Merge remote-tracking branch 'remotes/origin/master' into ks-flyway

# Conflicts:
#	src/changes/changes.xml

azure-pipelines.yml

@@ -13,19 +13,22 @@ pool:
 jobs:
   - job: Build
     timeoutInMinutes: 360
+    container: maven:3-jdk-11
     steps:
       - task: CacheBeta@0
         inputs:
           key: maven
           path: $(MAVEN_CACHE_FOLDER)
-          displayName: Cache Maven local repo
       - task: Maven@3
+        env:
+          JAVA_HOME_11_X64: /usr/local/openjdk-11
         inputs:
           goals: 'clean install'
           # These are Maven CLI options (and show up in the build logs) - "-nsu"=Don't update snapshots. We can remove this when Maven OSS is more healthy
-          options: '-P ALLMODULES,JACOCO -nsu'
+          options: '-P ALLMODULES,JACOCO,CI -nsu'
           # These are JVM options (and don't show up in the build logs)
           mavenOptions: '-Xmx2048m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS -Duser.timezone=America/Toronto'
+          jdkVersionOption: 1.11
       - script: bash <(curl https://codecov.io/bash) -t $(CODECOV_TOKEN)
         displayName: 'codecov'
       - task: PublishCodeCoverageResults@1

hapi-fhir-base/pom.xml

@@ -145,7 +145,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>

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

@@ -20,6 +20,12 @@ package ca.uhn.fhir.context;
  * #L%
  */
 
+import ca.uhn.fhir.model.api.ExtensionDt;
+import ca.uhn.fhir.model.api.IDatatype;
+import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
+import org.apache.commons.text.WordUtils;
+import org.hl7.fhir.instance.model.api.IBase;
+
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -27,18 +33,11 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import org.apache.commons.text.WordUtils;
-import org.hl7.fhir.instance.model.api.IBase;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-
-import ca.uhn.fhir.model.api.ExtensionDt;
-import ca.uhn.fhir.model.api.IDatatype;
-import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
-
 public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildDefinition {
 
 	private static final String VALUE_REFERENCE = "valueReference";
 	private static final String VALUE_RESOURCE = "valueResource";
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RuntimeChildUndeclaredExtensionDefinition.class);
 	private Map<String, BaseRuntimeElementDefinition<?>> myAttributeNameToDefinition;
 	private Map<Class<? extends IBase>, String> myDatatypeToAttributeName;
 	private Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myDatatypeToDefinition;
@@ -48,15 +47,13 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 	}
 
 	private void addReferenceBinding(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions, String value) {
-		List<Class<? extends IBaseResource>> types = new ArrayList<Class<? extends IBaseResource>>();
-		types.add(IBaseResource.class);
 		BaseRuntimeElementDefinition<?> def = findResourceReferenceDefinition(theClassToElementDefinitions);
 
 		myAttributeNameToDefinition.put(value, def);
 		/*
 		 * Resource reference - The correct name is 'valueReference' in DSTU2 and 'valueResource' in DSTU1
 		 */
-		if (value != VALUE_RESOURCE) {
+		if (!value.equals(VALUE_RESOURCE)) {
 			myDatatypeToAttributeName.put(theContext.getVersion().getResourceReferenceType(), value);
 			myDatatypeToDefinition.put(BaseResourceReferenceDt.class, def);
 			myDatatypeToDefinition.put(theContext.getVersion().getResourceReferenceType(), def);
@@ -71,10 +68,9 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 			public List<IBase> getValues(IBase theTarget) {
 				ExtensionDt target = (ExtensionDt) theTarget;
 				if (target.getValue() != null) {
-					return Collections.singletonList((IBase) target.getValue());
+					return Collections.singletonList(target.getValue());
 				}
-				ArrayList<IBase> retVal = new ArrayList<IBase>(target.getUndeclaredExtensions());
-				return retVal;
+				return new ArrayList<>(target.getUndeclaredExtensions());
 			}
 
 		};
@@ -116,22 +112,13 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 			@Override
 			public void addValue(IBase theTarget, IBase theValue) {
 				ExtensionDt target = (ExtensionDt) theTarget;
-				if (theValue instanceof IDatatype) {
-					target.setValue((IDatatype) theTarget);
-				} else {
-					target.getUndeclaredExtensions().add((ExtensionDt) theValue);
-				}
+				target.setValue((IDatatype) theTarget);
 			}
 
 			@Override
 			public void setValue(IBase theTarget, IBase theValue) {
 				ExtensionDt target = (ExtensionDt) theTarget;
-				if (theValue instanceof IDatatype) {
-					target.setValue((IDatatype) theTarget);
-				} else {
-					target.getUndeclaredExtensions().clear();
-					target.getUndeclaredExtensions().add((ExtensionDt) theValue);
-				}
+				target.setValue((IDatatype) theTarget);
 			}
 		};
 	}
@@ -146,8 +133,6 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 		return false;
 	}
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RuntimeChildUndeclaredExtensionDefinition.class);
-	
 	@Override
 	void sealAndInitialize(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
 		Map<String, BaseRuntimeElementDefinition<?>> datatypeAttributeNameToDefinition = new HashMap<>();
@@ -163,15 +148,15 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 				if (isSpecialization) {
 					ourLog.trace("Not adding specialization: {}", next.getImplementingClass());
 				}
-				
+
 				if (!isSpecialization) {
-					
+
 					if (!next.isStandardType()) {
 						continue;
 					}
-					
+
 					String qualifiedName = next.getImplementingClass().getName();
-					
+
 					/*
 					 * We don't want user-defined custom datatypes ending up overriding the built in
 					 * types here. It would probably be better for there to be a way for
@@ -183,7 +168,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 							continue;
 						}
 					}
-					
+
 					String attrName = createExtensionChildName(next);
 					if (datatypeAttributeNameToDefinition.containsKey(attrName)) {
 						BaseRuntimeElementDefinition<?> existing = datatypeAttributeNameToDefinition.get(attrName);
@@ -207,8 +192,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 	}
 
 	public static String createExtensionChildName(BaseRuntimeElementDefinition<?> next) {
-		String attrName = "value" + WordUtils.capitalize(next.getName());
-		return attrName;
+		return "value" + WordUtils.capitalize(next.getName());
 	}
 
 }

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

@@ -22,10 +22,16 @@ package ca.uhn.fhir.parser;
 
 import ca.uhn.fhir.context.*;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
-import ca.uhn.fhir.model.api.*;
+import ca.uhn.fhir.model.api.IIdentifiableElement;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.Tag;
+import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
 import org.apache.commons.lang3.StringUtils;
@@ -35,7 +41,13 @@ import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.hl7.fhir.instance.model.api.*;
 
 import javax.annotation.Nullable;
-import java.io.*;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.Writer;
 import java.lang.reflect.Modifier;
 import java.util.*;
 import java.util.stream.Collectors;
@@ -530,11 +542,6 @@ public abstract class BaseParser implements IParser {
 		return tags;
 	}
 
-	@Override
-	public Boolean getOverrideResourceIdWithBundleEntryFullUrl() {
-		return myOverrideResourceIdWithBundleEntryFullUrl;
-	}
-
 	@Override
 	public List<Class<? extends IBaseResource>> getPreferTypes() {
 		return myPreferTypes;
@@ -705,39 +712,38 @@ public abstract class BaseParser implements IParser {
 		RuntimeResourceDefinition def = myContext.getResourceDefinition(retVal);
 		if ("Bundle".equals(def.getName())) {
 
-			BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
-			BaseRuntimeElementCompositeDefinition<?> entryDef = (BaseRuntimeElementCompositeDefinition<?>) entryChild.getChildByName("entry");
-			List<IBase> entries = entryChild.getAccessor().getValues(retVal);
-			if (entries != null) {
-				for (IBase nextEntry : entries) {
-
-					/**
-					 * If Bundle.entry.fullUrl is populated, set the resource ID to that
-					 */
-					// TODO: should emit a warning and maybe notify the error handler if the resource ID doesn't match the
-					// fullUrl idPart
-					BaseRuntimeChildDefinition fullUrlChild = entryDef.getChildByName("fullUrl");
-					if (fullUrlChild == null) {
-						continue; // TODO: remove this once the data model in tinder plugin catches up to 1.2
-					}
-					if (isOverrideResourceIdWithBundleEntryFullUrl()) {
-						List<IBase> fullUrl = fullUrlChild.getAccessor().getValues(nextEntry);
-						if (fullUrl != null && !fullUrl.isEmpty()) {
-							IPrimitiveType<?> value = (IPrimitiveType<?>) fullUrl.get(0);
-							if (value.isEmpty() == false) {
-								List<IBase> entryResources = entryDef.getChildByName("resource").getAccessor().getValues(nextEntry);
-								if (entryResources != null && entryResources.size() > 0) {
-									IBaseResource res = (IBaseResource) entryResources.get(0);
-									String versionId = res.getIdElement().getVersionIdPart();
-									res.setId(value.getValueAsString());
-									if (isNotBlank(versionId) && res.getIdElement().hasVersionIdPart() == false) {
-										res.setId(res.getIdElement().withVersion(versionId));
+			if (isOverrideResourceIdWithBundleEntryFullUrl()) {
+				BundleUtil.processEntries(myContext, (IBaseBundle) retVal, t -> {
+					String fullUrl = t.getFullUrl();
+					if (fullUrl != null) {
+						IBaseResource resource = t.getResource();
+						if (resource != null) {
+							IIdType resourceId = resource.getIdElement();
+							if (isBlank(resourceId.getValue())) {
+								resourceId.setValue(fullUrl);
+							} else {
+								if (fullUrl.startsWith("urn:") && fullUrl.endsWith(":" + resourceId.getIdPart())) {
+									resourceId.setValue(fullUrl);
+								} else {
+									IIdType fullUrlId = myContext.getVersion().newIdType();
+									fullUrlId.setValue(fullUrl);
+									if (myContext.getVersion().getVersion().isOlderThan(FhirVersionEnum.DSTU3)) {
+										IIdType newId = fullUrlId;
+										if (!newId.hasVersionIdPart() && resourceId.hasVersionIdPart()) {
+											newId = newId.withVersion(resourceId.getVersionIdPart());
+										}
+										resourceId.setValue(newId.getValue());
+									} else if (StringUtils.equals(fullUrlId.getIdPart(), resourceId.getIdPart())) {
+										if (fullUrlId.hasBaseUrl()) {
+											IIdType newResourceId = resourceId.withServerBase(fullUrlId.getBaseUrl(), resourceId.getResourceType());
+											resourceId.setValue(newResourceId.getValue());
+										}
 									}
 								}
 							}
 						}
 					}
-				}
+				});
 			}
 
