Merging cleanup from local branch with commit from #153

hapi-fhir-android/pom.xml

@@ -147,7 +147,7 @@
 									<include>javax.xml.stream:stax-api</include>
 									<include>javax.servlet:javax.servlet-api</include>
 									<include>org.codehaus.woodstox:stax2-api</include>
-									<include>org.slf4j:slf4j*</include>
+									<!-- <include>org.slf4j:slf4j*</include>  -->
 									<include>org.apache.commons:*</include>
 									<include>org.apache.httpcomponents:*</include>
 									<include>org.glassfish:javax.json</include>

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

@@ -49,14 +49,13 @@ import javax.json.stream.JsonGenerator;
 import javax.json.stream.JsonGeneratorFactory;
 import javax.json.stream.JsonParsingException;
 
-import ca.uhn.fhir.model.base.composite.BaseCodingDt;
-import ca.uhn.fhir.model.primitive.*;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.IBase;
 import org.hl7.fhir.instance.model.IBaseResource;
 import org.hl7.fhir.instance.model.IPrimitiveType;
 import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseBinary;
 import org.hl7.fhir.instance.model.api.IBaseBooleanDatatype;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseDecimalDatatype;
@@ -89,19 +88,25 @@ 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.api.annotation.Child;
+import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.composite.BaseContainedDt;
 import ca.uhn.fhir.model.base.composite.BaseNarrativeDt;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
-import ca.uhn.fhir.model.base.resource.BaseBinary;
+import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.DecimalDt;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.IntegerDt;
 import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.model.primitive.UriDt;
 import ca.uhn.fhir.model.primitive.XhtmlDt;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.util.ElementUtil;
 import ca.uhn.fhir.util.UrlUtil;
 
+/**
+ * This class is the FHIR JSON parser/encoder. Users should not interact with this class directly, but should use {@link FhirContext#newJsonParser()} to get an instance.
+ */
 public class JsonParser extends BaseParser implements IParser {
 
 	private static final Set<String> BUNDLE_TEXTNODE_CHILDREN_DSTU1;
@@ -298,9 +303,9 @@ public class JsonParser extends BaseParser implements IParser {
 				// IResource nextResource = nextEntry.getResource();
 			}
 
-			if (nextEntry.getTransactionOperation().isEmpty() == false || nextEntry.getLinkSearch().isEmpty() == false) {
+			if (nextEntry.getTransactionMethod().isEmpty() == false || nextEntry.getLinkSearch().isEmpty() == false) {
 				theEventWriter.writeStartObject("transaction");
-				writeOptionalTagWithTextNode(theEventWriter, "operation", nextEntry.getTransactionOperation().getValue());
+				writeOptionalTagWithTextNode(theEventWriter, "method", nextEntry.getTransactionMethod().getValue());
 				writeOptionalTagWithTextNode(theEventWriter, "url", nextEntry.getLinkSearch().getValue());
 				theEventWriter.writeEnd();
 			}
@@ -343,7 +348,7 @@ public class JsonParser extends BaseParser implements IParser {
 	}
 
 	private void encodeChildElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonGenerator theWriter, IBase theNextValue,
-			BaseRuntimeElementDefinition<?> theChildDef, String theChildName, boolean theIsSubElementWithinResource) throws IOException {
+			BaseRuntimeElementDefinition<?> theChildDef, String theChildName, boolean theContainedResource) throws IOException {
 
 		switch (theChildDef.getChildType()) {
 		case PRIMITIVE_DATATYPE: {
@@ -391,7 +396,7 @@ public class JsonParser extends BaseParser implements IParser {
 			if (theNextValue instanceof ExtensionDt) {
 				theWriter.write("url", ((ExtensionDt) theNextValue).getUrlAsString());
 			}
-			encodeCompositeElementToStreamWriter(theResDef, theResource, theNextValue, theWriter, childCompositeDef, theIsSubElementWithinResource);
+			encodeCompositeElementToStreamWriter(theResDef, theResource, theNextValue, theWriter, childCompositeDef, theContainedResource);
 			theWriter.writeEnd();
 			break;
 		}
@@ -452,7 +457,7 @@ public class JsonParser extends BaseParser implements IParser {
 		case RESOURCE:
 			IBaseResource resource = (IBaseResource) theNextValue;
 			RuntimeResourceDefinition def = myContext.getResourceDefinition(resource);
-			encodeResourceToJsonStreamWriter(def, resource, theWriter, theChildName, true);
+			encodeResourceToJsonStreamWriter(def, resource, theWriter, theChildName, false);
 			break;
 		case UNDECL_EXT:
 		default:
@@ -462,7 +467,7 @@ public class JsonParser extends BaseParser implements IParser {
 	}
 
 	private void encodeCompositeElementChildrenToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theNextValue, JsonGenerator theEventWriter,
-			List<? extends BaseRuntimeChildDefinition> theChildren, boolean theIsSubElementWithinResource) throws IOException {
+			List<? extends BaseRuntimeChildDefinition> theChildren, boolean theContainedResource) throws IOException {
 		for (BaseRuntimeChildDefinition nextChild : theChildren) {
 			if (nextChild.getElementName().equals("extension") || nextChild.getElementName().equals("modifierExtension")) {
 				continue;
@@ -478,7 +483,7 @@ public class JsonParser extends BaseParser implements IParser {
 						RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
 						String childName = nextChild.getChildNameByDatatype(child.getDatatype());
 						BaseRuntimeElementDefinition<?> type = child.getChildByName(childName);
-						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, narr, type, childName, theIsSubElementWithinResource);
+						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, narr, type, childName, theContainedResource);
 						continue;
 					}
 				}
@@ -499,7 +504,7 @@ public class JsonParser extends BaseParser implements IParser {
 			for (IBase nextValue : values) {
 				if (nextValue == null || nextValue.isEmpty()) {
 					if (nextValue instanceof BaseContainedDt) {
-						if (theIsSubElementWithinResource || getContainedResources().isEmpty()) {
+						if (theContainedResource || getContainedResources().isEmpty()) {
 							continue;
 						}
 					} else {
@@ -515,7 +520,7 @@ public class JsonParser extends BaseParser implements IParser {
 				}
 				boolean primitive = childDef.getChildType() == ChildTypeEnum.PRIMITIVE_DATATYPE;
 
-				if (childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES && theIsSubElementWithinResource) {
+				if (childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES && theContainedResource) {
 					continue;
 				}
 
@@ -537,15 +542,15 @@ public class JsonParser extends BaseParser implements IParser {
 						if (nextChild.getMax() > 1 || nextChild.getMax() == Child.MAX_UNLIMITED) {
 							theEventWriter.writeStartArray(childName);
 							inArray = true;
-							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theIsSubElementWithinResource);
+							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource);
-						} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theIsSubElementWithinResource) {
+						} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
 							// suppress narratives from contained resources
 						} else {
-							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theIsSubElementWithinResource);
+							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theContainedResource);
 						}
 						currentChildName = childName;
 					} else {
-						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theIsSubElementWithinResource);
+						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource);
 					}
 
 					if (primitive) {
@@ -620,19 +625,19 @@ public class JsonParser extends BaseParser implements IParser {
 	}
 
 	private void encodeCompositeElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theNextValue, JsonGenerator theEventWriter,
-			BaseRuntimeElementCompositeDefinition<?> resDef, boolean theIsSubElementWithinResource) throws IOException, DataFormatException {
+			BaseRuntimeElementCompositeDefinition<?> resDef, boolean theContainedResource) throws IOException, DataFormatException {
 		extractAndWriteExtensionsAsDirectChild(theNextValue, theEventWriter, resDef, theResDef, theResource, null);
-		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, resDef.getExtensions(), theIsSubElementWithinResource);
+		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, resDef.getExtensions(), theContainedResource);
-		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, resDef.getChildren(), theIsSubElementWithinResource);
+		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, resDef.getChildren(), theContainedResource);
 	}
 
-	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonGenerator theEventWriter, String theObjectNameOrNull,
+	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonGenerator theEventWriter, String theObjectNameOrNull, boolean theContainedResource)
-			boolean theIsSubElementWithinResource) throws IOException {
+			throws IOException {
 		String resourceId = null;
 		if (theResource instanceof IResource) {
 			IResource res = (IResource) theResource;
 			if (StringUtils.isNotBlank(res.getId().getIdPart())) {
-				if (theIsSubElementWithinResource) {
+				if (theContainedResource) {
 					resourceId = res.getId().getIdPart();
 				} else if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
 					resourceId = res.getId().getIdPart();
@@ -640,17 +645,17 @@ public class JsonParser extends BaseParser implements IParser {
 			}
 		} else if (theResource instanceof IAnyResource) {
 			IAnyResource res = (IAnyResource) theResource;
-			if (theIsSubElementWithinResource && StringUtils.isNotBlank(res.getId())) {
+			if (theContainedResource && StringUtils.isNotBlank(res.getId())) {
 				resourceId = res.getId();
 			}
 		}
 
