, searchUuid2);
 
-		Thread.sleep(500);
+		sleepAtLeast(500);
 
 		// We're now past 500ms so we shouldn't reuse the search
 
@@ -150,7 +112,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
 			}
 		});
 
-		Thread.sleep(750);
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 1400);
 
 		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
 		newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@@ -166,7 +128,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
 			}
 		});
 
-		Thread.sleep(300);
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 2200);
 
 		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
 		newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@@ -178,4 +140,63 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
 		});
 
 	}
+
+	@Test
+	public void testExpirePagesAfterSingleUse() throws Exception {
+		IIdType pid1;
+		IIdType pid2;
+		{
+			Patient patient = new Patient();
+			patient.addName().setFamily("EXPIRE");
+			pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		Thread.sleep(10);
+		{
+			Patient patient = new Patient();
+			patient.addName().setFamily("EXPIRE");
+			pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		Thread.sleep(10);
+
+		final StopWatch sw = new StopWatch();
+
+		long start = System.currentTimeMillis();
+
+		SearchParameterMap params;
+		params = new SearchParameterMap();
+		params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
+		final IBundleProvider bundleProvider = myPatientDao.search(params);
+		assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
+		assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
+
+		myDaoConfig.setExpireSearchResultsAfterMillis(500);
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(start);
+
+		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
+		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
+		txTemplate.execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				assertNotNull("Failed after " + sw.toString(), mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
+			}
+		});
+
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 499);
+		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
+		txTemplate.execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				assertNotNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
+			}
+		});
+
+		StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 600);
+		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
+		txTemplate.execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				assertNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
+			}
+		});
+	}
 }

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

@@ -29,6 +29,7 @@ import java.util.regex.Pattern;
 
 import javax.servlet.http.HttpServletRequest;
 
+import ca.uhn.fhir.util.BinaryUtil;
 import org.hl7.fhir.instance.model.api.*;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -580,10 +581,17 @@ public class RestfulServerUtils {
 			} else {
 				contentType = Constants.CT_OCTET_STREAM;
 			}
+
 			// Force binary resources to download - This is a security measure to prevent
 			// malicious images or HTML blocks being served up as content.
 			response.addHeader(Constants.HEADER_CONTENT_DISPOSITION, "Attachment;");
 
+			IBaseReference securityContext = BinaryUtil.getSecurityContext(theServer.getFhirContext(), bin);
+			String securityContextRef = securityContext.getReferenceElement().getValue();
+			if (isNotBlank(securityContextRef)) {
+				response.addHeader(Constants.HEADER_X_SECURITY_CONTEXT, securityContextRef);
+			}
+
 			return response.sendAttachmentResponse(bin, theStausCode, contentType);
 		}
 

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

@@ -149,24 +149,6 @@ public abstract class BaseResourceReturningMethodBinding extends BaseMethodBindi
 
 		return theRequest.getResponse().streamResponseAsResource(response, prettyPrint, summaryMode, Constants.STATUS_HTTP_200_OK, null, theRequest.isRespondGzip(), isAddContentLocationHeader());
 
-		// DSTU1 Bundle
-		// // Is this request coming from a browser
-		// String uaHeader = theRequest.getHeader("user-agent");
-		// boolean requestIsBrowser = false;
-		// if (uaHeader != null && uaHeader.contains("Mozilla")) {
-		// requestIsBrowser = true;
-		// }
-		//
-		// for (int i = theServer.getInterceptors().size() - 1; i >= 0; i--) {
-		// IServerInterceptor next = theServer.getInterceptors().get(i);
-		// boolean continueProcessing = next.outgoingResponse(theRequest, responseObject.getDstu1Bundle());
-		// if (!continueProcessing) {
-		// ourLog.debug("Interceptor {} returned false, not continuing processing");
-		// return null;
-		// }
-		// }
-		//
-		// return theRequest.getResponse().streamResponseAsBundle(responseObject.getDstu1Bundle(), summaryMode, theRequest.isRespondGzip(), requestIsBrowser);
 	}
 
 	public IBaseResource doInvokeServer(IRestfulServer<?> theServer, RequestDetails theRequest) {