 		}

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

@@ -92,19 +92,6 @@ public interface IParser {
 	 */
 	Boolean getStripVersionsFromReferences();
 
-	/**
-	 * If set to <code>true</code> (which is the default), the Bundle.entry.fullUrl will override the Bundle.entry.resource's
-	 * resource id if the fullUrl is defined. This behavior happens when parsing the source data into a Bundle object. Set this
-	 * to <code>false</code> if this is not the desired behavior (e.g. the client code wishes to perform additional
-	 * validation checks between the fullUrl and the resource id).
-	 *
-	 * @return Returns the parser instance's configuration setting for overriding resource ids with Bundle.entry.fullUrl when
-	 *         parsing the source data into a Bundle object. This method will return <code>null</code> if no value is set, in
-	 *         which case the value from the {@link ParserOptions} will be used (default is <code>true</code>)
-	 * @see ParserOptions
-	 */
-	Boolean getOverrideResourceIdWithBundleEntryFullUrl();
-
 	/**
 	 * Is the parser in "summary mode"? See {@link #setSummaryMode(boolean)} for information
 	 * 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/StringParam.java

@@ -19,22 +19,25 @@ package ca.uhn.fhir.rest.param;
  * limitations under the License.
  * #L%
  */
-import static org.apache.commons.lang3.StringUtils.defaultString;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.builder.*;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.api.Constants;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
+
+import static org.apache.commons.lang3.StringUtils.defaultString;
 
 public class StringParam extends BaseParam implements IQueryParameterType {
 
 	private boolean myContains;
 	private boolean myExact;
 	private String myValue;
-	
+
 	/**
 	 * Constructor
 	 */
@@ -72,6 +75,16 @@ public class StringParam extends BaseParam implements IQueryParameterType {
 		return ParameterUtil.escape(myValue);
 	}
 
+	@Override
+	public int hashCode() {
+		return new HashCodeBuilder(17, 37)
+			.append(myExact)
+			.append(myContains)
+			.append(myValue)
+			.append(getMissing())
+			.toHashCode();
+	}
+
 	@Override
 	void doSetValueAsQueryToken(FhirContext theContext, String theParamName, String theQualifier, String theValue) {
 		if (Constants.PARAMQUALIFIER_STRING_EXACT.equals(theQualifier)) {
@@ -106,7 +119,7 @@ public class StringParam extends BaseParam implements IQueryParameterType {
 		eb.append(myContains, other.myContains);
 		eb.append(myValue, other.myValue);
 		eb.append(getMissing(), other.getMissing());
-		
+
 		return eb.isEquals();
 	}
 
@@ -114,6 +127,11 @@ public class StringParam extends BaseParam implements IQueryParameterType {
 		return myValue;
 	}
 
+	public StringParam setValue(String theValue) {
+		myValue = theValue;
+		return this;
+	}
+
 	public StringDt getValueAsStringDt() {
 		return new StringDt(myValue);
 	}
@@ -129,14 +147,6 @@ public class StringParam extends BaseParam implements IQueryParameterType {
 		return myContains;
 	}
 
-	public boolean isEmpty() {
-		return StringUtils.isEmpty(myValue);
-	}
-
-	public boolean isExact() {
-		return myExact;
-	}
-
 	/**
 	 * String parameter modifier <code>:contains</code>
 	 */
@@ -149,6 +159,14 @@ public class StringParam extends BaseParam implements IQueryParameterType {
 		return this;
 	}
 
+	public boolean isEmpty() {
+		return StringUtils.isEmpty(myValue);
+	}
+
+	public boolean isExact() {
+		return myExact;
+	}
+
 	public StringParam setExact(boolean theExact) {
 		myExact = theExact;
 		if (myExact) {
@@ -158,11 +176,6 @@ public class StringParam extends BaseParam implements IQueryParameterType {
 		return this;
 	}
 
-	public StringParam setValue(String theValue) {
-		myValue = theValue;
-		return this;
-	}
-
 	@Override
 	public String toString() {
 		ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);

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

@@ -168,6 +168,8 @@ public class BundleUtil {
 
 		BaseRuntimeElementCompositeDefinition<?> entryChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) entryChildDef.getChildByName("entry");
 
+		BaseRuntimeChildDefinition fullUrlChildDef = entryChildContentsDef.getChildByName("fullUrl");
+
 		BaseRuntimeChildDefinition resourceChildDef = entryChildContentsDef.getChildByName("resource");
 		BaseRuntimeChildDefinition requestChildDef = entryChildContentsDef.getChildByName("request");
 		BaseRuntimeElementCompositeDefinition<?> requestChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) requestChildDef.getChildByName("request");
@@ -180,6 +182,11 @@ public class BundleUtil {
 			String url = null;
 			RequestTypeEnum requestType = null;
 			String conditionalUrl = null;
+			String fullUrl = fullUrlChildDef
+				.getAccessor()
+				.getFirstValueOrNull(nextEntry)
+				.map(t->((IPrimitiveType<?>)t).getValueAsString())
+				.orElse(null);
 
 			for (IBase nextResource : resourceChildDef.getAccessor().getValues(nextEntry)) {
 				resource = (IBaseResource) nextResource;
@@ -217,7 +224,7 @@ public class BundleUtil {
 			 * order in the original bundle.
 			 */
 			BundleEntryMutator mutator = new BundleEntryMutator(nextEntry, requestChildDef, requestChildContentsDef);
-			ModifiableBundleEntry entry = new ModifiableBundleEntry(new BundleEntryParts(requestType, url, resource, conditionalUrl), mutator);
+			ModifiableBundleEntry entry = new ModifiableBundleEntry(new BundleEntryParts(fullUrl, requestType, url, resource, conditionalUrl), mutator);
 			theProcessor.accept(entry);
 		}
 	}

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

@@ -28,15 +28,21 @@ public class BundleEntryParts {
 	private final IBaseResource myResource;
 	private final String myUrl;
 	private final String myConditionalUrl;
+	private final String myFullUrl;
 
-	public BundleEntryParts(RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource, String theConditionalUrl) {
+	public BundleEntryParts(String theFullUrl, RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource, String theConditionalUrl) {
 		super();
+		myFullUrl = theFullUrl;
 		myRequestType = theRequestType;
 		myUrl = theUrl;
 		myResource = theResource;
 		myConditionalUrl = theConditionalUrl;
 	}
 
+	public String getFullUrl() {
+		return myFullUrl;
+	}
+
 	public RequestTypeEnum getRequestType() {
 		return myRequestType;
 	}

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.util.bundle;
  */
 
 import ca.uhn.fhir.context.FhirContext;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 
 public class ModifiableBundleEntry {
 	private final BundleEntryParts myBundleEntryParts;
@@ -39,7 +40,15 @@ public class ModifiableBundleEntry {
 		myBundleEntryMutator.setRequestUrl(theFhirContext, theRequestUrl);
 	}
 
+	public String getFullUrl() {
+		return myBundleEntryParts.getFullUrl();
+	}
+
 	public String getRequestUrl() {
 		return myBundleEntryParts.getUrl();
 	}
+
+	public IBaseResource getResource() {
+		return myBundleEntryParts.getResource();
+	}
 }

hapi-fhir-client/pom.xml

@@ -58,7 +58,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/ConditionalParamBinder.java

@@ -44,7 +44,7 @@ class ConditionalParamBinder implements IParameter {
 	@Override
 	public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
 		if (theOuterCollectionType != null || theInnerCollectionType != null || theParameterType.equals(String.class) == false) {
-			throw new ConfigurationException("Parameters annotated with @" + ConditionalUrlParam.class.getSimpleName()  + " must be of type String, found incorrect parameteter in method \"" + theMethod + "\"");
+			throw new ConfigurationException("Parameters annotated with @" + ConditionalUrlParam.class.getSimpleName()  + " must be of type String, found incorrect parameter in method \"" + theMethod + "\"");
 		}
 	}
 

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/MethodUtil.java

@@ -208,23 +208,10 @@ public class MethodUtil {
 		return b;
 	}
 
-	public static void extractDescription(SearchParameter theParameter, Annotation[] theAnnotations) {
-		for (Annotation annotation : theAnnotations) {
-			if (annotation instanceof Description) {
-				Description desc = (Description) annotation;
-				if (isNotBlank(desc.formalDefinition())) {
-					theParameter.setDescription(desc.formalDefinition());
-				} else {
-					theParameter.setDescription(desc.shortDefinition());
-				}
-			}
-		}
-	}
-
 	@SuppressWarnings("unchecked")
 	public static List<IParameter> getResourceParameters(final FhirContext theContext, Method theMethod,
 			Object theProvider, RestOperationTypeEnum theRestfulOperationTypeEnum) {
-		List<IParameter> parameters = new ArrayList<IParameter>();
+		List<IParameter> parameters = new ArrayList<>();
 