-		encodeResourceToJsonStreamWriter(theResDef, theResource, theEventWriter, theObjectNameOrNull, theIsSubElementWithinResource, resourceId);
+		encodeResourceToJsonStreamWriter(theResDef, theResource, theEventWriter, theObjectNameOrNull, theContainedResource, resourceId);
 	}
 
 	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonGenerator theEventWriter, String theObjectNameOrNull,
-			boolean theIsSubElementWithinResource, String theResourceId) throws IOException {
+			boolean theContainedResource, String theResourceId) throws IOException {
-		if (!theIsSubElementWithinResource) {
+		if (!theContainedResource) {
 			super.containResourcesForEncoding(theResource);
 		}
 
@@ -670,54 +675,65 @@ public class JsonParser extends BaseParser implements IParser {
 		if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1) && theResource instanceof IResource) {
 			IResource resource = (IResource) theResource;
 			// Object securityLabelRawObj =
-			List<BaseCodingDt> securityLabels = (List<BaseCodingDt>) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.SECURITY_LABELS);
+
-			if (!ElementUtil.isEmpty(resource.getId().getVersionIdPart(), ResourceMetadataKeyEnum.UPDATED.get(resource))
+			List<BaseCodingDt> securityLabels = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
-					|| (securityLabels != null && !securityLabels.isEmpty())) {
+			List<IdDt> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
+			TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(resource);
+			InstantDt updated = (InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
+			IdDt resourceId = resource.getId();
+			String versionIdPart = resourceId.getVersionIdPart();
+			if (isBlank(versionIdPart)) {
+				versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
+			}
+
+			if (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, profiles) == false) {
 				theEventWriter.writeStartObject("meta");
-				writeOptionalTagWithTextNode(theEventWriter, "versionId", resource.getId().getVersionIdPart());
+				writeOptionalTagWithTextNode(theEventWriter, "versionId", versionIdPart);
-				writeOptionalTagWithTextNode(theEventWriter, "lastUpdated", ResourceMetadataKeyEnum.UPDATED.get(resource));
+				writeOptionalTagWithTextNode(theEventWriter, "lastUpdated", updated);
 
-				if (securityLabels != null) {
+				if (profiles != null && profiles.isEmpty() == false) {
-					if (!securityLabels.isEmpty()) {
+					theEventWriter.writeStartArray("profile");
+					for (IdDt profile : profiles) {
+						if (profile != null && isNotBlank(profile.getValue())) {
+							theEventWriter.write(profile.getValue());
+						}
+					}
+					theEventWriter.writeEnd();
+				}
+
+				if (securityLabels.isEmpty() == false) {
 					theEventWriter.writeStartArray("security");
-
 					for (BaseCodingDt securityLabel : securityLabels) {
 						theEventWriter.writeStartObject();
-
+						BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(securityLabel.getClass());
-							UriDt system = securityLabel.getSystemElement();
+						encodeCompositeElementChildrenToStreamWriter(resDef, resource, securityLabel, theEventWriter, def.getChildren(), theContainedResource);
-							if (system != null && !system.isEmpty())
+						theEventWriter.writeEnd();
-								writeOptionalTagWithTextNode(theEventWriter, "system", system.getValueAsString());
-
-							CodeDt code = securityLabel.getCodeElement();
-
-							if (code != null && !code.isEmpty())
-								writeOptionalTagWithTextNode(theEventWriter, "code", code.getValueAsString());
-
-							StringDt display = securityLabel.getDisplayElement();
-							if (display != null && !display.isEmpty())
-								writeOptionalTagWithTextNode(theEventWriter, "display", display.getValueAsString());
-
-							/*todo: handle version
-							StringDt version = securityLabel.getVersion();
-							if (version != null && ! version.isEmpty())
-								writeOptionalTagWithTextNode(theEventWriter, "version", version.getValueAsString());
-                            */
-							theEventWriter.writeEnd(); //end the individual security label
 					}
-						theEventWriter.writeEnd(); //end security labels array
+					theEventWriter.writeEnd();
 				}
+
+				if (tags != null && tags.isEmpty() == false) {
+					theEventWriter.writeStartArray("tag");
+					for (Tag tag : tags) {
+						theEventWriter.writeStartObject();
+						writeOptionalTagWithTextNode(theEventWriter, "system", tag.getScheme());
+						writeOptionalTagWithTextNode(theEventWriter, "code", tag.getTerm());
+						writeOptionalTagWithTextNode(theEventWriter, "display", tag.getLabel());
+						theEventWriter.writeEnd();
+					}
+					theEventWriter.writeEnd();
 				}
 