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/ResourceParameter.java

@@ -19,7 +19,24 @@ package ca.uhn.fhir.rest.server.method;
  * limitations under the License.
  * #L%
  */
-import static org.apache.commons.lang3.StringUtils.isBlank;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServerUtils;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.BinaryUtil;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.api.IBaseBinary;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
@@ -30,27 +47,8 @@ import java.lang.reflect.Modifier;
 import java.nio.charset.Charset;
 import java.util.Collection;
 
-import org.apache.commons.io.IOUtils;
+import static org.apache.commons.lang3.StringUtils.isBlank;
-import org.apache.commons.lang3.Validate;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import org.hl7.fhir.instance.model.api.IBaseBinary;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
-import ca.uhn.fhir.model.api.TagList;
-import ca.uhn.fhir.parser.DataFormatException;
-import ca.uhn.fhir.parser.IParser;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.EncodingEnum;
-import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.param.ParameterUtil;
-import ca.uhn.fhir.rest.server.IResourceProvider;
-import ca.uhn.fhir.rest.server.RestfulServerUtils;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
 public class ResourceParameter implements IParameter {
 
@@ -193,11 +191,22 @@ public class ResourceParameter implements IParameter {
 			String ct = theRequest.getHeader(Constants.HEADER_CONTENT_TYPE);
 			if (EncodingEnum.forContentTypeStrict(ct) == null) {
 				FhirContext ctx = theRequest.getServer().getFhirContext();
-				IBaseBinary binary = (IBaseBinary) ctx.getResourceDefinition("Binary").newInstance();
+				IBaseBinary binary = BinaryUtil.newBinary(ctx);
 				binary.setId(theRequest.getId());
 				binary.setContentType(ct);
 				binary.setContent(theRequest.loadRequestContents());
 				retVal = binary;
+
+				/*
+				 * Security context header, which is only in
+				 * DSTU3+
+				 */
+				if (ctx.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
+					String securityContext = theRequest.getHeader(Constants.HEADER_X_SECURITY_CONTEXT);
+					if (isNotBlank(securityContext)) {
+						BinaryUtil.setSecurityContext(ctx, binary, securityContext);
+					}
+				}
 			}
 		}
 		

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java

@@ -51,8 +51,8 @@ import static org.mockito.Matchers.isNull;
 import static org.mockito.Mockito.*;
 
 public class JsonParserDstu3Test {
-	private static FhirContext ourCtx = FhirContext.forDstu3();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu3Test.class);
+	private static FhirContext ourCtx = FhirContext.forDstu3();
 
 	@After
 	public void after() {
@@ -77,22 +77,6 @@ public class JsonParserDstu3Test {
 		}
 	}
 
-
-	/**
-	 * See #720
-	 */
-	@Test
-	public void testParseCustomResourceType() {
-		String input = "{\"resourceType\":\"Bug720ResourceType\",\"meta\":{\"profile\":[\"http://example.com/StructureDefinition/dontuse#Bug720ResourceType\"]},\"supportedVersion\":\"2.5.x\",\"templatesConsentTemplate\":[{\"domainName\":\"name\",\"Name\":\"template_01\",\"version\":\"1.0\",\"title\":\"title\",\"comment\":\"comment\",\"contact\":{\"resourceType\":\"Person\",\"name\":[{\"family\":\"Mustermann\",\"given\":[\"Max\"]}],\"telecom\":[{\"system\":\"email\",\"value\":\"max.mustermann@mail.de\"},{\"system\":\"phone\",\"value\":\"+49 1234 23232\"}],\"address\":[{\"text\":\"street 1-2\",\"city\":\"city\",\"postalCode\":\"12345\",\"country\":\"Germany\"}]}}]}";
-		Bug720ResourceType parsed = ourCtx.newJsonParser().parseResource(Bug720ResourceType.class, input);
-
-		assertEquals(1, parsed.getTemplates().size());
-		assertEquals(Bug720Datatype.class, parsed.getTemplates().get(0).getClass());
-		assertEquals("Mustermann", ((Bug720Datatype)parsed.getTemplates().get(0)).getContact().getNameFirstRep().getFamily());
-
-		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(parsed));
-	}
-
 	/**
 	 * See #563
 	 */
@@ -110,6 +94,26 @@ public class JsonParserDstu3Test {
 		}
 	}
 