 		Class<?>[] parameterTypes = theMethod.getParameterTypes();
 		int paramIndex = 0;
@@ -271,7 +258,6 @@ public class MethodUtil {
 						parameter.setChainlists(((RequiredParam) nextAnnotation).chainWhitelist(),
 								((RequiredParam) nextAnnotation).chainBlacklist());
 						parameter.setType(theContext, parameterType, innerCollectionType, outerCollectionType);
-						MethodUtil.extractDescription(parameter, annotations);
 						param = parameter;
 					} else if (nextAnnotation instanceof OptionalParam) {
 						SearchParameter parameter = new SearchParameter();
@@ -282,7 +268,6 @@ public class MethodUtil {
 						parameter.setChainlists(((OptionalParam) nextAnnotation).chainWhitelist(),
 								((OptionalParam) nextAnnotation).chainBlacklist());
 						parameter.setType(theContext, parameterType, innerCollectionType, outerCollectionType);
-						MethodUtil.extractDescription(parameter, annotations);
 						param = parameter;
 					} else if (nextAnnotation instanceof RawParam) {
 						param = new RawParamsParmeter();

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

@@ -76,7 +76,7 @@ public class JaxRsRestfulClientFactory extends RestfulClientFactory {
 	}
 
 	@Override
-	public IHttpClient getHttpClient(StringBuilder url, Map<String, List<String>> theIfNoneExistParams, String theIfNoneExistString, RequestTypeEnum theRequestType, List<Header> theHeaders) {
+	public synchronized IHttpClient getHttpClient(StringBuilder url, Map<String, List<String>> theIfNoneExistParams, String theIfNoneExistString, RequestTypeEnum theRequestType, List<Header> theHeaders) {
 		Client client = getNativeClientClient();
 		return new JaxRsHttpClient(client, url, theIfNoneExistParams, theIfNoneExistString, theRequestType, theHeaders);
 	}
@@ -112,7 +112,7 @@ public class JaxRsRestfulClientFactory extends RestfulClientFactory {
 
 
 	@Override
-	protected JaxRsHttpClient getHttpClient(String theServerBase) {
+	protected synchronized JaxRsHttpClient getHttpClient(String theServerBase) {
 		return new JaxRsHttpClient(getNativeClientClient(), new StringBuilder(theServerBase), null, null, null, null);
 	}
   

hapi-fhir-jpaserver-base/pom.xml

@@ -698,7 +698,7 @@
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
 					<runOrder>alphabetical</runOrder>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx20484M -Xss128M -XX:MetaspaceSize=512M -XX:MaxMetaspaceSize=2048M -XX:+CMSClassUnloadingEnabled -XX:+UseConcMarkSweepGC</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 					<forkCount>0.6C</forkCount>
 					<excludes>*StressTest*</excludes>
 				</configuration>

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

@@ -96,6 +96,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 	public static final int DEFAULT_SYNC_SIZE = 250;
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchCoordinatorSvcImpl.class);
+	public static final String UNIT_TEST_CAPTURE_STACK = "unit_test_capture_stack";
 	private final ConcurrentHashMap<String, SearchTask> myIdToSearchTask = new ConcurrentHashMap<>();
 	@Autowired
 	private FhirContext myContext;
@@ -902,6 +903,10 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 					failureCode = ((BaseServerResponseException) t).getStatusCode();
 				}
 
+				if (System.getProperty(UNIT_TEST_CAPTURE_STACK) != null) {
+					failureMessage += "\n" + ExceptionUtils.getStackTrace(rootCause);
+				}
+
 				mySearch.setFailureMessage(failureMessage);
 				mySearch.setFailureCode(failureCode);
 				mySearch.setStatus(SearchStatusEnum.FAILED);

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

@@ -31,7 +31,7 @@ public interface IValueSetConceptAccumulator {
 
 	void includeConcept(String theSystem, String theCode, String theDisplay);
 
-	void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations);
+	void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, @Nullable Collection<TermConceptDesignation> theDesignations);
 
 	void excludeConcept(String theSystem, String theCode);
 

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

@@ -34,7 +34,9 @@ import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isAnyBlank;
+import static org.apache.commons.lang3.StringUtils.isNoneBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValueSetConceptAccumulator.class);
@@ -71,8 +73,10 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
 	@Override
 	public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
 		TermValueSetConcept concept = saveConcept(theSystem, theCode, theDisplay);
-		for (TermConceptDesignation designation : theDesignations) {
-			saveConceptDesignation(concept, designation);
+		if (theDesignations != null) {
+			for (TermConceptDesignation designation : theDesignations) {
+				saveConceptDesignation(concept, designation);
+			}
 		}
 	}
 

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

@@ -25,7 +25,6 @@ import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import org.apache.commons.csv.CSVRecord;
 import org.apache.commons.lang3.Validate;
-import org.hl7.fhir.r4.model.ValueSet;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -37,7 +36,6 @@ public class LoincPartHandler implements IRecordHandler {
 
 	private final Map<String, TermConcept> myCode2Concept;
 	private final TermCodeSystemVersion myCodeSystemVersion;
-	private final Map<String, ValueSet> myIdToValueSet = new HashMap<>();
 	private final Map<PartTypeAndPartName, String> myPartTypeAndPartNameToPartNumber = new HashMap<>();
 
 	public LoincPartHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.model.entity.*;
 import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap.EverythingModeEnum;
+import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
 import ca.uhn.fhir.jpa.util.TestUtil;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
@@ -229,6 +230,36 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 
 	}
 
+	@Test
+	public void testHasChain() {
+
+		Patient p = new Patient();
+		p.setId("P");
+		p.setActive(true);
+		myPatientDao.update(p);
+
+		Group group = new Group();
+		group.setId("G");
+		group.addMember().getEntity().setReference("Patient/P");
+		myGroupDao.update(group);
+
+		DiagnosticReport dr = new DiagnosticReport();
+		dr.setId("DR");
+		dr.getSubject().setReference("Patient/P");
+		myDiagnosticReportDao.update(dr);
+
+		SearchParameterMap map = new SearchParameterMap();
+		map.setLoadSynchronous(true);
+
+		ReferenceParam referenceParam = new ReferenceParam();
+		referenceParam.setValueAsQueryToken(myFhirCtx, "subject", "._has:Group:member:_id", "Group/G");
+		map.add("subject", referenceParam);
+		List<String> actual = toUnqualifiedVersionlessIdValues(myDiagnosticReportDao.search(map));
+		assertThat(actual, containsInAnyOrder("DiagnosticReport/DR"));
+
+		// http://hapi.fhir.org/baseR4/DiagnosticReport?subject._has:Group:member:_id=52152
+	}
+
 	@SuppressWarnings("unused")
 	@Test
 	public void testHasAndHas() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
@@ -2154,6 +2155,27 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testSearchResourceLinkOnCanonical() {
+
+		Questionnaire q = new Questionnaire();
+		q.setId("Q");
+		myQuestionnaireDao.update(q);
+
+		QuestionnaireResponse qr = new QuestionnaireResponse();
+		qr.setId("QR");
+		qr.setQuestionnaire("Questionnaire/Q");
+		String qrId = myQuestionnaireResponseDao.update(qr).getId().toUnqualifiedVersionless().getValue();
+
+		List<QuestionnaireResponse> result = toList(myQuestionnaireResponseDao
+			.search(new SearchParameterMap().setLoadSynchronous(true).add(QuestionnaireResponse.SP_QUESTIONNAIRE, new ReferenceParam("Questionnaire/Q"))));
+		assertEquals(1, result.size());
+		assertEquals(qrId, result.get(0).getIdElement().toUnqualifiedVersionless().getValue());
+
+
+	}
+
+
 	@Test
 	public void testSearchResourceLinkWithChain() {
 		Patient patient = new Patient();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java

@@ -10,6 +10,8 @@ import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
+import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -116,6 +118,8 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
 	private IResourceReindexingSvc myResourceReindexingSvc;
 	@Autowired
 	private IBulkDataExportSvc myBulkDataExportSvc;
+	@Autowired
+	private ITermReadSvc myTermSvc;
 
 	@Before
 	@Transactional()
@@ -190,6 +194,36 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
 		}
 	}
 
+	@Test
+		public void testExpandValueSet() {
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://fooCS");
+		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		cs.addConcept().setCode("CODEA");
+		cs.addConcept().setCode("CODEB");
+		myCodeSystemDao.create(cs);
+
+		ValueSet vs = new ValueSet();
+		vs.setUrl("http://fooVS");
+		vs.getCompose()
+			.addInclude()
+			.setSystem("http://fooCS")
+			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("CODEA"));
+
+		// Explicit expand
+		ValueSet outcome = myValueSetDao.expand(vs, null);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
+		assertEquals("CODEA", outcome.getExpansion().getContains().get(0).getCode());
+
+		// Deferred expand
+		IIdType id = myValueSetDao.create(vs).getId().toUnqualifiedVersionless();
+		myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
+		outcome = myValueSetDao.expand(id, null, mySrd);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
+		assertEquals("CODEA", outcome.getExpansion().getContains().get(0).getCode());
+	}
+
+
 	@Test
 	public void testSearchByCodeIn() {
 		CodeSystem cs = new CodeSystem();
@@ -207,6 +241,7 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
 			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("CODEA"));
 		myValueSetDao.create(vs);
 
