Merge branch 'master' into analyzer-def-using-search-mapping

.gitignore

@@ -141,6 +141,8 @@ local.properties
 **/.target
 **/.project
 **/.classpath
+**/.factorypath
+**/.springBeans
 
 
 # PDT-specific

.travis.yml

@@ -22,4 +22,4 @@ before_script:
 script:
 #  - mvn -e -B clean install && cd hapi-fhir-ra && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID clean test jacoco:report coveralls:report
 #  - mvn -Dci=true -e -B -P ALLMODULES,NOPARALLEL,ERRORPRONE clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report 
-  - mvn -Dci=true -e -B -P ALLMODULES,MINPARALLEL clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report 
+  - mvn -Dci=true -e -B -P ALLMODULES,MINPARALLEL,ERRORPRONE clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report 

hapi-deployable-pom/pom.xml

@@ -63,6 +63,65 @@
 					</dependency>
 				</dependencies>
 			</plugin>
+			<plugin>
+				<groupId>org.basepom.maven</groupId>
+				<artifactId>duplicate-finder-maven-plugin</artifactId>
+				<executions>
+					<execution>
+						<id>default</id>
+						<phase>verify</phase>
+						<goals>
+							<goal>check</goal>
+						</goals>
+						<inherited>true</inherited>
+					</execution>
+				</executions>
+				<configuration>
+					<printEqualFiles>false</printEqualFiles>
+					<failBuildInCaseOfDifferentContentConflict>true</failBuildInCaseOfDifferentContentConflict>
+					<failBuildInCaseOfEqualContentConflict>true</failBuildInCaseOfEqualContentConflict>
+					<failBuildInCaseOfConflict>true</failBuildInCaseOfConflict>
+					<checkCompileClasspath>true</checkCompileClasspath>
+					<checkRuntimeClasspath>false</checkRuntimeClasspath>
+					<checkTestClasspath>false</checkTestClasspath>
+					<skip>false</skip>
+					<quiet>false</quiet>
+					<preferLocal>true</preferLocal>
+					<useResultFile>true</useResultFile>
+					<resultFileMinClasspathCount>2</resultFileMinClasspathCount>
+					<resultFile>${project.build.directory}/duplicate-finder-result.xml</resultFile>
+					<ignoredDependencies>
+						<dependency>
+							<groupId>javax.el</groupId>
+							<artifactId>javax.el-api</artifactId>
+						</dependency>
+						<dependency>
+							<groupId>javax.mail</groupId>
+							<artifactId>javax.mail-api</artifactId>
+						</dependency>
+						<dependency>
+							<groupId>com.phloc</groupId>
+							<artifactId>phloc-commons</artifactId>
+						</dependency>
+						<dependency>
+							<groupId>commons-logging</groupId>
+							<artifactId>commons-logging</artifactId>
+						</dependency>
+						<dependency>
+							<groupId>org.jscience</groupId>
+							<artifactId>jscience</artifactId>
+						</dependency>
+						<dependency>
+							<groupId>org.springframework</groupId>
+							<artifactId>spring-jcl</artifactId>
+						</dependency>
+					</ignoredDependencies>
+					<ignoredResources>
+						<ignoredResource>changelog.txt</ignoredResource>
+						<ignoredResource>javac.bat</ignoredResource>
+					</ignoredResources>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 

hapi-fhir-android/pom.xml

@@ -35,6 +35,25 @@
 					<groupId>commons-codec</groupId>
 					<artifactId>commons-codec</artifactId>
 				</exclusion>
+				<exclusion>
+					<groupId>org.codehaus.woodstox</groupId>
+					<artifactId>woodstox-core-asl</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-client</artifactId>
+			<version>${project.version}</version>
+			<exclusions>
+				<exclusion>
+					<groupId>org.apache.httpcomponents</groupId>
+					<artifactId>httpcore</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.apache.httpcomponents</groupId>
+					<artifactId>httpclient</artifactId>
+				</exclusion>
 			</exclusions>
 		</dependency>
 		<dependency>
@@ -92,52 +111,14 @@
 				</configuration>
 				<executions>
 					<execution>
-						<id>dstu2_shade</id>
+						<id>it</id>
 						<goals>
 							<goal>integration-test</goal>
-							<goal>verify</goal>
 						</goals>
 						<configuration>
 							<includes>
-								<include>**/*Dstu2ShadeIT.java</include>
+								<include>**/*IT.java</include>
 							</includes>
-							<classpathDependencyExcludes>
-								<!--<classpathDependencyExclude>ca.uhn.hapi.fhir:*</classpathDependencyExclude>-->
-								<classpathDependencyExclude>org.codehaus.woodstox:woodstox-core-asl</classpathDependencyExclude>
-								<classpathDependencyExclude>org.codehaus.woodstox:stax2-api</classpathDependencyExclude>
-							</classpathDependencyExcludes>
-						</configuration>
-					</execution>
-					<execution>
-						<id>dstu2</id>
-						<goals>
-							<goal>integration-test</goal>
-							<goal>verify</goal>
-						</goals>
-						<configuration>
-							<includes>
-								<include>**/*Dstu2IT.java</include>
-							</includes>
-							<classpathDependencyExcludes>
-								<classpathDependencyExclude>org.codehaus.woodstox:woodstox-core-asl</classpathDependencyExclude>
-								<classpathDependencyExclude>org.codehaus.woodstox:stax2-api</classpathDependencyExclude>
-							</classpathDependencyExcludes>
-						</configuration>
-					</execution>
-					<execution>
-						<id>dstu3</id>
-						<goals>
-							<goal>integration-test</goal>
-							<goal>verify</goal>
-						</goals>
-						<configuration>
-							<includes>
-								<include>**/*Dstu3IT.java</include>
-							</includes>
-							<classpathDependencyExcludes>
-								<classpathDependencyExclude>org.codehaus.woodstox:woodstox-core-asl</classpathDependencyExclude>
-								<classpathDependencyExclude>org.codehaus.woodstox:stax2-api</classpathDependencyExclude>
-							</classpathDependencyExcludes>
 						</configuration>
 					</execution>
 				</executions>

hapi-fhir-android/src/test/java/ca/uhn/fhir/android/BuiltJarDstu2ShadeIT.java

@@ -9,6 +9,7 @@ import java.util.zip.ZipFile;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.filefilter.WildcardFileFilter;
+import org.junit.Ignore;
 import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -21,6 +22,7 @@ public class BuiltJarDstu2ShadeIT {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BuiltJarDstu2ShadeIT.class);
 
 	@Test
+	@Ignore
 	public void testParserXml() throws Exception {
 
 		FhirContext ctx = FhirContext.forDstu2();

hapi-fhir-android/src/test/java/ca/uhn/fhir/android/client/GenericClientDstu3IT.java

@@ -7,7 +7,6 @@ import static org.mockito.Mockito.when;
 import java.io.IOException;
 import java.util.Date;
 
-import org.apache.http.client.ClientProtocolException;
 import org.hl7.fhir.dstu3.model.*;
 import org.junit.*;
 import org.mockito.ArgumentCaptor;
@@ -82,6 +81,7 @@ public class GenericClientDstu3IT {
 	 * TODO: narratives don't work without stax
 	 */
 	@Test
+	@Ignore
 	public void testBinaryCreateWithFhirContentType() throws Exception {
 		IParser p = ourCtx.newXmlParser();
 
@@ -142,7 +142,7 @@ public class GenericClientDstu3IT {
       	.returnBundle(Bundle.class)
       	.execute();
 
-		assertEquals("http://example.com/fhir/Patient", capt.getAllValues().get(idx).url().toString());
+		assertEquals("http://example.com/fhir/Patient?_format=json", capt.getAllValues().get(idx).url().toString());
 		idx++;
 		
 	}
@@ -177,12 +177,12 @@ public class GenericClientDstu3IT {
 		Request request = capt.getAllValues().get(0);
 		ourLog.info(request.headers().toString());
 
-		assertEquals("http://example.com/fhir/Binary", request.url().toString());
+		assertEquals("http://example.com/fhir/Binary?_format=json", request.url().toString());
 		validateUserAgent(capt);
 
-		assertEquals(Constants.CT_FHIR_XML_NEW + ";charset=utf-8", request.body().contentType().toString().toLowerCase().replace(" ", ""));
+		assertEquals(Constants.CT_FHIR_JSON_NEW + ";charset=utf-8", request.body().contentType().toString().toLowerCase().replace(" ", ""));
-		assertEquals(Constants.HEADER_ACCEPT_VALUE_XML_NON_LEGACY, request.header("Accept"));
+		assertEquals(Constants.HEADER_ACCEPT_VALUE_JSON_NON_LEGACY, request.header("Accept"));
-		assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourCtx.newXmlParser().parseResource(Binary.class, extractBodyAsString(capt)).getContent());
+		assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourCtx.newJsonParser().parseResource(Binary.class, extractBodyAsString(capt)).getContent());
 
 	}
 
@@ -257,11 +257,11 @@ public class GenericClientDstu3IT {
 		assertNotNull(outcome.getResource());
 
 		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">FINAL VALUE</div>", ((Patient) outcome.getResource()).getText().getDivAsString());
-		assertEquals("http://example.com/fhir/Patient", capt.getAllValues().get(0).url().toString());
+		assertEquals("http://example.com/fhir/Patient?_format=json", capt.getAllValues().get(0).url().toString());
 	}
 
 	
-	private ArgumentCaptor<Request> prepareClientForSearchResponse() throws IOException, ClientProtocolException {
+	private ArgumentCaptor<Request> prepareClientForSearchResponse() throws IOException {
 		final String respString = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 		myHttpResponse = new Response.Builder()
 				.request(myRequest)

hapi-fhir-base/pom.xml

@@ -28,6 +28,7 @@
 		<dependency>
 			<groupId>org.codehaus.woodstox</groupId>
 			<artifactId>woodstox-core-asl</artifactId>
+			<optional>true</optional>
 		</dependency>
 
 		<!-- Only required for narrative generator support -->
@@ -124,6 +125,7 @@
 					<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
 				</configuration>
 			</plugin>
+			<!--
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-source-plugin</artifactId>
@@ -136,6 +138,7 @@
 					</execution>
 				</executions>
 			</plugin>
+			-->
 		</plugins>
 		<resources>
 			<resource>

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/context/RuntimeSearchParam.java

@@ -152,7 +152,8 @@ public class RuntimeSearchParam {
 	public enum RuntimeSearchParamStatusEnum {
 		ACTIVE,
 		DRAFT,
-		RETIRED
+		RETIRED,
+		UNKNOWN
 	}
 	
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/XhtmlDt.java

@@ -20,29 +20,29 @@ package ca.uhn.fhir.model.primitive;
  * #L%
  */
 
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLEventReader;
-import javax.xml.stream.XMLEventWriter;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.events.XMLEvent;
-
-import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.model.api.BasePrimitive;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
 import ca.uhn.fhir.model.api.annotation.SimpleSetter;
 import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.util.XmlDetectionUtil;
 import ca.uhn.fhir.util.XmlUtil;
 
+import java.util.List;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+/**
+ * Note that as of HAPI FHIR 3.1.0, this method no longer uses
+ * the StAX XMLEvent type as the XML representation, and uses a
+ * String instead. If you need to work with XML as StAX events, you
+ * can use the {@link XmlUtil#parse(String)} and {@link XmlUtil#encode(List)}
+ * methods to do so.
+ */
 @DatatypeDef(name = "xhtml")
-public class XhtmlDt extends BasePrimitive<List<XMLEvent>> {
+public class XhtmlDt extends BasePrimitive<String> {
 
 	private static final String DECL_XMLNS = " xmlns=\"http://www.w3.org/1999/xhtml\"";
-	private static final String DIV_OPEN_FIRST = "<div" + DECL_XMLNS + ">";
+	public static final String DIV_OPEN_FIRST = "<div" + DECL_XMLNS + ">";
 	private static final long serialVersionUID = 1L;
 
 	/**
@@ -63,29 +63,12 @@ public class XhtmlDt extends BasePrimitive<List<XMLEvent>> {
 	}
 
 	@Override
-	protected String encode(List<XMLEvent> theValue) {
+	protected String encode(String theValue) {
-		try {
+		return theValue;
-			StringWriter w = new StringWriter();
-			XMLEventWriter ew = XmlUtil.createXmlFragmentWriter(w);
-
-			for (XMLEvent next : getValue()) {
-				if (next.isCharacters()) {
-					ew.add(next);
-				} else {
-					ew.add(next);
-				}
-			}
-			ew.close();
-			return w.toString();
-		} catch (XMLStreamException e) {
-			throw new DataFormatException("Problem with the contained XML events", e);
-		} catch (FactoryConfigurationError e) {
-			throw new ConfigurationException(e);
-		}
 	}
 
 	public boolean hasContent() {
-		return getValue() != null && getValue().size() > 0;
+		return isNotBlank(getValue());
 	}
 
 	@Override
@@ -94,40 +77,37 @@ public class XhtmlDt extends BasePrimitive<List<XMLEvent>> {
 	}
 
 	@Override
-	protected List<XMLEvent> parse(String theValue) {
+	protected String parse(String theValue) {
-		String val = theValue.trim();
+		if (XmlDetectionUtil.isStaxPresent()) {
-		if (!val.startsWith("<")) {
+			// for validation
-			val = DIV_OPEN_FIRST + val + "</div>";
+			XmlUtil.parse(theValue);
-		}
-		boolean hasProcessingInstruction = val.startsWith("<?");
-		if (hasProcessingInstruction && val.endsWith("?>")) {
-			return null;
 		}
+		return theValue;
+	}
 
 
-		try {
+	/**
-			ArrayList<XMLEvent> value = new ArrayList<XMLEvent>();
+	 * Note that as of HAPI FHIR 3.1.0, this method no longer uses
-			StringReader reader = new StringReader(val);
+	 * the StAX XMLEvent type as the XML representation, and uses a
-			XMLEventReader er = XmlUtil.createXmlReader(reader);
+	 * String instead. If you need to work with XML as StAX events, you
-			boolean first = true;
+	 * can use the {@link XmlUtil#parse(String)} and {@link XmlUtil#encode(List)}
-			while (er.hasNext()) {
+	 * methods to do so.
-				XMLEvent next = er.nextEvent();
+	 */
-				if (first) {
+	@Override
-					first = false;
+	public String getValue() {
-					continue;
+		return super.getValue();
-				}
+	}
-				if (er.hasNext()) {
-					// don't add the last event
-					value.add(next);
-				}
-			}
-			return value;
 
-		} catch (XMLStreamException e) {
+	/**
-			throw new DataFormatException("String does not appear to be valid XML/XHTML (error is \"" + e.getMessage() + "\"): " + theValue, e);
+	 * Note that as of HAPI FHIR 3.1.0, this method no longer uses
-		} catch (FactoryConfigurationError e) {
+	 * the StAX XMLEvent type as the XML representation, and uses a
-			throw new ConfigurationException(e);
+	 * String instead. If you need to work with XML as StAX events, you
-		}
+	 * can use the {@link XmlUtil#parse(String)} and {@link XmlUtil#encode(List)}
+	 * methods to do so.
+	 */
+	@Override
+	public BasePrimitive<String> setValue(String theValue) throws DataFormatException {
+		return super.setValue(theValue);
 	}
 
 	/**

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

@@ -43,7 +43,7 @@ public abstract class BaseParser implements IParser {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
 
 	private ContainedResources myContainedResources;
-
+	private boolean myEncodeElementsAppliesToChildResourcesOnly;
 	private FhirContext myContext;
 	private Set<String> myDontEncodeElements;
 	private boolean myDontEncodeElementsIncludesStars;
@@ -556,6 +556,16 @@ public abstract class BaseParser implements IParser {
 			&& theIncludedResource == false;
 	}
 
+	@Override
+	public boolean isEncodeElementsAppliesToChildResourcesOnly() {
+		return myEncodeElementsAppliesToChildResourcesOnly;
+	}
+
+	@Override
+	public void setEncodeElementsAppliesToChildResourcesOnly(boolean theEncodeElementsAppliesToChildResourcesOnly) {
+		myEncodeElementsAppliesToChildResourcesOnly = theEncodeElementsAppliesToChildResourcesOnly;
+	}
+
 	@Override
 	public boolean isOmitResourceId() {
 		return myOmitResourceId;
@@ -1039,7 +1049,13 @@ public abstract class BaseParser implements IParser {
 		}
 
 		private boolean checkIfParentShouldBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
-			return checkIfPathMatchesForEncoding(thePathBuilder, theStarPass, myEncodeElementsAppliesToResourceTypes, myEncodeElements, true);
+			Set<String> encodeElements = myEncodeElements;
+			if (encodeElements != null && encodeElements.isEmpty() == false) {
+				if (isEncodeElementsAppliesToChildResourcesOnly() && !mySubResource) {
+					encodeElements = null;
+				}
+			}
+			return checkIfPathMatchesForEncoding(thePathBuilder, theStarPass, myEncodeElementsAppliesToResourceTypes, encodeElements, true);
 		}
 
 		private boolean checkIfParentShouldNotBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
@@ -1058,6 +1074,9 @@ public abstract class BaseParser implements IParser {
 				} else {
 					thePathBuilder.append(myResDef.getName());
 				}
+				if (theElements == null) {
+					return true;
+				}
 				if (theElements.contains(thePathBuilder.toString())) {
 					return true;
 				}

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

@@ -206,6 +206,22 @@ public interface IParser {
 	 */
 	void setEncodeElements(Set<String> theEncodeElements);
 
+	/**
+	 * If set to <code>true</code> (default is false), the values supplied
+	 * to {@link #setEncodeElements(Set)} will not be applied to the root
+	 * resource (typically a Bundle), but will be applied to any sub-resources
+	 * contained within it (i.e. search result resources in that bundle)
+	 */
+	void setEncodeElementsAppliesToChildResourcesOnly(boolean theEncodeElementsAppliesToChildResourcesOnly);
+
+	/**
+	 * If set to <code>true</code> (default is false), the values supplied
+	 * to {@link #setEncodeElements(Set)} will not be applied to the root
+	 * resource (typically a Bundle), but will be applied to any sub-resources
+	 * contained within it (i.e. search result resources in that bundle)
+	 */
+	boolean isEncodeElementsAppliesToChildResourcesOnly();
+
 	/**
 	 * If provided, tells the parse which resource types to apply {@link #setEncodeElements(Set) encode elements} to. Any
 	 * resource types not specified here will be encoded completely, with no elements excluded.

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;
@@ -46,9 +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 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
@@ -88,7 +93,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private boolean addToHeldExtensions(int valueIdx, List<? extends IBaseExtension<?, ?>> ext, ArrayList<ArrayList<HeldExtension>> list, boolean theIsModifier, CompositeChildElement theChildElem,
-			CompositeChildElement theParent) {
+													CompositeChildElement theParent) {
 		if (ext.size() > 0) {
 			list.ensureCapacity(valueIdx);
 			while (list.size() <= valueIdx) {
@@ -139,12 +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);
@@ -156,6 +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();
@@ -191,136 +196,136 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void encodeChildElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, IBase theNextValue,
-			BaseRuntimeElementDefinition<?> theChildDef, String theChildName, boolean theContainedResource, boolean theSubResource, CompositeChildElement theChildElem,
+																 BaseRuntimeElementDefinition<?> theChildDef, String theChildName, boolean theContainedResource, boolean theSubResource, CompositeChildElement theChildElem,
-			boolean theForceEmpty) throws IOException {
+																 boolean theForceEmpty) throws IOException {
 
 		switch (theChildDef.getChildType()) {
-		case ID_DATATYPE: {
+			case ID_DATATYPE: {
-			IIdType value = (IIdType) theNextValue;
+				IIdType value = (IIdType) theNextValue;
-			String encodedValue = "id".equals(theChildName) ? value.getIdPart() : value.getValue();
+				String encodedValue = "id".equals(theChildName) ? value.getIdPart() : value.getValue();
-			if (isBlank(encodedValue)) {
+				if (isBlank(encodedValue)) {
-				break;
+					break;
-			}
+				}
-			if (theChildName != null) {
+				if (theChildName != null) {
-				write(theEventWriter, theChildName, encodedValue);
+					write(theEventWriter, theChildName, encodedValue);
-			} else {
+				} else {
-				theEventWriter.write(encodedValue);
+					theEventWriter.write(encodedValue);
-			}
-			break;
-		}
-		case PRIMITIVE_DATATYPE: {
-			final IPrimitiveType<?> value = (IPrimitiveType<?>) theNextValue;
-			if (isBlank(value.getValueAsString())) {
-				if (theForceEmpty) {
-					theEventWriter.writeNull();
 				}
 				break;
 			}
-
+			case PRIMITIVE_DATATYPE: {
-			if (value instanceof IBaseIntegerDatatype) {
+				final IPrimitiveType<?> value = (IPrimitiveType<?>) theNextValue;
-				if (theChildName != null) {
+				if (isBlank(value.getValueAsString())) {
-					write(theEventWriter, theChildName, ((IBaseIntegerDatatype) value).getValue());
+					if (theForceEmpty) {
-				} else {
+						theEventWriter.writeNull();
-					theEventWriter.write(((IBaseIntegerDatatype) value).getValue());
-				}
-			} else if (value instanceof IBaseDecimalDatatype) {
-				BigDecimal decimalValue = ((IBaseDecimalDatatype) value).getValue();
-				decimalValue = new BigDecimal(decimalValue.toString()) {
-					private static final long serialVersionUID = 1L;
-
-					@Override
-					public String toString() {
-						return value.getValueAsString();
 					}
-				};
+					break;
-				if (theChildName != null) {
-					write(theEventWriter, theChildName, decimalValue);
-				} else {
-					theEventWriter.write(decimalValue);
 				}
-			} else if (value instanceof IBaseBooleanDatatype) {
+
-				if (theChildName != null) {
+				if (value instanceof IBaseIntegerDatatype) {
-					write(theEventWriter, theChildName, ((IBaseBooleanDatatype) value).getValue());
+					if (theChildName != null) {
+						write(theEventWriter, theChildName, ((IBaseIntegerDatatype) value).getValue());
+					} else {
+						theEventWriter.write(((IBaseIntegerDatatype) value).getValue());
+					}
+				} else if (value instanceof IBaseDecimalDatatype) {
+					BigDecimal decimalValue = ((IBaseDecimalDatatype) value).getValue();
+					decimalValue = new BigDecimal(decimalValue.toString()) {
+						private static final long serialVersionUID = 1L;
+
+						@Override
+						public String toString() {
+							return value.getValueAsString();
+						}
+					};
+					if (theChildName != null) {
+						write(theEventWriter, theChildName, decimalValue);
+					} else {
+						theEventWriter.write(decimalValue);
+					}
+				} else if (value instanceof IBaseBooleanDatatype) {
+					if (theChildName != null) {
+						write(theEventWriter, theChildName, ((IBaseBooleanDatatype) value).getValue());
+					} else {
+						Boolean booleanValue = ((IBaseBooleanDatatype) value).getValue();
+						if (booleanValue != null) {
+							theEventWriter.write(booleanValue.booleanValue());
+						}
+					}
 				} else {
-					Boolean booleanValue = ((IBaseBooleanDatatype) value).getValue();
+					String valueStr = value.getValueAsString();
-					if (booleanValue != null) {
+					if (theChildName != null) {
-						theEventWriter.write(booleanValue.booleanValue());
+						write(theEventWriter, theChildName, valueStr);
+					} else {
+						theEventWriter.write(valueStr);
 					}
 				}
-			} else {
+				break;
-				String valueStr = value.getValueAsString();
+			}
+			case RESOURCE_BLOCK:
+			case COMPOSITE_DATATYPE: {
 				if (theChildName != null) {
-					write(theEventWriter, theChildName, valueStr);
+					theEventWriter.beginObject(theChildName);
 				} else {
-					theEventWriter.write(valueStr);
+					theEventWriter.beginObject();
 				}
+				encodeCompositeElementToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, theContainedResource, theSubResource, theChildElem);
+				theEventWriter.endObject();
+				break;
 			}
-			break;
+			case CONTAINED_RESOURCE_LIST:
-		}
+			case CONTAINED_RESOURCES: {
-		case RESOURCE_BLOCK:
-		case COMPOSITE_DATATYPE: {
-			if (theChildName != null) {
-				theEventWriter.beginObject(theChildName);
-			} else {
-				theEventWriter.beginObject();
-			}
-			encodeCompositeElementToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, theContainedResource, theSubResource, theChildElem);
-			theEventWriter.endObject();
-			break;
-		}
-		case CONTAINED_RESOURCE_LIST:
-		case CONTAINED_RESOURCES: {
 			/*
 			 * Disabled per #103 ContainedDt value = (ContainedDt) theNextValue; for (IResource next :
 			 * value.getContainedResources()) { if (getContainedResources().getResourceId(next) != null) { continue; }
 			 * encodeResourceToJsonStreamWriter(theResDef, next, theWriter, null, true,
 			 * fixContainedResourceId(next.getId().getValue())); }
 			 */
-			List<IBaseResource> containedResources = getContainedResources().getContainedResources();
+				List<IBaseResource> containedResources = getContainedResources().getContainedResources();
-			if (containedResources.size() > 0) {
+				if (containedResources.size() > 0) {
-				beginArray(theEventWriter, theChildName);
+					beginArray(theEventWriter, theChildName);
 