+	@Test
+	public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
+		String refVal = "http://my.org/FooBar";
+
+		Patient fhirPat = new Patient();
+		fhirPat.addExtension().setUrl("x1").setValue(new Reference(refVal));
+
+		IParser parser = ourCtx.newJsonParser();
+
+		String output = parser.encodeResourceToString(fhirPat);
+		System.out.println("output: " + output);
+
+		// Deserialize then check that valueReference value is still correct
+		fhirPat = parser.parseResource(Patient.class, output);
+
+		List<Extension> extlst = fhirPat.getExtensionsByUrl("x1");
+		Assert.assertEquals(1, extlst.size());
+		Assert.assertEquals(refVal, ((Reference) extlst.get(0).getValue()).getReference());
+	}
+
 	/**
 	 * See #544
 	 */
@@ -506,6 +510,22 @@ public class JsonParserDstu3Test {
 		assertEquals("VERSION2", label.getVersion());
 	}
 
+	@Test
+	public void testEncodeBinaryWithSecurityContext() {
+		Binary bin = new Binary();
+		bin.setContentType("text/plain");
+		bin.setContent("Now is the time".getBytes());
+		Reference securityContext = new Reference();
+		securityContext.setReference("DiagnosticReport/1");
+		bin.setSecurityContext(securityContext);
+		String encoded = ourCtx.newJsonParser().encodeResourceToString(bin);
+		ourLog.info(encoded);
+		assertThat(encoded, containsString("Binary"));
+		assertThat(encoded, containsString("\"contentType\":\"text/plain\""));
+		assertThat(encoded, containsString("\"content\":\"Tm93IGlzIHRoZSB0aW1l\""));
+		assertThat(encoded, containsString("\"securityContext\":{\"reference\":\"DiagnosticReport/1\"}"));
+	}
+
 	@Test
 	public void testEncodeBundleNewBundleNoText() {
 
@@ -576,23 +596,6 @@ public class JsonParserDstu3Test {
 		assertEquals("{\"resourceType\":\"Binary\"}", output);
 	}
 
-	@Test
-	public void testEncodeBinaryWithSecurityContext() {
-            Binary bin = new Binary();
-            bin.setContentType("text/plain");
-            bin.setContent("Now is the time".getBytes());
-            Reference securityContext = new Reference();
-            securityContext.setReference("DiagnosticReport/1");
-            bin.setSecurityContext(securityContext);
-            String encoded = ourCtx.newJsonParser().encodeResourceToString(bin);
-            assertThat(encoded, containsString("Binary"));
-            assertThat(encoded, containsString("contentType"));
-            assertThat(encoded, containsString("text/plain"));
-            assertThat(encoded, containsString("Tm93IGlzIHRoZSB0aW1l"));
-            assertThat(encoded, containsString("securityContext"));
-            assertThat(encoded, containsString("{\"reference\":\"DiagnosticReport/1\"}"));
-        }
-
 	/**
 	 * #158
 	 */
@@ -1865,7 +1868,7 @@ public class JsonParserDstu3Test {
 		Binary patient = new Binary();
 		patient.setId(new IdType("http://base/Binary/11/_history/22"));
 		patient.setContentType("foo");
-		patient.setContent(new byte[] { 1, 2, 3, 4 });
+		patient.setContent(new byte[]{1, 2, 3, 4});
 
 		String val = ourCtx.newJsonParser().encodeResourceToString(patient);
 