 				theEventWriter.writeEnd(); // end meta
 			}
 		}
 
-		if (theResource instanceof BaseBinary) {
+		if (theResource instanceof IBaseBinary) {
-			BaseBinary bin = (BaseBinary) theResource;
+			IBaseBinary bin = (IBaseBinary) theResource;
 			theEventWriter.write("contentType", bin.getContentType());
 			theEventWriter.write("content", bin.getContentAsBase64());
 		} else {
-			encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, resDef, theIsSubElementWithinResource);
+			encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, resDef, theContainedResource);
 		}
 
 		theEventWriter.writeEnd();
@@ -1128,30 +1144,30 @@ public class JsonParser extends BaseParser implements IParser {
 		}
 	}
 
-	private void parseExtensionInDstu2Style(boolean theModifier, ParserState<?> theState, String theParentExtensionUrl, String theExtensionUrl, JsonArray theValues) {
+	// private void parseExtensionInDstu2Style(boolean theModifier, ParserState<?> theState, String theParentExtensionUrl, String theExtensionUrl, JsonArray theValues) {
-		String extUrl = UrlUtil.constructAbsoluteUrl(theParentExtensionUrl, theExtensionUrl);
+	// String extUrl = UrlUtil.constructAbsoluteUrl(theParentExtensionUrl, theExtensionUrl);
-		theState.enteringNewElementExtension(null, extUrl, theModifier);
+	// theState.enteringNewElementExtension(null, extUrl, theModifier);
-
+	//
-		for (int extIdx = 0; extIdx < theValues.size(); extIdx++) {
+	// for (int extIdx = 0; extIdx < theValues.size(); extIdx++) {
-			JsonObject nextExt = theValues.getJsonObject(extIdx);
+	// JsonObject nextExt = theValues.getJsonObject(extIdx);
-			for (String nextKey : nextExt.keySet()) {
+	// for (String nextKey : nextExt.keySet()) {
-				// if (nextKey.startsWith("value") && nextKey.length() > 5 &&
+	// // if (nextKey.startsWith("value") && nextKey.length() > 5 &&
-				// myContext.getRuntimeChildUndeclaredExtensionDefinition().getChildByName(nextKey) != null) {
+	// // myContext.getRuntimeChildUndeclaredExtensionDefinition().getChildByName(nextKey) != null) {
-				JsonValue jsonVal = nextExt.get(nextKey);
+	// JsonValue jsonVal = nextExt.get(nextKey);
-				if (jsonVal.getValueType() == ValueType.ARRAY) {
+	// if (jsonVal.getValueType() == ValueType.ARRAY) {
-					/*
+	// /*
-					 * Extension children which are arrays are sub-extensions. Any other value type should be treated as a value.
+	// * Extension children which are arrays are sub-extensions. Any other value type should be treated as a value.
-					 */
+	// */
-					JsonArray arrayValue = (JsonArray) jsonVal;
+	// JsonArray arrayValue = (JsonArray) jsonVal;
-					parseExtensionInDstu2Style(theModifier, theState, extUrl, nextKey, arrayValue);
+	// parseExtensionInDstu2Style(theModifier, theState, extUrl, nextKey, arrayValue);
-				} else {
+	// } else {
-					parseChildren(theState, nextKey, jsonVal, null, null);
+	// parseChildren(theState, nextKey, jsonVal, null, null);
-				}
+	// }
-			}
+	// }
-		}
+	// }
-
+	//
-		theState.endingElement();
+	// theState.endingElement();
-	}
+	// }
 