+
 		Observation obs = new Observation();
 		obs.getCode().addCoding().setSystem("http://fooCS").setCode("CODEA");
 		String obs1id = myObservationDao.create(obs).getId().toUnqualifiedVersionless().getValue();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java

@@ -77,11 +77,14 @@ public class SearchCoordinatorSvcImplTest {
 
 	@After
 	public void after() {
+		System.clearProperty(SearchCoordinatorSvcImpl.UNIT_TEST_CAPTURE_STACK);
 		verify(myCallingDao, atMost(myExpectedNumberOfSearchBuildersCreated)).newSearchBuilder();
 	}
 
 	@Before
 	public void before() {
+		System.setProperty(SearchCoordinatorSvcImpl.UNIT_TEST_CAPTURE_STACK, "true");
+
 		myCurrentSearch = null;
 
 		mySvc = new SearchCoordinatorSvcImpl();
@@ -148,7 +151,8 @@ public class SearchCoordinatorSvcImplTest {
 		try {
 			result.getResources(0, 100000);
 		} catch (InternalErrorException e) {
-			assertEquals("FAILED", e.getMessage());
+			assertThat(e.getMessage(), containsString("FAILED"));
+			assertThat(e.getMessage(), containsString("at ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImplTest"));
 		}
 
 	}
@@ -187,9 +191,7 @@ public class SearchCoordinatorSvcImplTest {
 		when(mySearchResultCacheSvc.fetchAllResultPids(any())).thenReturn(allResults);
 
 		when(mySearchCacheSvc.tryToMarkSearchAsInProgress(any())).thenAnswer(t->{
-			Object argument = t.getArgument(0);
-			Validate.isTrue( argument instanceof Search, "Argument is " + argument);
-			Search search = (Search) argument;
+			Search search = t.getArgument(0, Search.class);
 			assertEquals(SearchStatusEnum.PASSCMPLET, search.getStatus());
 			search.setStatus(SearchStatusEnum.LOADING);
 			return Optional.of(search);
@@ -202,7 +204,7 @@ public class SearchCoordinatorSvcImplTest {
 		List<IBaseResource> resources;
 
 		when(mySearchCacheSvc.save(any())).thenAnswer(t -> {
-			Search search = (Search) t.getArguments()[0];
+			Search search = t.getArgument(0, Search.class);
 			myCurrentSearch = search;
 			return search;
 		});
@@ -328,7 +330,8 @@ public class SearchCoordinatorSvcImplTest {
 		try {
 			result.getResources(10, 20);
 		} catch (InternalErrorException e) {
-			assertEquals("Abort has been requested", e.getMessage());
+			assertThat(e.getMessage(), containsString("Abort has been requested"));
+			assertThat(e.getMessage(), containsString("at ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl"));
 		}
 
 		completionLatch.await(10, TimeUnit.SECONDS);

hapi-fhir-jpaserver-base/src/test/resources/david_big_bundle.json

@@ -2666,7 +2666,7 @@
 			"fullUrl": "http://fhirtest.uhn.ca/baseDstu3/Practitioner/A45515",
 			"resource": {
 				"resourceType": "Practitioner",
-				"id": "45515",
+				"id": "A45515",
 				"meta": {
 					"versionId": "1",
 					"lastUpdated": "2016-05-07T11:45:53.918-04:00"

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -160,7 +160,7 @@
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
 					<runOrder>alphabetical</runOrder>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx20484M -Xss128M -XX:MetaspaceSize=512M -XX:MaxMetaspaceSize=2048M -XX:+CMSClassUnloadingEnabled -XX:+UseConcMarkSweepGC</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 					<forkCount>0.6C</forkCount>
 					<excludes>*StressTest*</excludes>
 				</configuration>

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/ResourceMetaParams.java

@@ -23,6 +23,8 @@ package ca.uhn.fhir.jpa.searchparam;
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.param.HasAndListParam;
+import ca.uhn.fhir.rest.param.HasParam;
 import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
@@ -61,6 +63,8 @@ public class ResourceMetaParams {
 		resourceMetaAndParams.put(Constants.PARAM_PROFILE, UriAndListParam.class);
 		resourceMetaParams.put(Constants.PARAM_SECURITY, TokenParam.class);
 		resourceMetaAndParams.put(Constants.PARAM_SECURITY, TokenAndListParam.class);
+		resourceMetaParams.put(Constants.PARAM_HAS, HasParam.class);
+		resourceMetaAndParams.put(Constants.PARAM_HAS, HasAndListParam.class);
 		RESOURCE_META_PARAMS = Collections.unmodifiableMap(resourceMetaParams);
 		RESOURCE_META_AND_PARAMS = Collections.unmodifiableMap(resourceMetaAndParams);
 

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java

@@ -51,6 +51,7 @@ import org.hl7.fhir.instance.model.api.IBaseReference;
 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.IdType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 
@@ -151,7 +152,31 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 
 			String nextType = toRootTypeName(value);
 			switch (nextType) {
+				case "uri":
 				case "canonical":
+					String typeName = toTypeName(value);
+
+					// Canonical has a root type of "uri"
+					if ("canonical".equals(typeName)) {
+						IPrimitiveType<?> valuePrimitive = (IPrimitiveType<?>) value;
+						IBaseReference fakeReference = (IBaseReference) myContext.getElementDefinition("Reference").newInstance();
+						fakeReference.setReference(valuePrimitive.getValueAsString());
+
+						/*
+						 * See #1583
+						 * Technically canonical fields should not allow local references (e.g.
+						 * Questionnaire/123) but it seems reasonable for us to interpret a canonical
+						 * containing a local reference for what it is, and allow people to seaerch
+						 * based on that.
+						 */
+						IIdType parsed = fakeReference.getReferenceElement();
+						if (parsed.hasIdPart() && parsed.hasResourceType() && !parsed.isAbsolute()) {
+							PathAndRef ref = new PathAndRef(searchParam.getName(), path, fakeReference);
+							params.add(ref);
+							break;
+						}
+					}
+
 					params.addWarning("Ignoring canonical reference (indexing canonical is not yet supported)");
 					break;
 				case "reference":
@@ -789,6 +814,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		return rootParentDefinition.getName();
 	}
 
+	private String toTypeName(IBase nextObject) {
+		BaseRuntimeElementDefinition<?> elementDefinition = getContext().getElementDefinition(nextObject.getClass());
+		return elementDefinition.getName();
+	}
+
 	@SuppressWarnings("unchecked")
 	private void addDateTimeTypes(String theResourceType, Set<ResourceIndexedSearchParamDate> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
 		IPrimitiveType<Date> nextBaseDateTime = (IPrimitiveType<Date>) theValue;

hapi-fhir-server/pom.xml

@@ -97,7 +97,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
             <plugin>

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

@@ -47,7 +47,7 @@ class ConditionalParamBinder implements IParameter {
 	public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
 		if (theOuterCollectionType != null || theInnerCollectionType != null || theParameterType.equals(String.class) == false) {
 			throw new ConfigurationException(
-					"Parameters annotated with @" + ConditionalUrlParam.class.getSimpleName() + " must be of type String, found incorrect parameteter in method \"" + theMethod + "\"");
+					"Parameters annotated with @" + ConditionalUrlParam.class.getSimpleName() + " must be of type String, found incorrect parameter in method \"" + theMethod + "\"");
 		}
 	}
 

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

@@ -28,6 +28,8 @@ import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.annotation.OptionalParam;
+import ca.uhn.fhir.rest.annotation.RequiredParam;
 import ca.uhn.fhir.rest.api.RequestTypeEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -91,6 +93,14 @@ public class OperationMethodBinding extends BaseResourceReturningMethodBinding {
 			myDescription = null;
 		}
 
+		for (Annotation[] nextParamAnnotations : theMethod.getParameterAnnotations()) {
+			for (Annotation nextParam : nextParamAnnotations) {
+				if (nextParam instanceof OptionalParam || nextParam instanceof RequiredParam) {
+					throw new ConfigurationException("Illegal method parameter annotation @" + nextParam.annotationType().getSimpleName() + " on method: " + theMethod.toString());
+				}
+			}
+		}
+
 		if (isBlank(theOperationName)) {
 			throw new ConfigurationException("Method '" + theMethod.getName() + "' on type " + theMethod.getDeclaringClass().getName() + " is annotated with @" + Operation.class.getSimpleName()
 				+ " but this annotation has no name defined");

hapi-fhir-structures-dstu/pom.xml

@@ -186,7 +186,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>

hapi-fhir-structures-dstu2.1/pom.xml

@@ -270,7 +270,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>

hapi-fhir-structures-dstu2/pom.xml

@@ -244,7 +244,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>-Dfile.encoding=UTF-8 -Xmx1024m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>

hapi-fhir-structures-dstu3/pom.xml

@@ -71,7 +71,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>
@@ -150,7 +150,7 @@
 		<dependency>
 			<groupId>javax.servlet</groupId>
 			<artifactId>javax.servlet-api</artifactId>
-			<version>3.0.1</version>
+			<version>3.1.0</version>
 			<optional>true</optional>
 		</dependency>
 

hapi-fhir-structures-hl7org-dstu2/pom.xml

@@ -269,7 +269,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>

hapi-fhir-structures-r4/pom.xml

@@ -315,7 +315,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java

@@ -23,6 +23,7 @@ import java.util.Set;
 import java.util.concurrent.TimeUnit;
 
 import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.stringContainsInOrder;
 import static org.hamcrest.core.IsNot.not;
 import static org.junit.Assert.*;
 import static org.mockito.Mockito.mock;
@@ -174,6 +175,34 @@ public class JsonParserR4Test extends BaseTest {
 		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">Copy © 1999</div>", p.getText().getDivAsString());
 	}
 