@@ -1927,6 +1930,21 @@ public class JsonParserDstu3Test {
 		assertEquals("patient family", p.getName().get(0).getFamilyElement().getValue());
 	}
 
+	/**
+	 * See #720
+	 */
+	@Test
+	public void testParseCustomResourceType() {
+		String input = "{\"resourceType\":\"Bug720ResourceType\",\"meta\":{\"profile\":[\"http://example.com/StructureDefinition/dontuse#Bug720ResourceType\"]},\"supportedVersion\":\"2.5.x\",\"templatesConsentTemplate\":[{\"domainName\":\"name\",\"Name\":\"template_01\",\"version\":\"1.0\",\"title\":\"title\",\"comment\":\"comment\",\"contact\":{\"resourceType\":\"Person\",\"name\":[{\"family\":\"Mustermann\",\"given\":[\"Max\"]}],\"telecom\":[{\"system\":\"email\",\"value\":\"max.mustermann@mail.de\"},{\"system\":\"phone\",\"value\":\"+49 1234 23232\"}],\"address\":[{\"text\":\"street 1-2\",\"city\":\"city\",\"postalCode\":\"12345\",\"country\":\"Germany\"}]}}]}";
+		Bug720ResourceType parsed = ourCtx.newJsonParser().parseResource(Bug720ResourceType.class, input);
+
+		assertEquals(1, parsed.getTemplates().size());
+		assertEquals(Bug720Datatype.class, parsed.getTemplates().get(0).getClass());
+		assertEquals("Mustermann", ((Bug720Datatype) parsed.getTemplates().get(0)).getContact().getNameFirstRep().getFamily());
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(parsed));
+	}
+
 	/**
 	 * #480
 	 */
@@ -2182,39 +2200,6 @@ public class JsonParserDstu3Test {
 		}
 	}
 
-	/**
-	 * See #344
-	 */
-	@Test
-	public void testParserIsCaseSensitive() {
-		Observation obs = new Observation();
-		SampledData data = new SampledData();
-		data.setData("1 2 3");
-		data.setOrigin((SimpleQuantity) new SimpleQuantity().setValue(0L));
-		data.setPeriod(1000L);
-		obs.setValue(data);
-
-		IParser p = ourCtx.newJsonParser().setPrettyPrint(true).setParserErrorHandler(new StrictErrorHandler());
-		String encoded = p.encodeResourceToString(obs);
-		ourLog.info(encoded);
-
-		p.parseResource(encoded);
-
-		try {
-			p.parseResource(encoded.replace("Observation", "observation"));
-			fail();
-		} catch (DataFormatException e) {
-			assertEquals("Unknown resource type 'observation': Resource names are case sensitive, found similar name: 'Observation'", e.getMessage());
-		}
-
-		try {
-			p.parseResource(encoded.replace("valueSampledData", "valueSampleddata"));
-			fail();
-		} catch (DataFormatException e) {
-			assertEquals("Unknown element 'valueSampleddata' found during parse", e.getMessage());
-		}
-	}
-
 	@Test
 	public void testParseWithPrecision() {
 		String input = "{\"resourceType\":\"Observation\",\"valueQuantity\":{\"value\":0.000000000000000100}}";
@@ -2252,6 +2237,39 @@ public class JsonParserDstu3Test {
 		}
 	}
 
+	/**
+	 * See #344
+	 */
+	@Test
+	public void testParserIsCaseSensitive() {
+		Observation obs = new Observation();
+		SampledData data = new SampledData();
+		data.setData("1 2 3");
+		data.setOrigin((SimpleQuantity) new SimpleQuantity().setValue(0L));
+		data.setPeriod(1000L);
+		obs.setValue(data);
+
+		IParser p = ourCtx.newJsonParser().setPrettyPrint(true).setParserErrorHandler(new StrictErrorHandler());
+		String encoded = p.encodeResourceToString(obs);
+		ourLog.info(encoded);
+
+		p.parseResource(encoded);
+
+		try {
+			p.parseResource(encoded.replace("Observation", "observation"));
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("Unknown resource type 'observation': Resource names are case sensitive, found similar name: 'Observation'", e.getMessage());
+		}
+
+		try {
+			p.parseResource(encoded.replace("valueSampledData", "valueSampleddata"));
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("Unknown element 'valueSampleddata' found during parse", e.getMessage());
+		}
+	}
+
 	/**
 	 * See #144 and #146
 	 */
@@ -2361,26 +2379,6 @@ public class JsonParserDstu3Test {
 		assertTrue(result.isSuccessful());
 	}
 