 	@Override
 	public <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) {

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

@@ -20,17 +20,17 @@ package ca.uhn.fhir.parser;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.io.IOException;
 import java.io.Reader;
 import java.io.StringWriter;
 import java.io.Writer;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Iterator;
 import java.util.List;
-import java.util.ListIterator;
 
 import javax.xml.namespace.QName;
 import javax.xml.stream.FactoryConfigurationError;
@@ -46,13 +46,12 @@ import javax.xml.stream.events.Namespace;
 import javax.xml.stream.events.StartElement;
 import javax.xml.stream.events.XMLEvent;
 
-import ca.uhn.fhir.model.base.composite.BaseCodingDt;
-import ca.uhn.fhir.model.primitive.*;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.IBase;
 import org.hl7.fhir.instance.model.IBaseResource;
 import org.hl7.fhir.instance.model.IPrimitiveType;
 import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseBinary;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
@@ -73,20 +72,22 @@ import ca.uhn.fhir.context.RuntimeChildUndeclaredExtensionDefinition;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.BundleEntry;
-import ca.uhn.fhir.model.api.ExtensionDt;
-import ca.uhn.fhir.model.api.IElement;
-import ca.uhn.fhir.model.api.IPrimitiveDatatype;
 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.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.composite.BaseContainedDt;
 import ca.uhn.fhir.model.base.composite.BaseNarrativeDt;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
-import ca.uhn.fhir.model.base.resource.BaseBinary;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.model.primitive.XhtmlDt;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
-import ca.uhn.fhir.rest.method.BaseMethodBinding;
+import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.util.ElementUtil;
 import ca.uhn.fhir.util.NonPrettyPrintWriterWrapper;
 import ca.uhn.fhir.util.PrettyPrintWriterWrapper;
 import ca.uhn.fhir.util.XmlUtil;
@@ -245,12 +246,12 @@ public class XmlParser extends BaseParser implements IParser {
 		writeTagWithTextNode(eventWriter, "title", theBundle.getTitle());
 		writeTagWithTextNode(eventWriter, "id", theBundle.getBundleId());
 
-		writeAtomLink(eventWriter, "self", theBundle.getLinkSelf());
+		writeAtomLink(eventWriter, Constants.LINK_SELF, theBundle.getLinkSelf());
-		writeAtomLink(eventWriter, "first", theBundle.getLinkFirst());
+		writeAtomLink(eventWriter, Constants.LINK_FIRST, theBundle.getLinkFirst());
-		writeAtomLink(eventWriter, "previous", theBundle.getLinkPrevious());
+		writeAtomLink(eventWriter, Constants.LINK_PREVIOUS, theBundle.getLinkPrevious());
-		writeAtomLink(eventWriter, "next", theBundle.getLinkNext());
+		writeAtomLink(eventWriter, Constants.LINK_NEXT, theBundle.getLinkNext());
-		writeAtomLink(eventWriter, "last", theBundle.getLinkLast());
+		writeAtomLink(eventWriter, Constants.LINK_LAST, theBundle.getLinkLast());
-		writeAtomLink(eventWriter, "fhir-base", theBundle.getLinkBase());
+		writeAtomLink(eventWriter, Constants.LINK_FHIR_BASE, theBundle.getLinkBase());
 
 		if (theBundle.getTotalResults().getValue() != null) {
 			eventWriter.writeStartElement("os", "totalResults", OPENSEARCH_NS);
@@ -412,9 +413,9 @@ public class XmlParser extends BaseParser implements IParser {
 				// IResource nextResource = nextEntry.getResource();
 			}
 
-			if (nextEntry.getTransactionOperation().isEmpty() == false || nextEntry.getLinkSearch().isEmpty() == false) {
+			if (nextEntry.getTransactionMethod().isEmpty() == false || nextEntry.getLinkSearch().isEmpty() == false) {
 				theEventWriter.writeStartElement("transaction");
-				writeOptionalTagWithValue(theEventWriter, "operation", nextEntry.getTransactionOperation().getValue());
+				writeOptionalTagWithValue(theEventWriter, "method", nextEntry.getTransactionMethod().getValue());
 				writeOptionalTagWithValue(theEventWriter, "url", nextEntry.getLinkSearch().getValue());
 				theEventWriter.writeEndElement();
 			}
@@ -733,69 +734,56 @@ public class XmlParser extends BaseParser implements IParser {
 			// HL7.org Structures
 			encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, resDef, theContainedResource);
 