+	@Test
+	public void testEncodeAndParseBundleWithFullUrlAndResourceIdMismatch() {
+
+		MessageHeader header = new MessageHeader();
+		header.setId("1.1.1.1");
+		header.setDefinition("Hello");
+
+		Bundle input = new Bundle();
+		input
+			.addEntry()
+			.setFullUrl("urn:uuid:0.0.0.0")
+			.setResource(header);
+
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input);
+
+		ourLog.info("Encoded: {}", encoded);
+		assertThat(encoded, stringContainsInOrder(
+			"\"fullUrl\": \"urn:uuid:0.0.0.0\"",
+			"\"id\": \"1.1.1.1\""
+		));
+
+		input = ourCtx.newJsonParser().parseResource(Bundle.class, encoded);
+		assertEquals("urn:uuid:0.0.0.0", input.getEntry().get(0).getFullUrl());
+		assertEquals("MessageHeader/1.1.1.1", input.getEntry().get(0).getResource().getId());
+
+	}
+
+
 	@Test
 	public void testEncodeBinary() {
 		Binary b = new Binary();

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/XmlParserR4Test.java

@@ -1,8 +1,13 @@
 package ca.uhn.fhir.parser;
 
+import static org.hamcrest.Matchers.stringContainsInOrder;
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertThat;
 
+import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Composition;
+import org.hl7.fhir.r4.model.MessageHeader;
 import org.hl7.fhir.r4.model.Narrative;
 import org.junit.Test;
 import org.slf4j.Logger;
@@ -41,5 +46,33 @@ public class XmlParserR4Test {
 		int idx = encoded.indexOf(sectionText);
 		assertNotEquals(-1, idx);
 	}
-	
+
+	@Test
+	public void testEncodeAndParseBundleWithFullUrlAndResourceIdMismatch() {
+
+		MessageHeader header = new MessageHeader();
+		header.setId("1.1.1.1");
+		header.setDefinition("Hello");
+
+		Bundle input = new Bundle();
+		input
+			.addEntry()
+			.setFullUrl("urn:uuid:0.0.0.0")
+			.setResource(header);
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(input);
+
+		ourLog.info("Encoded: {}", encoded);
+		assertThat(encoded, stringContainsInOrder(
+			"<fullUrl value=\"urn:uuid:0.0.0.0\"/>",
+			"<id value=\"1.1.1.1\"/>"
+		));
+
+		input = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
+		assertEquals("urn:uuid:0.0.0.0", input.getEntry().get(0).getFullUrl());
+		assertEquals("MessageHeader/1.1.1.1", input.getEntry().get(0).getResource().getId());
+
+	}
+
+
 }

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/ClientR4Test.java

@@ -1,14 +1,21 @@
 package ca.uhn.fhir.rest.client;
 
+import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.annotation.Elements;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.IncludeParam;
+import ca.uhn.fhir.rest.annotation.OptionalParam;
+import ca.uhn.fhir.rest.annotation.RequiredParam;
+import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.SummaryEnum;
 import ca.uhn.fhir.rest.client.apache.ApacheHttpRequest;
+import ca.uhn.fhir.rest.client.apache.ResourceEntity;
 import ca.uhn.fhir.rest.client.api.IBasicClient;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
@@ -47,13 +54,24 @@ import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
 import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
 
+import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringReader;
-import java.nio.charset.Charset;
-import java.util.*;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
-import static org.hamcrest.Matchers.*;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.either;
+import static org.hamcrest.Matchers.equalTo;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
@@ -144,7 +162,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 201, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_TEXT + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), StandardCharsets.UTF_8));
 		when(myHttpResponse.getAllHeaders()).thenReturn(toHeaderArray("Location", "http://example.com/fhir/Patient/100/_history/200"));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
@@ -173,7 +191,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 400, "foobar"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_TEXT + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader("foobar"), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader("foobar"), StandardCharsets.UTF_8));
 
 		try {
 			ourCtx.newRestfulClient(ITestClient.class, "http://foo").createPatient(patient);
@@ -197,7 +215,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 201, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(ourCtx.newXmlParser().encodeResourceToString(patient)), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(ourCtx.newXmlParser().encodeResourceToString(patient)), StandardCharsets.UTF_8));
 		when(myHttpResponse.getAllHeaders()).thenReturn(toHeaderArray("Location", "http://example.com/fhir/Patient/100/_history/200"));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
@@ -221,7 +239,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 201, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(resp), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(resp), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		MethodOutcome response = client.deletePatient(new IdType("1234"));
@@ -238,7 +256,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 204, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_TEXT + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		client.deleteDiagnosticReport(new IdType("1234"));
@@ -259,7 +277,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		CapabilityStatement response = (CapabilityStatement) client.getServerConformanceStatement();
@@ -278,7 +296,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML_NEW + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		Bundle response = client.getHistoryPatientInstance(new IdType("111"));
@@ -298,7 +316,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML_NEW + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		Bundle response = client.getHistoryPatientType();
@@ -316,7 +334,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML_NEW + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		Bundle response = client.getHistoryServer();
@@ -340,7 +358,7 @@ public class ClientR4Test {
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
 			@Override
 			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
-				return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
+				return new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8);
 			}
 		});
 
@@ -410,7 +428,7 @@ public class ClientR4Test {
 
 		when(myHttpResponse.getAllHeaders()).thenReturn(headers);
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		// Patient response = client.findPatientByMrn(new
@@ -422,7 +440,7 @@ public class ClientR4Test {
 
 		assertEquals("http://foo.com/Patient/123/_history/2333", response.getId());
 
-		InstantType lm = (InstantType) response.getMeta().getLastUpdatedElement();
+		InstantType lm = response.getMeta().getLastUpdatedElement();
 		lm.setTimeZoneZulu(true);
 		assertEquals("1995-11-15T04:58:08.000Z", lm.getValueAsString());
 
@@ -447,7 +465,7 @@ public class ClientR4Test {
 		headers[0] = new BasicHeader(Constants.HEADER_LAST_MODIFIED, "2011-01-02T22:01:02");
 		when(myHttpResponse.getAllHeaders()).thenReturn(headers);
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_TEXT));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader("Internal Failure"), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader("Internal Failure"), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		try {
@@ -474,7 +492,7 @@ public class ClientR4Test {
 		headers[0] = new BasicHeader(Constants.HEADER_LAST_MODIFIED, "2011-01-02T22:01:02");
 		when(myHttpResponse.getAllHeaders()).thenReturn(headers);
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		try {
@@ -498,7 +516,7 @@ public class ClientR4Test {
 		headers[0] = new BasicHeader(Constants.HEADER_LAST_MODIFIED, "Wed, 15 Nov 1995 04:58:08 GMT");
 		when(myHttpResponse.getAllHeaders()).thenReturn(headers);
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		// Patient response = client.findPatientByMrn(new
@@ -508,7 +526,7 @@ public class ClientR4Test {
 		assertEquals("http://foo/Patient/111", capt.getValue().getURI().toString());
 		assertEquals("PRP1660", response.getIdentifier().get(0).getValueElement().getValue());
 
-		InstantType lm = (InstantType) response.getMeta().getLastUpdatedElement();
+		InstantType lm = response.getMeta().getLastUpdatedElement();
 		lm.setTimeZoneZulu(true);
 		assertEquals("1995-11-15T04:58:08.000Z", lm.getValueAsString());
 
@@ -523,7 +541,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", "application/fhir+xml; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		// Patient response = client.findPatientByMrn(new
@@ -544,7 +562,7 @@ public class ClientR4Test {
 
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 
@@ -572,7 +590,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		StringParam str = new StringParam("FOO$BAR");
@@ -592,7 +610,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		DateRangeParam param = new DateRangeParam();
@@ -613,7 +631,7 @@ public class ClientR4Test {
 
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		// httpResponse = new BasicHttpResponse(statusline, catalog, locale)
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
@@ -635,7 +653,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		Patient response = client.findPatientQuantity(new QuantityParam(ParamPrefixEnum.GREATERTHAN, 123L, "foo", "bar"));
@@ -654,7 +672,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		Patient response = client.findPatientByMrn(new TokenParam("urn:foo", "123"));
@@ -673,7 +691,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		client.getPatientNoParams();
@@ -691,7 +709,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		client.getPatientOneParam(new StringParam("BB"));
@@ -709,7 +727,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		TokenOrListParam identifiers = new TokenOrListParam();
@@ -730,7 +748,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClientWithCustomType client = ourCtx.newRestfulClient(ITestClientWithCustomType.class, "http://foo");
 		CustomPatient response = client.getPatientByDob(new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, "2011-01-02"));
@@ -749,7 +767,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClientWithCustomTypeList client = ourCtx.newRestfulClient(ITestClientWithCustomTypeList.class, "http://foo");
 		List<CustomPatient> response = client.getPatientByDob(new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, "2011-01-02"));
@@ -771,7 +789,7 @@ public class ClientR4Test {
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
 			@Override
 			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
-				return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
+				return new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8);
 			}
 		});
 
@@ -813,7 +831,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		StringAndListParam andListParam = new StringAndListParam();
@@ -837,7 +855,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		// TODO: document this
 
@@ -845,13 +863,13 @@ public class ClientR4Test {
 		client.getPatientByDob(new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, "2011-01-02"));
 		assertEquals("http://foo/Patient?birthdate=ge2011-01-02", capt.getAllValues().get(0).getURI().toString());
 