-	@Test
-	public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
-		String refVal = "http://my.org/FooBar";
-
-		Patient fhirPat = new Patient();
-		fhirPat.addExtension().setUrl("x1").setValue(new Reference(refVal));
-
-		IParser parser = ourCtx.newJsonParser();
-
-		String output = parser.encodeResourceToString(fhirPat);
-		System.out.println("output: " + output);
-
-		// Deserialize then check that valueReference value is still correct
-		fhirPat = parser.parseResource(Patient.class, output);
-
-		List<Extension> extlst = fhirPat.getExtensionsByUrl("x1");
-		Assert.assertEquals(1, extlst.size());
-		Assert.assertEquals(refVal, ((Reference) extlst.get(0).getValue()).getReference());
-	}
-
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java

@@ -82,6 +82,23 @@ public class XmlParserDstu3Test {
 		ourCtx.setNarrativeGenerator(null);
 	}
 
+	@Test
+	public void testEncodeBinaryWithSecurityContext() {
+		Binary bin = new Binary();
+		bin.setContentType("text/plain");
+		bin.setContent("Now is the time".getBytes());
+		Reference securityContext = new Reference();
+		securityContext.setReference("DiagnosticReport/1");
+		bin.setSecurityContext(securityContext);
+		String encoded = ourCtx.newXmlParser().encodeResourceToString(bin);
+		ourLog.info(encoded);
+		assertThat(encoded, containsString("Binary"));
+		assertThat(encoded, containsString("<contentType value=\"text/plain\"/>"));
+		assertThat(encoded, containsString("<securityContext><reference value=\"DiagnosticReport/1\"/></securityContext>"));
+		assertThat(encoded, containsString("<content value=\"Tm93IGlzIHRoZSB0aW1l\"/>"));
+	}
+
+
 	/**
 	 * See #544
 	 */

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/BinaryServerR4Test.java

@@ -1,14 +1,16 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.junit.Assert.assertArrayEquals;
+import ca.uhn.fhir.context.FhirContext;
-import static org.junit.Assert.assertEquals;
+import ca.uhn.fhir.rest.annotation.*;
-import static org.junit.Assert.assertNull;
+import ca.uhn.fhir.rest.api.Constants;
-
+import ca.uhn.fhir.rest.api.MethodOutcome;
-import java.util.concurrent.TimeUnit;
+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.client.methods.HttpPost;
+import org.apache.http.client.methods.HttpPut;
 import org.apache.http.entity.ByteArrayEntity;
 import org.apache.http.entity.StringEntity;
 import org.apache.http.impl.client.CloseableHttpClient;
@@ -18,18 +20,20 @@ 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.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.Binary;
-import org.junit.*;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Reference;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
 
-import ca.uhn.fhir.context.FhirContext;
+import java.util.concurrent.TimeUnit;
-import ca.uhn.fhir.rest.annotation.Create;
-import ca.uhn.fhir.rest.annotation.ResourceParam;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.util.PortUtil;
-import ca.uhn.fhir.util.TestUtil;
 
-public class CreateBinaryR4Test {
+import static org.junit.Assert.*;
+
+public class BinaryServerR4Test {
 	private static CloseableHttpClient ourClient;
 	private static FhirContext ourCtx = FhirContext.forR4();
 	private static Binary ourLastBinary;
@@ -37,24 +41,73 @@ public class CreateBinaryR4Test {
 	private static String ourLastBinaryString;
 	private static int ourPort;
 	private static Server ourServer;
+	private static IdType ourLastId;
+	private static Binary ourNextBinary;
 