-
 		} else {
 
 			if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
 
 				// DSTU2+
 
-
 				IResource resource = (IResource) theResource;
 				writeOptionalTagWithValue(theEventWriter, "id", theResourceId);
 
-
 				InstantDt updated = (InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
-				//Object securityLabelRawObj = resource.getResourceMetadata().get(ResourceMetadataKeyEnum.SECURITY_LABELS);
-				List<BaseCodingDt> securityLabels = (List<BaseCodingDt>) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.SECURITY_LABELS);
 				IdDt resourceId = resource.getId();
-				if (resourceId != null && isNotBlank(resourceId.getVersionIdPart())
-						|| (updated != null && !updated.isEmpty())
-						|| (securityLabels != null && !securityLabels.isEmpty())) {
-					theEventWriter.writeStartElement("meta");
 				String versionIdPart = resourceId.getVersionIdPart();
 				if (isBlank(versionIdPart)) {
 					versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
 				}
+				List<BaseCodingDt> securityLabels = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
+				List<IdDt> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
+				TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(resource);
+				if (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, profiles) == false) {
+					theEventWriter.writeStartElement("meta");
 					writeOptionalTagWithValue(theEventWriter, "versionId", versionIdPart);
 					if (updated != null) {
 						writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
 					}
 
-					if (securityLabels != null) {
+					for (IdDt profile : profiles) {
-
+						theEventWriter.writeStartElement("profile");
-						if (!securityLabels.isEmpty()) {
+						theEventWriter.writeAttribute("value", profile.getValue());
-
+						theEventWriter.writeEndElement();
+					}
 					for (BaseCodingDt securityLabel : securityLabels) {
 						theEventWriter.writeStartElement("security");
-
+						BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(securityLabel.getClass());
-								UriDt system = securityLabel.getSystemElement();
+						encodeCompositeElementChildrenToStreamWriter(resource, securityLabel, theEventWriter, def.getChildren(), theContainedResource);
-								if (system != null && !system.isEmpty())
-									writeOptionalTagWithValue(theEventWriter, "system", system.getValueAsString());
-
-								CodeDt code = securityLabel.getCodeElement();
-								if (code != null && !code.isEmpty())
-									writeOptionalTagWithValue(theEventWriter, "code", code.getValueAsString());
-
-								StringDt display = securityLabel.getDisplayElement();
-								if (display != null && !display.isEmpty())
-									writeOptionalTagWithValue(theEventWriter, "display", display.getValueAsString());
-
-							/*todo: handle version
-							StringDt version = securityLabel.getVersion();
-							if (version != null && ! version.isEmpty())
-								writeOptionalTagWithValue(theEventWriter, "version", version.getValueAsString());
-                            */
 						theEventWriter.writeEndElement();
 					}
-
+					if (tags != null) {
+						for (Tag tag : tags) {
+							theEventWriter.writeStartElement("tag");
+							writeOptionalTagWithValue(theEventWriter, "system", tag.getScheme());
+							writeOptionalTagWithValue(theEventWriter, "code", tag.getTerm());
+							writeOptionalTagWithValue(theEventWriter, "display", tag.getLabel());
+							theEventWriter.writeEndElement();
 						}
 					}
 					theEventWriter.writeEndElement();
 				}
 
-				if (theResource instanceof BaseBinary) {
+				if (theResource instanceof IBaseBinary) {
-					BaseBinary bin = (BaseBinary) theResource;
+					IBaseBinary bin = (IBaseBinary) theResource;
 					writeOptionalTagWithValue(theEventWriter, "contentType", bin.getContentType());
 					writeOptionalTagWithValue(theEventWriter, "content", bin.getContentAsBase64());
 				} else {
@@ -809,8 +797,8 @@ public class XmlParser extends BaseParser implements IParser {
 					theEventWriter.writeAttribute("id", theResourceId);
 				}
 
-				if (theResource instanceof BaseBinary) {
+				if (theResource instanceof IBaseBinary) {
-					BaseBinary bin = (BaseBinary) theResource;
+					IBaseBinary bin = (IBaseBinary) theResource;
 					if (bin.getContentType() != null) {
 						theEventWriter.writeAttribute("contentType", bin.getContentType());
 					}