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 		client.setEncoding(EncodingEnum.JSON); // this needs to be actually
 		// implemented
 		client.getPatientByDob(new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, "2011-01-02"));
 		assertEquals("http://foo/Patient?birthdate=ge2011-01-02&_format=json", capt.getAllValues().get(1).getURI().toString());
 
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 		client.setPrettyPrint(true);
 		client.getPatientByDob(new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, "2011-01-02"));
 		assertEquals("http://foo/Patient?birthdate=ge2011-01-02&_format=json&_pretty=true", capt.getAllValues().get(2).getURI().toString());
@@ -877,7 +895,7 @@ public class ClientR4Test {
 
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		// httpResponse = new BasicHttpResponse(statusline, catalog, locale)
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
@@ -900,7 +918,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		client.setSummary(SummaryEnum.DATA);
@@ -919,10 +937,10 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
-		client.getPatientWithIncludes(new StringParam("aaa"), Arrays.asList(new Include[]{new Include("inc1"), new Include("inc2", true), new Include("inc3", true)}));
+		client.getPatientWithIncludes(new StringParam("aaa"), Arrays.asList(new Include("inc1"), new Include("inc2", true), new Include("inc3", true)));
 
 		assertEquals("http://foo/Patient?withIncludes=aaa&_include=inc1&_include%3Aiterate=inc2&_include%3Aiterate=inc3", capt.getValue().getURI().toString());
 
@@ -937,7 +955,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		Bundle response = client.findPatientByName(new StringParam("AAA"), null);
@@ -950,7 +968,7 @@ public class ClientR4Test {
 		 * Now with a first name
 		 */
 
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 		client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		response = client.findPatientByName(new StringParam("AAA"), new StringParam("BBB"));
 
@@ -970,7 +988,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClientWithStringIncludes client = ourCtx.newRestfulClient(ITestClientWithStringIncludes.class, "http://foo");
 		client.getPatientWithIncludes(new StringParam("aaa"), "inc1");
@@ -991,7 +1009,7 @@ public class ClientR4Test {
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
 			@Override
 			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
-				return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
+				return new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8);
 			}
 		});
 
@@ -1037,7 +1055,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 201, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_TEXT + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), StandardCharsets.UTF_8));
 		when(myHttpResponse.getAllHeaders()).thenReturn(toHeaderArray("Location", "http://example.com/fhir/Patient/100/_history/200"));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
@@ -1065,7 +1083,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 201, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), StandardCharsets.UTF_8));
 		when(myHttpResponse.getAllHeaders()).thenReturn(toHeaderArray(Constants.HEADER_LOCATION, "http://example.com/fhir/Patient/100/_history/200"));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
@@ -1088,7 +1106,7 @@ public class ClientR4Test {
 		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), StandardCharsets.UTF_8));
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), Constants.STATUS_HTTP_409_CONFLICT, "Conflict"));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
@@ -1105,7 +1123,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 201, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_TEXT + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), StandardCharsets.UTF_8));
 		when(myHttpResponse.getAllHeaders()).thenReturn(toHeaderArray("Location", "http://example.com/fhir/Patient/100/_history/200"));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
@@ -1129,7 +1147,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), Constants.STATUS_HTTP_204_NO_CONTENT, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_TEXT + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), StandardCharsets.UTF_8));
 		when(myHttpResponse.getAllHeaders()).thenReturn(toHeaderArray("Location", "http://example.com/fhir/Patient/100/_history/200"));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
@@ -1152,7 +1170,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(response), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(response), StandardCharsets.UTF_8));
 
 		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.ONCE);
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://testValidateServerBaseWithInvalidResponse");
@@ -1180,7 +1198,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON_NEW + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(resp), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(resp), StandardCharsets.UTF_8));
 		when(myHttpResponse.getAllHeaders()).thenReturn(toHeaderArray("Location", "http://example.com/fhir/Patient/100/_history/200"));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
@@ -1215,7 +1233,7 @@ public class ClientR4Test {
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), StandardCharsets.UTF_8));
 
 		ITestClient client = ourCtx.newRestfulClient(ITestClient.class, "http://foo");
 		// Patient response = client.findPatientByMrn(new
@@ -1227,6 +1245,67 @@ public class ClientR4Test {
 
 	}
 
+	@Test
+	public void testClientWithAndOrList() throws IOException {
+
+		Bundle response = new Bundle().setType(Bundle.BundleType.SEARCHSET);
+
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(myHttpResponse.getEntity()).thenReturn(new ResourceEntity(ourCtx, response));
+
+		ITestClientWithAndOr client = ourCtx.newRestfulClient(ITestClientWithAndOr.class, "http://foo");
+		StringAndListParam andList = new StringAndListParam();
+		StringOrListParam orListA = new StringOrListParam();
+		orListA.add(new StringParam("A1"));
+		orListA.add(new StringParam("A2"));
+		andList.addAnd(orListA);
+		StringOrListParam orListB = new StringOrListParam();
+		orListB.add(new StringParam("B1"));
+		orListB.add(new StringParam("B2"));
+		andList.addAnd(orListB);
+		client.search(andList);
+
+		assertEquals("http://foo/Patient?foo=A1%2CA2&foo=B1%2CB2", capt.getValue().getURI().toString());
+	}
+
+	@Test
+	public void testClientWithAndOrList2() throws IOException {
+
+		Bundle response = new Bundle().setType(Bundle.BundleType.SEARCHSET);
+
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(myHttpResponse.getEntity()).thenReturn(new ResourceEntity(ourCtx, response));
+
+		try {
+			ourCtx.newRestfulClient(ITestClientWithAndOr2.class, "http://foo");
+		} catch (ConfigurationException e) {
+			assertEquals("Argument #0 of Method 'search' in type 'ca.uhn.fhir.rest.client.ClientR4Test.ITestClientWithAndOr2' is of an invalid generic type (can not be a collection of a collection of a collection)", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testClientWithAndOrList3() throws IOException {
+
+		Bundle response = new Bundle().setType(Bundle.BundleType.SEARCHSET);
+
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(myHttpResponse.getEntity()).thenReturn(new ResourceEntity(ourCtx, response));
+
+		ITestClientWithAndOr3 client = ourCtx.newRestfulClient(ITestClientWithAndOr3.class, "http://foo");
+		Set<Include> orListA = new HashSet<>();
+		orListA.add(new Include("a"));
+		orListA.add(new Include("b"));
+		client.search(orListA);
+
+		assertEquals("http://foo/Patient?_include=a&_include=b", capt.getValue().getURI().toString());
+	}
+
 	private Header[] toHeaderArray(String theName, String theValue) {
 		return new Header[]{new BasicHeader(theName, theValue)};
 	}
@@ -1245,40 +1324,61 @@ public class ClientR4Test {
 		}
 	}
 
+	interface ITestClientWithAndOr extends IBasicClient {
+
+		@Search()
+		List<Patient> search(@OptionalParam(name = "foo") StringAndListParam theParam);
+
+	}
+
+	interface ITestClientWithAndOr2 extends IBasicClient {
+
+		@Search()
+		List<Patient> search(@OptionalParam(name = "foo") List<List<String>> theParam);
+
+	}
+
+	public interface ITestClientWithAndOr3 extends IBasicClient {
+
+		@Search()
+		List<Patient> search(@IncludeParam Set<Include> theParam);
+
+	}
+
 	private interface ClientWithoutAnnotation extends IBasicClient {
 		Patient read(@IdParam IdType theId);
 	}
 
 	public interface ITestClientWithCustomType extends IBasicClient {
 		@Search()
-		public CustomPatient getPatientByDob(@RequiredParam(name = Patient.SP_BIRTHDATE) DateParam theBirthDate);
+		CustomPatient getPatientByDob(@RequiredParam(name = Patient.SP_BIRTHDATE) DateParam theBirthDate);
 	}
 
 	public interface ITestClientWithCustomTypeList extends IBasicClient {
 		@Search()
-		public List<CustomPatient> getPatientByDob(@RequiredParam(name = Patient.SP_BIRTHDATE) DateParam theBirthDate);
+		List<CustomPatient> getPatientByDob(@RequiredParam(name = Patient.SP_BIRTHDATE) DateParam theBirthDate);
 	}
 
 	public interface ITestClientWithElements extends IBasicClient {
 		@Search()
-		public List<Patient> getPatientWithIncludes(@Elements Set<String> theElements);
+		List<Patient> getPatientWithIncludes(@Elements Set<String> theElements);
 
 		@Search()
-		public List<Patient> getPatientWithIncludes(@Elements String theElements);
+		List<Patient> getPatientWithIncludes(@Elements String theElements);
 
 	}
 
 	public interface ITestClientWithStringIncludes extends IBasicClient {
 		@Search()
-		public Patient getPatientWithIncludes(@RequiredParam(name = "withIncludes") StringParam theString, @IncludeParam String theInclude);
+		Patient getPatientWithIncludes(@RequiredParam(name = "withIncludes") StringParam theString, @IncludeParam String theInclude);
 	}
 
 	public interface ITestClientWithSummary extends IBasicClient {
 		@Search()
-		public List<Patient> getPatientWithIncludes(List<SummaryEnum> theSummary);
+		List<Patient> getPatientWithIncludes(List<SummaryEnum> theSummary);
 
 		@Search()
-		public List<Patient> getPatientWithIncludes(SummaryEnum theSummary);
+		List<Patient> getPatientWithIncludes(SummaryEnum theSummary);
 