 	@Before
 	public void before() {
 		ourLastBinary = null;
 		ourLastBinaryBytes = null;
 		ourLastBinaryString = null;
+		ourLastId = null;
+		ourNextBinary = null;
 	}
 
 	@Test
-	public void testRawBytesBinaryContentType() throws Exception {
+	public void testGetWithNoAccept() throws Exception {
+
+		ourNextBinary = new Binary();
+		ourNextBinary.setId("Binary/A/_history/222");
+		ourNextBinary.setContent(new byte[]{0, 1, 2, 3, 4});
+		ourNextBinary.setSecurityContext(new Reference("Patient/1"));
+		ourNextBinary.setContentType("application/foo");
+
+		HttpGet get = new HttpGet("http://localhost:" + ourPort + "/Binary/A");
+		get.addHeader("Content-Type", "application/foo");
+		CloseableHttpResponse status = ourClient.execute(get);
+		try {
+			assertEquals(200, status.getStatusLine().getStatusCode());
+			assertEquals("application/foo", status.getEntity().getContentType().getValue());
+			assertEquals("Patient/1", status.getFirstHeader(Constants.HEADER_X_SECURITY_CONTEXT).getValue());
+			assertEquals("W/\"222\"", status.getFirstHeader(Constants.HEADER_ETAG).getValue());
+			assertEquals("http://localhost:" + ourPort + "/Binary/A/_history/222", status.getFirstHeader(Constants.HEADER_LOCATION).getValue());
+
+			byte[] content = IOUtils.toByteArray(status.getEntity().getContent());
+			assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, content);
+		} finally {
+			IOUtils.closeQuietly(status);
+		}
+	}
+
+	@Test
+	public void testPostBinaryWithSecurityContext() throws Exception {
 		HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
-		post.setEntity(new ByteArrayEntity(new byte[] { 0, 1, 2, 3, 4 }));
+		post.setEntity(new ByteArrayEntity(new byte[]{0, 1, 2, 3, 4}));
+		post.addHeader("Content-Type", "application/foo");
+		post.addHeader(Constants.HEADER_X_SECURITY_CONTEXT, "Encounter/2");
+		CloseableHttpResponse status = ourClient.execute(post);
+		try {
+			assertNull(ourLastId);
+			assertEquals("application/foo", ourLastBinary.getContentType());
+			assertEquals("Encounter/2", ourLastBinary.getSecurityContext().getReference());
+			assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinary.getContent());
+			assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinaryBytes);
+		} finally {
+			IOUtils.closeQuietly(status);
+		}
+	}
+
+	@Test
+	public void testPostRawBytesBinaryContentType() throws Exception {
+		HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
+		post.setEntity(new ByteArrayEntity(new byte[]{0, 1, 2, 3, 4}));
 		post.addHeader("Content-Type", "application/foo");
 		CloseableHttpResponse status = ourClient.execute(post);
 		try {
+			assertNull(ourLastId);
 			assertEquals("application/foo", ourLastBinary.getContentType());
-			assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourLastBinary.getContent());
+			assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinary.getContent());
-			assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourLastBinaryBytes);
+			assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinaryBytes);
 		} finally {
 			IOUtils.closeQuietly(status);
 		}
@@ -64,11 +117,11 @@ public class CreateBinaryR4Test {
 	 * Technically the client shouldn't be doing it this way, but we'll be accepting
 	 */
 	@Test
-	public void testRawBytesFhirContentType() throws Exception {
+	public void testPostRawBytesFhirContentType() throws Exception {
 
 		Binary b = new Binary();
 		b.setContentType("application/foo");
-		b.setContent(new byte[] { 0, 1, 2, 3, 4 });
+		b.setContent(new byte[]{0, 1, 2, 3, 4});
 		String encoded = ourCtx.newJsonParser().encodeResourceToString(b);
 