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

@@ -30,10 +30,19 @@ import org.apache.commons.lang3.StringUtils;
  */
 public class IncomingRequestAddressStrategy implements IServerAddressStrategy {
 
+	private String myServletPath;
+
 	@Override
 	public String determineServerBase(ServletContext theServletContext, HttpServletRequest theRequest) {
 		String requestFullPath = StringUtils.defaultString(theRequest.getRequestURI());
-		String servletPath = StringUtils.defaultString(theRequest.getServletPath());
+		
+		String servletPath;
+		if (myServletPath != null) {
+			servletPath = myServletPath;
+		} else {
+			servletPath = StringUtils.defaultString(theRequest.getServletPath());
+		}
+		
 		StringBuffer requestUrl = theRequest.getRequestURL();
 		String servletContextPath = "";
 		if (theServletContext != null) {
@@ -48,7 +57,9 @@ public class IncomingRequestAddressStrategy implements IServerAddressStrategy {
 		}
 
 		int startOfPath = requestUrl.indexOf("//");
-		if (startOfPath != -1 && (startOfPath + 2) < requestUrl.length()) {
+		int requestUrlLength = requestUrl.length();
+
+		if (startOfPath != -1 && (startOfPath + 2) < requestUrlLength) {
 			startOfPath = requestUrl.indexOf("/", startOfPath + 2);
 		}
 		if (startOfPath == -1) {
@@ -56,9 +67,9 @@ public class IncomingRequestAddressStrategy implements IServerAddressStrategy {
 		}
 
 		int contextIndex;
-		if (servletPath.length() == 0) {
+		if (servletPath.length() == 0 || servletPath.equals("/")) {
 			if (requestPath.length() == 0) {
-				contextIndex = requestUrl.length();
+				contextIndex = requestUrlLength;
 			} else {
 				contextIndex = requestUrl.indexOf(requestPath, startOfPath);
 			}
@@ -68,8 +79,30 @@ public class IncomingRequestAddressStrategy implements IServerAddressStrategy {
 
 		String fhirServerBase;
 		int length = contextIndex + servletPath.length();
+		if (length > requestUrlLength) {
+			length = requestUrlLength;
+		}
 		fhirServerBase = requestUrl.substring(0, length);
 		return fhirServerBase;
 	}
 
+	/**
+	 * If set to a non-null value (default is <code>null</code>), this address strategy assumes that the FHIR endpoint is deployed to the given servlet path within the context. This is useful in some
+	 * deployments where it isn't obvious to the servlet which part of the path is actually the root path to reach the servlet.
+	 * <p>
+	 * Example values could be:
+	 * <ul>
+	 * <li>null</li>
+	 * <li>/</li>
+	 * <li>/base</li>
+	 * </ul>
+	 * </p>
+	 * <p>
+	 * <b>Wildcards are not supported!</b>
+	 * </p>
+	 */
+	public void setServletPath(String theServletPath) {
+		myServletPath = theServletPath;
+	}
+
 }

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java

@@ -7,18 +7,16 @@ import javax.servlet.ServletContext;
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 
-import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
-
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.context.ApplicationContext;
 import org.springframework.web.context.ContextLoaderListener;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
-import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
 import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu1;
+import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
 import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1;
+import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.server.ETagSupportEnum;
 import ca.uhn.fhir.rest.server.EncodingEnum;
@@ -26,7 +24,7 @@ import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
 import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 
 public class TestRestfulServer extends RestfulServer {
 
@@ -165,18 +163,12 @@ public class TestRestfulServer extends RestfulServer {
 		setPagingProvider(new FifoMemoryPagingProvider(10));
 
 		/*
-		 * Do some fancy logging to create a nice access log that has details
+		 * Load interceptors for the server from Spring (these are defined in hapi-fhir-server-config.xml
-		 * about each incoming request. 
 		 */
 		List<IServerInterceptor> interceptorBeans = myAppCtx.getBean("myServerInterceptors", List.class);
-		for (IServerInterceptor interceptor : interceptorBeans)
+		for (IServerInterceptor interceptor : interceptorBeans) {
 			this.registerInterceptor(interceptor);
-
+		}
-		/*LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
-		loggingInterceptor.setLoggerName("fhirtest.access");
-		loggingInterceptor.setMessageFormat("Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}]");
-		this.registerInterceptor(loggingInterceptor);
-		*/
 
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/hapi-fhir-server-config.xml

@@ -24,6 +24,11 @@
 	<util:list id="myServerInterceptors">
 		<ref bean="myLoggingInterceptor"/>
 	</util:list>
+	
+	<!-- 
+	Do some fancy logging to create a nice access log that has details
+	about each incoming request.
+	-->
 	<bean id="myLoggingInterceptor" class="ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor">
 		<property name="loggerName" value="fhirtest.access"/>
 		<property name="messageFormat"

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/IncomingRequestAddressStrategyTest.java

@@ -1,7 +1,8 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 import java.io.IOException;
 import java.util.concurrent.TimeUnit;
@@ -24,8 +25,6 @@ import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.rest.server.ServerBaseTest.DummyProvider;
 import ca.uhn.fhir.util.RandomServerPortProvider;
 
 public class IncomingRequestAddressStrategyTest {
@@ -99,9 +98,33 @@ public class IncomingRequestAddressStrategyTest {
 
 		startServer(port, contextPath, servletPath);
 
+		httpGet("http://localhost:" + port + "/ctx");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/Patient?_pretty=true");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/Patient/123/_history/222");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
 		httpGet("http://localhost:" + port);
 		assertEquals(null, ourLastBase);
 		
+	}
+
+	@Test
+	public void testUnderJettyWithContextPathServletRootContextOnly() throws Exception {
+		int port = RandomServerPortProvider.findFreePort();
+
+		String contextPath = "/ctx";
+		String servletPath = "/";
+
+		startServer(port, contextPath, servletPath);
+		ourStrategy.setServletPath("");
+
 		httpGet("http://localhost:" + port + "/ctx");
 		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
 
@@ -113,6 +136,37 @@ public class IncomingRequestAddressStrategyTest {
 
 		httpGet("http://localhost:" + port + "/ctx/Patient/123/_history/222");
 		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port);
+		assertEquals(null, ourLastBase);
+		
+	}
+
+	
+	@Test
+	public void testUnderJettyWithContextPathServletRoot2() throws Exception {
+		int port = RandomServerPortProvider.findFreePort();
+
+		String contextPath = "/ctx";
+		String servletPath = "/foo/bar/*"; // not /* but still this should work
+
+		startServer(port, contextPath, servletPath);
+
+		httpGet("http://localhost:" + port + "/ctx/foo/bar/Patient?_pretty=true");
+		assertEquals("http://localhost:" + port + "/ctx/foo/bar", ourLastBase);
+		
+		httpGet("http://localhost:" + port + "/ctx/foo/bar");
+		assertEquals("http://localhost:" + port + "/ctx/foo/bar", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/foo/bar/");
+		assertEquals("http://localhost:" + port + "/ctx/foo/bar", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/foo/bar/Patient/123/_history/222");
+		assertEquals("http://localhost:" + port + "/ctx/foo/bar", ourLastBase);
+
+		httpGet("http://localhost:" + port);
+		assertEquals(null, ourLastBase);
+		
 	}
 
 	@Test
@@ -168,6 +222,9 @@ public class IncomingRequestAddressStrategyTest {
 
 		@Override
 		protected void doGet(HttpServletRequest theReq, HttpServletResponse theResp) throws ServletException, IOException {
+			
+//			ourLog.info("Ctx: {}", theReq.)
+			
 			ourLastBase = ourStrategy.determineServerBase(getServletContext(), theReq);
 			theResp.setContentType("text/plain");
 			theResp.getWriter().append("Success");

hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/model/HomeRequest.java

@@ -49,7 +49,9 @@ public class HomeRequest {
 		}
 
 		if (retVal.contains("${serverBase}")) {
-			String base = new IncomingRequestAddressStrategy().determineServerBase(theRequest.getServletContext(), theRequest);
+			IncomingRequestAddressStrategy strategy = new IncomingRequestAddressStrategy();
+			strategy.setServletPath("");
+			String base = strategy.determineServerBase(theRequest.getServletContext(), theRequest);
 			if (base.endsWith("/")) {
 				base = base.substring(0, base.length() - 1);
 			}