-				for (IBaseResource next : containedResources) {
+					for (IBaseResource next : containedResources) {
-					IIdType resourceId = getContainedResources().getResourceId(next);
+						IIdType resourceId = getContainedResources().getResourceId(next);
-					encodeResourceToJsonStreamWriter(theResDef, next, theEventWriter, null, true, false, fixContainedResourceId(resourceId.getValue()));
+						encodeResourceToJsonStreamWriter(theResDef, next, theEventWriter, null, true, false, fixContainedResourceId(resourceId.getValue()));
-				}
+					}
 
-				theEventWriter.endArray();
+					theEventWriter.endArray();
-			}
-			break;
-		}
-		case PRIMITIVE_XHTML_HL7ORG:
-		case PRIMITIVE_XHTML: {
-			if (!isSuppressNarratives()) {
-				IPrimitiveType<?> dt = (IPrimitiveType<?>) theNextValue;
-				if (theChildName != null) {
-					write(theEventWriter, theChildName, dt.getValueAsString());
-				} else {
-					theEventWriter.write(dt.getValueAsString());
-				}
-			} else {
-				if (theChildName != null) {
-					// do nothing
-				} else {
-					theEventWriter.writeNull();
 				}
+				break;
 			}
-			break;
+			case PRIMITIVE_XHTML_HL7ORG:
-		}
+			case PRIMITIVE_XHTML: {
-		case RESOURCE:
+				if (!isSuppressNarratives()) {
-			IBaseResource resource = (IBaseResource) theNextValue;
+					IPrimitiveType<?> dt = (IPrimitiveType<?>) theNextValue;
-			RuntimeResourceDefinition def = myContext.getResourceDefinition(resource);
+					if (theChildName != null) {
-			encodeResourceToJsonStreamWriter(def, resource, theEventWriter, theChildName, false, true);
+						write(theEventWriter, theChildName, dt.getValueAsString());
-			break;
+					} else {
-		case UNDECL_EXT:
+						theEventWriter.write(dt.getValueAsString());
-		default:
+					}
-			throw new IllegalStateException("Should not have this state here: " + theChildDef.getChildType().name());
+				} else {
+					if (theChildName != null) {
+						// do nothing
+					} else {
+						theEventWriter.writeNull();
+					}
+				}
+				break;
+			}
+			case RESOURCE:
+				IBaseResource resource = (IBaseResource) theNextValue;
+				RuntimeResourceDefinition def = myContext.getResourceDefinition(resource);
+				encodeResourceToJsonStreamWriter(def, resource, theEventWriter, theChildName, false, true);
+				break;
+			case UNDECL_EXT:
+			default:
+				throw new IllegalStateException("Should not have this state here: " + theChildDef.getChildType().name());
 		}
 
 	}
 
 	private void encodeCompositeElementChildrenToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theElement, JsonLikeWriter theEventWriter,
-			boolean theContainedResource, boolean theSubResource, CompositeChildElement theParent) throws IOException {
+																				 boolean theContainedResource, boolean theSubResource, CompositeChildElement theParent) throws IOException {
 
 		{
 			String elementId = getCompositeElementId(theElement);
@@ -335,7 +340,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
 
 			if (nextChildElem.getDef().getElementName().equals("extension") || nextChildElem.getDef().getElementName().equals("modifierExtension")
-					|| nextChild instanceof RuntimeChildDeclaredExtensionDefinition) {
+				|| nextChild instanceof RuntimeChildDeclaredExtensionDefinition) {
 				if (!haveWrittenExtensions) {
 					extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, myContext.getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem, theParent);
 					haveWrittenExtensions = true;
@@ -451,15 +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++;
@@ -541,7 +546,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void encodeCompositeElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theNextValue, JsonLikeWriter theEventWriter, boolean theContainedResource, boolean theSubResource,
-			CompositeChildElement theParent) throws IOException, DataFormatException {
+																	  CompositeChildElement theParent) throws IOException, DataFormatException {
 
 		writeCommentsPreAndPost(theNextValue, theEventWriter);
 		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, theContainedResource, theSubResource, theParent);
@@ -554,14 +559,14 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 
 		if (theResource.getStructureFhirVersionEnum() != myContext.getVersion().getVersion()) {
 			throw new IllegalArgumentException(
-					"This parser is for FHIR version " + myContext.getVersion().getVersion() + " - Can not encode a structure for version " + theResource.getStructureFhirVersionEnum());
+				"This parser is for FHIR version " + myContext.getVersion().getVersion() + " - Can not encode a structure for version " + theResource.getStructureFhirVersionEnum());
 		}
 
 		doEncodeResourceToJsonLikeWriter(theResource, theJsonLikeWriter);
 	}
 
 	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, String theObjectNameOrNull,
-			boolean theContainedResource, boolean theSubResource) throws IOException {
+																 boolean theContainedResource, boolean theSubResource) throws IOException {
 		IIdType resourceId = null;
 		// if (theResource instanceof IResource) {
 		// IResource res = (IResource) theResource;
@@ -598,7 +603,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, String theObjectNameOrNull,
-			boolean theContainedResource, boolean theSubResource, IIdType theResourceId) throws IOException {
+																 boolean theContainedResource, boolean theSubResource, IIdType theResourceId) throws IOException {
 		if (!theContainedResource) {
 			super.containResourcesForEncoding(theResource);
 		}
@@ -612,28 +617,28 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		}
 
 		write(theEventWriter, "resourceType", resDef.getName());
-    if (theResourceId != null && theResourceId.hasIdPart()) {
+		if (theResourceId != null && theResourceId.hasIdPart()) {
-      write(theEventWriter, "id", theResourceId.getIdPart());
+			write(theEventWriter, "id", theResourceId.getIdPart());
-      final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
+			final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
-      final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
+			final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
-      // Undeclared extensions
+			// Undeclared extensions
-      extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null);
+			extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null);
-      boolean haveExtension = false;
+			boolean haveExtension = false;
-      if (!extensions.isEmpty()) {
+			if (!extensions.isEmpty()) {
-        haveExtension = true;
+				haveExtension = true;
-      }
+			}
 
-      if (theResourceId.hasFormatComment() || haveExtension) {
+			if (theResourceId.hasFormatComment() || haveExtension) {
-        beginObject(theEventWriter, "_id");
+				beginObject(theEventWriter, "_id");
-        if (theResourceId.hasFormatComment()) {
+				if (theResourceId.hasFormatComment()) {
-          writeCommentsPreAndPost(theResourceId, theEventWriter);
+					writeCommentsPreAndPost(theResourceId, theEventWriter);
-        }
+				}
-        if (haveExtension) {
+				if (haveExtension) {
-          writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
+					writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
-        }
+				}
-        theEventWriter.endObject();
+				theEventWriter.endObject();
-      }
+			}
-    }
+		}
 
 		if (theResource instanceof IResource) {
 			IResource resource = (IResource) theResource;
@@ -695,19 +700,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 			}
 		}
 
-		if (theResource instanceof IBaseBinary) {
+		encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
-			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);
-			}
-		} else {
-			encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
-		}
 
 		theEventWriter.endObject();
 	}
@@ -720,7 +713,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	 * @param theParent
 	 */
 	private void extractAndWriteExtensionsAsDirectChild(IBase theElement, JsonLikeWriter theEventWriter, BaseRuntimeElementDefinition<?> theElementDef, RuntimeResourceDefinition theResDef,
-			IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent) throws IOException {
+																		 IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent) throws IOException {
 		List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
 		List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
 
@@ -737,7 +730,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void extractDeclaredExtensions(IBase theResource, BaseRuntimeElementDefinition<?> resDef, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions,
-			CompositeChildElement theChildElem) {
+														CompositeChildElement theChildElem) {
 		for (RuntimeChildDeclaredExtensionDefinition nextDef : resDef.getExtensionsNonModifier()) {
 			for (IBase nextValue : nextDef.getAccessor().getValues(theResource)) {
 				if (nextValue != null) {
@@ -761,7 +754,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void extractUndeclaredExtensions(IBase theElement, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions, CompositeChildElement theChildElem,
-			CompositeChildElement theParent) {
+														  CompositeChildElement theParent) {
 		if (theElement instanceof ISupportsUndeclaredExtensions) {
 			ISupportsUndeclaredExtensions element = (ISupportsUndeclaredExtensions) theElement;
 			List<ExtensionDt> ext = element.getUndeclaredExtensions();
@@ -1029,78 +1022,78 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		}
 	}
 
-  private void parseExtension(ParserState<?> theState, JsonLikeArray theValues, boolean theIsModifier) {
+	private void parseExtension(ParserState<?> theState, JsonLikeArray theValues, boolean theIsModifier) {
-    int allUnderscoreNames = 0;
+		int allUnderscoreNames = 0;
-    int handledUnderscoreNames = 0;
+		int handledUnderscoreNames = 0;
 
-    for (int i = 0; i < theValues.size(); i++) {
+		for (int i = 0; i < theValues.size(); i++) {
-      JsonLikeObject nextExtObj = JsonLikeValue.asObject(theValues.get(i));
+			JsonLikeObject nextExtObj = JsonLikeValue.asObject(theValues.get(i));
-      JsonLikeValue jsonElement = nextExtObj.get("url");
+			JsonLikeValue jsonElement = nextExtObj.get("url");
-      String url;
+			String url;
-      if (null == jsonElement || !(jsonElement.isScalar())) {
+			if (null == jsonElement || !(jsonElement.isScalar())) {
-        String parentElementName;
+				String parentElementName;
-        if (theIsModifier) {
+				if (theIsModifier) {
-          parentElementName = "modifierExtension";
+					parentElementName = "modifierExtension";
-        } else {
+				} else {
-          parentElementName = "extension";
+					parentElementName = "extension";
-        }
+				}
-        getErrorHandler().missingRequiredElement(new ParseLocation(parentElementName), "url");
+				getErrorHandler().missingRequiredElement(new ParseLocation(parentElementName), "url");
-        url = null;
+				url = null;
-      } else {
+			} else {
-        url = getExtensionUrl(jsonElement.getAsString());
+				url = getExtensionUrl(jsonElement.getAsString());
-      }
+			}
-      theState.enteringNewElementExtension(null, url, theIsModifier, getServerBaseUrl());
+			theState.enteringNewElementExtension(null, url, theIsModifier, getServerBaseUrl());
-      for (String next : nextExtObj.keySet()) {
+			for (String next : nextExtObj.keySet()) {
-        if ("url".equals(next)) {
+				if ("url".equals(next)) {
-          continue;
+					continue;
-        } else if ("extension".equals(next)) {
+				} else if ("extension".equals(next)) {
-          JsonLikeArray jsonVal = JsonLikeValue.asArray(nextExtObj.get(next));
+					JsonLikeArray jsonVal = JsonLikeValue.asArray(nextExtObj.get(next));
-          parseExtension(theState, jsonVal, false);
+					parseExtension(theState, jsonVal, false);
-        } else if ("modifierExtension".equals(next)) {
+				} else if ("modifierExtension".equals(next)) {
-          JsonLikeArray jsonVal = JsonLikeValue.asArray(nextExtObj.get(next));
+					JsonLikeArray jsonVal = JsonLikeValue.asArray(nextExtObj.get(next));
-          parseExtension(theState, jsonVal, true);
+					parseExtension(theState, jsonVal, true);
-        } else if (next.charAt(0) == '_') {
+				} else if (next.charAt(0) == '_') {
-          allUnderscoreNames++;
+					allUnderscoreNames++;
-          continue;
+					continue;
-        } else {
+				} else {
-          JsonLikeValue jsonVal = nextExtObj.get(next);
+					JsonLikeValue jsonVal = nextExtObj.get(next);
-          String alternateName = '_' + next;
+					String alternateName = '_' + next;
-          JsonLikeValue alternateVal = nextExtObj.get(alternateName);
+					JsonLikeValue alternateVal = nextExtObj.get(alternateName);
-          if (alternateVal != null) {
+					if (alternateVal != null) {
-            handledUnderscoreNames++;
+						handledUnderscoreNames++;
-          }
+					}
-          parseChildren(theState, next, jsonVal, alternateVal, alternateName, false);
+					parseChildren(theState, next, jsonVal, alternateVal, alternateName, false);
-        }
+				}
-      }
+			}
 
       /*
-       * This happens if an element has an extension but no actual value. I.e.
+		 * This happens if an element has an extension but no actual value. I.e.
 		   * if a resource has a "_status" element but no corresponding "status"
 		   * element. This could be used to handle a null value with an extension
 		   * for example.
 		  */
-      if (allUnderscoreNames > handledUnderscoreNames) {
+			if (allUnderscoreNames > handledUnderscoreNames) {
-        for (String alternateName : nextExtObj.keySet()) {
+				for (String alternateName : nextExtObj.keySet()) {
-          if (alternateName.startsWith("_") && alternateName.length() > 1) {
+					if (alternateName.startsWith("_") && alternateName.length() > 1) {
-            JsonLikeValue nextValue = nextExtObj.get(alternateName);
+						JsonLikeValue nextValue = nextExtObj.get(alternateName);
-            if (nextValue != null) {
+						if (nextValue != null) {
-              if (nextValue.isObject()) {
+							if (nextValue.isObject()) {
-                String nextName = alternateName.substring(1);
+								String nextName = alternateName.substring(1);
-                if (nextExtObj.get(nextName) == null) {
+								if (nextExtObj.get(nextName) == null) {
-                  theState.enteringNewElement(null, nextName);
+									theState.enteringNewElement(null, nextName);
-                  parseAlternates(nextValue, theState, alternateName, alternateName);
+									parseAlternates(nextValue, theState, alternateName, alternateName);
-                  theState.endingElement();
+									theState.endingElement();
-                }
+								}
-              } else {
+							} else {
-                getErrorHandler().incorrectJsonType(null, alternateName, ValueType.OBJECT, null, nextValue.getJsonType(), null);
+								getErrorHandler().incorrectJsonType(null, alternateName, ValueType.OBJECT, null, nextValue.getJsonType(), null);
-              }
+							}
-             }
+						}
-          }
+					}
-        }
+				}
-      }
+			}
-      theState.endingElement();
+			theState.endingElement();
-    }
+		}
-  }
+	}
 
 	private void parseFhirComments(JsonLikeValue theObject, ParserState<?> theState) {
 		if (theObject.isArray()) {
@@ -1254,7 +1247,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	}
 
 	private void writeExtensionsAsDirectChild(IBaseResource theResource, JsonLikeWriter theEventWriter, RuntimeResourceDefinition resDef, List<HeldExtension> extensions,
-			List<HeldExtension> modifierExtensions) throws IOException {
+															List<HeldExtension> modifierExtensions) throws IOException {
 		if (extensions.isEmpty() == false) {
 			beginArray(theEventWriter, "extension");
 			for (HeldExtension next : extensions) {
@@ -1328,6 +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);
@@ -1367,7 +1382,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				} else {
 					String childName = myDef.getChildNameByDatatype(myValue.getClass());
 					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName, false, false, myParent, false);
-          managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName);
+					managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName);
 				}
 
 				theEventWriter.endObject();
@@ -1422,34 +1437,12 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					throw new ConfigurationException("Unable to encode extension, unregognized child element type: " + value.getClass().getCanonicalName());
 				}
 				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, true, false, myParent, false);
-        managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName);
+				managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName);
 			}
 
 			// theEventWriter.name(myUndeclaredExtension.get);
 
 			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/parser/ParserState.java

@@ -606,7 +606,7 @@ class ParserState<T> {
 				return;
 			}
 			case RESOURCE: {
-				if (myInstance instanceof IAnyResource || myInstance instanceof IBaseBackboneElement) {
+				if (myInstance instanceof IAnyResource || myInstance instanceof IBaseBackboneElement || myInstance instanceof IBaseElement) {
 					ParserState<T>.PreResourceStateHl7Org state = new PreResourceStateHl7Org(myInstance, child.getMutator(), null);
 					push(state);
 				} else {
@@ -1559,7 +1559,8 @@ class ParserState<T> {
 
 			if (theEvent.isEndElement()) {
 				if (myDepth == 0) {
-					myDt.setValue(myEvents);
+					String eventsAsString = XmlUtil.encode(myEvents);
+					myDt.setValue(eventsAsString);
 					doPop();
 				}
 			}

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

@@ -24,6 +24,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.io.Reader;
+import java.io.StringReader;
 import java.io.Writer;
 import java.util.*;
 
@@ -605,13 +606,16 @@ public class XmlParser extends BaseParser /* implements IParser */ {
 		}
 	}
 
+
 	private void encodeXhtml(XhtmlDt theDt, XMLStreamWriter theEventWriter) throws XMLStreamException {
 		if (theDt == null || theDt.getValue() == null) {
 			return;
 		}
 
+		List<XMLEvent> events = XmlUtil.parse(theDt.getValue());
 		boolean firstElement = true;
-		for (XMLEvent event : theDt.getValue()) {
+
+		for (XMLEvent event : events) {
 			switch (event.getEventType()) {
 			case XMLStreamConstants.ATTRIBUTE:
 				Attribute attr = (Attribute) event;

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

@@ -31,6 +31,16 @@ public class Constants {
 	public static final String CHARSET_NAME_UTF8 = "UTF-8";
 	public static final Charset CHARSET_UTF8;
 	public static final String CHARSET_UTF8_CTSUFFIX = "; charset=" + CHARSET_NAME_UTF8;
+	/**
+	 * Contains a standard set of headers which are used by FHIR / HAPI FHIR, and therefore
+	 * would make a useful set for CORS AllowedHeader declarations
+	 */
+	public static final Set<String> CORS_ALLOWED_HEADERS;
+	/**
+	 * Contains a standard set of HTTP Methods which are used by FHIR / HAPI FHIR, and therefore
+	 * would make a useful set for CORS AllowedMethod declarations
+	 */
+	public static final Set<String> CORS_ALLWED_METHODS;
 	public static final String CT_FHIR_JSON = "application/json+fhir";
 	public static final String CT_FHIR_JSON_NEW = "application/fhir+json";
 	public static final String CT_FHIR_XML = "application/xml+fhir";
@@ -176,12 +186,13 @@ public class Constants {
 	public static final String URL_TOKEN_METADATA = "metadata";
 	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);
 
-		HashMap<Integer, String> statusNames = new HashMap<Integer, String>();
+		HashMap<Integer, String> statusNames = new HashMap<>();
-
 		statusNames.put(200, "OK");
 		statusNames.put(201, "Created");
 		statusNames.put(202, "Accepted");
@@ -246,11 +257,31 @@ public class Constants {
 		statusNames.put(511, "Network Authentication Required");
 		HTTP_STATUS_NAMES = Collections.unmodifiableMap(statusNames);
 		
-		Set<String> formatsHtml = new HashSet<String>();
+		Set<String> formatsHtml = new HashSet<>();
 		formatsHtml.add(CT_HTML);
 		formatsHtml.add(FORMAT_HTML);
 		FORMATS_HTML = Collections.unmodifiableSet(formatsHtml);
 
+		// *********************************************************
+		// Update CorsInterceptor's constructor documentation if you change these:
+		// *********************************************************
+		HashSet<String> corsAllowedHeaders = new HashSet<>();
+		corsAllowedHeaders.add("Accept");
+		corsAllowedHeaders.add("Access-Control-Request-Headers");
+		corsAllowedHeaders.add("Access-Control-Request-Method");
+		corsAllowedHeaders.add("Cache-Control");
+		corsAllowedHeaders.add("Content-Type");
+		corsAllowedHeaders.add("Origin");
+		corsAllowedHeaders.add("Prefer");
+		corsAllowedHeaders.add("X-Requested-With");
+		CORS_ALLOWED_HEADERS = Collections.unmodifiableSet(corsAllowedHeaders);
+
+		// *********************************************************
+		// Update CorsInterceptor's constructor documentation if you change these:
+		// *********************************************************
+		HashSet<String> corsAllowedMethods = new HashSet<>();
+		corsAllowedMethods.addAll(Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH"));
+		CORS_ALLWED_METHODS = Collections.unmodifiableSet(corsAllowedMethods);
 	}
 
 }

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

@@ -35,7 +35,7 @@ public interface IVersionSpecificBundleFactory {
 
 	void addResourcesToBundle(List<IBaseResource> theResult, BundleTypeEnum theBundleType, String theServerBase, BundleInclusionRule theBundleInclusionRule, Set<Include> theIncludes);
 
-	void addRootPropertiesToBundle(String theAuthor, String theServerBase, String theLinkSelf, String theLinkPrev, String theLinkNext, Integer theTotalResults, BundleTypeEnum theBundleType, IPrimitiveType<Date> theLastUpdated);
+	void addRootPropertiesToBundle(String theId, String theServerBase, String theLinkSelf, String theLinkPrev, String theLinkNext, Integer theTotalResults, BundleTypeEnum theBundleType, IPrimitiveType<Date> theLastUpdated);
 
 	IBaseResource getResourceBundle();
 

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

@@ -0,0 +1,47 @@
+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");
+		IBaseReference retVal = null;
+		if (child != null) {
+			List<IBase> values = child.getAccessor().getValues(theBinary);
+			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-base/src/main/java/ca/uhn/fhir/util/PortUtil.java

@@ -21,12 +21,14 @@ package ca.uhn.fhir.util;
  */
 
 import java.net.ServerSocket;
+import java.util.LinkedHashSet;
 
 /**
  * Provides server ports
  */
 @CoverageIgnore
 public class PortUtil {
+	private static LinkedHashSet<Integer> ourPorts = new LinkedHashSet<>();
 
 	/*
 	 * Non instantiable
@@ -41,9 +43,13 @@ public class PortUtil {
 	public static int findFreePort() {
 		ServerSocket server;
 		try {
-			server = new ServerSocket(0);
+			int port;
-			int port = server.getLocalPort();
+			do {
-			server.close();
+				server = new ServerSocket(0);
+				port = server.getLocalPort();
+				server.close();
+			} while (!ourPorts.add(port));
+
 			Thread.sleep(500);
 			return port;
 		} catch (Exception e) {

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

@@ -20,26 +20,27 @@ package ca.uhn.fhir.util;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.i18n.HapiLocalizer;
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
+import ch.qos.logback.classic.LoggerContext;
+import org.slf4j.LoggerFactory;
+
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
 import java.util.Arrays;
 import java.util.Locale;
 import java.util.TimeZone;
 
-import org.slf4j.LoggerFactory;
+import static org.apache.commons.lang3.StringUtils.defaultString;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.i18n.HapiLocalizer;
-import ch.qos.logback.classic.Level;
-import ch.qos.logback.classic.Logger;
-import ch.qos.logback.classic.LoggerContext;
 
 public class TestUtil {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestUtil.class);
 
 	/**
 	 * <b>THIS IS FOR UNIT TESTS ONLY - DO NOT CALL THIS METHOD FROM USER CODE</b>
-	 * 
+	 * <p>
 	 * When we run the unit tests in cobertura, JUnit doesn't seem to clean up static fields which leads to
 	 * tons of memory being used by the end and the JVM crashes in Travis. Manually clearing all of the
 	 * static fields seems to solve this.
@@ -104,7 +105,7 @@ public class TestUtil {
 	 * environment
 	 */
 	public static void randomizeLocale() {
-		Locale[] availableLocales = { Locale.CANADA, Locale.GERMANY, Locale.TAIWAN };
+		Locale[] availableLocales = {Locale.CANADA, Locale.GERMANY, Locale.TAIWAN};
 		Locale.setDefault(availableLocales[(int) (Math.random() * availableLocales.length)]);
 		ourLog.info("Tests are running in locale: " + Locale.getDefault().getDisplayName());
 		if (Math.random() < 0.5) {
@@ -116,10 +117,19 @@ public class TestUtil {
 			System.setProperty("file.encoding", "UTF-8");
 			System.setProperty("line.separator", "\n");
 		}
-		String availableTimeZones[] = { "GMT+08:00", "GMT-05:00", "GMT+00:00", "GMT+03:30" };
+		String availableTimeZones[] = {"GMT+08:00", "GMT-05:00", "GMT+00:00", "GMT+03:30"};
 		String timeZone = availableTimeZones[(int) (Math.random() * availableTimeZones.length)];
 		TimeZone.setDefault(TimeZone.getTimeZone(timeZone));
 		ourLog.info("Tests are using time zone: {}", TimeZone.getDefault().getID());
 	}
 
+	/**
+	 * <b>THIS IS FOR UNIT TESTS ONLY - DO NOT CALL THIS METHOD FROM USER CODE</b>
+	 * <p>
+	 * Strip \r chars from a string to account for line ending platform differences
+	 */
+	public static String stripReturns(String theString) {
+		return defaultString(theString).replace("\r", "");
+	}
+
 }

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

@@ -0,0 +1,57 @@
+package ca.uhn.fhir.util;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2017 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.Reader;
+import java.io.StringReader;
+
+public class XmlDetectionUtil {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(XmlDetectionUtil.class);
+	private static Boolean ourStaxPresent;
+
+	/**
+	 * This method will return <code>true</code> if a StAX XML parsing library is present
+	 * on the classpath
+	 */
+	public static boolean isStaxPresent() {
+		Boolean retVal = ourStaxPresent;
+		if (retVal == null) {
+			try {
+				Class.forName("javax.xml.stream.events.XMLEvent");
+				Class<?> xmlUtilClazz = Class.forName("ca.uhn.fhir.util.XmlUtil");
+				xmlUtilClazz.getMethod("createXmlReader", Reader.class).invoke(xmlUtilClazz, new StringReader(""));
+				ourStaxPresent = Boolean.TRUE;
+				retVal = Boolean.TRUE;
+			} catch (Throwable t) {
+				ourLog.info("StAX not detected on classpath, XML processing will be disabled");
+				ourStaxPresent = Boolean.FALSE;
+				retVal = Boolean.FALSE;
+			}
+		}
+		return retVal;
+	}
+
+	
+}

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

@@ -20,12 +20,13 @@ package ca.uhn.fhir.util;
  * #L%
  */
 import java.io.*;
-import java.util.Collections;
+import java.util.*;
-import java.util.HashMap;
-import java.util.Map;
 
 import javax.xml.stream.*;
+import javax.xml.stream.events.XMLEvent;
 
+import ca.uhn.fhir.model.primitive.XhtmlDt;
+import ca.uhn.fhir.parser.DataFormatException;
 import org.apache.commons.lang3.StringEscapeUtils;
 import org.codehaus.stax2.XMLOutputFactory2;
 import org.codehaus.stax2.io.EscapingWriterFactory;
@@ -37,21 +38,22 @@ import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.util.jar.DependencyLogFactory;
 import ca.uhn.fhir.util.jar.IDependencyLog;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
 /**
  * Utility methods for working with the StAX API.
  * 
  * This class contains code adapted from the Apache Axiom project.
  */
 public class XmlUtil {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlUtil.class);
+	private static final Map<String, Integer> VALID_ENTITY_NAMES;
+	private static final ExtendedEntityReplacingXmlResolver XML_RESOLVER = new ExtendedEntityReplacingXmlResolver();
 	private static XMLOutputFactory ourFragmentOutputFactory;
 	private static volatile boolean ourHaveLoggedStaxImplementation;
 	private static volatile XMLInputFactory ourInputFactory;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlUtil.class);
 	private static Throwable ourNextException;
 	private static volatile XMLOutputFactory ourOutputFactory;
-	private static Boolean ourStaxPresent;
-	private static final Map<String, Integer> VALID_ENTITY_NAMES;
-	private static final ExtendedEntityReplacingXmlResolver XML_RESOLVER = new ExtendedEntityReplacingXmlResolver();
 
 	static {
 		HashMap<String, Integer> validEntityNames = new HashMap<String, Integer>(1448);
@@ -1567,6 +1569,30 @@ public class XmlUtil {
 		return retVal;
 	}
 
+	/**
+	 * Encode a set of StAX events into a String
+	 */
+	public static String encode(List<XMLEvent> theEvents) {
+		try {
+			StringWriter w = new StringWriter();
+			XMLEventWriter ew = XmlUtil.createXmlFragmentWriter(w);
+
+			for (XMLEvent next : theEvents) {
+				if (next.isCharacters()) {
+					ew.add(next);
+				} else {
+					ew.add(next);
+				}
+			}
+			ew.close();
+			return w.toString();
+		} catch (XMLStreamException e) {
+			throw new DataFormatException("Problem with the contained XML events", e);
+		} catch (FactoryConfigurationError e) {
+			throw new ConfigurationException(e);
+		}
+	}
+
 	private static XMLOutputFactory getOrCreateFragmentOutputFactory() throws FactoryConfigurationError {
 		XMLOutputFactory retVal = ourFragmentOutputFactory;
 		if (retVal == null) {
@@ -1652,6 +1678,7 @@ public class XmlUtil {
 		return ourOutputFactory;
 	}
 
+
 	private static void logStaxImplementation(Class<?> theClass) {
 		IDependencyLog logger = DependencyLogFactory.createJarLogger();
 		if (logger != null) {
@@ -1683,6 +1710,49 @@ public class XmlUtil {
 		return outputFactory;
 	}
 
+	/**
+	 * Parses an XML string into a set of StAX events
+	 */
+	public static List<XMLEvent> parse(String theValue) {
+		if (isBlank(theValue)) {
+			return Collections.emptyList();
+		}
+
+		String val = theValue.trim();
+		if (!val.startsWith("<")) {
+			val = XhtmlDt.DIV_OPEN_FIRST + val + "</div>";
+		}
+		boolean hasProcessingInstruction = val.startsWith("<?");
+		if (hasProcessingInstruction && val.endsWith("?>")) {
+			return null;
+		}
+
+
+		try {
+			ArrayList<XMLEvent> value = new ArrayList<>();
+			StringReader reader = new StringReader(val);
+			XMLEventReader er = XmlUtil.createXmlReader(reader);
+			boolean first = true;
+			while (er.hasNext()) {
+				XMLEvent next = er.nextEvent();
+				if (first) {
+					first = false;
+					continue;
+				}
+				if (er.hasNext()) {
+					// don't add the last event
+					value.add(next);
+				}
+			}
+			return value;
+
+		} catch (XMLStreamException e) {
+			throw new DataFormatException("String does not appear to be valid XML/XHTML (error is \"" + e.getMessage() + "\"): " + theValue, e);
+		} catch (FactoryConfigurationError e) {
+			throw new ConfigurationException(e);
+		}
+	}
+
 	/**
 	 * FOR UNIT TESTS ONLY - Throw this exception for the next operation
 	 */
@@ -1712,26 +1782,6 @@ public class XmlUtil {
 		}
 	}
 	
-	/**
-	 * This method will return <code>true</code> if a StAX XML parsing library is present
-	 * on the classpath 
-	 */
-	public static boolean isStaxPresent() {
-		Boolean retVal = ourStaxPresent;
-		if (retVal == null) {
-			try {
-				newInputFactory();
-				ourStaxPresent = Boolean.TRUE;
-				retVal = Boolean.TRUE;
-			} catch (ConfigurationException e) {
-				ourLog.info("StAX not detected on classpath, XML processing will be disabled");
-				ourStaxPresent = Boolean.FALSE;
-				retVal = Boolean.FALSE;
-			}
-		}
-		return retVal;
-	}
-	
 	public static class MyEscaper implements EscapingWriterFactory {
 
 		@Override

hapi-fhir-base/src/main/java/org/hl7/fhir/exceptions/DefinitionException.java

@@ -1,44 +0,0 @@
-package org.hl7.fhir.exceptions;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2017 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-public class DefinitionException extends FHIRException {
-
-	private static final long serialVersionUID = 8175803009974854088L;
-
-	public DefinitionException() {
-		super();
-	}
-
-	public DefinitionException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-	public DefinitionException(String message) {
-		super(message);
-	}
-
-	public DefinitionException(Throwable cause) {
-		super(cause);
-	}
-
-}

hapi-fhir-base/src/main/java/org/hl7/fhir/exceptions/FHIRException.java

@@ -1,46 +0,0 @@
-package org.hl7.fhir.exceptions;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2017 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-public class FHIRException extends Exception {
-
-	// Note that the 4-argument constructor has been removed as it is not JDK6 compatible
-	
-	private static final long serialVersionUID = -1793365096090608037L;
-
-	public FHIRException() {
-		super();
-	}
-
-	public FHIRException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-	public FHIRException(String message) {
-		super(message);
-	}
-
-	public FHIRException(Throwable cause) {
-		super(cause);
-	}
-
-}

hapi-fhir-base/src/main/java/org/hl7/fhir/exceptions/FHIRFormatError.java

@@ -1,44 +0,0 @@
-package org.hl7.fhir.exceptions;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2017 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-public class FHIRFormatError extends FHIRException {
-
-	private static final long serialVersionUID = 1L;
-
-	public FHIRFormatError() {
-		super();
-	}
-
-	public FHIRFormatError(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-	public FHIRFormatError(String message) {
-		super(message);
-	}
-
-	public FHIRFormatError(Throwable cause) {
-		super(cause);
-	}
-
-}

hapi-fhir-base/src/main/java/org/hl7/fhir/exceptions/NoTerminologyServiceException.java

@@ -1,44 +0,0 @@
-package org.hl7.fhir.exceptions;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2017 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-public class NoTerminologyServiceException extends FHIRException {
-
-	private static final long serialVersionUID = 8196224236579018584L;
-
-	public NoTerminologyServiceException() {
-		super();
-	}
-
-	public NoTerminologyServiceException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-	public NoTerminologyServiceException(String message) {
-		super(message);
-	}
-
-	public NoTerminologyServiceException(Throwable cause) {
-		super(cause);
-	}
-
-}

hapi-fhir-base/src/main/java/org/hl7/fhir/exceptions/PathEngineException.java

@@ -1,44 +0,0 @@
-package org.hl7.fhir.exceptions;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2017 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-public class PathEngineException extends FHIRException {
-
-	private static final long serialVersionUID = -8550234068917355391L;
-
-	public PathEngineException() {
-		super();
-	}
-
-	public PathEngineException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-	public PathEngineException(String message) {
-		super(message);
-	}
-
-	public PathEngineException(Throwable cause) {
-		super(cause);
-	}
-
-}

hapi-fhir-base/src/main/java/org/hl7/fhir/exceptions/TerminologyServiceException.java

@@ -1,44 +0,0 @@
-package org.hl7.fhir.exceptions;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2017 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-public class TerminologyServiceException extends FHIRException {
-
-	private static final long serialVersionUID = -1547510329455394225L;
-
-	public TerminologyServiceException() {
-		super();
-	}
-
-	public TerminologyServiceException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-	public TerminologyServiceException(String message) {
-		super(message);
-	}
-
-	public TerminologyServiceException(Throwable cause) {
-		super(cause);
-	}
-
-}

hapi-fhir-base/src/main/java/org/hl7/fhir/exceptions/UcumException.java

@@ -1,44 +0,0 @@
-package org.hl7.fhir.exceptions;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2017 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-public class UcumException extends FHIRException {
-
-	private static final long serialVersionUID = -8535757334881835619L;
-
-	public UcumException() {
-		super();
-	}
-
-	public UcumException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-	public UcumException(String message) {
-		super(message);
-	}
-
-	public UcumException(Throwable cause) {
-		super(cause);
-	}
-
-}

hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/IgPackUploader.java

@@ -73,6 +73,7 @@ public class IgPackUploader extends BaseCommand {
 							.and(StructureDefinition.URL.matches().value(nextResourceUrl))
 							.execute();
 					}
+					break;
 				default:
 					throw new ParseException("This command does not support FHIR version " + ctx.getVersion().getVersion());
 			}

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

@@ -1,28 +1,36 @@
 package ca.uhn.fhir.jpa.demo;
 
-import java.util.*;
-
-import javax.servlet.ServletException;
-
-import org.springframework.web.context.ContextLoaderListener;
-import org.springframework.web.context.WebApplicationContext;
-import org.springframework.web.cors.CorsConfiguration;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
 import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
-import ca.uhn.fhir.jpa.provider.dstu3.*;
+import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
-import ca.uhn.fhir.jpa.provider.r4.*;
+import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
+import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
+import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
+import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
+import ca.uhn.fhir.jpa.provider.r4.TerminologyUploaderProviderR4;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.api.EncodingEnum;
-import ca.uhn.fhir.rest.server.*;
+import ca.uhn.fhir.rest.server.ETagSupportEnum;
+import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import org.springframework.web.context.ContextLoaderListener;
+import org.springframework.web.context.WebApplicationContext;
+import org.springframework.web.cors.CorsConfiguration;
+
+import javax.servlet.ServletException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
 
 public class JpaServerDemo extends RestfulServer {
 
@@ -134,19 +142,7 @@ public class JpaServerDemo extends RestfulServer {
 		setPagingProvider(new FifoMemoryPagingProvider(10));
 
 		// Register a CORS filter
-		CorsConfiguration config = new CorsConfiguration();
+		CorsInterceptor corsInterceptor = new CorsInterceptor();
-		CorsInterceptor corsInterceptor = new CorsInterceptor(config);
-		config.addAllowedHeader("x-fhir-starter");
-		config.addAllowedHeader("Origin");
-		config.addAllowedHeader("Accept");
-		config.addAllowedHeader("X-Requested-With");
-		config.addAllowedHeader("Content-Type");
-		config.addAllowedHeader("Access-Control-Request-Method");
-		config.addAllowedHeader("Access-Control-Request-Headers");
-		config.addAllowedOrigin("*");
-		config.addExposedHeader("Location");
-		config.addExposedHeader("Content-Location");
-		config.setAllowedMethods(Arrays.asList("GET","POST","PUT","DELETE","OPTIONS"));
 		registerInterceptor(corsInterceptor);
 
 		/*

hapi-fhir-client-okhttp/pom.xml

@@ -59,6 +59,11 @@
 		</dependency>
 
 		<!-- Unit test dependencies -->
+      <dependency>
+         <groupId>org.codehaus.woodstox</groupId>
+         <artifactId>woodstox-core-asl</artifactId>
+         <scope>test</scope>
+      </dependency>
 		<dependency>
 			<groupId>com.google.guava</groupId>
 			<artifactId>guava</artifactId>

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/apache/ApacheHttpResponse.java

@@ -98,24 +98,23 @@ public class ApacheHttpResponse implements IHttpResponse {
 		}
 		if (charset == null) {
 			if (Constants.STATUS_HTTP_204_NO_CONTENT != myResponse.getStatusLine().getStatusCode()) {
-				ourLog.warn("Response did not specify a charset.");
+				ourLog.debug("Response did not specify a charset, defaulting to utf-8");
 			}
 			charset = Charset.forName("UTF-8");
 		}
 
-		Reader reader = new InputStreamReader(readEntity(), charset);
+		return new InputStreamReader(readEntity(), charset);
-		return reader;
 	}
 
 	@Override
 	public Map<String, List<String>> getAllHeaders() {
-		Map<String, List<String>> headers = new HashMap<String, List<String>>();
+		Map<String, List<String>> headers = new HashMap<>();
 		if (myResponse.getAllHeaders() != null) {
 			for (Header next : myResponse.getAllHeaders()) {
 				String name = next.getName().toLowerCase();
 				List<String> list = headers.get(name);
 				if (list == null) {
-					list = new ArrayList<String>();
+					list = new ArrayList<>();
 					headers.put(name, list);
 				}
 				list.add(next.getValue());
@@ -131,7 +130,7 @@ public class ApacheHttpResponse implements IHttpResponse {
 		if (headers == null) {
 			headers = new Header[0];
 		}
-		List<String> retVal = new ArrayList<String>();
+		List<String> retVal = new ArrayList<>();
 		for (Header next : headers) {
 			retVal.add(next.getValue());
 		}

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/impl/BaseClient.java

@@ -35,6 +35,7 @@ import java.util.Map;
 import java.util.Set;
 
 import ca.uhn.fhir.rest.api.CacheControlDirective;
+import ca.uhn.fhir.util.XmlDetectionUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
@@ -110,7 +111,7 @@ public abstract class BaseClient implements IRestfulClient {
 			setKeepResponses(true);
 		}
 
-		if (XmlUtil.isStaxPresent() == false) {
+		if (XmlDetectionUtil.isStaxPresent() == false) {
 			myEncoding = EncodingEnum.JSON;
 		}
 

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/impl/RestfulClientFactory.java

@@ -330,6 +330,8 @@ public abstract class RestfulClientFactory implements IRestfulClientFactory {
 				serverFhirVersionEnum = FhirVersionEnum.DSTU2_1;
 			} else if (serverFhirVersionString.equals(FhirVersionEnum.DSTU3.getFhirVersionString())) {
 				serverFhirVersionEnum = FhirVersionEnum.DSTU3;
+			} else if (serverFhirVersionString.equals(FhirVersionEnum.R4.getFhirVersionString())) {
+				serverFhirVersionEnum = FhirVersionEnum.R4;
 			} else {
 				// we'll be lenient and accept this
 				ourLog.debug("Server conformance statement indicates unknown FHIR version: {}", serverFhirVersionString);

hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_14_40.java

@@ -1346,7 +1346,7 @@ public class VersionConvertor_14_40 {
     org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionSlicingComponent tgt = new org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionSlicingComponent();
     copyElement(src, tgt);
     for (org.hl7.fhir.dstu2016may.model.StringType t : src.getDiscriminator())
-      tgt.addDiscriminator(ProfileUtilities.interpretR2Discriminator(t.getValue()));
+      tgt.addDiscriminator(ProfileUtilities.interpretR2Discriminator(t.getValue(), true));
     if (src.hasDescription())
       tgt.setDescription(src.getDescription());
     if (src.hasOrdered())

hapi-fhir-converter/src/main/java/org/hl7/fhir/utilities/OIDUtils.java

@@ -1,83 +0,0 @@
-package org.hl7.fhir.utilities;
-
-/*
- * #%L
- * HAPI FHIR - Converter
- * %%
- * Copyright (C) 2014 - 2017 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-public class OIDUtils {
-
-	/*
-  2.16.840.1.113883.3.72.5.2 - NIST owns this
-  2.16.840.1.113883.4.6 - National Provider Identifier
-  2.16.840.1.113883.6.21 - UB92
-  2.16.840.1.113883.6.69 - NDC
-	 */
-
-	public static String getUriForOid(String r) {
-		if (r.equals("2.16.840.1.113883.6.96"))
-			return "http://snomed.info/sct";
-		if (r.equals("2.16.840.1.113883.6.1"))
-			return "http://loinc.org";
-		if (r.equals("2.16.840.1.113883.6.8"))
-			return "http://unitsofmeasure.org";
-		if (r.equals("2.16.840.1.113883.6.3"))
-			return "http://hl7.org/fhir/sid/icd-10";
-		if (r.equals("2.16.840.1.113883.6.42"))
-			return "http://hl7.org/fhir/sid/icd-9";
-		if (r.equals("2.16.840.1.113883.6.104"))
-			return "http://hl7.org/fhir/sid/icd-9";
-		if (r.equals("2.16.840.1.113883.6.103"))
-			return "http://hl7.org/fhir/sid/icd-9"; //todo: confirm this		
-		if (r.equals("2.16.840.1.113883.6.73"))
-			return "http://hl7.org/fhir/sid/atc";
-		if (r.equals("2.16.840.1.113883.3.26.1.1"))
-			return "http://ncimeta.nci.nih.gov";
-		if (r.equals("2.16.840.1.113883.3.26.1.1.1"))
-			return "http://ncimeta.nci.nih.gov";
-		if (r.equals("2.16.840.1.113883.6.88"))
-			return "http://www.nlm.nih.gov/research/umls/rxnorm"; // todo: confirm this
-
-		if (r.equals("2.16.840.1.113883.5.1008"))
-			return "http://hl7.org/fhir/v3/NullFlavor";
-		if (r.equals("2.16.840.1.113883.5.111"))
-			return "http://hl7.org/fhir/v3/RoleCode";
-		if (r.equals("2.16.840.1.113883.5.4"))
-			return "http://hl7.org/fhir/v3/ActCode";
-		if (r.equals("2.16.840.1.113883.5.8"))
-			return "http://hl7.org/fhir/v3/ActReason";
-		if (r.equals("2.16.840.1.113883.5.83"))
-			return "http://hl7.org/fhir/v3/ObservationInterpretation";
-		if (r.equals("2.16.840.1.113883.6.238"))
-			return "http://hl7.org/fhir/v3/Race";
-
-		if (r.equals("2.16.840.1.113883.6.59"))
-			return "http://hl7.org/fhir/sid/cvx";
-		if (r.equals("2.16.840.1.113883.12.292"))
-			return "http://hl7.org/fhir/sid/cvx";
-
-		if (r.equals("2.16.840.1.113883.6.12"))
-			return "http://www.ama-assn.org/go/cpt";
-
-		if (r.startsWith("2.16.840.1.113883.12."))
-			return "http://hl7.org/fhir/sid/v2-"+r.substring(21);
-		return null;
-	}
-
-}

hapi-fhir-converter/src/main/java/org/hl7/fhir/utilities/ucum/UcumService.java

@@ -1,193 +0,0 @@
-package org.hl7.fhir.utilities.ucum;
-
-/*
- * #%L
- * HAPI FHIR - Converter
- * %%
- * Copyright (C) 2014 - 2017 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-/*******************************************************************************
- * Crown Copyright (c) 2006+, Copyright (c) 2006 - 2014 Kestral Computing & Health Intersections.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License v1.0
- * which accompanies this distribution, and is available at
- * http://www.eclipse.org/legal/epl-v10.html
- * 
- * Contributors:
- *    Kestral Computing P/L - initial implementation
- *    Health Intersections - ongoing maintenance
- *******************************************************************************/
-
-import java.util.Date;
-import java.util.List;
-import java.util.Set;
-
-import org.hl7.fhir.exceptions.UcumException;
-
-
-/**
- * General Ucum Service
- * 
- * UCUM functionality that is useful for applications that make use of UCUM codes
- * 
- * This is a tightly bound interface - consumers use the internal model classes
- * 
- * @author Grahame Grieve
- *
- */
-public interface UcumService {
-
-	public class UcumVersionDetails {
-		private Date releaseDate;
-		private String version;
-		/**
-		 * @param releaseDate
-		 * @param version
-		 */
-		public UcumVersionDetails(Date releaseDate, String version) {
-			super();
-			this.releaseDate = releaseDate;
-			this.version = version;
-		}
-		/**
-		 * @return the releaseDate
-		 */
-		public Date getReleaseDate() {
-			return releaseDate;
-		}
-		/**
-		 * @return the version
-		 */
-		public String getVersion() {
-			return version;
-		}
-		
-	}
-	
-	/**
-	 * return Ucum Identification details for the version in use
-	 */
-	public abstract UcumVersionDetails ucumIdentification();
-
-
-	/**
-	 * Check UCUM. Note that this stands as a test of the service
-	 * more than UCUM itself (for version 1.7, there are no known
-	 * semantic errors in UCUM). But you should always run this test at least
-	 * once with the version of UCUM you are using to ensure that 
-	 * the service implementation correctly understands the UCUM data
-	 * to which it is bound
-	 *   
-	 * @return a list of internal errors in the UCUM spec.
-	 * 
-	 */
-	public abstract List<String> validateUCUM();
-
-
-	/**
-	 * return a list of the defined types of units in this UCUM version
-	 * 
-	 * @return
-	 */
-	public abstract Set<String> getProperties();
-
-	/**
-	 * validate whether a unit code are valid UCUM units
-	 *  
-	 * @param units - the unit code to check
-	 * @return nil if valid, or an error message describing the problem
-	 */
-	public abstract String validate(String unit);
-
-	/**
-	 * given a unit, return a formal description of what the units stand for using
-	 * full names 
-	 * @param units the unit code
-	 * @return formal description
-	 * @throws UcumException 
-	 * @throws OHFException 
-	 */
-	public String analyse(String unit) throws UcumException ;
-	
-	/**
-	 * validate whether a units are valid UCUM units and additionally require that the 
-	 * units from a particular property
-	 *  
-	 * @param units - the unit code to check
-	 * @return nil if valid, or an error message describing the problem
-	 */
-	public abstract String validateInProperty(String unit, String property);
-
-	/**
-	 * validate whether a units are valid UCUM units and additionally require that the 
-	 * units match a particular base canonical unit
-	 *  
-	 * @param units - the unit code to check
-	 * @return nil if valid, or an error message describing the problem
-	 */
-	public abstract String validateCanonicalUnits(String unit, String canonical);
-
-	/**
-	 * given a set of units, return their canonical form
-	 * @param unit
-	 * @return the canonical form
-	 * @throws UcumException 
-	 * @throws OHFException 
-	 */
-	public abstract String getCanonicalUnits(String unit) throws UcumException ;
-
-  /**
-   * given two pairs of units, return true if they sahre the same canonical base
-   * 
-   * @param units1
-   * @param units2
-   * @return
-   * @throws UcumException 
-   * @ 
-   */
-  public abstract boolean isComparable(String units1, String units2) throws UcumException ;
-  
-
-	/**
-	 * given a value and source unit, return the value in the given dest unit
-	 * an exception is thrown if the conversion is not possible
-	 * 
-	 * @param value
-	 * @param sourceUnit
-	 * @param destUnit
-	 * @return the value if a conversion is possible
-	 * @throws UcumException 
-	 * @throws OHFException
-	 */
-	public abstract Decimal convert(Decimal value, String sourceUnit, String destUnit) throws UcumException ;
-
-
-
-	/**
-	 * given a set of UCUM units, return a likely preferred human dense form
-	 * 
-	 * SI units - as is. 
-	 * Other units - improved by manual fixes, or the removal of [] 
-	 * 
-	 * @param code
-	 * @return the preferred human display form
-	 */
-	public abstract String getCommonDisplay(String code);
-
-
-
-}

hapi-fhir-jacoco/pom.xml

@@ -1,8 +1,13 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+			xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
-	<!-- The parent of this project is the deployable POM. This project isn't deployable, but this keeps it before the root pom in the reactor order when building the site. I don't know why this works... 
+	<!--
-		Need to investigate this. -->
+	The parent of this project is the deployable POM. This project isn't
+	deployable, but this keeps it before the root pom in the reactor
+	order when building the site. I don't know why this works...
+	Need to investigate this.
+	-->
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
@@ -225,14 +230,14 @@
 			<artifactId>spring-web</artifactId>
 		</dependency>
 
-      <!--
+		<!--
       For some reason JavaDoc crashed during site generation unless we have this dependency
       -->
-      <dependency>
+		<dependency>
-          <groupId>javax.interceptor</groupId>
+			<groupId>javax.interceptor</groupId>
-          <artifactId>javax.interceptor-api</artifactId>
+			<artifactId>javax.interceptor-api</artifactId>
-          <scope>provided</scope>
+			<scope>provided</scope>
-      </dependency>
+		</dependency>
 
 
 	</dependencies>
@@ -253,6 +258,13 @@
 			</plugins>
 		</pluginManagement>
 		<plugins>
+			<plugin>
+				<groupId>org.basepom.maven</groupId>
+				<artifactId>duplicate-finder-maven-plugin</artifactId>
+				<configuration>
+					<skip>true</skip>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>org.jacoco</groupId>
 				<artifactId>jacoco-maven-plugin</artifactId>
@@ -285,19 +297,17 @@
 							</fileSets>
 						</configuration>
 					</execution>
-<execution>
+					<execution>
-            <id>post-integration-test</id>
+						<id>post-integration-test</id>
-					<phase>install</phase>
+						<phase>install</phase>
-            <goals>
+						<goals>
-					<goal>report</goal>
+							<goal>report</goal>
-            </goals>
+						</goals>
-            <configuration>
+						<configuration>
-					<dataFile>${project.build.directory}/jacoco.exec</dataFile>
+							<dataFile>${project.build.directory}/jacoco.exec</dataFile>
-               <outputDirectory>${project.reporting.outputDirectory}/jacoco-report</outputDirectory>
+							<outputDirectory>${project.reporting.outputDirectory}/jacoco-report</outputDirectory>
-            </configuration>
+						</configuration>
-        </execution>
+					</execution>
-
-
 				</executions>
 			</plugin>
 			<plugin>

hapi-fhir-jaxrsserver-base/pom.xml

@@ -74,6 +74,11 @@
 		</dependency>
 
 		<!-- Unit test dependencies -->
+      <dependency>
+         <groupId>org.codehaus.woodstox</groupId>
+         <artifactId>woodstox-core-asl</artifactId>
+         <scope>test</scope>
+      </dependency>
 		<dependency>
 			<groupId>com.google.guava</groupId>
 			<artifactId>guava</artifactId>

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/client/JaxRsRestfulClientFactory.java

@@ -34,12 +34,14 @@ import ca.uhn.fhir.rest.client.impl.RestfulClientFactory;
 
 /**
  * A Restful Client Factory, based on Jax Rs
- * 
+ * Default Jax-Rs client is NOT thread safe in static context, you should create a new factory every time or
+ * use a specific Jax-Rs client implementation which managed connection pool. 
  * @author Peter Van Houte | peter.vanhoute@agfa.com | Agfa Healthcare
  */
 public class JaxRsRestfulClientFactory extends RestfulClientFactory {
 
 	private Client myNativeClient;
+  private List<Class<?>> registeredComponents;
   
 	/**
 	 * Constructor. Note that you must set the {@link FhirContext} manually using {@link #setFhirContext(FhirContext)} if this constructor is used!
@@ -64,6 +66,12 @@ public class JaxRsRestfulClientFactory extends RestfulClientFactory {
 			myNativeClient = builder.build();
 		}
 
+    if (registeredComponents != null && !registeredComponents.isEmpty()) {
+      for (Class<?> c : registeredComponents) {
+        myNativeClient = myNativeClient.register(c);
+      }
+    }
+
 		return myNativeClient;
 	}
 
@@ -73,29 +81,46 @@ public class JaxRsRestfulClientFactory extends RestfulClientFactory {
 		return new JaxRsHttpClient(client, url, theIfNoneExistParams, theIfNoneExistString, theRequestType, theHeaders);
 	}
 
+  /***
+  * Not supported with default Jax-Rs client implementation
+  * @param theHost
+  *            The host (or null to disable proxying, as is the default)
+  * @param thePort
+  */
 	@Override
 	public void setProxy(String theHost, Integer thePort) {
 		throw new UnsupportedOperationException("Proxies are not supported yet in JAX-RS client");
 	}
   
-	/**
+  /**
-	 * Only accept clients of type javax.ws.rs.client.Client
+  * Only accept clients of type javax.ws.rs.client.Client
-	 * 
+  * Can be used to set a specific Client implementation
-	 * @param theHttpClient
+  * @param theHttpClient
-	 */
+  */
 	@Override
 	public synchronized void setHttpClient(Object theHttpClient) {
 		this.myNativeClient = (Client) theHttpClient;
 	}
 
+  /**
+  * Register a list of Jax-Rs component (provider, filter...)
+  * @param components list of Jax-Rs components to register
+  */
+  public void register(List<Class<?>> components) {
+    registeredComponents = components;
+  }
+
+
 	@Override
 	protected JaxRsHttpClient getHttpClient(String theServerBase) {
 		return new JaxRsHttpClient(getNativeClientClient(), new StringBuilder(theServerBase), null, null, null, null);
 	}
   
-	@Override
+  @Override
-	protected void resetHttpClient() {
+  protected void resetHttpClient() {
-		this.myNativeClient = null;
+    if (myNativeClient != null) 
-	}
+      myNativeClient.close(); // close client to avoid memory leak
+    myNativeClient = null;
+  }
 
 }

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/JaxRsRestfulClientFactoryTest.java

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.jaxrs.client;
+
+import ca.uhn.fhir.context.FhirContext;
+import org.junit.Before;
+import org.junit.Test;
+
+import javax.ws.rs.client.Client;
+import java.util.ArrayList;
+import java.util.Arrays;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+/**
+ * Created by Sebastien Riviere on 31/07/2017.
+ */
+public class JaxRsRestfulClientFactoryTest {
+
+    private final FhirContext context = FhirContext.forDstu2();
+    private JaxRsRestfulClientFactory factory;
+
+    @Before
+    public void setUp() {
+        factory = new JaxRsRestfulClientFactory(context);
+    }
+
+    @Test
+    public void emptyConstructorTest() {
+        assertNotNull(new JaxRsRestfulClientFactory());
+    }
+
+    @Test
+    public void getDefaultNativeClientTest() {
+        assertNotNull(factory.getNativeClientClient());
+    }
+
+    @Test
+    public void getNativeClientEmptyRegisteredComponentListTest() {
+        factory.register(new ArrayList<Class<?>>());
+        final Client result = factory.getNativeClientClient();
+        assertNotNull(result);
+        assertTrue(result.getConfiguration().getClasses().isEmpty());
+    }
+
+    @Test
+    public void getNativeClientRegisteredComponentListTest() {
+        factory.register(Arrays.asList(MyFilter.class, String.class));
+        final Client result = factory.getNativeClientClient();
+        assertNotNull(result);
+        assertEquals(1, result.getConfiguration().getClasses().size());
+    }
+}

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/MyFilter.java

@@ -0,0 +1,18 @@
+package ca.uhn.fhir.jaxrs.client;
+
+import javax.ws.rs.client.ClientRequestContext;
+import javax.ws.rs.client.ClientResponseContext;
+import javax.ws.rs.client.ClientResponseFilter;
+import javax.ws.rs.ext.Provider;
+import java.io.IOException;
+
+/**
+ * Created by Sebastien Riviere on 31/07/2017.
+ */
+@Provider
+public class MyFilter implements ClientResponseFilter {
+    @Override
+    public void filter(final ClientRequestContext requestContext, final ClientResponseContext responseContext) throws IOException {
+
+    }
+}

hapi-fhir-jpaserver-base/pom.xml

@@ -1,4 +1,4 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
@@ -32,6 +32,12 @@
 			<version>3.5</version>
 		</dependency>
 -->
+
+		<dependency>
+			<groupId>org.codehaus.woodstox</groupId>
+			<artifactId>woodstox-core-asl</artifactId>
+     </dependency>
+
 		<dependency>
 			<groupId>net.sf.saxon</groupId>
 			<artifactId>Saxon-HE</artifactId>
@@ -105,10 +111,12 @@
 			<version>${project.version}</version>
 		</dependency>
 
+		<!--
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>jcl-over-slf4j</artifactId>
 		</dependency>
+		-->
 
 		<dependency>
 			<groupId>ch.qos.logback</groupId>
@@ -163,7 +171,7 @@
 			<artifactId>thymeleaf-spring4</artifactId>
 		</dependency>
 
-		<!-- For UCUM -->
+		<!-- For UCUM: TODO we should replace this with org.fhir UCUM -->
 		<dependency>
 			<groupId>org.jscience</groupId>
 			<artifactId>jscience</artifactId>
@@ -233,10 +241,12 @@
 		<!-- <dependency> <groupId>org.hsqldb</groupId> <artifactId>hsqldb</artifactId> <version>2.3.2</version> </dependency> -->
 
 		<!-- Spring -->
+		<!--
 		<dependency>
 			<groupId>aopalliance</groupId>
 			<artifactId>aopalliance</artifactId>
 		</dependency>
+		-->
 		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-core</artifactId>
@@ -358,6 +368,7 @@
 		<dependency>
 			<groupId>javax.mail</groupId>
 			<artifactId>javax.mail-api</artifactId>
+			<scope>provided</scope>
 		</dependency>
 		<dependency>
 			<groupId>com.sun.mail</groupId>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
 import ca.uhn.fhir.jpa.search.*;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.sp.SearchParamPresenceSvcImpl;
+import ca.uhn.fhir.jpa.subscription.email.SubscriptionEmailInterceptor;
 import ca.uhn.fhir.jpa.subscription.resthook.SubscriptionRestHookInterceptor;
 import ca.uhn.fhir.jpa.subscription.websocket.SubscriptionWebsocketInterceptor;
 import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
@@ -93,15 +94,6 @@ public class BaseConfig implements SchedulingConfigurer {
 		return new StaleSearchDeletingSvcImpl();
 	}
 
-	// @PostConstruct
-	// public void wireResourceDaos() {
-	// Map<String, IDao> daoBeans = myAppCtx.getBeansOfType(IDao.class);
-	// List bean = myAppCtx.getBean("myResourceProvidersDstu2", List.class);
-	// for (IDao next : daoBeans.values()) {
-	// next.setResourceDaos(bean);
-	// }
-	// }
-
 	@Bean
 	@Lazy
 	public SubscriptionRestHookInterceptor subscriptionRestHookInterceptor() {
@@ -114,15 +106,23 @@ public class BaseConfig implements SchedulingConfigurer {
 		return new SubscriptionWebsocketInterceptor();
 	}
 
+	/**
+	 * Note: If you're going to use this, you need to provide a bean
+	 * of type {@link ca.uhn.fhir.jpa.subscription.email.IEmailSender}
+	 * in your own Spring config
+	 */
+	@Bean
+	@Lazy
+	public SubscriptionEmailInterceptor subscriptionEmailInterceptor() {
+		return new SubscriptionEmailInterceptor();
+	}
+
 	@Bean
 	public TaskScheduler taskScheduler() {
 		ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
 		retVal.setConcurrentExecutor(scheduledExecutorService().getObject());
 		retVal.setScheduledExecutor(scheduledExecutorService().getObject());
 		return retVal;
-//		ThreadPoolTaskScheduler retVal = new ThreadPoolTaskScheduler();
-//		retVal.setPoolSize(5);
-//		return retVal;
 	}
 
 	/**

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

@@ -29,7 +29,6 @@ import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.jpa.util.DeleteConflict;
-import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.model.api.*;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
@@ -51,10 +50,7 @@ import ca.uhn.fhir.rest.server.exceptions.*;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
-import ca.uhn.fhir.util.CoverageIgnore;
+import ca.uhn.fhir.util.*;
-import ca.uhn.fhir.util.FhirTerser;
-import ca.uhn.fhir.util.OperationOutcomeUtil;
-import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Sets;
@@ -2044,7 +2040,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		StringBuilder b = new StringBuilder();
 		if (theResource instanceof IResource) {
 			IResource resource = (IResource) theResource;
-			List<XMLEvent> xmlEvents = resource.getText().getDiv().getValue();
+			List<XMLEvent> xmlEvents = XmlUtil.parse(resource.getText().getDiv().getValue());
 			if (xmlEvents != null) {
 				for (XMLEvent next : xmlEvents) {
 					if (next.isCharacters()) {
@@ -2057,8 +2053,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			IDomainResource resource = (IDomainResource) theResource;
 			try {
 				String divAsString = resource.getText().getDivAsString();
-				XhtmlDt xhtml = new XhtmlDt(divAsString);
+				List<XMLEvent> xmlEvents = XmlUtil.parse(divAsString);
-				List<XMLEvent> xmlEvents = xhtml.getValue();
 				if (xmlEvents != null) {
 					for (XMLEvent next : xmlEvents) {
 						if (next.isCharacters()) {

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

@@ -30,6 +30,7 @@ import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils;
@@ -61,6 +62,7 @@ import org.springframework.transaction.annotation.Transactional;
 import javax.annotation.PostConstruct;
 import javax.persistence.NoResultException;
 import javax.persistence.TypedQuery;
+import javax.servlet.http.HttpServletResponse;
 import java.util.*;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -894,6 +896,12 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Transactional(propagation = Propagation.SUPPORTS)
 	@Override
 	public IBundleProvider search(final SearchParameterMap theParams, RequestDetails theRequestDetails) {
+		return search(theParams, theRequestDetails, null);
+	}
+
+	@Transactional(propagation = Propagation.SUPPORTS)
+	@Override
+	public IBundleProvider search(final SearchParameterMap theParams, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
 
 		if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.DISABLED) {
 			for (List<List<? extends IQueryParameterType>> nextAnds : theParams.values()) {
@@ -930,7 +938,19 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			cacheControlDirective.parse(theRequestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL));
 		}
 
-		return mySearchCoordinatorSvc.registerSearch(this, theParams, getResourceName(), cacheControlDirective);
+		IBundleProvider retVal = mySearchCoordinatorSvc.registerSearch(this, theParams, getResourceName(), cacheControlDirective);
+
+		if (retVal instanceof PersistedJpaBundleProvider) {
+			PersistedJpaBundleProvider provider = (PersistedJpaBundleProvider) retVal;
+			if (provider.isCacheHit()) {
+				if (theServletResponse != null && theRequestDetails != null) {
+					String value = "HIT from " + theRequestDetails.getFhirServerBase();
+					theServletResponse.addHeader(Constants.HEADER_X_CACHE, value);
+				}
+			}
+		}
+
+		return retVal;
 	}
 
 	@Override

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

@@ -108,6 +108,7 @@ public class DaoConfig {
 	private Set<String> myTreatReferencesAsLogical = new HashSet<String>(DEFAULT_LOGICAL_BASE_URLS);
 	private boolean myAutoCreatePlaceholderReferenceTargets;
 	private Integer myCacheControlNoStoreMaxResultsUpperLimit = 1000;
+	private Integer myCountSearchResultsUpTo = null;
 
 	/**
 	 * Constructor
@@ -152,6 +153,56 @@ public class DaoConfig {
 		myCacheControlNoStoreMaxResultsUpperLimit = theCacheControlNoStoreMaxResults;
 	}
 