 		HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
@@ -77,14 +130,14 @@ public class CreateBinaryR4Test {
 		CloseableHttpResponse status = ourClient.execute(post);
 		try {
 			assertEquals("application/foo", ourLastBinary.getContentType());
-			assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourLastBinary.getContent());
+			assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinary.getContent());
 		} finally {
 			IOUtils.closeQuietly(status);
 		}
 	}
 
 	@Test
-	public void testRawBytesFhirContentTypeContainingFhir() throws Exception {
+	public void testPostRawBytesFhirContentTypeContainingFhir() throws Exception {
 
 		Patient p = new Patient();
 		p.getText().setDivAsString("A PATIENT");
@@ -109,13 +162,32 @@ public class CreateBinaryR4Test {
 	}
 
 	@Test
-	public void testRawBytesNoContentType() throws Exception {
+	public void testPostRawBytesNoContentType() throws Exception {
 		HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
-		post.setEntity(new ByteArrayEntity(new byte[] { 0, 1, 2, 3, 4 }));
+		post.setEntity(new ByteArrayEntity(new byte[]{0, 1, 2, 3, 4}));
 		CloseableHttpResponse status = ourClient.execute(post);
 		try {
 			assertNull(ourLastBinary.getContentType());
-			assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourLastBinary.getContent());
+			assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinary.getContent());
+		} finally {
+			IOUtils.closeQuietly(status);
+		}
+	}
+
+	@Test
+	public void testPutBinaryWithSecurityContext() throws Exception {
+		HttpPut post = new HttpPut("http://localhost:" + ourPort + "/Binary/A");
+		post.setEntity(new ByteArrayEntity(new byte[]{0, 1, 2, 3, 4}));
+		post.addHeader("Content-Type", "application/foo");
+		post.addHeader(Constants.HEADER_X_SECURITY_CONTEXT, "Encounter/2");
+		CloseableHttpResponse status = ourClient.execute(post);
+		try {
+			assertEquals("Binary/A", ourLastId.getValue());
+			assertEquals("Binary/A", ourLastBinary.getId());
+			assertEquals("application/foo", ourLastBinary.getContentType());
+			assertEquals("Encounter/2", ourLastBinary.getSecurityContext().getReference());
+			assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinary.getContent());
+			assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinaryBytes);
 		} finally {
 			IOUtils.closeQuietly(status);
 		}
@@ -149,7 +221,6 @@ public class CreateBinaryR4Test {
 	}
 
 	public static class BinaryProvider implements IResourceProvider {
-
 		@Create()
 		public MethodOutcome createBinary(@ResourceParam Binary theBinary, @ResourceParam String theBinaryString, @ResourceParam byte[] theBinaryBytes) {
 			ourLastBinary = theBinary;
@@ -163,6 +234,20 @@ public class CreateBinaryR4Test {
 			return Binary.class;
 		}
 
+		@Read
+		public Binary read(@IdParam IdType theId) {
+			return ourNextBinary;
+		}
+
+		@Update()
+		public MethodOutcome updateBinary(@IdParam IdType theId, @ResourceParam Binary theBinary, @ResourceParam String theBinaryString, @ResourceParam byte[] theBinaryBytes) {
+			ourLastId = theId;
+			ourLastBinary = theBinary;
+			ourLastBinaryString = theBinaryString;
+			ourLastBinaryBytes = theBinaryBytes;
+			return new MethodOutcome(new IdType("Binary/001/_history/002"));
+		}
+
 	}
 
 }

src/changes/changes.xml

@@ -175,6 +175,11 @@
 				was not encoded correctly. Thanks to Malcolm McRoberts for the pull
 				request with fix and test case!
 			</action>
+			<action type="add">
+				The Binary resource endpoint now supports the `X-Security-Context` header when
+				reading or writing Binary contents using their native Content-Type (i.e exchanging
+				the raw binary with the server, as opposed to exchanging a FHIR resource).
+			</action>
 		</release>
 		<release version="3.0.0" date="2017-09-27">
 			<action type="add">