 	}
 

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/BlockingContentR4Test.java

@@ -0,0 +1,113 @@
+package ca.uhn.fhir.rest.server;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.annotation.Transaction;
+import ca.uhn.fhir.rest.annotation.TransactionParam;
+import ca.uhn.fhir.test.utilities.server.ResourceProviderRule;
+import ca.uhn.fhir.test.utilities.server.RestfulServerRule;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.HttpEntity;
+import org.apache.http.client.config.RequestConfig;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.InputStreamEntity;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.ClassRule;
+import org.junit.Rule;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Arrays;
+import java.util.concurrent.TimeUnit;
+
+public class BlockingContentR4Test {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(BlockingContentR4Test.class);
+	private static FhirContext ourCtx = FhirContext.forR4();
+	@ClassRule
+	public static RestfulServerRule ourServerRule = new RestfulServerRule(ourCtx);
+	@Rule
+	public ResourceProviderRule myPatientProviderRule = new ResourceProviderRule(ourServerRule, new SystemProvider());
+
+	@Test
+	public void testCreateWith100Continue() throws Exception {
+		Patient patient = new Patient();
+		patient.setActive(true);
+
+		Bundle input = new Bundle();
+		input.setType(Bundle.BundleType.TRANSACTION);
+		input.addEntry().setResource(patient).setFullUrl("Patient/").getRequest().setMethod(Bundle.HTTPVerb.POST);
+
+		RequestConfig config = RequestConfig.custom().setExpectContinueEnabled(true).build();
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		builder.setDefaultRequestConfig(config);
+		try (CloseableHttpClient client = builder.build()) {
+
+			String resourceAsString = ourCtx.newJsonParser().encodeResourceToString(input);
+
+//			InputStream inputStream = new BlockingInputStream(resourceAsString.getBytes(Charsets.UTF_8));
+			byte[] bytes = resourceAsString.getBytes(Charsets.UTF_8);
+			InputStream inputStream = new ByteArrayInputStream(bytes);
+			HttpEntity entity = new InputStreamEntity(inputStream, ContentType.parse("application/fhir+json")){
+				@Override
+				public long getContentLength() {
+					return bytes.length + 100;
+				}
+			};
+
+			HttpPost post = new HttpPost("http://localhost:" + ourServerRule.getPort() + "/");
+			post.setEntity(entity);
+			try (CloseableHttpResponse resp = client.execute(post)) {
+				ourLog.info(Arrays.asList(resp.getAllHeaders()).toString().replace(", ", "\n"));
+				ourLog.info(resp.toString());
+				ourLog.info(IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8));
+			}
+
+		}
+	}
+
+	private static class BlockingInputStream extends InputStream {
+		private final ByteArrayInputStream myWrap;
+		private int myByteCount = 0;
+
+		public BlockingInputStream(byte[] theBytes) {
+			myWrap = new ByteArrayInputStream(theBytes);
+		}
+
+		@Override
+		public int read() throws IOException {
+			if (myByteCount++ == 10) {
+				ourLog.info("About to block...");
+				try {
+					Thread.sleep(30000);
+				} catch (InterruptedException e) {
+					ourLog.warn("Interrupted", e);
+				}
+			}
+			return myWrap.read();
+		}
+	}
+
+
+	public static class SystemProvider {
+
+		@Transaction
+		public Bundle transaction(@TransactionParam Bundle theInput) {
+			return theInput;
+		}
+
+	}
+
+}

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/ServerInvalidDefinitionR4Test.java

@@ -1,30 +1,30 @@
 package ca.uhn.fhir.rest.server;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OptionalParam;
+import ca.uhn.fhir.rest.annotation.ResourceParam;
+import ca.uhn.fhir.rest.annotation.Update;
+import ca.uhn.fhir.rest.annotation.Validate;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.util.TestUtil;
+import org.hamcrest.core.StringContains;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.StringType;
+import org.junit.AfterClass;
+import org.junit.Test;
+
+import javax.servlet.ServletException;
+
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.fail;
 
-import javax.servlet.ServletException;
+public class ServerInvalidDefinitionR4Test {
 
-import org.hamcrest.core.StringContains;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.junit.AfterClass;
-import org.junit.Test;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.rest.annotation.*;
-import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.param.TokenParam;
-import ca.uhn.fhir.util.TestUtil;
-
-public class ServerInvalidDefinitionDstu2Test {
-
-	private static FhirContext ourCtx = FhirContext.forDstu2();
-
-	@AfterClass
-	public static void afterClassClearContext() {
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
+	private static FhirContext ourCtx = FhirContext.forR4();
 
 	@Test
 	public void testWrongConditionalUrlType() {
@@ -38,7 +38,7 @@ public class ServerInvalidDefinitionDstu2Test {
 		} catch (ServletException e) {
 			assertThat(e.getCause().toString(), StringContains.containsString("ConfigurationException"));
 			assertThat(e.getCause().toString(), StringContains.containsString(
-					"Parameters annotated with @ConditionalUrlParam must be of type String, found incorrect parameteter in method \"public ca.uhn.fhir.rest.api.MethodOutcome ca.uhn.fhir.rest.server.ServerInvalidDefinitionDstu2Test$UpdateWithWrongConditionalUrlType.update(ca.uhn.fhir.rest.param.TokenParam,ca.uhn.fhir.model.dstu2.resource.Patient)"));
+				"Parameters annotated with @ConditionalUrlParam must be of type String, found incorrect parameter in method \"public ca.uhn.fhir.rest.api.MethodOutcome ca.uhn.fhir.rest.server.ServerInvalidDefinitionR4Test$UpdateWithWrongConditionalUrlType.update(ca.uhn.fhir.rest.param.TokenParam,org.hl7.fhir.r4.model.Patient)"));
 		}
 	}
 
@@ -54,7 +54,7 @@ public class ServerInvalidDefinitionDstu2Test {
 		} catch (ServletException e) {
 			assertThat(e.getCause().toString(), StringContains.containsString("ConfigurationException"));
 			assertThat(e.getCause().toString(), StringContains
-					.containsString("Method 'update' is annotated with @ResourceParam but has a type that is not an implemtation of org.hl7.fhir.instance.model.api.IBaseResource or String or byte[]"));
+				.containsString("Method 'update' is annotated with @ResourceParam but has a type that is not an implemtation of org.hl7.fhir.instance.model.api.IBaseResource or String or byte[]"));
 		}
 	}
 
@@ -88,6 +88,29 @@ public class ServerInvalidDefinitionDstu2Test {
 		}
 	}
 
+	@Test
+	public void testWrongParameterAnnotationOnOperation() {
+		class MyProvider {
+
+			@Operation(name = "foo")
+			public MethodOutcome update(@OptionalParam(name = "foo") StringType theFoo) {
+				return null;
+			}
+
+		}
+
+		RestfulServer srv = new RestfulServer(ourCtx);
+		srv.setFhirContext(ourCtx);
+		srv.registerProvider(new MyProvider());
+
+		try {
+			srv.init();
+			fail();
+		} catch (ServletException e) {
+			assertThat(e.getCause().toString(), StringContains.containsString("Failure scanning class MyProvider: Illegal method parameter annotation @OptionalParam on method: public ca.uhn.fhir.rest.api.MethodOutcome ca.uhn.fhir.rest.server.ServerInvalidDefinitionR4Test$1MyProvider.update(org.hl7.fhir.r4.model.StringType)"));
+		}
+	}
+
 	public static class UpdateWithWrongConditionalUrlType implements IResourceProvider {
 
 		@Override
@@ -144,4 +167,9 @@ public class ServerInvalidDefinitionDstu2Test {
 
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
 }

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/ServerMimetypeR4Test.java

@@ -1,18 +1,17 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.hamcrest.Matchers.contains;
-import static org.hamcrest.Matchers.containsString;
-import static org.hamcrest.Matchers.not;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertThat;
-
-import java.io.IOException;
-import java.net.URI;
-import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.TimeUnit;
-
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.annotation.Create;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Read;
+import ca.uhn.fhir.rest.annotation.ResourceParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.client.MyPatientWithExtensions;
+import ca.uhn.fhir.test.utilities.JettyUtil;
+import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.CloseableHttpResponse;
@@ -40,18 +39,18 @@ import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.rest.annotation.Create;
-import ca.uhn.fhir.rest.annotation.IdParam;
-import ca.uhn.fhir.rest.annotation.Read;
-import ca.uhn.fhir.rest.annotation.ResourceParam;
-import ca.uhn.fhir.rest.annotation.Search;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.EncodingEnum;
-import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.client.MyPatientWithExtensions;
-import ca.uhn.fhir.test.utilities.JettyUtil;
-import ca.uhn.fhir.util.TestUtil;
+import java.io.IOException;
+import java.net.URI;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.not;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
 
 public class ServerMimetypeR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerMimetypeR4Test.class);
@@ -406,45 +405,16 @@ public class ServerMimetypeR4Test {
 		return retVal;
 	}
 
-	@AfterClass
-	public static void afterClassClearContext() throws Exception {
-		JettyUtil.closeServer(ourServer);
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-	@BeforeClass
-	public static void beforeClass() throws Exception {
-		ourServer = new Server(0);
-
-		PatientProvider patientProvider = new PatientProvider();
-
-		ServletHandler proxyHandler = new ServletHandler();
-		ourServlet = new RestfulServer(ourCtx);
-
-		ourServlet.setResourceProviders(patientProvider);
-		ServletHolder servletHolder = new ServletHolder(ourServlet);
-		proxyHandler.addServletWithMapping(servletHolder, "/*");
-		ourServer.setHandler(proxyHandler);
-		JettyUtil.startServer(ourServer);
-        ourPort = JettyUtil.getPortForStartedServer(ourServer);
-
-		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
-		HttpClientBuilder builder = HttpClientBuilder.create();
-		builder.setConnectionManager(connectionManager);
-		ourClient = builder.build();
-
-	}
-
 	public static class PatientProvider implements IResourceProvider {
 