+	/**
+	 * When searching, if set to a non-null value (default is <code>null</code>) the
+	 * search coordinator will attempt to find at least this many results
+	 * before returning a response to the client. This parameter mainly affects
+	 * whether a "total count" is included in the response bundle for searches that
+	 * return large amounts of data.
+	 * <p>
+	 *    For a search that returns 10000 results, if this value is set to
+	 *    10000 the search coordinator will find all 10000 results
+	 *    prior to returning, so the initial response bundle will have the
+	 *    total set to 10000. If this value is null (or less than 10000)
+	 *    the response bundle will likely return slightly faster, but will
+	 *    not include the total. Subsequent page requests will likely
+	 *    include the total however, if they are performed after the
+	 *    search coordinator has found all results.
+	 * </p>
+	 * <p>
+	 *    Set this value to <code>0</code> to always load all
+	 *    results before returning.
+	 * </p>
+	 */
+	public Integer getCountSearchResultsUpTo() {
+		return myCountSearchResultsUpTo;
+	}
+
+	/**
+	 * When searching, if set to a non-null value (default is <code>null</code>) the
+	 * search coordinator will attempt to find at least this many results
+	 * before returning a response to the client. This parameter mainly affects
+	 * whether a "total count" is included in the response bundle for searches that
+	 * return large amounts of data.
+	 * <p>
+	 *    For a search that returns 10000 results, if this value is set to
+	 *    10000 the search coordinator will find all 10000 results
+	 *    prior to returning, so the initial response bundle will have the
+	 *    total set to 10000. If this value is null (or less than 10000)
+	 *    the response bundle will likely return slightly faster, but will
+	 *    not include the total. Subsequent page requests will likely
+	 *    include the total however, if they are performed after the
+	 *    search coordinator has found all results.
+	 * </p>
+	 * <p>
+	 *    Set this value to <code>0</code> to always load all
+	 *    results before returning.
+	 * </p>
+	 */
+	public void setCountSearchResultsUpTo(Integer theCountSearchResultsUpTo) {
+		myCountSearchResultsUpTo = theCountSearchResultsUpTo;
+	}
+
 	/**
 	 * When a code system is added that contains more than this number of codes,
 	 * the code system will be indexed later in an incremental process in order to
@@ -357,11 +408,8 @@ public class DaoConfig {
 	/**
 	 * This may be used to optionally register server interceptors directly against the DAOs.
 	 */
-	public void setInterceptors(IServerInterceptor... theInterceptor) {
+	public void setInterceptors(List<IServerInterceptor> theInterceptors) {
-		setInterceptors(new ArrayList<IServerInterceptor>());
+		myInterceptors = theInterceptors;
-		if (theInterceptor != null && theInterceptor.length != 0) {
-			getInterceptors().addAll(Arrays.asList(theInterceptor));
-		}
 	}
 
 	/**
@@ -959,8 +1007,11 @@ public class DaoConfig {
 	/**
 	 * This may be used to optionally register server interceptors directly against the DAOs.
 	 */
-	public void setInterceptors(List<IServerInterceptor> theInterceptors) {
+	public void setInterceptors(IServerInterceptor... theInterceptor) {
-		myInterceptors = theInterceptors;
+		setInterceptors(new ArrayList<IServerInterceptor>());
+		if (theInterceptor != null && theInterceptor.length != 0) {
+			getInterceptors().addAll(Arrays.asList(theInterceptor));
+		}
 	}
 
 	/**

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

@@ -33,6 +33,10 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
+
+import javax.servlet.http.HttpServletResponse;
 
 public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 
@@ -179,6 +183,9 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 
 	IBundleProvider search(SearchParameterMap theParams, RequestDetails theRequestDetails);
 
+	@Transactional(propagation = Propagation.SUPPORTS)
+	IBundleProvider search(SearchParameterMap theParams, RequestDetails theRequestDetails, HttpServletResponse theServletResponse);
+
 	Set<Long> searchForIds(SearchParameterMap theParams);
 
 	/**

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

@@ -274,14 +274,6 @@ public class SearchParameterMap extends LinkedHashMap<String, List<List<? extend
 		return this;
 	}
 
-	/**
-	 * @deprecated As of HAPI FHIR 2.4 this method no longer does anything
-	 */
-	@Deprecated
-	public void setPersistResults(boolean thePersistResults) {
-		// does nothing as of HAPI FHIR 2.4
-	}
-
 	public void setRevIncludes(Set<Include> theRevIncludes) {
 		myRevIncludes = theRevIncludes;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java

@@ -29,6 +29,7 @@ import java.util.Map.Entry;
 import javax.persistence.TypedQuery;
 
 import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.rest.param.ParameterUtil;
 import org.apache.commons.lang3.Validate;
 import org.apache.http.NameValuePair;
 import org.hibernate.Session;
@@ -438,7 +439,11 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				DaoMethodOutcome outcome;
 				UrlParts parts = UrlUtil.parseUrl(url);
 				if (isNotBlank(parts.getResourceId())) {
-					res.setId(new IdType(parts.getResourceType(), parts.getResourceId()));
+					String version = null;
+					if (isNotBlank(nextReqEntry.getRequest().getIfMatch())) {
+						version = ParameterUtil.parseETagValue(nextReqEntry.getRequest().getIfMatch());
+					}
+					res.setId(new IdType(parts.getResourceType(), parts.getResourceId(), version));
 					outcome = resourceDao.update(res, null, false, theRequestDetails);
 				} else {
 					res.setId((String) null);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamRegistryDstu3.java

@@ -215,6 +215,9 @@ public class SearchParamRegistryDstu3 extends BaseSearchParamRegistry {
 			case RETIRED:
 				status = RuntimeSearchParamStatusEnum.RETIRED;
 				break;
+			case UNKNOWN:
+				status = RuntimeSearchParamStatusEnum.UNKNOWN;
+				break;
 			case NULL:
 				break;
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4.java

@@ -28,6 +28,7 @@ import java.util.Map.Entry;
 
 import javax.persistence.TypedQuery;
 
+import ca.uhn.fhir.rest.param.ParameterUtil;
 import org.apache.commons.lang3.Validate;
 import org.apache.http.NameValuePair;
 import org.hl7.fhir.r4.model.*;
@@ -435,7 +436,11 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				DaoMethodOutcome outcome;
 				UrlParts parts = UrlUtil.parseUrl(url);
 				if (isNotBlank(parts.getResourceId())) {
-					res.setId(new IdType(parts.getResourceType(), parts.getResourceId()));
+					String version = null;
+					if (isNotBlank(nextReqEntry.getRequest().getIfMatch())) {
+						version = ParameterUtil.parseETagValue(nextReqEntry.getRequest().getIfMatch());
+					}
+					res.setId(new IdType(parts.getResourceType(), parts.getResourceId(), version));
 					outcome = resourceDao.update(res, null, false, theRequestDetails);
 				} else {
 					res.setId((String) null);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/SearchParamRegistryR4.java

@@ -216,6 +216,9 @@ public class SearchParamRegistryR4 extends BaseSearchParamRegistry {
 			case RETIRED:
 				status = RuntimeSearchParamStatusEnum.RETIRED;
 				break;
+			case UNKNOWN:
+				status = RuntimeSearchParamStatusEnum.UNKNOWN;
+				break;
 			case NULL:
 				break;
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/JpaStorageServices.java

@@ -115,6 +115,8 @@ public class JpaStorageServices extends BaseHapiFhirDao<IBaseResource> implement
 						break;
 					case URI:
 						break;
+					case HAS:
+						break;
 				}
 
 				params.add(nextArgument.getName(), param);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/JpaSystemProviderDstu2.java

@@ -24,6 +24,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 import java.util.*;
 import java.util.Map.Entry;
 
+import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 
@@ -47,7 +48,7 @@ public class JpaSystemProviderDstu2 extends BaseJpaSystemProviderDstu2Plus<Bundl
 	@Qualifier("mySystemDaoDstu2")
 	private IFhirSystemDao<Bundle, MetaDt> mySystemDao;
 
-	@Autowired
+	@Autowired(required = false)
 	private IFulltextSearchSvc mySearchDao;
 	
 	//@formatter:off
@@ -178,6 +179,7 @@ public class JpaSystemProviderDstu2 extends BaseJpaSystemProviderDstu2Plus<Bundl
 			@OperationParam(name="searchParam", min=1, max=1) String theSearchParam,
 			@OperationParam(name="text", min=1, max=1) String theText
 		) {
+		JpaSystemProviderDstu3.validateFulltextSearchEnabled(mySearchDao);
 
 		if (isBlank(theContext)) {
 			throw new InvalidRequestException("Parameter 'context' must be provided");
@@ -193,11 +195,9 @@ public class JpaSystemProviderDstu2 extends BaseJpaSystemProviderDstu2Plus<Bundl
 		
 		Parameters retVal = new Parameters();
 		for (Suggestion next : keywords) {
-			//@formatter:off
 			retVal.addParameter()
 					.addPart(new Parameter().setName("keyword").setValue(new StringDt(next.getTerm())))
 					.addPart(new Parameter().setName("score").setValue(new DecimalDt(next.getScore())));
-			//@formatter:on
 		}
 
 		return retVal;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaSystemProviderDstu3.java

@@ -1,5 +1,27 @@
 package ca.uhn.fhir.jpa.provider.dstu3;
 
+import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl.Suggestion;
+import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
+import ca.uhn.fhir.jpa.provider.BaseJpaSystemProviderDstu2Plus;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.annotation.Transaction;
+import ca.uhn.fhir.rest.annotation.TransactionParam;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
 /*
@@ -21,23 +43,6 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
  * limitations under the License.
  * #L%
  */
-import java.util.*;
-import java.util.Map.Entry;
-
-import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
-
-import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl.Suggestion;
-import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
-import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
-import ca.uhn.fhir.jpa.provider.BaseJpaSystemProviderDstu2Plus;
-import ca.uhn.fhir.model.api.annotation.Description;
-import ca.uhn.fhir.rest.annotation.*;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 
 public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundle, Meta> {
 
@@ -45,106 +50,106 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
 	@Qualifier("mySystemDaoDstu3")
 	private IFhirSystemDao<Bundle, Meta> mySystemDao;
 
-	@Autowired
+	@Autowired(required = false)
 	private IFulltextSearchSvc mySearchDao;
 
 	//@formatter:off
 	// This is generated by hand:
 	// ls hapi-fhir-structures-dstu2/target/generated-sources/tinder/ca/uhn/fhir/model/dstu2/resource/ | sort | sed "s/.java//" | sed "s/^/@OperationParam(name=\"/" | sed "s/$/\", type=IntegerType.class, min=0, max=1),/"
-	@Operation(name="$get-resource-counts", idempotent=true, returnParameters= {
+	@Operation(name = "$get-resource-counts", idempotent = true, returnParameters = {
-		@OperationParam(name="AllergyIntolerance", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "AllergyIntolerance", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Appointment", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Appointment", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="AppointmentResponse", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "AppointmentResponse", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="AuditEvent", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "AuditEvent", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Basic", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Basic", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Binary", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Binary", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="BodySite", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "BodySite", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Bundle", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Bundle", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="CarePlan", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "CarePlan", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="CarePlan2", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "CarePlan2", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Claim", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Claim", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ClaimResponse", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ClaimResponse", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ClinicalImpression", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ClinicalImpression", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Communication", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Communication", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="CommunicationRequest", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "CommunicationRequest", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Composition", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Composition", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ConceptMap", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ConceptMap", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Condition", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Condition", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Conformance", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Conformance", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Contract", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Contract", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Contraindication", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Contraindication", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Coverage", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Coverage", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="DataElement", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "DataElement", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Device", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Device", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="DeviceComponent", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "DeviceComponent", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="DeviceMetric", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "DeviceMetric", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="DeviceUseRequest", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "DeviceUseRequest", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="DeviceUseStatement", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "DeviceUseStatement", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="DiagnosticOrder", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "DiagnosticOrder", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="DiagnosticReport", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "DiagnosticReport", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="DocumentManifest", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "DocumentManifest", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="DocumentReference", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "DocumentReference", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="EligibilityRequest", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "EligibilityRequest", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="EligibilityResponse", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "EligibilityResponse", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Encounter", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Encounter", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="EnrollmentRequest", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "EnrollmentRequest", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="EnrollmentResponse", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "EnrollmentResponse", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="EpisodeOfCare", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "EpisodeOfCare", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ExplanationOfBenefit", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ExplanationOfBenefit", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="FamilyMemberHistory", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "FamilyMemberHistory", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Flag", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Flag", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Goal", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Goal", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Group", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Group", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="HealthcareService", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "HealthcareService", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ImagingObjectSelection", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ImagingObjectSelection", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ImagingStudy", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ImagingStudy", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Immunization", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Immunization", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ImmunizationRecommendation", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ImmunizationRecommendation", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ListResource", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ListResource", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Location", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Location", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Media", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Media", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Medication", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Medication", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="MedicationAdministration", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "MedicationAdministration", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="MedicationDispense", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "MedicationDispense", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="MedicationPrescription", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "MedicationPrescription", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="MedicationStatement", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "MedicationStatement", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="MessageHeader", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "MessageHeader", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="NamingSystem", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "NamingSystem", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="NutritionOrder", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "NutritionOrder", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Observation", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Observation", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="OperationDefinition", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "OperationDefinition", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="OperationOutcome", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "OperationOutcome", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Order", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Order", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="OrderResponse", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "OrderResponse", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Organization", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Organization", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Parameters", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Parameters", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Patient", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Patient", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="PaymentNotice", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "PaymentNotice", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="PaymentReconciliation", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "PaymentReconciliation", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Person", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Person", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Practitioner", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Practitioner", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Procedure", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Procedure", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ProcedureRequest", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ProcedureRequest", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ProcessRequest", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ProcessRequest", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ProcessResponse", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ProcessResponse", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Provenance", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Provenance", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Questionnaire", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Questionnaire", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="QuestionnaireAnswers", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "QuestionnaireAnswers", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ReferralRequest", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ReferralRequest", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="RelatedPerson", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "RelatedPerson", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="RiskAssessment", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "RiskAssessment", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Schedule", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Schedule", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="SearchParameter", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "SearchParameter", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Slot", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Slot", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Specimen", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Specimen", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="StructureDefinition", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "StructureDefinition", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Subscription", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Subscription", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Substance", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Substance", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="Supply", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "Supply", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="ValueSet", type=IntegerType.class, min=0, max=1),
+		@OperationParam(name = "ValueSet", type = IntegerType.class, min = 0, max = 1),
-		@OperationParam(name="VisionPrescription", type=IntegerType.class, min=0, max=1)
+		@OperationParam(name = "VisionPrescription", type = IntegerType.class, min = 0, max = 1)
 	})
-	@Description(shortDefinition="Provides the number of resources currently stored on the server, broken down by resource type")
+	@Description(shortDefinition = "Provides the number of resources currently stored on the server, broken down by resource type")
 	//@formatter:on
 	public Parameters getResourceCounts() {
 		Parameters retVal = new Parameters();
@@ -159,8 +164,8 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
 	}
 
 	//@formatter:off
-	@Operation(name="$meta", idempotent=true, returnParameters= {
+	@Operation(name = "$meta", idempotent = true, returnParameters = {
-		@OperationParam(name="return", type=Meta.class)
+		@OperationParam(name = "return", type = Meta.class)
 	})
 	//@formatter:on
 	public Parameters meta(RequestDetails theRequestDetails) {
@@ -169,12 +174,13 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
 		return parameters;
 	}
 
-	@Operation(name="$suggest-keywords", idempotent=true)
+	@Operation(name = "$suggest-keywords", idempotent = true)
 	public Parameters suggestKeywords(
-			@OperationParam(name="context", min=1, max=1) String theContext,
+		@OperationParam(name = "context", min = 1, max = 1) String theContext,
-			@OperationParam(name="searchParam", min=1, max=1) String theSearchParam,
+		@OperationParam(name = "searchParam", min = 1, max = 1) String theSearchParam,
-			@OperationParam(name="text", min=1, max=1) String theText
+		@OperationParam(name = "text", min = 1, max = 1) String theText
-		) {
+	) {
+
 
 		if (isBlank(theContext)) {
 			throw new InvalidRequestException("Parameter 'context' must be provided");
@@ -192,8 +198,8 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
 		for (Suggestion next : keywords) {
 			//@formatter:off
 			retVal.addParameter()
-					.addPart(new ParametersParameterComponent().setName("keyword").setValue(new StringType(next.getTerm())))
+				.addPart(new ParametersParameterComponent().setName("keyword").setValue(new StringType(next.getTerm())))
-					.addPart(new ParametersParameterComponent().setName("score").setValue(new DecimalType(next.getScore())));
+				.addPart(new ParametersParameterComponent().setName("score").setValue(new DecimalType(next.getScore())));
 			//@formatter:on
 		}
 
@@ -210,4 +216,10 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
 		}
 	}
 
+	public static void validateFulltextSearchEnabled(IFulltextSearchSvc theSearchDao) {
+		if (theSearchDao == null || theSearchDao.isDisabled()) {
+			throw new InvalidRequestException("Fulltext searching is disabled on this server");
+		}
+	}
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/JpaSystemProviderR4.java

@@ -45,7 +45,7 @@ public class JpaSystemProviderR4 extends BaseJpaSystemProviderDstu2Plus<Bundle,
 	@Qualifier("mySystemDaoR4")
 	private IFhirSystemDao<Bundle, Meta> mySystemDao;
 
-	@Autowired
+	@Autowired(required = false)
 	private IFulltextSearchSvc mySearchDao;
 	
 	//@formatter:off
@@ -175,6 +175,7 @@ public class JpaSystemProviderR4 extends BaseJpaSystemProviderDstu2Plus<Bundle,
 			@OperationParam(name="searchParam", min=1, max=1) String theSearchParam,
 			@OperationParam(name="text", min=1, max=1) String theText
 		) {
+		ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3.validateFulltextSearchEnabled(mySearchDao);
 		
 		if (isBlank(theContext)) {
 			throw new InvalidRequestException("Parameter 'context' must be provided");

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

@@ -19,23 +19,32 @@ package ca.uhn.fhir.jpa.search;
  * limitations under the License.
  * #L%
  */
-import java.util.*;
-
-import javax.persistence.*;
-import javax.persistence.criteria.*;
-
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.TransactionStatus;
-import org.springframework.transaction.support.*;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.IDao;
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
 import ca.uhn.fhir.jpa.dao.data.ISearchDao;
-import ca.uhn.fhir.jpa.entity.*;
+import ca.uhn.fhir.jpa.entity.BaseHasResource;
+import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
+import ca.uhn.fhir.jpa.entity.Search;
+import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallback;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import javax.persistence.EntityManager;
+import javax.persistence.NoResultException;
+import javax.persistence.TypedQuery;
+import javax.persistence.criteria.CriteriaBuilder;
+import javax.persistence.criteria.CriteriaQuery;
+import javax.persistence.criteria.Predicate;
+import javax.persistence.criteria.Root;
+import java.util.*;
 
 public class PersistedJpaBundleProvider implements IBundleProvider {
 
@@ -47,6 +56,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 	private ISearchDao mySearchDao;
 	private Search mySearchEntity;
 	private String myUuid;
+	private boolean myCacheHit;
 
 	public PersistedJpaBundleProvider(String theSearchUuid, IDao theDao) {
 		myUuid = theSearchUuid;
@@ -179,17 +189,17 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		});
 
 		switch (mySearchEntity.getSearchType()) {
-		case HISTORY:
+			case HISTORY:
-			return template.execute(new TransactionCallback<List<IBaseResource>>() {
+				return template.execute(new TransactionCallback<List<IBaseResource>>() {
-				@Override
+					@Override
-				public List<IBaseResource> doInTransaction(TransactionStatus theStatus) {
+					public List<IBaseResource> doInTransaction(TransactionStatus theStatus) {
-					return doHistoryInTransaction(theFromIndex, theToIndex);
+						return doHistoryInTransaction(theFromIndex, theToIndex);
-				}
+					}
-			});
+				});
-		case SEARCH:
+			case SEARCH:
-		case EVERYTHING:
+			case EVERYTHING:
-		default:
+			default:
-			return doSearchOrEverything(theFromIndex, theToIndex);
+				return doSearchOrEverything(theFromIndex, theToIndex);
 		}
 	}
 
@@ -197,6 +207,14 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		return myUuid;
 	}
 
+	public boolean isCacheHit() {
+		return myCacheHit;
+	}
+
+	public void setCacheHit(boolean theCacheHit) {
+		myCacheHit = theCacheHit;
+	}
+
 	@Override
 	public Integer preferredPageSize() {
 		ensureSearchEntityLoaded();

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

@@ -67,8 +67,11 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
 
 	@Override
 	public Integer size() {
-		mySearchTask.awaitInitialSync();
+		Integer size = mySearchTask.awaitInitialSync();
 		SearchCoordinatorSvcImpl.verifySearchHasntFailedOrThrowInternalErrorException(mySearch);
+		if (size != null) {
+			return size;
+		}
 		return super.size();
 	}
 

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

@@ -17,7 +17,7 @@ package ca.uhn.fhir.jpa.search;
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- * #L%
+ * #L%family
  */
 import java.util.*;
 import java.util.concurrent.*;
@@ -184,6 +184,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		StopWatch w = new StopWatch();
 		final String searchUuid = UUID.randomUUID().toString();
 
+		ourLog.debug("Registering new search {}", searchUuid);
+
 		Class<? extends IBaseResource> resourceTypeClass = myContext.getResourceDefinition(theResourceType).getImplementingClass();
 		final ISearchBuilder sb = theCallingDao.newSearchBuilder();
 		sb.setType(resourceTypeClass, theResourceType);
@@ -204,6 +206,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 		if (theParams.isLoadSynchronous() || loadSynchronousUpTo != null) {
 
+			ourLog.debug("Search {} is loading in synchronous mode", searchUuid);
+
 			// Execute the query and make sure we return distinct results
 			TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
 			txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
@@ -281,6 +285,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 							mySearchDao.updateSearchLastReturned(searchToUse.getId(), new Date());
 
 							retVal = new PersistedJpaBundleProvider(searchToUse.getUuid(), theCallingDao);
+							retVal.setCacheHit(true);
+
 							populateBundleProvider(retVal);
 						}
 
@@ -437,7 +443,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			mySearchUuid = theSearchUuid;
 		}
 
-		public void awaitInitialSync() {
+		public Integer awaitInitialSync() {
 			ourLog.trace("Awaiting initial sync");
 			do {
 				try {
@@ -449,6 +455,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				}
 			} while (mySearch.getStatus() == SearchStatusEnum.LOADING);
 			ourLog.trace("Initial sync completed");
+
+			return mySearch.getTotalCount();
 		}
 
 		@Override
@@ -507,6 +515,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			}
 
 			myIdToSearchTask.remove(mySearch.getUuid());
+			myInitialCollectionLatch.countDown();
 			myCompletionLatch.countDown();
 			return null;
 		}
@@ -552,27 +561,27 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		public List<Long> getResourcePids(int theFromIndex, int theToIndex) {
 			ourLog.info("Requesting search PIDs from {}-{}", theFromIndex, theToIndex);
 
-			CountDownLatch latch = null;
+			boolean keepWaiting;
-			synchronized (mySyncedPids) {
+			do {
-				if (mySyncedPids.size() < theToIndex && mySearch.getStatus() == SearchStatusEnum.LOADING) {
+				synchronized (mySyncedPids) {
-					int latchSize = theToIndex - mySyncedPids.size();
+					keepWaiting = false;
-					ourLog.trace("Registering latch to await {} results (want {} total)", latchSize, theToIndex);
+					if (mySyncedPids.size() < theToIndex && mySearch.getStatus() == SearchStatusEnum.LOADING) {
-					latch = new CountDownLatch(latchSize);
+						keepWaiting = true;
-				}
-			}
-
-			if (latch != null) {
-				while (latch.getCount() > 0 && mySearch.getStatus() == SearchStatusEnum.LOADING) {
-					try {
-						ourLog.trace("Awaiting latch with {}", latch.getCount());
-						latch.await(500, TimeUnit.MILLISECONDS);
-					} catch (InterruptedException e) {
-						// ok
 					}
 				}
-			}
+				if (keepWaiting) {
+					ourLog.info("Waiting, as we only have {} results", mySyncedPids.size());
+					try {
+						Thread.sleep(500);
+					} catch (InterruptedException theE) {
+						// ignore
+					}
+				}
+			} while (keepWaiting);
 
-			ArrayList<Long> retVal = new ArrayList<Long>();
+			ourLog.info("Proceeding, as we have {} results", mySyncedPids.size());
+
+			ArrayList<Long> retVal = new ArrayList<>();
 			synchronized (mySyncedPids) {
 				verifySearchHasntFailedOrThrowInternalErrorException(mySearch);
 
@@ -585,6 +594,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				}
 			}
 
+			ourLog.info("Done syncing results", mySyncedPids.size());
+
 			return retVal;
 		}
 
@@ -633,8 +644,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 						myUnsyncedPids.clear();
 
 						if (theResultIter.hasNext() == false) {
-							mySearch.setStatus(SearchStatusEnum.FINISHED);
 							mySearch.setTotalCount(myCountSaved);
+							mySearch.setStatus(SearchStatusEnum.FINISHED);
 						}
 					}
 					mySearch.setNumFound(myCountSaved);
@@ -643,7 +654,16 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				}
 			});
 
-			myInitialCollectionLatch.countDown();
+			int numSynced;
+			synchronized (mySyncedPids) {
+				numSynced = mySyncedPids.size();
+			}
+
+			if (myDaoConfig.getCountSearchResultsUpTo() == null ||
+				myDaoConfig.getCountSearchResultsUpTo() <= 0 ||
+				myDaoConfig.getCountSearchResultsUpTo() <= numSynced) {
+				myInitialCollectionLatch.countDown();
+			}
 		}
 
 	}

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
@@ -46,35 +46,32 @@ 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;
 
 	private void deleteSearch(final Long theSearchPid) {
 		Search searchToDelete = mySearchDao.findOne(theSearchPid);
-		ourLog.info("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), searchToDelete.getCreated(), searchToDelete.getSearchLastReturned());
+		if (searchToDelete != null) {
-		mySearchIncludeDao.deleteForSearch(searchToDelete.getId());
+			ourLog.info("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), searchToDelete.getCreated(), searchToDelete.getSearchLastReturned());
-		mySearchResultDao.deleteForSearch(searchToDelete.getId());
+			mySearchIncludeDao.deleteForSearch(searchToDelete.getId());
-		mySearchDao.delete(searchToDelete);
+			mySearchResultDao.deleteForSearch(searchToDelete.getId());
+			mySearchDao.delete(searchToDelete);
+		}
 	}
 
 	@Override
@@ -85,7 +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);
 
@@ -129,4 +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/subscription/BaseSubscriptionInterceptor.java

@@ -156,13 +156,11 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
 				try {
 					from = subscription.getChannel().getExtensionString(JpaConstants.EXT_SUBSCRIPTION_EMAIL_FROM);
 					subjectTemplate = subscription.getChannel().getExtensionString(JpaConstants.EXT_SUBSCRIPTION_SUBJECT_TEMPLATE);
-					bodyTemplate = subscription.getChannel().getExtensionString(JpaConstants.EXT_SUBSCRIPTION_BODY_TEMPLATE);
 				} catch (FHIRException theE) {
 					throw new ConfigurationException("Failed to extract subscription extension(s): " + theE.getMessage(), theE);
 				}
 				retVal.getEmailDetails().setFrom(from);
 				retVal.getEmailDetails().setSubjectTemplate(subjectTemplate);
-				retVal.getEmailDetails().setBodyTemplate(bodyTemplate);
 			}
 
 		} catch (FHIRException theE) {
@@ -191,13 +189,11 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
 			try {
 				from = subscription.getChannel().getExtensionString(JpaConstants.EXT_SUBSCRIPTION_EMAIL_FROM);
 				subjectTemplate = subscription.getChannel().getExtensionString(JpaConstants.EXT_SUBSCRIPTION_SUBJECT_TEMPLATE);
-				bodyTemplate = subscription.getChannel().getExtensionString(JpaConstants.EXT_SUBSCRIPTION_BODY_TEMPLATE);
 			} catch (FHIRException theE) {
 				throw new ConfigurationException("Failed to extract subscription extension(s): " + theE.getMessage(), theE);
 			}
 			retVal.getEmailDetails().setFrom(from);
 			retVal.getEmailDetails().setSubjectTemplate(subjectTemplate);
-			retVal.getEmailDetails().setBodyTemplate(bodyTemplate);
 		}
 
 		List<org.hl7.fhir.r4.model.Extension> topicExts = subscription.getExtensionsByUrl("http://hl7.org/fhir/subscription/topics");
@@ -459,7 +455,7 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
 		}
 
 		if (mySubscriptionActivatingSubscriber == null) {
-			mySubscriptionActivatingSubscriber = new SubscriptionActivatingSubscriber(getSubscriptionDao(), getChannelType(), this);
+			mySubscriptionActivatingSubscriber = new SubscriptionActivatingSubscriber(getSubscriptionDao(), getChannelType(), this, myTxManager);
 		}
 
 		registerSubscriptionCheckingSubscriber();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/CanonicalSubscription.java

@@ -131,10 +131,12 @@ public class CanonicalSubscription implements Serializable {
 		return myHeaders;
 	}
 
-	public void setHeaders(String theHeaders) {
+	public void setHeaders(List<? extends IPrimitiveType<String>> theHeader) {
 		myHeaders = new ArrayList<>();
-		if (isNotBlank(theHeaders)) {
+		for (IPrimitiveType<String> next : theHeader) {
-			myHeaders.add(theHeaders);
+			if (isNotBlank(next.getValueAsString())) {
+				myHeaders.add(next.getValueAsString());
+			}
 		}
 	}
 
@@ -189,12 +191,10 @@ public class CanonicalSubscription implements Serializable {
 		}
 	}
 
-	public void setHeaders(List<? extends IPrimitiveType<String>> theHeader) {
+	public void setHeaders(String theHeaders) {
 		myHeaders = new ArrayList<>();
-		for (IPrimitiveType<String> next : theHeader) {
+		if (isNotBlank(theHeaders)) {
-			if (isNotBlank(next.getValueAsString())) {
+			myHeaders.add(theHeaders);
-				myHeaders.add(next.getValueAsString());
-			}
 		}
 	}
 
@@ -212,16 +212,6 @@ public class CanonicalSubscription implements Serializable {
 		private String myFrom;
 		@JsonProperty("subjectTemplate")
 		private String mySubjectTemplate;
-		@JsonProperty("bodyTemplate")
-		private String myBodyTemplate;
-
-		public String getBodyTemplate() {
-			return myBodyTemplate;
-		}
-
-		public void setBodyTemplate(String theBodyTemplate) {
-			myBodyTemplate = theBodyTemplate;
-		}
 
 		public String getFrom() {
 			return myFrom;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/SubscriptionActivatingSubscriber.java

@@ -27,20 +27,21 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.Subscription;
-import org.hl7.fhir.utilities.ucum.Canonical;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.messaging.Message;
 import org.springframework.messaging.MessagingException;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionSynchronizationAdapter;
 import org.springframework.transaction.support.TransactionSynchronizationManager;
-
+import org.springframework.transaction.support.TransactionTemplate;
-import java.util.concurrent.ConcurrentHashMap;
 
 @SuppressWarnings("unchecked")
 public class SubscriptionActivatingSubscriber {
 	private final IFhirResourceDao mySubscriptionDao;
 	private final BaseSubscriptionInterceptor mySubscriptionInterceptor;
+	private final PlatformTransactionManager myTransactionManager;
 	private Logger ourLog = LoggerFactory.getLogger(SubscriptionActivatingSubscriber.class);
 	private FhirContext myCtx;
 	private Subscription.SubscriptionChannelType myChannelType;
@@ -48,11 +49,12 @@ public class SubscriptionActivatingSubscriber {
 	/**
 	 * Constructor
 	 */
-	public SubscriptionActivatingSubscriber(IFhirResourceDao<? extends IBaseResource> theSubscriptionDao, Subscription.SubscriptionChannelType theChannelType, BaseSubscriptionInterceptor theSubscriptionInterceptor) {
+	public SubscriptionActivatingSubscriber(IFhirResourceDao<? extends IBaseResource> theSubscriptionDao, Subscription.SubscriptionChannelType theChannelType, BaseSubscriptionInterceptor theSubscriptionInterceptor, PlatformTransactionManager theTransactionManager) {
 		mySubscriptionDao = theSubscriptionDao;
 		mySubscriptionInterceptor = theSubscriptionInterceptor;
 		myChannelType = theChannelType;
 		myCtx = theSubscriptionDao.getContext();
+		myTransactionManager = theTransactionManager;
 	}
 
 	public void activateAndRegisterSubscriptionIfRequired(final IBaseResource theSubscription) {
@@ -67,15 +69,16 @@ public class SubscriptionActivatingSubscriber {
 		final String requestedStatus = Subscription.SubscriptionStatus.REQUESTED.toCode();
 		final String activeStatus = Subscription.SubscriptionStatus.ACTIVE.toCode();
 		if (requestedStatus.equals(statusString)) {
-			TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronizationAdapter() {
+			if (TransactionSynchronizationManager.isSynchronizationActive()) {
-				@Override
+				TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronizationAdapter() {
-				public void afterCommit() {
+					@Override
-					status.setValueAsString(activeStatus);
+					public void afterCommit() {
-					ourLog.info("Activating and registering subscription {} from status {} to {}", theSubscription.getIdElement().toUnqualified().getValue(), requestedStatus, activeStatus);
+						activateSubscription(status, activeStatus, theSubscription, requestedStatus);
-					mySubscriptionDao.update(theSubscription);
+					}
-					mySubscriptionInterceptor.registerSubscription(theSubscription.getIdElement(), theSubscription);
+				});
-				}
+			} else {
-			});
+				activateSubscription(status, activeStatus, theSubscription, requestedStatus);
+			}
 		} else if (activeStatus.equals(statusString)) {
 			if (!mySubscriptionInterceptor.hasSubscription(theSubscription.getIdElement())) {
 				ourLog.info("Registering active subscription {}", theSubscription.getIdElement().toUnqualified().getValue());
@@ -89,8 +92,15 @@ public class SubscriptionActivatingSubscriber {
 		}
 	}
 
+	private void activateSubscription(IPrimitiveType<?> theStatus, String theActiveStatus, IBaseResource theSubscription, String theRequestedStatus) {
+		theStatus.setValueAsString(theActiveStatus);
+		ourLog.info("Activating and registering subscription {} from status {} to {}", theSubscription.getIdElement().toUnqualified().getValue(), theRequestedStatus, theActiveStatus);
+		mySubscriptionDao.update(theSubscription);
+		mySubscriptionInterceptor.registerSubscription(theSubscription.getIdElement(), theSubscription);
+	}
 
-	public void handleMessage(RestOperationTypeEnum theOperationType, IIdType theId, IBaseResource theSubscription) throws MessagingException {
+
+	public void handleMessage(RestOperationTypeEnum theOperationType, IIdType theId, final IBaseResource theSubscription) throws MessagingException {
 
 		switch (theOperationType) {
 			case DELETE:
@@ -101,7 +111,15 @@ public class SubscriptionActivatingSubscriber {
 				if (!theId.getResourceType().equals("Subscription")) {
 					return;
 				}
-				activateAndRegisterSubscriptionIfRequired(theSubscription);
+				TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
+				txTemplate.execute(new TransactionCallbackWithoutResult() {
+					@Override
+					protected void doInTransactionWithoutResult(TransactionStatus status) {
+						activateAndRegisterSubscriptionIfRequired(theSubscription);
+					}
+				});
+				break;
+			default:
 				break;
 		}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/email/EmailDetails.java

@@ -20,6 +20,8 @@ package ca.uhn.fhir.jpa.subscription.email;
  * #L%
  */
 
+import org.hl7.fhir.instance.model.api.IIdType;
+
 import java.util.List;
 
 public class EmailDetails {
@@ -27,6 +29,7 @@ public class EmailDetails {
 	private String myBodyTemplate;
 	private List<String> myTo;
 	private String myFrom;
+	private IIdType mySubscription;
 
 	public String getBodyTemplate() {
 		return myBodyTemplate;
@@ -52,6 +55,14 @@ public class EmailDetails {
 		mySubjectTemplate = theSubjectTemplate;
 	}
 
+	public IIdType getSubscription() {
+		return mySubscription;
+	}
+
+	public void setSubscription(IIdType theSubscription) {
+		mySubscription = theSubscription;
+	}
+
 	public List<String> getTo() {
 		return myTo;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/email/JavaMailEmailSender.java

@@ -22,11 +22,11 @@ package ca.uhn.fhir.jpa.subscription.email;
 
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.mail.SimpleMailMessage;
-import org.springframework.mail.javamail.JavaMailSender;
 import org.springframework.mail.javamail.JavaMailSenderImpl;
 import org.thymeleaf.context.Context;
 import org.thymeleaf.spring4.SpringTemplateEngine;
@@ -35,6 +35,9 @@ import org.thymeleaf.templatemode.TemplateMode;
 import org.thymeleaf.templateresolver.StringTemplateResolver;
 
 import javax.annotation.PostConstruct;
+import javax.mail.Message;
+import javax.mail.MessagingException;
+import javax.mail.internet.MimeMessage;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
@@ -42,26 +45,57 @@ import java.util.List;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.apache.commons.lang3.StringUtils.trim;
 
-public class EmailSender implements IEmailSender {
+public class JavaMailEmailSender implements IEmailSender {
 
-	private static final Logger ourLog = LoggerFactory.getLogger(EmailSender.class);
+	private static final Logger ourLog = LoggerFactory.getLogger(JavaMailEmailSender.class);
-	private String mySmtpServerHost;
+	private String mySmtpServerHostname;
 	private int mySmtpServerPort = 25;
 	private JavaMailSenderImpl mySender;
+	private String mySmtpServerUsername;
+	private String mySmtpServerPassword;
 
-	@PostConstruct
+	public String getSmtpServerHostname() {
-	public void start() {
+		return mySmtpServerHostname;
-		Validate.notBlank(mySmtpServerHost, "No SMTP host defined");
+	}
 
-		mySender = new JavaMailSenderImpl();
+	/**
-		mySender.setHost(mySmtpServerHost);
+	 * Set the SMTP server host to use for outbound mail
-		mySender.setPort(mySmtpServerPort);
+	 */
-		mySender.setDefaultEncoding(Constants.CHARSET_UTF8.name());
+	public void setSmtpServerHostname(String theSmtpServerHostname) {
+		mySmtpServerHostname = theSmtpServerHostname;
+	}
+
+	public String getSmtpServerPassword() {
+		return mySmtpServerPassword;
+	}
+
+	public void setSmtpServerPassword(String theSmtpServerPassword) {
+		mySmtpServerPassword = theSmtpServerPassword;
+	}
+
+	public int getSmtpServerPort() {
+		return mySmtpServerPort;
+	}
+
+	/**
+	 * Set the SMTP server port to use for outbound mail
+	 */
+	public void setSmtpServerPort(int theSmtpServerPort) {
+		mySmtpServerPort = theSmtpServerPort;
+	}
+
+	public String getSmtpServerUsername() {
+		return mySmtpServerUsername;
+	}
+
+	public void setSmtpServerUsername(String theSmtpServerUsername) {
+		mySmtpServerUsername = theSmtpServerUsername;
 	}
 
 	@Override
 	public void send(EmailDetails theDetails) {
-		ourLog.info("Sending email to recipients: {}", theDetails.getTo());
+		String subscriptionId = theDetails.getSubscription().toUnqualifiedVersionless().getValue();
+		ourLog.info("Sending email for subscription {} to recipients: {}", subscriptionId, theDetails.getTo());
 		StopWatch sw = new StopWatch();
 
 		StringTemplateResolver templateResolver = new StringTemplateResolver();
@@ -80,39 +114,44 @@ public class EmailSender implements IEmailSender {
 		String body = engine.process(theDetails.getBodyTemplate(), context);
 		String subject = engine.process(theDetails.getSubjectTemplate(), context);
 
-		SimpleMailMessage email = new SimpleMailMessage();
+		MimeMessage email = mySender.createMimeMessage();
-		email.setFrom(trim(theDetails.getFrom()));
+
-		email.setTo(toTrimmedStringArray(theDetails.getTo()));
+		try {
-		email.setSubject(subject);
+			email.setFrom(trim(theDetails.getFrom()));
-		email.setText(body);
+			email.setRecipients(Message.RecipientType.TO, toTrimmedCommaSeparatedString(theDetails.getTo()));
-		email.setSentDate(new Date());
+			email.setSubject(subject);
+			email.setText(body);
+			email.setSentDate(new Date());
+			email.addHeader("X-FHIR-Subscription", subscriptionId);
+		} catch (MessagingException e) {
+			throw new InternalErrorException("Failed to create email messaage", e);
+		}
 
 		mySender.send(email);
 
 		ourLog.info("Done sending email (took {}ms)", sw.getMillis());
 	}
 
-	/**
+	@PostConstruct
-	 * Set the SMTP server host to use for outbound mail
+	public void start() {
-	 */
+		Validate.notBlank(mySmtpServerHostname, "No SMTP host defined");
-	public void setSmtpServerHost(String theSmtpServerHost) {
+
-		mySmtpServerHost = theSmtpServerHost;
+		mySender = new JavaMailSenderImpl();
+		mySender.setHost(getSmtpServerHostname());
+		mySender.setPort(getSmtpServerPort());
+		mySender.setUsername(getSmtpServerUsername());
+		mySender.setPassword(getSmtpServerPassword());
+		mySender.setDefaultEncoding(Constants.CHARSET_UTF8.name());
 	}
 
-	/**
+	private static String toTrimmedCommaSeparatedString(List<String> theTo) {
-	 * Set the SMTP server port to use for outbound mail
-	 */
-	public void setSmtpServerPort(int theSmtpServerPort) {
-		mySmtpServerPort = theSmtpServerPort;
-	}
-
-	private static String[] toTrimmedStringArray(List<String> theTo) {
 		List<String> to = new ArrayList<>();
 		for (String next : theTo) {
 			if (isNotBlank(next)) {
 				to.add(next);
 			}
 		}
-		return to.toArray(new String[to.size()]);
+
+		return StringUtils.join(to, ",");
 	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/email/SubscriptionDeliveringEmailSubscriber.java

@@ -54,32 +54,29 @@ public class SubscriptionDeliveringEmailSubscriber extends BaseSubscriptionDeliv
 		List<String> destinationAddresses = new ArrayList<>();
 		String[] destinationAddressStrings = StringUtils.split(endpointUrl, ",");
 		for (String next : destinationAddressStrings) {
+			next = trim(defaultString(next));
+			if (next.startsWith("mailto:")) {
+				next = next.substring("mailto:".length());
+			}
 			if (isNotBlank(next)) {
-				destinationAddresses.add(trim(next));
+				destinationAddresses.add(next);
 			}
 		}
 
-		String from = defaultString(subscription.getEmailDetails().getFrom(), provideDefaultFrom());
+		String from = defaultString(subscription.getEmailDetails().getFrom(), mySubscriptionEmailInterceptor.getDefaultFromAddress());
 		String subjectTemplate = defaultString(subscription.getEmailDetails().getSubjectTemplate(), provideDefaultSubjectTemplate());
-		String bodyTemplate = defaultString(subscription.getEmailDetails().getBodyTemplate(), provideDefaultBodyTemplate());
 
 		EmailDetails details = new EmailDetails();
 		details.setTo(destinationAddresses);
 		details.setFrom(from);
-		details.setBodyTemplate(bodyTemplate);
+		details.setBodyTemplate(subscription.getPayloadString());
 		details.setSubjectTemplate(subjectTemplate);
+		details.setSubscription(subscription.getIdElement(getContext()));
 
 		IEmailSender emailSender = mySubscriptionEmailInterceptor.getEmailSender();
 		emailSender.send(details);
 	}
 
-	private String provideDefaultBodyTemplate() {
-		return "A subscription update has been received";
-	}
-
-	private String provideDefaultFrom() {
-		return "unknown@sender.com";
-	}
 
 	private String provideDefaultSubjectTemplate() {
 		return "HAPI FHIR Subscriptions";

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/email/SubscriptionEmailInterceptor.java

@@ -20,28 +20,51 @@ package ca.uhn.fhir.jpa.subscription.email;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.subscription.BaseSubscriptionInterceptor;
 import org.apache.commons.lang3.Validate;
-import org.springframework.beans.factory.annotation.Required;
+import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.PostConstruct;
-import java.util.List;
 
 public class SubscriptionEmailInterceptor extends BaseSubscriptionInterceptor {
 	private SubscriptionDeliveringEmailSubscriber mySubscriptionDeliverySubscriber;
+
+	/**
+	 * This is set to autowired=false just so that implementors can supply this
+	 * with a mechanism other than autowiring if they want
+	 */
+	@Autowired(required = false)
 	private IEmailSender myEmailSender;
+	private String myDefaultFromAddress = "noreply@unknown.com";
 
 	@Override
 	public org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType getChannelType() {
 		return org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType.EMAIL;
 	}
 
+	/**
+	 * The "from" address to use for any sent emails that to not explicitly specity a from address
+	 */
+	public String getDefaultFromAddress() {
+		return myDefaultFromAddress;
+	}
+
+	/**
+	 * The "from" address to use for any sent emails that to not explicitly specity a from address
+	 */
+	public void setDefaultFromAddress(String theDefaultFromAddress) {
+		Validate.notBlank(theDefaultFromAddress, "theDefaultFromAddress must not be null or blank");
+		myDefaultFromAddress = theDefaultFromAddress;
+	}
+
 	public IEmailSender getEmailSender() {
 		return myEmailSender;
 	}
 
-	@Required
+	/**
+	 * Set the email sender (this method does not need to be explicitly called if you
+	 * are using autowiring to supply the sender)
+	 */
 	public void setEmailSender(IEmailSender theEmailSender) {
 		myEmailSender = theEmailSender;
 	}
@@ -54,12 +77,12 @@ public class SubscriptionEmailInterceptor extends BaseSubscriptionInterceptor {
 		getDeliveryChannel().subscribe(mySubscriptionDeliverySubscriber);
 	}
 
-	@PostConstruct
+//	@PostConstruct
-	public void start() {
+//	public void start() {
-		Validate.notNull(myEmailSender, "emailSender has not been configured");
+//		Validate.notNull(myEmailSender, "emailSender has not been configured");
-
+//
-		super.start();
+//		super.start();
-	}
+//	}
 
 	@Override
 	protected void unregisterDeliverySubscriber() {

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

@@ -24,8 +24,20 @@ public class JpaConstants {
 
 	public static final String EXT_SP_UNIQUE = "http://hapifhir.io/fhir/StructureDefinition/sp-unique";
 
+	/**
+	 * <p>
+	 * This extension should be of type <code>string</code> and should be
+	 * placed on the <code>Subscription.channel</code> element
+	 * </p>
+	 */
 	public static final String EXT_SUBSCRIPTION_EMAIL_FROM = "http://hapifhir.io/fhir/StructureDefinition/subscription-email-from";
+
+	/**
+	 * <p>
+	 * This extension should be of type <code>string</code> and should be
+	 * placed on the <code>Subscription.channel</code> element
+	 * </p>
+	 */
 	public static final String EXT_SUBSCRIPTION_SUBJECT_TEMPLATE = "http://hapifhir.io/fhir/StructureDefinition/subscription-email-subject-template";
-	public static final String EXT_SUBSCRIPTION_BODY_TEMPLATE = "http://hapifhir.io/fhir/StructureDefinition/subscription-email-body-template";
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/SubscriptionsRequireManualActivationInterceptorDstu2.java

@@ -42,7 +42,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 public class SubscriptionsRequireManualActivationInterceptorDstu2 extends ServerOperationInterceptorAdapter {
 
 	@Autowired
-	@Qualifier("mySubscriptionDaoR4")
+	@Qualifier("mySubscriptionDaoDstu2")
 	private IFhirResourceDao<Subscription> myDao;
 
 	@Override

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/config/ConnectionWrapper.java

@@ -97,7 +97,7 @@ public class ConnectionWrapper implements Connection {
 
 	@Override
 	public String getClientInfo(String theName) throws SQLException {
-		return getClientInfo(theName);
+		return myWrap.getClientInfo(theName);
 	}
 
 	@Override

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

@@ -10,19 +10,30 @@ import javax.sql.DataSource;
 
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.subscription.email.IEmailSender;
+import ca.uhn.fhir.jpa.subscription.email.JavaMailEmailSender;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.hibernate.jpa.HibernatePersistenceProvider;
-import org.springframework.context.annotation.*;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import ca.uhn.fhir.jpa.dao.DaoConfig;
+import javax.persistence.EntityManagerFactory;
-import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import javax.sql.DataSource;
-import ca.uhn.fhir.validation.ResultSeverityEnum;
+import java.sql.Connection;
-import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
+import java.sql.SQLException;
+import java.util.Properties;
+import java.util.concurrent.TimeUnit;
 
-import static org.junit.Assert.fail;
+import static org.junit.Assert.*;
 
 @Configuration
 @EnableTransactionManagement()
@@ -31,11 +42,6 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 	static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestDstu3Config.class);
 	private Exception myLastStackTrace;
 
-	@Bean()
-	public DaoConfig daoConfig() {
-		return new DaoConfig();
-	}
-
 	@Bean()
 	public BasicDataSource basicDataSource() {
 		BasicDataSource retVal = new BasicDataSource() {
@@ -50,7 +56,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 					ourLog.error("Exceeded maximum wait for connection", e);
 					logGetConnectionStackTrace();
 //					if ("true".equals(System.getProperty("ci"))) {
-					fail("Exceeded maximum wait for connection: "+ e.toString());
+					fail("Exceeded maximum wait for connection: " + e.toString());
 //					}
 //					System.exit(1);
 					retVal = null;
@@ -100,20 +106,33 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		return retVal;
 	}
 
+	@Bean()
+	public DaoConfig daoConfig() {
+		return new DaoConfig();
+	}
+
 	@Bean()
 	@Primary()
 	public DataSource dataSource() {
 
 		DataSource dataSource = ProxyDataSourceBuilder
-				.create(basicDataSource())
+			.create(basicDataSource())
 //				.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
-				.logSlowQueryBySlf4j(1000, TimeUnit.MILLISECONDS)
+			.logSlowQueryBySlf4j(1000, TimeUnit.MILLISECONDS)
-				.countQuery()
+			.countQuery()
-				.build();
+			.build();
 
 		return dataSource;
 	}
 
+	@Bean
+	public IEmailSender emailSender() {
+		JavaMailEmailSender retVal = new JavaMailEmailSender();
+		retVal.setSmtpServerHostname("localhost");
+		retVal.setSmtpServerPort(3025);
+		return retVal;
+	}
+
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
 		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();

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

@@ -118,8 +118,13 @@ public abstract class BaseJpaTest {
 
 	protected List<String> toUnqualifiedVersionlessIdValues(IBundleProvider theFound) {
 		List<String> retVal = new ArrayList<String>();
-		int size = theFound.size();
+		Integer size = theFound.size();
 		ourLog.info("Found {} results", size);
+
+		if (size == null) {
+			size = 99999;
+		}
+
 		List<IBaseResource> resources = theFound.getResources(0, size);
 		for (IBaseResource next : resources) {
 			retVal.add(next.getIdElement().toUnqualifiedVersionless().getValue());
@@ -298,7 +303,7 @@ public abstract class BaseJpaTest {
 
 	public static void waitForSize(int theTarget, List<?> theList) {
 		StopWatch sw = new StopWatch();
-		while (theList.size() != theTarget && sw.getMillis() < 10000) {
+		while (theList.size() != theTarget && sw.getMillis() <= 15000) {
 			try {
 				Thread.sleep(50);
 			} catch (InterruptedException theE) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java

@@ -120,7 +120,7 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	protected Object myResourceProviders;
 	@Autowired
 	protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
-	@Autowired
+	@Autowired(required = false)
 	protected IFulltextSearchSvc mySearchDao;
 	@Autowired
 	protected ISearchParamPresenceSvc mySearchParamPresenceSvc;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java

@@ -56,6 +56,30 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		myDaoConfig.setTreatReferencesAsLogical(new DaoConfig().getTreatReferencesAsLogical());
 	}
 
+	/**
+	 * See #773
+	 */
+	@Test
+	public void testDeleteResourceWithOutboundDeletedResources() {
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
+
+		Organization org = new Organization();
+		org.setId("ORG");
+		org.setName("ORG");
+		myOrganizationDao.update(org);
+
+		Patient pat = new Patient();
+		pat.setId("PAT");
+		pat.setActive(true);
+		pat.setManagingOrganization(new ResourceReferenceDt("Organization/ORG"));
+		myPatientDao.update(pat);
+
+		myOrganizationDao.delete(new IdDt("Organization/ORG"));
+
+		myPatientDao.delete(new IdDt("Patient/PAT"));
+	}
+
+
 	private void assertGone(IIdType theId) {
 		try {
 			assertNotGone(theId);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2ValidateTest.java

@@ -102,6 +102,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
 			} catch (PreconditionFailedException e) {
 				return (OperationOutcome) e.getOperationOutcome();
 			}
+			break;
 		case XML:
 			encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
 			try {
@@ -110,6 +111,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
 			} catch (PreconditionFailedException e) {
 				return (OperationOutcome) e.getOperationOutcome();
 			}
+			break;
 		}
 
 		throw new IllegalStateException(); // shouldn't get here

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -172,7 +172,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	protected IResourceTagDao myResourceTagDao;
 	@Autowired
 	protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
-	@Autowired
+	@Autowired(required = false)
 	protected IFulltextSearchSvc mySearchDao;
 	@Autowired
 	protected ISearchDao mySearchEntityDao;

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/dstu3/FhirResourceDaoDstu3ValidateTest.java

@@ -133,6 +133,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
 			} catch (PreconditionFailedException e) {
 				return (OperationOutcome) e.getOperationOutcome();
 			}
+			break;
 		case XML:
 			encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
 			try {
@@ -141,6 +142,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
 			} catch (PreconditionFailedException e) {
 				return (OperationOutcome) e.getOperationOutcome();
 			}
+			break;
 		}
 
 		throw new IllegalStateException(); // shouldn't get here

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java

@@ -1879,6 +1879,91 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		assertNull(nextEntry.getResource());
 	}
 
+	@Test
+	public void testTransactionWithIfMatch() {
+		Patient p = new Patient();
+		p.setId("P1");
+		p.setActive(true);
+		myPatientDao.update(p);
+
+		p.setActive(false);
+		Bundle b = new Bundle();
+		b.setType(BundleType.TRANSACTION);
+		b.addEntry()
+			.setFullUrl("Patient/P1")
+			.setResource(p)
+			.getRequest()
+			.setMethod(HTTPVerb.PUT)
+			.setUrl("Patient/P1")
+			.setIfMatch("2");
+
+		try {
+			mySystemDao.transaction(mySrd, b);
+		} catch (ResourceVersionConflictException e) {
+			assertEquals("Trying to update Patient/P1/_history/2 but this is not the current version", e.getMessage());
+		}
+
+		b = new Bundle();
+		b.setType(BundleType.TRANSACTION);
+		b.addEntry()
+			.setFullUrl("Patient/P1")
+			.setResource(p)
+			.getRequest()
+			.setMethod(HTTPVerb.PUT)
+			.setUrl("Patient/P1")
+			.setIfMatch("1");
+
+		Bundle resp = mySystemDao.transaction(mySrd, b);
+		assertEquals("Patient/P1/_history/2", new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualified().getValue());
+
+
+	}
+
+	@Test
+	public void testTransactionWithIfNoneExist() {
+		Patient p = new Patient();
+		p.setId("P1");
+		p.setActive(true);
+		myPatientDao.update(p);
+
+		p = new Patient();
+		p.setActive(true);
+		p.addName().setFamily("AAA");
+
+		Bundle b = new Bundle();
+		b.setType(BundleType.TRANSACTION);
+		b.addEntry()
+			.setFullUrl("Patient")
+			.setResource(p)
+			.getRequest()
+			.setMethod(HTTPVerb.POST)
+			.setUrl("Patient/P1")
+			.setIfNoneExist("Patient?active=true");
+
+		Bundle resp = mySystemDao.transaction(mySrd, b);
+		assertEquals("Patient/P1/_history/1", new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualified().getValue());
+
+		p = new Patient();
+		p.setActive(true);
+		p.addName().setFamily("AAA");
+
+		b = new Bundle();
+		b.setType(BundleType.TRANSACTION);
+		b.addEntry()
+			.setFullUrl("Patient")
+			.setResource(p)
+			.getRequest()
+			.setMethod(HTTPVerb.POST)
+			.setUrl("Patient/P1")
+			.setIfNoneExist("Patient?active=false");
+
+		resp = mySystemDao.transaction(mySrd, b);
+		assertThat( new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualified().getValue(), matchesPattern("Patient/[0-9]+/_history/1"));
+
+
+	}
+
+
 	@Test
 	public void testTransactionSearchWithCount() {
 		String methodName = "testTransactionSearchWithCount";

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -181,7 +181,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	protected IResourceTagDao myResourceTagDao;
 	@Autowired
 	protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
-	@Autowired
+	@Autowired(required = false)
 	protected IFulltextSearchSvc mySearchDao;
 	@Autowired
 	protected ISearchDao mySearchEntityDao;

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-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -55,6 +55,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	public final void after() {
 		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
 		myDaoConfig.setTreatReferencesAsLogical(new DaoConfig().getTreatReferencesAsLogical());
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(new DaoConfig().isEnforceReferentialIntegrityOnDelete());
 	}
 
 	private void assertGone(IIdType theId) {
@@ -98,6 +99,29 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	}
 
 
+	/**
+	 * See #773
+	 */
+	@Test
+	public void testDeleteResourceWithOutboundDeletedResources() {
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
+
+		Organization org = new Organization();
+		org.setId("ORG");
+		org.setName("ORG");
+		myOrganizationDao.update(org);
+
+		Patient pat = new Patient();
+		pat.setId("PAT");
+		pat.setActive(true);
+		pat.setManagingOrganization(new Reference("Organization/ORG"));
+		myPatientDao.update(pat);
+
+		myOrganizationDao.delete(new IdType("Organization/ORG"));
+
+		myPatientDao.delete(new IdType("Patient/PAT"));
+	}
+
 
 	@Before
 	public void beforeDisableResultReuse() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -133,6 +133,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 			} catch (PreconditionFailedException e) {
 				return (OperationOutcome) e.getOperationOutcome();
 			}
+			break;
 		case XML:
 			encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
 			try {
@@ -141,6 +142,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 			} catch (PreconditionFailedException e) {
 				return (OperationOutcome) e.getOperationOutcome();
 			}
+			break;
 		}
 
 		throw new IllegalStateException(); // shouldn't get here

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java

@@ -587,6 +587,90 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
 
 	}
 
+	@Test
+	public void testTransactionWithIfMatch() {
+		Patient p = new Patient();
+		p.setId("P1");
+		p.setActive(true);
+		myPatientDao.update(p);
+
+		p.setActive(false);
+		Bundle b = new Bundle();
+		b.setType(BundleType.TRANSACTION);
+		b.addEntry()
+			.setFullUrl("Patient/P1")
+			.setResource(p)
+			.getRequest()
+			.setMethod(HTTPVerb.PUT)
+			.setUrl("Patient/P1")
+			.setIfMatch("2");
+
+		try {
+			mySystemDao.transaction(mySrd, b);
+		} catch (ResourceVersionConflictException e) {
+			assertEquals("Trying to update Patient/P1/_history/2 but this is not the current version", e.getMessage());
+		}
+
+		b = new Bundle();
+		b.setType(BundleType.TRANSACTION);
+		b.addEntry()
+			.setFullUrl("Patient/P1")
+			.setResource(p)
+			.getRequest()
+			.setMethod(HTTPVerb.PUT)
+			.setUrl("Patient/P1")
+			.setIfMatch("1");
+
+		Bundle resp = mySystemDao.transaction(mySrd, b);
+		assertEquals("Patient/P1/_history/2", new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualified().getValue());
+
+
+	}
+
+	@Test
+	public void testTransactionWithIfNoneExist() {
+		Patient p = new Patient();
+		p.setId("P1");
+		p.setActive(true);
+		myPatientDao.update(p);
+
+		p = new Patient();
+		p.setActive(true);
+		p.addName().setFamily("AAA");
+
+		Bundle b = new Bundle();
+		b.setType(BundleType.TRANSACTION);
+		b.addEntry()
+			.setFullUrl("Patient")
+			.setResource(p)
+			.getRequest()
+			.setMethod(HTTPVerb.POST)
+			.setUrl("Patient/P1")
+			.setIfNoneExist("Patient?active=true");
+
+		Bundle resp = mySystemDao.transaction(mySrd, b);
+		assertEquals("Patient/P1/_history/1", new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualified().getValue());
+
+		p = new Patient();
+		p.setActive(true);
+		p.addName().setFamily("AAA");
+
+		b = new Bundle();
+		b.setType(BundleType.TRANSACTION);
+		b.addEntry()
+			.setFullUrl("Patient")
+			.setResource(p)
+			.getRequest()
+			.setMethod(HTTPVerb.POST)
+			.setUrl("Patient/P1")
+			.setIfNoneExist("Patient?active=false");
+
+		resp = mySystemDao.transaction(mySrd, b);
+		assertThat( new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualified().getValue(), matchesPattern("Patient/[0-9]+/_history/1"));
+
+
+	}
+
 	@Test
 	public void testTransaction1() throws IOException {
 		String inputBundleString = loadClasspath("/david-bundle-error.json");

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

@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
 import ca.uhn.fhir.jpa.dao.dstu3.SearchParamRegistryDstu3;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
+import ca.uhn.fhir.jpa.subscription.email.SubscriptionEmailInterceptor;
 import ca.uhn.fhir.jpa.subscription.resthook.SubscriptionRestHookInterceptor;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
@@ -58,6 +59,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 	protected static SearchParamRegistryDstu3 ourSearchParamRegistry;
 	protected static DatabaseBackedPagingProvider ourPagingProvider;
 	protected static SubscriptionRestHookInterceptor ourRestHookSubscriptionInterceptor;
+	protected static SubscriptionEmailInterceptor ourEmailSubscriptionInterceptor;
 	protected static ISearchDao mySearchEntityDao;
 	protected static ISearchCoordinatorSvc mySearchCoordinatorSvc;
 
@@ -111,13 +113,9 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 			ourWebApplicationContext = new GenericWebApplicationContext();
 			ourWebApplicationContext.setParent(myAppCtx);
 			ourWebApplicationContext.refresh();
-			// ContextLoaderListener loaderListener = new ContextLoaderListener(webApplicationContext);
-			// loaderListener.initWebApplicationContext(mock(ServletContext.class));
-			//
 			proxyHandler.getServletContext().setAttribute(WebApplicationContext.ROOT_WEB_APPLICATION_CONTEXT_ATTRIBUTE, ourWebApplicationContext);
 
 			DispatcherServlet dispatcherServlet = new DispatcherServlet();
-			// dispatcherServlet.setApplicationContext(webApplicationContext);
 			dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
 			ServletHolder subsServletHolder = new ServletHolder();
 			subsServletHolder.setServlet(dispatcherServlet);
@@ -150,6 +148,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 			mySearchCoordinatorSvc = wac.getBean(ISearchCoordinatorSvc.class);
 			mySearchEntityDao = wac.getBean(ISearchDao.class);
 			ourRestHookSubscriptionInterceptor = wac.getBean(SubscriptionRestHookInterceptor.class);
+			ourEmailSubscriptionInterceptor = wac.getBean(SubscriptionEmailInterceptor.class);
 			ourSearchParamRegistry = wac.getBean(SearchParamRegistryDstu3.class);
 
 			myFhirCtx.getRestfulClientFactory().setSocketTimeout(5000000);

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

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.jpa.provider.dstu3;
 
 import ca.uhn.fhir.jpa.provider.r4.ResourceProviderInterceptorR4Test;
-import ca.uhn.fhir.model.dstu2.resource.Conformance;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
@@ -61,8 +60,8 @@ public class ResourceProviderInterceptorDstu3Test extends BaseResourceProviderDs
 	public void before() throws Exception {
 		super.before();
 
-		myServerInterceptor = mock(IServerInterceptor.class);
+		myServerInterceptor = mock(IServerInterceptor.class, withSettings().verboseLogging());
-		myDaoInterceptor = mock(IServerInterceptor.class);
+		myDaoInterceptor = mock(IServerInterceptor.class, withSettings().verboseLogging());
 
 		resetServerInterceptor();
 
@@ -125,6 +124,8 @@ public class ResourceProviderInterceptorDstu3Test extends BaseResourceProviderDs
 	public void testCreateResourceInTransaction() throws IOException, ServletException {
 		String methodName = "testCreateResourceInTransaction";
 
+		ourLog.info("** Starting {}", methodName);
+
 		Patient pt = new Patient();
 		pt.addName().setFamily(methodName);
 
@@ -140,6 +141,11 @@ public class ResourceProviderInterceptorDstu3Test extends BaseResourceProviderDs
 
 		resetServerInterceptor();
 
+		ArgumentCaptor<ActionRequestDetails> ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
+		ArgumentCaptor<RestOperationTypeEnum> opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
+		verify(myDaoInterceptor, times(0)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
+		verify(myServerInterceptor, times(0)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
+
 		HttpPost post = new HttpPost(ourServerBase + "/");
 		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
 		CloseableHttpResponse response = ourHttpClient.execute(post);
@@ -153,8 +159,8 @@ public class ResourceProviderInterceptorDstu3Test extends BaseResourceProviderDs
 		 * Server Interceptor
 		 */
 
-		ArgumentCaptor<ActionRequestDetails> ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
+		ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
-		ArgumentCaptor<RestOperationTypeEnum> opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
+		opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
 		verify(myServerInterceptor, times(2)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
 		assertEquals(RestOperationTypeEnum.TRANSACTION, opTypeCaptor.getAllValues().get(0));
 		assertEquals(null, ardCaptor.getAllValues().get(0).getResourceType());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/AuthorizationInterceptorResourceProviderR4Test.java

@@ -9,6 +9,8 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import org.apache.http.client.methods.*;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
@@ -69,19 +71,68 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
 		Patient patient = new Patient();
 		patient.addIdentifier().setSystem("http://uhn.ca/mrns").setValue("100");
 		patient.addName().setFamily("Tester").addGiven("Raghad");
-		IIdType id = ourClient.create().resource(patient).execute().getId();
+		IIdType id = myClient.create().resource(patient).execute().getId();
 
 		try {
-			ourClient.delete().resourceById(id.toUnqualifiedVersionless()).execute();
+			myClient.delete().resourceById(id.toUnqualifiedVersionless()).execute();
 			fail();
 		} catch (ForbiddenOperationException e) {
 			// good
 		}
 		
-		patient = ourClient.read().resource(Patient.class).withId(id.toUnqualifiedVersionless()).execute();
+		patient = myClient.read().resource(Patient.class).withId(id.toUnqualifiedVersionless()).execute();
 		assertEquals(id.getValue(), patient.getId());
 	}
 
+	/**
+	 * See #751
+	 */
+	@Test
+	public void testDeleteInCompartmentIsBlocked() {
+
+		Patient patient = new Patient();
+		patient.setId("Patient/A");
+		patient.addIdentifier().setSystem("http://uhn.ca/mrns").setValue("100");
+		patient.addName().setFamily("Tester").addGiven("Raghad");
+		IIdType id = myClient.update().resource(patient).execute().getId();
+
+		Observation obs = new Observation();
+		obs.setId("Observation/B");
+		obs.getSubject().setReference("Patient/A");
+		myClient.update().resource(obs).execute();
+
+		obs = new Observation();
+		obs.setId("Observation/C");
+		obs.setStatus(ObservationStatus.FINAL);
+		myClient.update().resource(obs).execute();
+
+		ourRestServer.registerInterceptor(new AuthorizationInterceptor(PolicyEnum.DENY) {
+			@Override
+			public List<IAuthRule> buildRuleList(RequestDetails theRequestDetails) {
+				return new RuleBuilder()
+					.allow().delete().allResources().inCompartment("Patient", new IdType("Patient/A")).andThen()
+					.allow().read().allResources().withAnyId().andThen()
+					.denyAll()
+					.build();
+			}
+		});
+
+		myClient.delete().resourceById(new IdType("Observation/B")).execute();
+
+		try {
+			myClient.read().resource(Observation.class).withId("Observation/B").execute();
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		try {
+			myClient.delete().resourceById(new IdType("Observation/C")).execute();
+			fail();
+		} catch (ForbiddenOperationException e) {
+			// good
+		}
+	}
 
 	/**
 	 * See #503
@@ -92,16 +143,16 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
 		Patient patient = new Patient();
 		patient.addIdentifier().setSystem("http://uhn.ca/mrns").setValue("100");
 		patient.addName().setFamily("Tester").addGiven("Raghad");
-		final IIdType id = ourClient.create().resource(patient).execute().getId();
+		final IIdType id = myClient.create().resource(patient).execute().getId();
 		
 		Observation obsInCompartment = new Observation();
 		obsInCompartment.setStatus(ObservationStatus.FINAL);
 		obsInCompartment.getSubject().setReferenceElement(id.toUnqualifiedVersionless());
-		IIdType obsInCompartmentId = ourClient.create().resource(obsInCompartment).execute().getId().toUnqualifiedVersionless();
+		IIdType obsInCompartmentId = myClient.create().resource(obsInCompartment).execute().getId().toUnqualifiedVersionless();
 		
 		Observation obsNotInCompartment = new Observation();
 		obsNotInCompartment.setStatus(ObservationStatus.FINAL);
-		IIdType obsNotInCompartmentId = ourClient.create().resource(obsNotInCompartment).execute().getId().toUnqualifiedVersionless();
+		IIdType obsNotInCompartmentId = myClient.create().resource(obsNotInCompartment).execute().getId().toUnqualifiedVersionless();
 		
 		ourRestServer.registerInterceptor(new AuthorizationInterceptor(PolicyEnum.DENY) {
 			@Override
@@ -114,10 +165,10 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
 			}
 		});
 		
-		ourClient.delete().resourceById(obsInCompartmentId.toUnqualifiedVersionless()).execute();
+		myClient.delete().resourceById(obsInCompartmentId.toUnqualifiedVersionless()).execute();
 
 		try {
-			ourClient.delete().resourceById(obsNotInCompartmentId.toUnqualifiedVersionless()).execute();
+			myClient.delete().resourceById(obsNotInCompartmentId.toUnqualifiedVersionless()).execute();
 			fail();
 		} catch (ForbiddenOperationException e) {
 			// good
@@ -130,7 +181,7 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
 		Patient patient = new Patient();
 		patient.addIdentifier().setSystem("http://uhn.ca/mrns").setValue("100");
 		patient.addName().setFamily("Tester").addGiven("Raghad");
-		final MethodOutcome output1 = ourClient.update().resource(patient).conditionalByUrl("Patient?identifier=http://uhn.ca/mrns|100").execute();
+		final MethodOutcome output1 = myClient.update().resource(patient).conditionalByUrl("Patient?identifier=http://uhn.ca/mrns|100").execute();
 
 		ourRestServer.registerInterceptor(new AuthorizationInterceptor(PolicyEnum.DENY) {
 			@Override
@@ -148,7 +199,7 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
 		patient.setId(output1.getId().toUnqualifiedVersionless());
 		patient.addIdentifier().setSystem("http://uhn.ca/mrns").setValue("100");
 		patient.addName().setFamily("Tester").addGiven("Raghad");
-		MethodOutcome output2 = ourClient.update().resource(patient).conditionalByUrl("Patient?identifier=http://uhn.ca/mrns|100").execute();
+		MethodOutcome output2 = myClient.update().resource(patient).conditionalByUrl("Patient?identifier=http://uhn.ca/mrns|100").execute();
 
 		assertEquals(output1.getId().getIdPart(), output2.getId().getIdPart());
 		
@@ -156,7 +207,7 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
 		patient.addIdentifier().setSystem("http://uhn.ca/mrns").setValue("100");
 		patient.addName().setFamily("Tester").addGiven("Raghad");
 		try {
-			ourClient.update().resource(patient).conditionalByUrl("Patient?identifier=http://uhn.ca/mrns|101").execute();
+			myClient.update().resource(patient).conditionalByUrl("Patient?identifier=http://uhn.ca/mrns|101").execute();
 			fail();
 		} catch (ForbiddenOperationException e) {
 			assertEquals("HTTP 403 Forbidden: Access denied by default policy (no applicable rules)", e.getMessage());
@@ -167,7 +218,7 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
 		patient.addIdentifier().setSystem("http://uhn.ca/mrns").setValue("100");
 		patient.addName().setFamily("Tester").addGiven("Raghad");
 		try {
-			ourClient.update().resource(patient).execute();
+			myClient.update().resource(patient).execute();
 			fail();
 		} catch (ForbiddenOperationException e) {
 			assertEquals("HTTP 403 Forbidden: Access denied by default policy (no applicable rules)", e.getMessage());
@@ -182,11 +233,11 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
 	public void testBlockUpdatingPatientUserDoesnNotHaveAccessTo() throws IOException {
 		Patient pt1 = new Patient();
 		pt1.setActive(true);
-		final IIdType pid1 = ourClient.create().resource(pt1).execute().getId().toUnqualifiedVersionless();
+		final IIdType pid1 = myClient.create().resource(pt1).execute().getId().toUnqualifiedVersionless();
 
 		Patient pt2 = new Patient();
 		pt2.setActive(false);
-		final IIdType pid2 = ourClient.create().resource(pt2).execute().getId().toUnqualifiedVersionless();
+		final IIdType pid2 = myClient.create().resource(pt2).execute().getId().toUnqualifiedVersionless();
 
 		ourRestServer.registerInterceptor(new AuthorizationInterceptor(PolicyEnum.DENY) {
 			@Override
@@ -200,7 +251,7 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
 		Observation obs = new Observation();
 		obs.setStatus(ObservationStatus.FINAL);
 		obs.setSubject(new Reference(pid1));
-		IIdType oid = ourClient.create().resource(obs).execute().getId().toUnqualified();
+		IIdType oid = myClient.create().resource(obs).execute().getId().toUnqualified();
 
 		
 		unregisterInterceptors();
@@ -224,7 +275,7 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
 		obs.setSubject(new Reference(pid2));
 		
 		try {
-			ourClient.update().resource(obs).execute();
+			myClient.update().resource(obs).execute();
 			fail();
 		} catch (ForbiddenOperationException e) {
 			// good

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java

@@ -47,7 +47,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 
 	protected static JpaValidationSupportChainR4 myValidationSupport;
-	protected static IGenericClient ourClient;
+	protected IGenericClient myClient;
 	protected static CloseableHttpClient ourHttpClient;
 	protected static int ourPort;
 	protected static RestfulServer ourRestServer;
@@ -150,10 +150,6 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 			ourSearchParamRegistry = wac.getBean(SearchParamRegistryR4.class);
 
 			myFhirCtx.getRestfulClientFactory().setSocketTimeout(5000000);
-			ourClient = myFhirCtx.newRestfulGenericClient(ourServerBase);
-			if (shouldLogClient()) {
-				ourClient.registerInterceptor(new LoggingInterceptor());
-			}
 
 			PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
 			HttpClientBuilder builder = HttpClientBuilder.create();
@@ -165,6 +161,11 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 		}
 
 		ourRestServer.setPagingProvider(ourPagingProvider);
+
+		myClient = myFhirCtx.newRestfulGenericClient(ourServerBase);
+		if (shouldLogClient()) {
+			myClient.registerInterceptor(new LoggingInterceptor());
+		}
 	}
 
 	/**

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/GraphQLProviderR4Test.java

@@ -1,11 +1,11 @@
 package ca.uhn.fhir.jpa.provider.r4;
 
+import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Patient;
 import org.junit.Test;
 import org.slf4j.Logger;
@@ -31,14 +31,14 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
 		try {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
-			assertEquals(resp, "{\n" +
+			assertEquals(TestUtil.stripReturns(resp), TestUtil.stripReturns("{\n" +
 				"  \"name\":[{\n" +
 				"    \"family\":\"FAM\",\n" +
 				"    \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
 				"  },{\n" +
 				"    \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
 				"  }]\n" +
-				"}");
+				"}"));
 		} finally {
 			IOUtils.closeQuietly(response);
 		}
@@ -56,7 +56,7 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
 		try {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
-			assertEquals(resp, "{\n" +
+			assertEquals(TestUtil.stripReturns(resp), TestUtil.stripReturns("{\n" +
 				"  \"PatientList\":[{\n" +
 				"    \"name\":[{\n" +
 				"      \"family\":\"FAM\",\n" +
@@ -69,7 +69,7 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
 				"      \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
 				"    }]\n" +
 				"  }]\n" +
-				"}");
+				"}"));
 		} finally {
 			IOUtils.closeQuietly(response);
 		}
@@ -85,13 +85,13 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
 		p.addName()
 			.addGiven("GivenOnly1")
 			.addGiven("GivenOnly2");
-		myPatientId0 = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
+		myPatientId0 = myClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
 
 		p = new Patient();
 		p.addName()
 			.addGiven("GivenOnlyB1")
 			.addGiven("GivenOnlyB2");
-		ourClient.create().resource(p).execute();
+		myClient.create().resource(p).execute();
 	}
 
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/PatientEverythingR4Test.java

@@ -57,41 +57,41 @@ public class PatientEverythingR4Test extends BaseResourceProviderR4Test {
 		
 		Organization org = new Organization();
 		org.setName("an org");
-		orgId = ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless().getValue();
+		orgId = myClient.create().resource(org).execute().getId().toUnqualifiedVersionless().getValue();
 		ourLog.info("OrgId: {}", orgId);
 
 		Patient patient = new Patient();
 		patient.getManagingOrganization().setReference(orgId);
-		patId = ourClient.create().resource(patient).execute().getId().toUnqualifiedVersionless().getValue();
+		patId = myClient.create().resource(patient).execute().getId().toUnqualifiedVersionless().getValue();
 
 		Patient patient2 = new Patient();
 		patient2.getManagingOrganization().setReference(orgId);
-		myWrongPatId = ourClient.create().resource(patient2).execute().getId().toUnqualifiedVersionless().getValue();
+		myWrongPatId = myClient.create().resource(patient2).execute().getId().toUnqualifiedVersionless().getValue();
 
 		Encounter enc1 = new Encounter();
 		enc1.setStatus(EncounterStatus.CANCELLED);
 		enc1.getSubject().setReference(patId);
 		enc1.getServiceProvider().setReference(orgId);
-		encId1 = ourClient.create().resource(enc1).execute().getId().toUnqualifiedVersionless().getValue();
+		encId1 = myClient.create().resource(enc1).execute().getId().toUnqualifiedVersionless().getValue();
 
 		Encounter enc2 = new Encounter();
 		enc2.setStatus(EncounterStatus.ARRIVED);
 		enc2.getSubject().setReference(patId);
 		enc2.getServiceProvider().setReference(orgId);
-		encId2 = ourClient.create().resource(enc2).execute().getId().toUnqualifiedVersionless().getValue();
+		encId2 = myClient.create().resource(enc2).execute().getId().toUnqualifiedVersionless().getValue();
 
 		Encounter wrongEnc1 = new Encounter();
 		wrongEnc1.setStatus(EncounterStatus.ARRIVED);
 		wrongEnc1.getSubject().setReference(myWrongPatId);
 		wrongEnc1.getServiceProvider().setReference(orgId);
-		myWrongEnc1 = ourClient.create().resource(wrongEnc1).execute().getId().toUnqualifiedVersionless().getValue();
+		myWrongEnc1 = myClient.create().resource(wrongEnc1).execute().getId().toUnqualifiedVersionless().getValue();
 
 		myObsIds = new ArrayList<String>();
 		for (int i = 0; i < 20; i++) {
 			Observation obs = new Observation();
 			obs.getSubject().setReference(patId);
 			obs.setStatus(ObservationStatus.FINAL);
-			String obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless().getValue();
+			String obsId = myClient.create().resource(obs).execute().getId().toUnqualifiedVersionless().getValue();
 			myObsIds.add(obsId);
 		}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java

@@ -54,7 +54,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 		sp.setTitle("Foo Param");
 
 		try {
-			ourClient.create().resource(sp).execute();
+			myClient.create().resource(sp).execute();
 			fail();
 		} catch (UnprocessableEntityException e) {
 			assertEquals("HTTP 422 Unprocessable Entity: SearchParameter.status is missing or invalid: null", e.getMessage());
@@ -120,7 +120,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(eyeColourSp));
 
-		ourClient
+		myClient
 				.create()
 				.resource(eyeColourSp)
 				.execute();
@@ -139,7 +139,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 		p2.addExtension().setUrl("http://acme.org/eyecolour").setValue(new CodeType("green"));
 		IIdType p2id = myPatientDao.create(p2).getId().toUnqualifiedVersionless();
 
-		Bundle bundle = ourClient
+		Bundle bundle = myClient
 				.search()
 				.forResource(Patient.class)
 				.where(new TokenClientParam("eyecolour").exactly().code("blue"))
@@ -168,7 +168,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 	public void testConformanceOverrideAllowed() {
 		myDaoConfig.setDefaultSearchParamsCanBeOverridden(true);
 
-		CapabilityStatement conformance = ourClient
+		CapabilityStatement conformance = myClient
 				.fetchConformance()
 				.ofType(CapabilityStatement.class)
 				.execute();
@@ -220,7 +220,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 			}
 		});
 
-		conformance = ourClient
+		conformance = myClient
 				.fetchConformance()
 				.ofType(CapabilityStatement.class)
 				.execute();
@@ -238,7 +238,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 	public void testConformanceOverrideNotAllowed() {
 		myDaoConfig.setDefaultSearchParamsCanBeOverridden(false);
 
-		CapabilityStatement conformance = ourClient
+		CapabilityStatement conformance = myClient
 				.fetchConformance()
 				.ofType(CapabilityStatement.class)
 				.execute();
@@ -274,7 +274,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 
 		mySearchParamRegsitry.forceRefresh();
 
-		conformance = ourClient
+		conformance = myClient
 				.fetchConformance()
 				.ofType(CapabilityStatement.class)
 				.execute();
@@ -332,7 +332,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 		List<String> foundResources;
 		Bundle result;
 
-		result = ourClient
+		result = myClient
 				.search()
 				.forResource(Patient.class)
 				.where(new TokenClientParam("foo").exactly().code("male"))
@@ -409,7 +409,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 		List<String> foundResources;
 		Bundle result;
 
-		result = ourClient
+		result = myClient
 				.search()
 				.forResource(Observation.class)
 				.where(new ReferenceClientParam("foo").hasChainedProperty(Patient.GENDER.exactly().code("male")))

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInterceptorR4Test.java

@@ -198,7 +198,7 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 
 		Organization org = new Organization();
 		org.setName("orgName");
-		IIdType orgId = ourClient.create().resource(org).execute().getId().toUnqualified();
+		IIdType orgId = myClient.create().resource(org).execute().getId().toUnqualified();
 		assertNotNull(orgId.getVersionIdPartAsLong());
 
 		resetServerInterceptor();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderQuestionnaireResponseR4Test.java

@@ -72,7 +72,7 @@ public class ResourceProviderQuestionnaireResponseR4Test extends BaseResourcePro
 		qr1.setStatus(QuestionnaireResponseStatus.COMPLETED);
 		qr1.addItem().setLinkId("link1").addAnswer().setValue(new DecimalType(123));
 		try {
-			ourClient.create().resource(qr1).execute();
+			myClient.create().resource(qr1).execute();
 			fail();
 		} catch (UnprocessableEntityException e) {
 			assertThat(e.toString(), containsString("Answer value must be of type string"));
@@ -95,7 +95,7 @@ public class ResourceProviderQuestionnaireResponseR4Test extends BaseResourcePro
 		qr1.setStatus(QuestionnaireResponseStatus.COMPLETED);
 		qr1.addItem().setLinkId("link1").addAnswer().setValue(new DecimalType(123));
 		try {
-			ourClient.create().resource(qr1).execute();
+			myClient.create().resource(qr1).execute();
 			fail();
 		} catch (UnprocessableEntityException e) {
 			assertThat(e.toString(), containsString("Answer value must be of type string"));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4BundleTest.java

@@ -34,9 +34,9 @@ public class ResourceProviderR4BundleTest extends BaseResourceProviderR4Test {
 		composition.setTitle("Visit Summary");
 		bundle.addEntry().setFullUrl("http://foo").setResource(composition);
 		
-		IIdType id = ourClient.create().resource(bundle).execute().getId();
+		IIdType id = myClient.create().resource(bundle).execute().getId();
 		
-		Bundle retBundle = ourClient.read().resource(Bundle.class).withId(id).execute();
+		Bundle retBundle = myClient.read().resource(Bundle.class).withId(id).execute();
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(retBundle));
 		
 		assertEquals("http://foo", bundle.getEntry().get(0).getFullUrl());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CacheTest.java

@@ -4,6 +4,8 @@ import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
 import ca.uhn.fhir.parser.StrictErrorHandler;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.r4.model.Bundle;
@@ -14,13 +16,17 @@ import org.junit.Test;
 import org.springframework.test.util.AopTestUtils;
 
 import java.io.IOException;
+import java.util.Date;
 
+import static org.hamcrest.Matchers.*;
+import static org.hamcrest.core.IsNot.not;
 import static org.junit.Assert.*;
 
 public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4CacheTest.class);
 	private SearchCoordinatorSvcImpl mySearchCoordinatorSvcRaw;
+	private CapturingInterceptor myCapturingInterceptor;
 
 	@Override
 	@After
@@ -28,6 +34,8 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 		super.after();
 		myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
 		myDaoConfig.setCacheControlNoStoreMaxResultsUpperLimit(new DaoConfig().getCacheControlNoStoreMaxResultsUpperLimit());
+
+		myClient.unregisterInterceptor(myCapturingInterceptor);
 	}
 
 	@Override
@@ -35,6 +43,9 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 		super.before();
 		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
 		mySearchCoordinatorSvcRaw = AopTestUtils.getTargetObject(mySearchCoordinatorSvc);
+
+		myCapturingInterceptor = new CapturingInterceptor();
+		myClient.registerInterceptor(myCapturingInterceptor);
 	}
 
 	@Test
@@ -42,9 +53,9 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 
 		Patient pt1 = new Patient();
 		pt1.addName().setFamily("FAM");
-		ourClient.create().resource(pt1).execute();
+		myClient.create().resource(pt1).execute();
 
-		Bundle results = ourClient
+		Bundle results = myClient
 			.search()
 			.forResource("Patient")
 			.where(Patient.FAMILY.matches().value("FAM"))
@@ -53,12 +64,13 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 			.execute();
 		assertEquals(1, results.getEntry().size());
 		assertEquals(0, mySearchEntityDao.count());
+		assertThat(myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE), empty());
 
 		Patient pt2 = new Patient();
 		pt2.addName().setFamily("FAM");
-		ourClient.create().resource(pt2).execute();
+		myClient.create().resource(pt2).execute();
 
-		results = ourClient
+		results = myClient
 			.search()
 			.forResource("Patient")
 			.where(Patient.FAMILY.matches().value("FAM"))
@@ -67,6 +79,7 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 			.execute();
 		assertEquals(2, results.getEntry().size());
 		assertEquals(0, mySearchEntityDao.count());
+		assertThat(myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE), empty());
 
 	}
 
@@ -76,10 +89,10 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 		for (int i = 0; i < 10; i++) {
 			Patient pt1 = new Patient();
 			pt1.addName().setFamily("FAM" + i);
-			ourClient.create().resource(pt1).execute();
+			myClient.create().resource(pt1).execute();
 		}
 
-		Bundle results = ourClient
+		Bundle results = myClient
 			.search()
 			.forResource("Patient")
 			.where(Patient.FAMILY.matches().value("FAM"))
@@ -88,6 +101,7 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 			.execute();
 		assertEquals(5, results.getEntry().size());
 		assertEquals(0, mySearchEntityDao.count());
+		assertThat(myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE), empty());
 
 	}
 
@@ -95,7 +109,7 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 	public void testCacheNoStoreMaxResultsWithIllegalValue() throws IOException {
 		myDaoConfig.setCacheControlNoStoreMaxResultsUpperLimit(123);
 		try {
-			ourClient
+			myClient
 				.search()
 				.forResource("Patient")
 				.where(Patient.FAMILY.matches().value("FAM"))
@@ -113,17 +127,18 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 
 		Patient pt1 = new Patient();
 		pt1.addName().setFamily("FAM");
-		ourClient.create().resource(pt1).execute();
+		myClient.create().resource(pt1).execute();
 
-		Bundle results = ourClient.search().forResource("Patient").where(Patient.FAMILY.matches().value("FAM")).returnBundle(Bundle.class).execute();
+		Bundle results = myClient.search().forResource("Patient").where(Patient.FAMILY.matches().value("FAM")).returnBundle(Bundle.class).execute();
 		assertEquals(1, results.getEntry().size());
 		assertEquals(1, mySearchEntityDao.count());
+		assertThat(myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE), empty());
 
 		Patient pt2 = new Patient();
 		pt2.addName().setFamily("FAM");
-		ourClient.create().resource(pt2).execute();
+		myClient.create().resource(pt2).execute();
 
-		results = ourClient
+		results = myClient
 			.search()
 			.forResource("Patient")
 			.where(Patient.FAMILY.matches().value("FAM"))
@@ -132,6 +147,7 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 			.execute();
 		assertEquals(2, results.getEntry().size());
 		assertEquals(2, mySearchEntityDao.count());
+		assertThat(myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE), empty());
 
 	}
 
@@ -140,20 +156,28 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 
 		Patient pt1 = new Patient();
 		pt1.addName().setFamily("FAM");
-		ourClient.create().resource(pt1).execute();
+		myClient.create().resource(pt1).execute();
 
-		Bundle results = ourClient.search().forResource("Patient").where(Patient.FAMILY.matches().value("FAM")).returnBundle(Bundle.class).execute();
+		Date beforeFirst = new Date();
-		assertEquals(1, results.getEntry().size());
+
+		Bundle results1 = myClient.search().forResource("Patient").where(Patient.FAMILY.matches().value("FAM")).returnBundle(Bundle.class).execute();
+		assertEquals(1, results1.getEntry().size());
 		assertEquals(1, mySearchEntityDao.count());
+		assertThat(myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE), empty());
+		assertThat(results1.getMeta().getLastUpdated(), greaterThan(beforeFirst));
+		assertThat(results1.getMeta().getLastUpdated(), lessThan(new Date()));
+		assertThat(results1.getId(), not(blankOrNullString()));
 
 		Patient pt2 = new Patient();
 		pt2.addName().setFamily("FAM");
-		ourClient.create().resource(pt2).execute();
+		myClient.create().resource(pt2).execute();
 
-		results = ourClient.search().forResource("Patient").where(Patient.FAMILY.matches().value("FAM")).returnBundle(Bundle.class).execute();
+		Bundle results2 = myClient.search().forResource("Patient").where(Patient.FAMILY.matches().value("FAM")).returnBundle(Bundle.class).execute();
-		assertEquals(1, results.getEntry().size());
+		assertEquals(1, results2.getEntry().size());
 		assertEquals(1, mySearchEntityDao.count());
-
+		assertEquals("HIT from " + ourServerBase, myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE).get(0));
+		assertEquals(results1.getMeta().getLastUpdated(), results2.getMeta().getLastUpdated());
+		assertEquals(results1.getId(), results2.getId());
 	}
 
 	@AfterClass