 		@Create()
 		public MethodOutcome create(@ResourceParam Patient theIdParam) {
 			OperationOutcome oo = new OperationOutcome();
 			oo.addIssue().setDiagnostics(theIdParam.getNameFirstRep().getFamily());
-			
+
 			theIdParam.setId("1");
 			theIdParam.getMeta().setVersionId("1");
-			
+
 			return new MethodOutcome(new IdType("Patient", "1"), true).setOperationOutcome(oo).setResource(theIdParam);
 		}
 
@@ -480,4 +450,33 @@ public class ServerMimetypeR4Test {
 
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		JettyUtil.closeServer(ourServer);
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourServer = new Server(0);
+
+		PatientProvider patientProvider = new PatientProvider();
+
+		ServletHandler proxyHandler = new ServletHandler();
+		ourServlet = new RestfulServer(ourCtx);
+
+		ourServlet.setResourceProviders(patientProvider);
+		ServletHolder servletHolder = new ServletHolder(ourServlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		JettyUtil.startServer(ourServer);
+		ourPort = JettyUtil.getPortForStartedServer(ourServer);
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
 }

hapi-fhir-structures-r5/pom.xml

@@ -308,7 +308,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>

hapi-fhir-test-utilities/pom.xml

@@ -81,7 +81,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>

hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/server/ResourceProviderRule.java

@@ -0,0 +1,55 @@
+package ca.uhn.fhir.test.utilities.server;
+
+/*-
+ * #%L
+ * HAPI FHIR Test Utilities
+ * %%
+ * Copyright (C) 2014 - 2019 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.junit.rules.TestRule;
+import org.junit.runner.Description;
+import org.junit.runners.model.Statement;
+
+public class ResourceProviderRule implements TestRule {
+
+	private final RestfulServerRule myRestfulServerRule;
+	private Object myProvider;
+
+	/**
+	 * Constructor
+	 */
+	public ResourceProviderRule(RestfulServerRule theRestfulServerRule, Object theProvider) {
+		myRestfulServerRule = theRestfulServerRule;
+		myProvider = theProvider;
+	}
+
+	@Override
+	public Statement apply(Statement base, Description description) {
+		return new Statement() {
+			@Override
+			public void evaluate() throws Throwable {
+				myRestfulServerRule.getRestfulServer().registerProvider(myProvider);
+				try {
+					base.evaluate();
+				} finally {
+					myRestfulServerRule.getRestfulServer().unregisterProvider(myProvider);
+				}
+			}
+		};
+	}
+
+}

hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/server/RestfulServerRule.java

@@ -112,4 +112,8 @@ public class RestfulServerRule implements TestRule {
 	public RestfulServer getRestfulServer() {
 		return myServlet;
 	}
+
+	public int getPort() {
+		return myPort;
+	}
 }

hapi-fhir-testpage-overlay/src/main/webapp/js/RestfulTester.js

@@ -540,7 +540,7 @@ function updateURLParameter(url, param, paramVal){
     var temp = "";
     if (additionalURL) {
         tempArray = additionalURL.split("&");
-        for (i=0; i<tempArray.length; i++){
+        for (var i=0; i<tempArray.length; i++){
             if(tempArray[i].split('=')[0] !== param){
                 newAdditionalURL += temp + tempArray[i];
                 temp = "&";

hapi-fhir-validation/pom.xml

@@ -275,7 +275,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 				</configuration>
 			</plugin>
 			<plugin>

pom.xml

@@ -582,9 +582,11 @@
 
 	<properties>
 
-		<fhir_core_version>4.1.0</fhir_core_version>
+		<fhir_core_version>4.1.7-SNAPSHOT</fhir_core_version>
 		<ucum_version>1.0.2</ucum_version>
 
+		<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx1024m</surefire_jvm_args>
+
 		<!-- configure timestamp in MANIFEST.MF for maven-war-provider -->
 		<maven.build.timestamp.format>yyyy-MM-dd'T'HH:mm:ss'Z'</maven.build.timestamp.format>
 
@@ -615,7 +617,7 @@
 		<jaxb_runtime_version>2.3.1</jaxb_runtime_version>
 		<jersey_version>2.25.1</jersey_version>
 		<!-- 9.4.17 seems to have issues -->
-		<jetty_version>9.4.14.v20181114</jetty_version>
+		<jetty_version>9.4.23.v20191118</jetty_version>
 		<jsr305_version>3.0.2</jsr305_version>
 		<flyway_version>6.0.8</flyway_version>
 		<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
@@ -712,7 +714,7 @@
 			<dependency>
 				<groupId>com.icegreen</groupId>
 				<artifactId>greenmail</artifactId>
-				<version>1.5.10</version>
+				<version>1.5.11</version>
 			</dependency>
 			<dependency>
 				<groupId>com.icegreen</groupId>
@@ -1663,9 +1665,9 @@
 					<configuration>
 						<redirectTestOutputToFile>true</redirectTestOutputToFile>
 						<runOrder>random</runOrder>
-						<argLine>-Dfile.encoding=UTF-8 -Xmx1024m</argLine>
+						<argLine>@{argLine} ${surefire_jvm_args}</argLine>
 						<forkCount>1.0C</forkCount>
-                        <trimStackTrace>false</trimStackTrace>
+						<trimStackTrace>false</trimStackTrace>
 					</configuration>
 				</plugin>
 				<plugin>
@@ -2494,6 +2496,31 @@
 			<modules>
 				<module>hapi-fhir-jacoco</module>
 			</modules>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.jacoco</groupId>
+						<artifactId>jacoco-maven-plugin</artifactId>
+						<configuration>
+							<dumpOnExit>true</dumpOnExit>
+						</configuration>
+						<executions>
+							<execution>
+								<id>default-prepare-agent</id>
+								<goals>
+									<goal>prepare-agent</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+		<profile>
+			<id>CI</id>
+			<properties>
+				<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m -XX:TieredStopAtLevel=1 -XX:+UseParallelGC -Xverify:none  -Dfile.encoding=UTF-8 -Xss128M -XX:MetaspaceSize=512M -XX:MaxMetaspaceSize=2048M</surefire_jvm_args>
+			</properties>
 		</profile>
 		<profile>
 			<id>NOPARALLEL</id>

src/changes/changes.xml

@@ -6,7 +6,48 @@
 		<title>HAPI FHIR Changelog</title>
 	</properties>
 	<body>
-		<release version="4.2.0" date="2019-02-01" description="K">
+		<release version="4.2.0" date="TBD">
+			<action type="add">
+				The version of a few dependencies have been bumped to the
+				latest versions (dependent HAPI modules listed in brackets):
+				<![CDATA[
+				<ul>
+					<li>Jetty (CLI): 9.4.14.v20181114 -&gt; 9.4.23.v20191118</li>
+				</ul>
+				]]>
+			</action>
+			<action type="fix" issue="1583">
+				As of FHIR R4, some fields that were previously of type reference are now of type canonical.
+				One example is QuestionnaireResponse.questionnaire. Technically this means that this field
+				should no longer contain a relative reference, but as they are sometimes used that way, HAPI
+				FHIR will now try to be permissive and will index relative link canonical fields
+				such as (Questionnaire/123) as though it actually was a local relative link. Thanks to
+				Dean Atchley for reporting and providing a test case!
+			</action>
+			<action type="fix">
+				ValueSet PreCalculation did not successfully expand valuesets when Lucene was not enabled
+				in the JPA server. This has been corrected.
+			</action>
+			<action type="change">
+				When parsing Bundle resources containing other resources, XML/JSON parsers have an option called
+				"override resource ID with bundle entry fullUrl". This option previously caused any value
+				found in Bundle.entry.fullUrl to override any value found in
+				Bundle.entry.resource.id (meaning that the parsed resource would take its ID from
+				the fullUrl even if that ID disagreed with the ID found in the resource itself. As of
+				HAPI FHIR 4.1.0 the value in Bundle.entry.fullUrl will only be used to set the parsed resource
+				ID if the resource has no ID present.
+			</action>
+			<action type="add">
+				Chained searches using the _has search parameter as the chain value are now supported by
+				the JPA server.
+			</action>
+			<action type="change">
+				Changed database migration to use flyway.  This adds a new table called flyway_schema_history that records all
+				database migration tasks that have already been applied.  The hapi-fhir-cli migrate tool has been changed
+				to use flyway.  Learn more about flyway on https://flywaydb.org/.
+			</action>
+		</release>
+		<release version="4.1.0" date="2019-11-13" description="Jitterbug">
 			<action type="add">
 				The version of a few dependencies have been bumped to the
 				latest versions (dependent HAPI modules listed in brackets):
@@ -33,13 +74,6 @@
 			format. Thanks to Raul Estrada for the pull request!
 		</action>
 		-->
-			<action type="change">
-				Changed database migration to use flyway.  This adds a new table called flyway_schema_history that records all
-				database migration tasks that have already been applied.  The hapi-fhir-cli migrate tool has been changed
-				to use flyway.  Learn more about flyway on https://flywaydb.org/.
-			</action>
-		</release>
-		<release version="4.1.0" date="2019-11-13" description="Jitterbug">
 			<action type="add">
 				<![CDATA[
 				<b>New Feature</b>: