Merged with the latest master snapshot.

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

@@ -73,6 +73,7 @@ import ca.uhn.fhir.validation.FhirValidator;
 public class FhirContext {
 
 	private static final List<Class<? extends IBaseResource>> EMPTY_LIST = Collections.emptyList();
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirContext.class);
 	private volatile Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinition = Collections.emptyMap();
 	private volatile Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = Collections.emptyMap();
 	private HapiLocalizer myLocalizer = new HapiLocalizer();
@@ -82,6 +83,7 @@ public class FhirContext {
 	private volatile IRestfulClientFactory myRestfulClientFactory;
 	private volatile RuntimeChildUndeclaredExtensionDefinition myRuntimeChildUndeclaredExtensionDefinition;
 	private final IFhirVersion myVersion;
+
 	private Map<FhirVersionEnum, Map<String, Class<? extends IBaseResource>>> myVersionToNameToResourceType = Collections.emptyMap();
 
 	/**
@@ -125,6 +127,8 @@ public class FhirContext {
 			throw new IllegalStateException(getLocalizer().getMessage(FhirContext.class, "noStructures"));
 		}
 
+		ourLog.info("Creating new FHIR context for FHIR version [{}]", myVersion.getVersion().name());
+
 		scanResourceTypes(toElementList(theResourceTypes));
 	}
 
@@ -214,14 +218,14 @@ public class FhirContext {
 			nameToType = new HashMap<String, Class<? extends IBaseResource>>();
 			ModelScanner.scanVersionPropertyFile(null, nameToType, theVersion);
 
-			Map<FhirVersionEnum, Map<String, Class<? extends IBaseResource>>> newVersionToNameToResourceType = new HashMap<FhirVersionEnum, Map<String,Class<? extends IBaseResource>>>();
+			Map<FhirVersionEnum, Map<String, Class<? extends IBaseResource>>> newVersionToNameToResourceType = new HashMap<FhirVersionEnum, Map<String, Class<? extends IBaseResource>>>();
 			newVersionToNameToResourceType.putAll(myVersionToNameToResourceType);
 			newVersionToNameToResourceType.put(theVersion, nameToType);
 			myVersionToNameToResourceType = newVersionToNameToResourceType;
 		}
 
 		Class<? extends IBaseResource> resourceType = nameToType.get(theResourceName.toLowerCase());
-		if (resourceType==null) {
+		if (resourceType == null) {
 			throw new DataFormatException(createUnknownResourceNameError(theResourceName, theVersion));
 		}
 
@@ -475,6 +479,10 @@ public class FhirContext {
 		return new FhirContext(FhirVersionEnum.DSTU2);
 	}
 
+	public static FhirContext forDstu2Hl7Org() {
+		return new FhirContext(FhirVersionEnum.DSTU2_HL7ORG);
+	}
+
 	private static Collection<Class<? extends IBaseResource>> toCollection(Class<? extends IBaseResource> theResourceType) {
 		ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<Class<? extends IBaseResource>>(1);
 		retVal.add(theResourceType);
@@ -493,8 +501,4 @@ public class FhirContext {
 		return retVal;
 	}
 
-	public static FhirContext forDstu2Hl7Org() {
-		return new FhirContext(FhirVersionEnum.DSTU2_HL7ORG);
-	}
-
 }

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

@@ -216,7 +216,7 @@ class ModelScanner {
 
 		long time = System.currentTimeMillis() - start;
 		int size = myClassToElementDefinitions.size() - startSize;
-		ourLog.info("Done scanning FHIR library, found {} model entries in {}ms", size, time);
+		ourLog.debug("Done scanning FHIR library, found {} model entries in {}ms", size, time);
 	}
 
 	/**

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

@@ -113,6 +113,18 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String> {
 		this(theResourceType, toPlainStringWithNpeThrowIfNeeded(theIdPart));
 	}
 
+	/**
+	 * Constructor
+	 * 
+	 * @param theResourceType
+	 *            The resource type (e.g. "Patient")
+	 * @param theIdPart
+	 *            The ID (e.g. "123")
+	 */
+	public IdDt(String theResourceType, Long theIdPart) {
+		this(theResourceType, toPlainStringWithNpeThrowIfNeeded(theIdPart));
+	}
+
 	/**
 	 * Constructor
 	 * 
@@ -515,6 +527,13 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String> {
 		return theIdPart.toPlainString();
 	}
 
+	private static String toPlainStringWithNpeThrowIfNeeded(Long theIdPart) {
+		if (theIdPart == null) {
+			throw new NullPointerException("Long ID can not be null");
+		}
+		return theIdPart.toString();
+	}
+
 	@Override
 	public boolean isEmpty() {
 		return isBlank(getValue());

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

@@ -146,8 +146,9 @@ public class MethodOutcome {
 	 *            If not null, indicates whether the resource was created (as opposed to being updated). This is generally not needed, since the server can assume based on the method being called
 	 *            whether the result was a creation or an update. However, it can be useful if you are implementing an update method that does a create if the ID doesn't already exist.
 	 */
-	public void setCreated(Boolean theCreated) {
+	public MethodOutcome setCreated(Boolean theCreated) {
 		myCreated = theCreated;
+		return this;
 	}
 
 	/**

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

@@ -182,8 +182,13 @@ public abstract class BaseClient {
 		}
 
 		try {
+			String mimeType;
+			if (Constants.STATUS_HTTP_204_NO_CONTENT == response.getStatusLine().getStatusCode()) {
+				mimeType = null;
+			} else {
 				ContentType ct = ContentType.get(response.getEntity());
-			String mimeType = ct != null ? ct.getMimeType() : null;
+				mimeType = ct != null ? ct.getMimeType() : null;
+			}
 			
 			Map<String, List<String>> headers = new HashMap<String, List<String>>();
 			if (response.getAllHeaders() != null) {
@@ -398,7 +403,9 @@ public abstract class BaseClient {
 			charset = ct.getCharset();
 		}
 		if (charset == null) {
+			if (Constants.STATUS_HTTP_204_NO_CONTENT != theResponse.getStatusLine().getStatusCode()) {
 				ourLog.warn("Response did not specify a charset.");
+			}
 			charset = Charset.forName("UTF-8");
 		}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/BaseHttpClientInvocation.java

@@ -59,6 +59,9 @@ public abstract class BaseHttpClientInvocation {
 	public abstract HttpRequestBase asHttpRequest(String theUrlBase, Map<String, List<String>> theExtraParams, EncodingEnum theEncoding);
 
 	protected static void appendExtraParamsWithQuestionMark(Map<String, List<String>> theExtraParams, StringBuilder theUrlBuilder, boolean theWithQuestionMark) {
+		if (theExtraParams==null) {
+			return;
+		}
 		boolean first = theWithQuestionMark;
 
 		if (theExtraParams != null && theExtraParams.isEmpty() == false) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/GenericClient.java

@@ -56,10 +56,14 @@ import ca.uhn.fhir.rest.client.exceptions.NonFhirResponseException;
 import ca.uhn.fhir.rest.gclient.IClientExecutable;
 import ca.uhn.fhir.rest.gclient.ICreate;
 import ca.uhn.fhir.rest.gclient.ICreateTyped;
+import ca.uhn.fhir.rest.gclient.ICreateWithQuery;
+import ca.uhn.fhir.rest.gclient.ICreateWithQueryTyped;
 import ca.uhn.fhir.rest.gclient.ICriterion;
 import ca.uhn.fhir.rest.gclient.ICriterionInternal;
 import ca.uhn.fhir.rest.gclient.IDelete;
 import ca.uhn.fhir.rest.gclient.IDeleteTyped;
+import ca.uhn.fhir.rest.gclient.IDeleteWithQuery;
+import ca.uhn.fhir.rest.gclient.IDeleteWithQueryTyped;
 import ca.uhn.fhir.rest.gclient.IGetPage;
 import ca.uhn.fhir.rest.gclient.IGetPageTyped;
 import ca.uhn.fhir.rest.gclient.IGetTags;
@@ -76,6 +80,8 @@ import ca.uhn.fhir.rest.gclient.IUntypedQuery;
 import ca.uhn.fhir.rest.gclient.IUpdate;
 import ca.uhn.fhir.rest.gclient.IUpdateExecutable;
 import ca.uhn.fhir.rest.gclient.IUpdateTyped;
+import ca.uhn.fhir.rest.gclient.IUpdateWithQuery;
+import ca.uhn.fhir.rest.gclient.IUpdateWithQueryTyped;
 import ca.uhn.fhir.rest.method.DeleteMethodBinding;
 import ca.uhn.fhir.rest.method.HistoryMethodBinding;
 import ca.uhn.fhir.rest.method.HttpDeleteClientInvocation;
@@ -237,10 +243,10 @@ public class GenericClient extends BaseClient implements IGenericClient {
 		return new LoadPageInternal();
 	}
 
-//	@Override
+	// @Override
-//	public <T extends IBaseResource> T read(final Class<T> theType, IdDt theId) {
+	// public <T extends IBaseResource> T read(final Class<T> theType, IdDt theId) {
-//		return doReadOrVRead(theType, theId, false, null, null);
+	// return doReadOrVRead(theType, theId, false, null, null);
-//	}
+	// }
 
 	@Override
 	public <T extends IBaseResource> T read(Class<T> theType, String theId) {
@@ -249,7 +255,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 
 	@Override
 	public <T extends IBaseResource> T read(final Class<T> theType, UriDt theUrl) {
-		IdDt id = theUrl instanceof IdDt ? ((IdDt)theUrl) : new IdDt(theUrl);
+		IdDt id = theUrl instanceof IdDt ? ((IdDt) theUrl) : new IdDt(theUrl);
 		return doReadOrVRead(theType, id, false, null, null);
 	}
 
@@ -475,18 +481,18 @@ public class GenericClient extends BaseClient implements IGenericClient {
 		return vread(theType, resId);
 	}
 
-	private abstract class BaseClientExecutable<T extends IClientExecutable<?, ?>, Y> implements IClientExecutable<T, Y> {
+	private static void addParam(Map<String, List<String>> params, String parameterName, String parameterValue) {
-		private EncodingEnum myParamEncoding;
-		private Boolean myPrettyPrint;
-		private boolean myQueryLogRequestAndResponse;
-
-		protected void addParam(Map<String, List<String>> params, String parameterName, String parameterValue) {
 		if (!params.containsKey(parameterName)) {
 			params.put(parameterName, new ArrayList<String>());
 		}
 		params.get(parameterName).add(parameterValue);
 	}
 
+	private abstract class BaseClientExecutable<T extends IClientExecutable<?, ?>, Y> implements IClientExecutable<T, Y> {
+		private EncodingEnum myParamEncoding;
+		private Boolean myPrettyPrint;
+		private boolean myQueryLogRequestAndResponse;
+
 		@SuppressWarnings("unchecked")
 		@Override
 		public T andLogRequestAndResponse(boolean theLogRequestAndResponse) {
@@ -575,11 +581,13 @@ public class GenericClient extends BaseClient implements IGenericClient {
 		}
 	}
 
-	private class CreateInternal extends BaseClientExecutable<ICreateTyped, MethodOutcome> implements ICreate, ICreateTyped {
+	private class CreateInternal extends BaseClientExecutable<ICreateTyped, MethodOutcome> implements ICreate, ICreateTyped, ICreateWithQuery, ICreateWithQueryTyped {
 
 		private String myId;
 		private IResource myResource;
 		private String myResourceBody;
+		private String mySearchUrl;
+		private CriterionList myCriterionList;
 
 		@Override
 		public MethodOutcome execute() {
@@ -593,7 +601,14 @@ public class GenericClient extends BaseClient implements IGenericClient {
 				myResourceBody = null;
 			}
 
-			BaseHttpClientInvocation invocation = MethodUtil.createCreateInvocation(myResource, myResourceBody, myId, myContext);
+			BaseHttpClientInvocation invocation;
+			if (mySearchUrl != null) {
+				invocation = MethodUtil.createCreateInvocation(myResource, myResourceBody, myId, myContext, mySearchUrl);
+			} else if (myCriterionList != null) {
+				invocation = MethodUtil.createCreateInvocation(myResource, myResourceBody, myId, myContext, myCriterionList.toParamList());
+			} else {
+				invocation = MethodUtil.createCreateInvocation(myResource, myResourceBody, myId, myContext);
+			}
 
 			RuntimeResourceDefinition def = myContext.getResourceDefinition(myResource);
 			final String resourceName = def.getName();
@@ -631,15 +646,50 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			return this;
 		}
 
+		@Override
+		public ICreateTyped conditionalByUrl(String theSearchUrl) {
+			mySearchUrl = theSearchUrl;
+			return this;
 		}
 
-	private class DeleteInternal extends BaseClientExecutable<IDeleteTyped, BaseOperationOutcome> implements IDelete, IDeleteTyped {
+		@Override
+		public ICreateWithQuery conditional() {
+			myCriterionList = new CriterionList();
+			return this;
+		}
+
+		@Override
+		public ICreateWithQueryTyped where(ICriterion<?> theCriterion) {
+			myCriterionList.add((ICriterionInternal) theCriterion);
+			return this;
+		}
+
+		@Override
+		public ICreateWithQueryTyped and(ICriterion<?> theCriterion) {
+			myCriterionList.add((ICriterionInternal) theCriterion);
+			return this;
+		}
+
+	}
+
+	private class DeleteInternal extends BaseClientExecutable<IDeleteTyped, BaseOperationOutcome> implements IDelete, IDeleteTyped, IDeleteWithQuery, IDeleteWithQueryTyped {
 
 		private IdDt myId;
+		private String mySearchUrl;
+		private String myResourceType;
+		private CriterionList myCriterionList;
 
 		@Override
 		public BaseOperationOutcome execute() {
-			HttpDeleteClientInvocation invocation = DeleteMethodBinding.createDeleteInvocation(myId);
+			HttpDeleteClientInvocation invocation;
+			if (myId != null) {
+				invocation = DeleteMethodBinding.createDeleteInvocation(myId);
+			} else if (myCriterionList != null) {
+				Map<String, List<String>> params = myCriterionList.toParamList();
+				invocation = DeleteMethodBinding.createDeleteInvocation(myResourceType, params);
+			} else {
+				invocation = DeleteMethodBinding.createDeleteInvocation(mySearchUrl);
+			}
 			OperationOutcomeResponseHandler binding = new OperationOutcomeResponseHandler();
 			Map<String, List<String>> params = new HashMap<String, List<String>>();
 			return invoke(params, binding, invocation);
@@ -680,6 +730,56 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			myId = new IdDt(theResourceType, theLogicalId);
 			return this;
 		}
+
+		@Override
+		public IDeleteTyped resourceConditionalByUrl(String theSearchUrl) {
+			Validate.notBlank(theSearchUrl, "theSearchUrl can not be blank/null");
+			mySearchUrl = theSearchUrl;
+			return this;
+		}
+
+		@Override
+		public IDeleteWithQuery resourceConditionalByType(String theResourceType) {
+			Validate.notBlank(theResourceType, "theResourceType can not be blank/null");
+			if (myContext.getResourceDefinition(theResourceType) == null) {
+				throw new IllegalArgumentException("Unknown resource type: " + theResourceType);
+			}
+			myResourceType = theResourceType;
+			myCriterionList = new CriterionList();
+			return this;
+		}
+
+		@Override
+		public IDeleteWithQueryTyped where(ICriterion<?> theCriterion) {
+			myCriterionList.add((ICriterionInternal) theCriterion);
+			return this;
+		}
+
+		@Override
+		public IDeleteWithQueryTyped and(ICriterion<?> theCriterion) {
+			myCriterionList.add((ICriterionInternal) theCriterion);
+			return this;
+		}
+	}
+
+	private static class CriterionList extends ArrayList<ICriterionInternal> {
+
+		private static final long serialVersionUID = 1L;
+
+		public void populateParamList(Map<String, List<String>> theParams) {
+			for (ICriterionInternal next : this) {
+				String parameterName = next.getParameterName();
+				String parameterValue = next.getParameterValue();
+				addParam(theParams, parameterName, parameterValue);
+			}
+		}
+
+		public Map<String, List<String>> toParamList() {
+			LinkedHashMap<String, List<String>> retVal = new LinkedHashMap<String, List<String>>();
+			populateParamList(retVal);
+			return retVal;
+		}
+
 	}
 
 	private class GetPageInternal extends BaseClientExecutable<IGetPageTyped, Bundle> implements IGetPageTyped {
@@ -996,7 +1096,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 	private class SearchInternal extends BaseClientExecutable<IQuery, Bundle> implements IQuery, IUntypedQuery {
 
 		private String myCompartmentName;
-		private List<ICriterionInternal> myCriterion = new ArrayList<ICriterionInternal>();
+		private CriterionList myCriterion = new CriterionList();
 		private List<Include> myInclude = new ArrayList<Include>();
 		private Integer myParamLimit;
 		private String myResourceId;
@@ -1025,11 +1125,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			// params.putAll(initial);
 			// }
 
-			for (ICriterionInternal next : myCriterion) {
+			myCriterion.populateParamList(params);
-				String parameterName = next.getParameterName();
-				String parameterValue = next.getParameterValue();
-				addParam(params, parameterName, parameterValue);
-			}
 
 			for (Include next : myInclude) {
 				addParam(params, Constants.PARAM_INCLUDE, next.getValue());
@@ -1224,30 +1320,39 @@ public class GenericClient extends BaseClient implements IGenericClient {
 
 	}
 
-	private class UpdateInternal extends BaseClientExecutable<IUpdateExecutable, MethodOutcome> implements IUpdate, IUpdateTyped, IUpdateExecutable {
+	private class UpdateInternal extends BaseClientExecutable<IUpdateExecutable, MethodOutcome> implements IUpdate, IUpdateTyped, IUpdateExecutable, IUpdateWithQuery, IUpdateWithQueryTyped {
 
 		private IdDt myId;
 		private IResource myResource;
 		private String myResourceBody;
+		private String mySearchUrl;
+		private CriterionList myCriterionList;
 
 		@Override
 		public MethodOutcome execute() {
 			if (myResource == null) {
 				myResource = parseResourceBody(myResourceBody);
 			}
-			if (myId == null) {
-				myId = myResource.getId();
-			}
-			if (myId == null || myId.hasIdPart() == false) {
-				throw new InvalidRequestException("No ID supplied for resource to update, can not invoke server");
-			}
 
 			// If an explicit encoding is chosen, we will re-serialize to ensure the right encoding
 			if (getParamEncoding() != null) {
 				myResourceBody = null;
 			}
 
-			BaseHttpClientInvocation invocation = MethodUtil.createUpdateInvocation(myResource, myResourceBody, myId, myContext);
+			BaseHttpClientInvocation invocation;
+			if (mySearchUrl != null) {
+				invocation = MethodUtil.createUpdateInvocation(myContext, myResource, myResourceBody, mySearchUrl);
+			} else if (myCriterionList != null) {
+				invocation = MethodUtil.createUpdateInvocation(myContext, myResource, myResourceBody, myCriterionList.toParamList());
+			} else {
+				if (myId == null) {
+					myId = myResource.getId();
+				}
+				if (myId == null || myId.hasIdPart() == false) {
+					throw new InvalidRequestException("No ID supplied for resource to update, can not invoke server");
+				}
+				invocation = MethodUtil.createUpdateInvocation(myResource, myResourceBody, myId, myContext);
+			}
 
 			RuntimeResourceDefinition def = myContext.getResourceDefinition(myResource);
 			final String resourceName = def.getName();
@@ -1297,6 +1402,30 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			return this;
 		}
 
+		@Override
+		public IUpdateTyped conditionalByUrl(String theSearchUrl) {
+			mySearchUrl = theSearchUrl;
+			return this;
+		}
+
+		@Override
+		public IUpdateWithQuery conditional() {
+			myCriterionList = new CriterionList();
+			return this;
+		}
+
+		@Override
+		public IUpdateWithQueryTyped where(ICriterion<?> theCriterion) {
+			myCriterionList.add((ICriterionInternal) theCriterion);
+			return this;
+		}
+
+		@Override
+		public IUpdateWithQueryTyped and(ICriterion<?> theCriterion) {
+			myCriterionList.add((ICriterionInternal) theCriterion);
+			return this;
+		}
+
 	}
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IBaseQuery.java

@@ -0,0 +1,9 @@
+package ca.uhn.fhir.rest.gclient;
+
+public interface IBaseQuery<T> {
+
+	T where(ICriterion<?> theCriterion);
+
+	T and(ICriterion<?> theCriterion);
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/ICreateTyped.java

@@ -37,4 +37,20 @@ public interface ICreateTyped extends IClientExecutable<ICreateTyped, MethodOutc
 	 */
 	ICreateTyped withId(IdDt theId);
 
+	/**
+	 * Specifies that the create should be performed as a conditional create 
+	 * against a given search URL. 
+	 * 
+	 * @param theSearchUrl The search URL to use. The format of this URL should be of the form <code>[ResourceType]?[Parameters]</code>,
+	 * for example: <code>Patient?name=Smith&amp;identifier=13.2.4.11.4%7C847366</code>
+	 * 
+	 * @since HAPI 0.9 / FHIR DSTU 2
+	 */
+	ICreateTyped conditionalByUrl(String theSearchUrl);
+
+	/**
+	 * @since HAPI 0.9 / FHIR DSTU 2
+	 */
+	ICreateWithQuery conditional();
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/ICreateWithQuery.java

@@ -0,0 +1,6 @@
+package ca.uhn.fhir.rest.gclient;
+
+
+public interface ICreateWithQuery extends IBaseQuery<ICreateWithQueryTyped> {
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/ICreateWithQueryTyped.java

@@ -0,0 +1,5 @@
+package ca.uhn.fhir.rest.gclient;
+
+public interface ICreateWithQueryTyped extends ICreateTyped, ICreateWithQuery {
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IDelete.java

@@ -31,4 +31,20 @@ public interface IDelete {
 	
 	IDeleteTyped resourceById(String theResourceType, String theLogicalId);
 
+	/**
+	 * Specifies that the delete should be performed as a conditional delete 
+	 * against a given search URL. 
+	 * 
+	 * @param theSearchUrl The search URL to use. The format of this URL should be of the form <code>[ResourceType]?[Parameters]</code>,
+	 * for example: <code>Patient?name=Smith&amp;identifier=13.2.4.11.4%7C847366</code>
+	 * 
+	 * @since HAPI 0.9 / FHIR DSTU 2
+	 */
+	IDeleteTyped resourceConditionalByUrl(String theSearchUrl);
+
+	/**
+	 * @since HAPI 0.9 / FHIR DSTU 2
+	 */
+	IDeleteWithQuery resourceConditionalByType(String theResourceType);
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IDeleteWithQuery.java

@@ -0,0 +1,5 @@
+package ca.uhn.fhir.rest.gclient;
+
+public interface IDeleteWithQuery extends IBaseQuery<IDeleteWithQueryTyped> {
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IDeleteWithQueryTyped.java

@@ -0,0 +1,5 @@
+package ca.uhn.fhir.rest.gclient;
+
+public interface IDeleteWithQueryTyped extends IDeleteTyped, IDeleteWithQuery {
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IQuery.java

@@ -24,11 +24,7 @@ import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.method.SearchStyleEnum;
 
-public interface IQuery extends IClientExecutable<IQuery,Bundle> {
+public interface IQuery extends IClientExecutable<IQuery,Bundle>, IBaseQuery<IQuery> {
-
-	IQuery where(ICriterion<?> theCriterion);
-
-	IQuery and(ICriterion<?> theCriterion);
 
 	IQuery include(Include theIncludeManagingorganization);
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IUpdateTyped.java

@@ -28,4 +28,20 @@ public interface IUpdateTyped extends IUpdateExecutable {
 
 	IUpdateExecutable withId(String theId);
 
+	/**
+	 * Specifies that the update should be performed as a conditional create 
+	 * against a given search URL. 
+	 * 
+	 * @param theSearchUrl The search URL to use. The format of this URL should be of the form <code>[ResourceType]?[Parameters]</code>,
+	 * for example: <code>Patient?name=Smith&amp;identifier=13.2.4.11.4%7C847366</code>
+	 * 
+	 * @since HAPI 0.9 / FHIR DSTU 2
+	 */
+	IUpdateTyped conditionalByUrl(String theSearchUrl);
+
+	/**
+	 * @since HAPI 0.9 / FHIR DSTU 2
+	 */
+	IUpdateWithQuery conditional();
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IUpdateWithQuery.java

@@ -0,0 +1,6 @@
+package ca.uhn.fhir.rest.gclient;
+
+
+public interface IUpdateWithQuery extends IBaseQuery<IUpdateWithQueryTyped> {
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/IUpdateWithQueryTyped.java

@@ -0,0 +1,5 @@
+package ca.uhn.fhir.rest.gclient;
+
+public interface IUpdateWithQueryTyped extends IUpdateTyped, IUpdateWithQuery {
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseHttpClientInvocationWithContents.java

@@ -143,29 +143,55 @@ abstract class BaseHttpClientInvocationWithContents extends BaseHttpClientInvoca
 		myBundleType = null;
 	}
 
+	public BaseHttpClientInvocationWithContents(FhirContext theContext, String theContents, Map<String, List<String>> theParams, String... theUrlPath) {
+		myContext = theContext;
+		myResource = null;
+		myTagList = null;
+		myUrlPath = StringUtils.join(theUrlPath, '/');
+		myResources = null;
+		myBundle = null;
+		myContents = theContents;
+		myContentsIsBundle = false;
+		myParams = theParams;
+		myBundleType = null;
+	}
+
+	public BaseHttpClientInvocationWithContents(FhirContext theContext, IResource theResource, Map<String, List<String>> theParams, String... theUrlPath) {
+		myContext = theContext;
+		myResource = theResource;
+		myTagList = null;
+		myUrlPath = StringUtils.join(theUrlPath, '/');
+		myResources = null;
+		myBundle = null;
+		myContents = null;
+		myContentsIsBundle = false;
+		myParams = theParams;
+		myBundleType = null;
+	}
+	
 	@Override
 	public HttpRequestBase asHttpRequest(String theUrlBase, Map<String, List<String>> theExtraParams, EncodingEnum theEncoding) throws DataFormatException {
-		StringBuilder b = new StringBuilder();
+		StringBuilder url = new StringBuilder();
 
 		if (myUrlPath == null) {
-			b.append(theUrlBase);
+			url.append(theUrlBase);
 		} else {
 			if (!myUrlPath.contains("://")) {
-				b.append(theUrlBase);
+				url.append(theUrlBase);
 				if (!theUrlBase.endsWith("/")) {
-					b.append('/');
+					url.append('/');
 				}
 			}
-			b.append(myUrlPath);
+			url.append(myUrlPath);
 		}
 
-		appendExtraParamsWithQuestionMark(theExtraParams, b, b.indexOf("?") == -1);
+		appendExtraParamsWithQuestionMark(theExtraParams, url, url.indexOf("?") == -1);
-		String url = b.toString();
 
 		if (myResource != null && BaseBinary.class.isAssignableFrom(myResource.getClass())) {
 			BaseBinary binary = (BaseBinary) myResource;
 			ByteArrayEntity entity = new ByteArrayEntity(binary.getContent(), ContentType.parse(binary.getContentType()));
 			HttpRequestBase retVal = createRequest(url, entity);
+			addMatchHeaders(retVal, url);
 			return retVal;
 		}
 
@@ -187,11 +213,11 @@ abstract class BaseHttpClientInvocationWithContents extends BaseHttpClientInvoca
 
 		AbstractHttpEntity entity;
 		if (myParams != null) {
-			contentType= null;
+			contentType = null;
 			List<NameValuePair> parameters = new ArrayList<NameValuePair>();
 			for (Entry<String, List<String>> nextParam : myParams.entrySet()) {
 				List<String> value = nextParam.getValue();
-				for(String s: value){
+				for (String s : value) {
 					parameters.add(new BasicNameValuePair(nextParam.getKey(), s));
 				}
 			}
@@ -228,6 +254,7 @@ abstract class BaseHttpClientInvocationWithContents extends BaseHttpClientInvoca
 
 		HttpRequestBase retVal = createRequest(url, entity);
 		super.addHeadersToRequest(retVal);
+		addMatchHeaders(retVal, url);
 
 		if (contentType != null) {
 			retVal.addHeader(Constants.HEADER_CONTENT_TYPE, contentType + Constants.HEADER_SUFFIX_CT_UTF_8);
@@ -236,6 +263,41 @@ abstract class BaseHttpClientInvocationWithContents extends BaseHttpClientInvoca
 		return retVal;
 	}
 
-	protected abstract HttpRequestBase createRequest(String url, AbstractHttpEntity theEntity);
+	private void addMatchHeaders(HttpRequestBase theHttpRequest, StringBuilder theUrlBase) {
+		if (myIfNoneExistParams != null) {
+			StringBuilder b = newHeaderBuilder(theUrlBase);
+			appendExtraParamsWithQuestionMark(myIfNoneExistParams, b, b.indexOf("?") == -1);
+			theHttpRequest.addHeader(Constants.HEADER_IF_NONE_EXIST, b.toString());
+		}
+
+		if (myIfNoneExistString != null) {
+			StringBuilder b = newHeaderBuilder(theUrlBase);
+			b.append(b.indexOf("?") == -1 ? '?' : '&');
+			b.append(myIfNoneExistString.substring(myIfNoneExistString.indexOf('?') + 1));
+			theHttpRequest.addHeader(Constants.HEADER_IF_NONE_EXIST, b.toString());
+		}
+	}
+
+	private StringBuilder newHeaderBuilder(StringBuilder theUrlBase) {
+		StringBuilder b = new StringBuilder();
+		b.append(theUrlBase);
+		if (theUrlBase.length() > 0 && theUrlBase.charAt(theUrlBase.length() - 1) == '/') {
+			b.deleteCharAt(b.length() - 1);
+		}
+		return b;
+	}
+
+	protected abstract HttpRequestBase createRequest(StringBuilder theUrl, AbstractHttpEntity theEntity);
+
+	private Map<String, List<String>> myIfNoneExistParams;
+	private String myIfNoneExistString;
+
+	public void setIfNoneExistParams(Map<String, List<String>> theIfNoneExist) {
+		myIfNoneExistParams = theIfNoneExist;
+	}
+
+	public void setIfNoneExistString(String theIfNoneExistString) {
+		myIfNoneExistString = theIfNoneExistString;
+	}
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/DeleteMethodBinding.java

@@ -22,6 +22,8 @@ package ca.uhn.fhir.rest.method;
 
 import java.lang.reflect.Method;
 import java.util.Collections;
+import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import ca.uhn.fhir.context.ConfigurationException;
@@ -154,5 +156,14 @@ public class DeleteMethodBinding extends BaseOutcomeReturningMethodBinding {
 		return null;
 	}
 
+	public static HttpDeleteClientInvocation createDeleteInvocation(String theSearchUrl) {
+		HttpDeleteClientInvocation retVal = new HttpDeleteClientInvocation(theSearchUrl);
+		return retVal;
+	}
+
+	public static HttpDeleteClientInvocation createDeleteInvocation(String theResourceType, Map<String, List<String>> theParams) {
+		return new HttpDeleteClientInvocation(theResourceType, theParams);
+	}
+
 	
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/HttpDeleteClientInvocation.java

@@ -33,12 +33,22 @@ import ca.uhn.fhir.rest.server.EncodingEnum;
 public class HttpDeleteClientInvocation extends BaseHttpClientInvocation {
 
 	private String myUrlPath;
+	private Map<String, List<String>> myParams;
 
 	public HttpDeleteClientInvocation(IdDt theId) {
 		super();
 		myUrlPath = theId.toUnqualifiedVersionless().getValue();
 	}
 
+	public HttpDeleteClientInvocation(String theSearchUrl) {
+		myUrlPath = theSearchUrl;
+	}
+
+	public HttpDeleteClientInvocation(String theResourceType, Map<String, List<String>> theParams) {
+		myUrlPath = theResourceType;
+		myParams = theParams;
+	}
+
 	@Override
 	public HttpRequestBase asHttpRequest(String theUrlBase, Map<String, List<String>> theExtraParams, EncodingEnum theEncoding) {
 		StringBuilder b = new StringBuilder();
@@ -48,12 +58,12 @@ public class HttpDeleteClientInvocation extends BaseHttpClientInvocation {
 		}
 		b.append(myUrlPath);
 
-		appendExtraParamsWithQuestionMark(theExtraParams, b,b.indexOf("?") == -1);
+		appendExtraParamsWithQuestionMark(myParams, b, b.indexOf("?") == -1);
+		appendExtraParamsWithQuestionMark(theExtraParams, b, b.indexOf("?") == -1);
 
 		HttpDelete retVal = new HttpDelete(b.toString());
 		super.addHeadersToRequest(retVal);
 		return retVal;
 	}
 
-
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/HttpPostClientInvocation.java

@@ -34,38 +34,34 @@ import ca.uhn.fhir.model.valueset.BundleTypeEnum;
 
 public class HttpPostClientInvocation extends BaseHttpClientInvocationWithContents {
 
+
 	public HttpPostClientInvocation(FhirContext theContext, IResource theResource, String theUrlExtension) {
 		super(theContext, theResource, theUrlExtension);
 	}
 
-	
 	public HttpPostClientInvocation(FhirContext theContext, TagList theTagList, String... theUrlExtension) {
 		super(theContext, theTagList, theUrlExtension);
 	}
 
-
 	public HttpPostClientInvocation(FhirContext theContext, List<IResource> theResources, BundleTypeEnum theBundleType) {
 		super(theContext, theResources, theBundleType);
 	}
 
-
 	public HttpPostClientInvocation(FhirContext theContext, Bundle theBundle) {
-		super(theContext,theBundle);
+		super(theContext, theBundle);
 	}
 
 	public HttpPostClientInvocation(FhirContext theContext, String theContents, boolean theIsBundle, String theUrlExtension) {
-		super(theContext,theContents, theIsBundle, theUrlExtension);
+		super(theContext, theContents, theIsBundle, theUrlExtension);
 	}
 
-
 	public HttpPostClientInvocation(FhirContext theContext, Map<String, List<String>> theParams, String... theUrlExtension) {
 		super(theContext, theParams, theUrlExtension);
 	}
 
-
 	@Override
-	protected HttpPost createRequest(String url, AbstractHttpEntity theEntity) {
+	protected HttpPost createRequest(StringBuilder theUrlBase, AbstractHttpEntity theEntity) {
-		HttpPost retVal = new HttpPost(url);
+		HttpPost retVal = new HttpPost(theUrlBase.toString());
 		retVal.setEntity(theEntity);
 		return retVal;
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/HttpPutClientInvocation.java

@@ -34,15 +34,14 @@ public class HttpPutClientInvocation extends BaseHttpClientInvocationWithContent
 	}
 
 	public HttpPutClientInvocation(FhirContext theContext, String theContents, boolean theIsBundle, String theUrlExtension) {
-		super(theContext,theContents, theIsBundle, theUrlExtension);
+		super(theContext, theContents, theIsBundle, theUrlExtension);
 	}
 
 	@Override
-	protected HttpRequestBase createRequest(String url, AbstractHttpEntity theEntity) {
+	protected HttpRequestBase createRequest(StringBuilder theUrl, AbstractHttpEntity theEntity) {
-		HttpPut retVal = new HttpPut(url);
+		HttpPut retVal = new HttpPut(theUrl.toString());
 		retVal.setEntity(theEntity);
 		return retVal;
 	}
 
-
 }

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

@@ -5,14 +5,17 @@ import static org.apache.commons.lang3.StringUtils.*;
 import java.io.IOException;
 import java.io.PushbackReader;
 import java.io.Reader;
+import java.io.UnsupportedEncodingException;
 import java.lang.annotation.Annotation;
 import java.lang.reflect.Method;
+import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 
 import javax.servlet.ServletRequest;
 import javax.servlet.ServletResponse;
@@ -95,9 +98,65 @@ import ca.uhn.fhir.util.ReflectionUtil;
 
 public class MethodUtil {
 	private static final String LABEL = "label=\"";
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(MethodUtil.class);
+
 	private static final String SCHEME = "scheme=\"";
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(MethodUtil.class);
+	static void addTagsToPostOrPut(IResource resource, BaseHttpClientInvocation retVal) {
+		TagList list = (TagList) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.TAG_LIST);
+		if (list != null) {
+			for (Tag tag : list) {
+				if (StringUtils.isNotBlank(tag.getTerm())) {
+					retVal.addHeader(Constants.HEADER_CATEGORY, tag.toHeaderValue());
+				}
+			}
+		}
+	}
+
+	public static HttpGetClientInvocation createConformanceInvocation() {
+		return new HttpGetClientInvocation("metadata");
+	}
+
+	public static HttpPostClientInvocation createCreateInvocation(IResource theResource, FhirContext theContext) {
+		return createCreateInvocation(theResource, null, null, theContext);
+	}
+
+	public static HttpPostClientInvocation createCreateInvocation(IResource theResource, String theResourceBody, String theId, FhirContext theContext) {
+		RuntimeResourceDefinition def = theContext.getResourceDefinition(theResource);
+		String resourceName = def.getName();
+
+		StringBuilder urlExtension = new StringBuilder();
+		urlExtension.append(resourceName);
+
+		if (StringUtils.isNotBlank(theId)) {
+			urlExtension.append('/');
+			urlExtension.append(theId);
+		}
+
+		HttpPostClientInvocation retVal;
+		if (StringUtils.isBlank(theResourceBody)) {
+			retVal = new HttpPostClientInvocation(theContext, theResource, urlExtension.toString());
+		} else {
+			retVal = new HttpPostClientInvocation(theContext, theResourceBody, false, urlExtension.toString());
+		}
+		addTagsToPostOrPut(theResource, retVal);
+
+		// addContentTypeHeaderBasedOnDetectedType(retVal, theResourceBody);
+
+		return retVal;
+	}
+
+	public static HttpPostClientInvocation createCreateInvocation(IResource theResource, String theResourceBody, String theId, FhirContext theContext, Map<String, List<String>> theIfNoneExistParams) {
+		HttpPostClientInvocation retVal = createCreateInvocation(theResource, theResourceBody, theId, theContext);
+		retVal.setIfNoneExistParams(theIfNoneExistParams);
+		return retVal;
+	}
+
+	public static HttpPostClientInvocation createCreateInvocation(IResource theResource, String theResourceBody, String theId, FhirContext theContext, String theIfNoneExistUrl) {
+		HttpPostClientInvocation retVal = createCreateInvocation(theResource, theResourceBody, theId, theContext);
+		retVal.setIfNoneExistString(theIfNoneExistUrl);
+		return retVal;
+	}
 
 	public static HttpPutClientInvocation createUpdateInvocation(IResource theResource, String theResourceBody, IdDt theId, FhirContext theContext) {
 		String resourceName = theContext.getResourceDefinition(theResource).getName();
@@ -105,9 +164,9 @@ public class MethodUtil {
 		urlBuilder.append(resourceName);
 		urlBuilder.append('/');
 		urlBuilder.append(theId.getIdPart());
+		String urlExtension = urlBuilder.toString();
 
 		HttpPutClientInvocation retVal;
-		String urlExtension = urlBuilder.toString();
 		if (StringUtils.isBlank(theResourceBody)) {
 			retVal = new HttpPutClientInvocation(theContext, theResource, urlExtension);
 		} else {
@@ -135,203 +194,49 @@ public class MethodUtil {
 		return retVal;
 	}
 
-	public static void parseClientRequestResourceHeaders(IdDt theRequestedId, Map<String, List<String>> theHeaders, IBaseResource resource) {
+	public static HttpPutClientInvocation createUpdateInvocation(FhirContext theContext, IResource theResource, String theResourceBody, Map<String, List<String>> theMatchParams) {
-		List<String> lmHeaders = theHeaders.get(Constants.HEADER_LAST_MODIFIED_LOWERCASE);
+		StringBuilder b = new StringBuilder();
-		if (lmHeaders != null && lmHeaders.size() > 0 && StringUtils.isNotBlank(lmHeaders.get(0))) {
+		
-			String headerValue = lmHeaders.get(0);
+		String resourceType = theContext.getResourceDefinition(theResource).getName();
-			Date headerDateValue;
+		b.append(resourceType);
+		
+		boolean haveQuestionMark=false;
+		for (Entry<String, List<String>> nextEntry : theMatchParams.entrySet()) {
+			for (String nextValue : nextEntry.getValue()) {
+				b.append(haveQuestionMark ? '&' : '?');
+				haveQuestionMark = true;
 				try {
-				headerDateValue = DateUtils.parseDate(headerValue);
+					b.append(URLEncoder.encode(nextEntry.getKey(), "UTF-8"));
-				if (resource instanceof IResource) {
+					b.append('=');
-					InstantDt lmValue = new InstantDt(headerDateValue);
+					b.append(URLEncoder.encode(nextValue, "UTF-8"));
-					((IResource) resource).getResourceMetadata().put(ResourceMetadataKeyEnum.UPDATED, lmValue);
+				} catch (UnsupportedEncodingException e) {
-				} else if (resource instanceof IAnyResource) {
+					throw new ConfigurationException("UTF-8 not supported on this platform");
-					((IAnyResource) resource).getMeta().setLastUpdated(headerDateValue);
-				}
-			} catch (Exception e) {
-				ourLog.warn("Unable to parse date string '{}'. Error is: {}", headerValue, e.toString());
-			}
-		}
-
-		List<String> clHeaders = theHeaders.get(Constants.HEADER_CONTENT_LOCATION_LC);
-		if (clHeaders != null && clHeaders.size() > 0 && StringUtils.isNotBlank(clHeaders.get(0))) {
-			String headerValue = clHeaders.get(0);
-			if (isNotBlank(headerValue)) {
-				new IdDt(headerValue).applyTo(resource);
-			}
-		}
-
-		IdDt existing = IdDt.of(resource);
-
-		List<String> eTagHeaders = theHeaders.get(Constants.HEADER_ETAG_LC);
-		String eTagVersion = null;
-		if (eTagHeaders != null && eTagHeaders.size() > 0) {
-			eTagVersion = parseETagValue(eTagHeaders.get(0));
-		}
-		if (isNotBlank(eTagVersion)) {
-			if (existing == null || existing.isEmpty()) {
-				if (theRequestedId != null) {
-					theRequestedId.withVersion(eTagVersion).applyTo(resource);
-				}
-			} else if (existing.hasVersionIdPart() == false) {
-				existing.withVersion(eTagVersion).applyTo(resource);
-			}
-		} else if (existing == null || existing.isEmpty()) {
-			if (theRequestedId != null) {
-				theRequestedId.applyTo(resource);
-			}
-		}
-
-		List<String> categoryHeaders = theHeaders.get(Constants.HEADER_CATEGORY_LC);
-		if (categoryHeaders != null && categoryHeaders.size() > 0 && StringUtils.isNotBlank(categoryHeaders.get(0))) {
-			TagList tagList = new TagList();
-			for (String header : categoryHeaders) {
-				parseTagValue(tagList, header);
-			}
-			if (resource instanceof IResource) {
-				ResourceMetadataKeyEnum.TAG_LIST.put((IResource) resource, tagList);
-			} else if (resource instanceof IAnyResource) {
-				IMetaType meta = ((IAnyResource) resource).getMeta();
-				for (Tag next : tagList) {
-					meta.addTag().setSystem(next.getScheme()).setCode(next.getTerm()).setDisplay(next.getLabel());
-				}
 				}
 			}
 		}
 
-	public static String parseETagValue(String value) {
-		String eTagVersion;
-		value = value.trim();
-		if (value.length() > 1) {
-			if (value.charAt(value.length() - 1) == '"') {
-				if (value.charAt(0) == '"') {
-					eTagVersion = value.substring(1, value.length() - 1);
-				} else if (value.length() > 3 && value.charAt(0) == 'W' && value.charAt(1) == '/' && value.charAt(2) == '"') {
-					eTagVersion = value.substring(3, value.length() - 1);
-				} else {
-					eTagVersion = value;
-				}
-			} else {
-				eTagVersion = value;
-			}
-		} else {
-			eTagVersion = value;
-		}
-		return eTagVersion;
-	}
 		
-	public static void parseTagValue(TagList tagList, String nextTagComplete) {
+		HttpPutClientInvocation retVal;
-		StringBuilder next = new StringBuilder(nextTagComplete);
-		parseTagValue(tagList, nextTagComplete, next);
-	}
-
-	private static void parseTagValue(TagList theTagList, String theCompleteHeaderValue, StringBuilder theBuffer) {
-		int firstSemicolon = theBuffer.indexOf(";");
-		int deleteTo;
-		if (firstSemicolon == -1) {
-			firstSemicolon = theBuffer.indexOf(",");
-			if (firstSemicolon == -1) {
-				firstSemicolon = theBuffer.length();
-				deleteTo = theBuffer.length();
-			} else {
-				deleteTo = firstSemicolon;
-			}
-		} else {
-			deleteTo = firstSemicolon + 1;
-		}
-
-		String term = theBuffer.substring(0, firstSemicolon);
-		String scheme = null;
-		String label = null;
-		if (isBlank(term)) {
-			return;
-		}
-
-		theBuffer.delete(0, deleteTo);
-		while (theBuffer.length() > 0 && theBuffer.charAt(0) == ' ') {
-			theBuffer.deleteCharAt(0);
-		}
-
-		while (theBuffer.length() > 0) {
-			boolean foundSomething = false;
-			if (theBuffer.length() > SCHEME.length() && theBuffer.substring(0, SCHEME.length()).equals(SCHEME)) {
-				int closeIdx = theBuffer.indexOf("\"", SCHEME.length());
-				scheme = theBuffer.substring(SCHEME.length(), closeIdx);
-				theBuffer.delete(0, closeIdx + 1);
-				foundSomething = true;
-			}
-			if (theBuffer.length() > LABEL.length() && theBuffer.substring(0, LABEL.length()).equals(LABEL)) {
-				int closeIdx = theBuffer.indexOf("\"", LABEL.length());
-				label = theBuffer.substring(LABEL.length(), closeIdx);
-				theBuffer.delete(0, closeIdx + 1);
-				foundSomething = true;
-			}
-			// TODO: support enc2231-string as described in
-			// http://tools.ietf.org/html/draft-johnston-http-category-header-02
-			// TODO: support multiple tags in one header as described in
-			// http://hl7.org/implement/standards/fhir/http.html#tags
-
-			while (theBuffer.length() > 0 && (theBuffer.charAt(0) == ' ' || theBuffer.charAt(0) == ';')) {
-				theBuffer.deleteCharAt(0);
-			}
-
-			if (!foundSomething) {
-				break;
-			}
-		}
-
-		if (theBuffer.length() > 0 && theBuffer.charAt(0) == ',') {
-			theBuffer.deleteCharAt(0);
-			while (theBuffer.length() > 0 && theBuffer.charAt(0) == ' ') {
-				theBuffer.deleteCharAt(0);
-			}
-			theTagList.add(new Tag(scheme, term, label));
-			parseTagValue(theTagList, theCompleteHeaderValue, theBuffer);
-		} else {
-			theTagList.add(new Tag(scheme, term, label));
-		}
-
-		if (theBuffer.length() > 0) {
-			ourLog.warn("Ignoring extra text at the end of " + Constants.HEADER_CATEGORY + " tag '" + theBuffer.toString() + "' - Complete tag value was: " + theCompleteHeaderValue);
-		}
-
-	}
-
-	static void addTagsToPostOrPut(IResource resource, BaseHttpClientInvocation retVal) {
-		TagList list = (TagList) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.TAG_LIST);
-		if (list != null) {
-			for (Tag tag : list) {
-				if (StringUtils.isNotBlank(tag.getTerm())) {
-					retVal.addHeader(Constants.HEADER_CATEGORY, tag.toHeaderValue());
-				}
-			}
-		}
-	}
-
-	public static HttpPostClientInvocation createCreateInvocation(IResource theResource, FhirContext theContext) {
-		return createCreateInvocation(theResource, null, null, theContext);
-	}
-
-	public static HttpPostClientInvocation createCreateInvocation(IResource theResource, String theResourceBody, String theId, FhirContext theContext) {
-		RuntimeResourceDefinition def = theContext.getResourceDefinition(theResource);
-		String resourceName = def.getName();
-
-		StringBuilder urlExtension = new StringBuilder();
-		urlExtension.append(resourceName);
-		if (StringUtils.isNotBlank(theId)) {
-			urlExtension.append('/');
-			urlExtension.append(theId);
-		}
-
-		HttpPostClientInvocation retVal;
 		if (StringUtils.isBlank(theResourceBody)) {
-			retVal = new HttpPostClientInvocation(theContext, theResource, urlExtension.toString());
+			retVal = new HttpPutClientInvocation(theContext, theResource, b.toString());
 		} else {
-			retVal = new HttpPostClientInvocation(theContext, theResourceBody, false, urlExtension.toString());
+			retVal = new HttpPutClientInvocation(theContext, theResourceBody, false, b.toString());
 		}
+
 		addTagsToPostOrPut(theResource, retVal);
 
-		// addContentTypeHeaderBasedOnDetectedType(retVal, theResourceBody);
+		return retVal;
+	}
+
+	public static HttpPutClientInvocation createUpdateInvocation(FhirContext theContext, IResource theResource, String theResourceBody, String theMatchUrl) {
+		HttpPutClientInvocation retVal;
+		if (StringUtils.isBlank(theResourceBody)) {
+			retVal = new HttpPutClientInvocation(theContext, theResource,  theMatchUrl);
+		} else {
+			retVal = new HttpPutClientInvocation(theContext, theResourceBody, false,theMatchUrl);
+		}
+
+		addTagsToPostOrPut(theResource, retVal);
 
 		return retVal;
 	}
@@ -348,57 +253,21 @@ public class MethodUtil {
 		return EncodingEnum.XML;
 	}
 
-	public static HttpGetClientInvocation createConformanceInvocation() {
+	public static void extractDescription(SearchParameter theParameter, Annotation[] theAnnotations) {
-		return new HttpGetClientInvocation("metadata");
+		for (Annotation annotation : theAnnotations) {
-	}
+			if (annotation instanceof Description) {
-
+				Description desc = (Description) annotation;
-	public static MethodOutcome process2xxResponse(FhirContext theContext, String theResourceName, int theResponseStatusCode, String theResponseMimeType, Reader theResponseReader, Map<String, List<String>> theHeaders) {
+				if (isNotBlank(desc.formalDefinition())) {
-		List<String> locationHeaders = new ArrayList<String>();
+					theParameter.setDescription(desc.formalDefinition());
-		List<String> lh = theHeaders.get(Constants.HEADER_LOCATION_LC);
-		if (lh != null) {
-			locationHeaders.addAll(lh);
-		}
-		List<String> clh = theHeaders.get(Constants.HEADER_CONTENT_LOCATION_LC);
-		if (clh != null) {
-			locationHeaders.addAll(clh);
-		}
-
-		MethodOutcome retVal = new MethodOutcome();
-		if (locationHeaders != null && locationHeaders.size() > 0) {
-			String locationHeader = locationHeaders.get(0);
-			BaseOutcomeReturningMethodBinding.parseContentLocation(retVal, theResourceName, locationHeader);
-		}
-		if (theResponseStatusCode != Constants.STATUS_HTTP_204_NO_CONTENT) {
-			EncodingEnum ct = EncodingEnum.forContentType(theResponseMimeType);
-			if (ct != null) {
-				PushbackReader reader = new PushbackReader(theResponseReader);
-
-				try {
-					int firstByte = reader.read();
-					if (firstByte == -1) {
-						BaseOutcomeReturningMethodBinding.ourLog.debug("No content in response, not going to read");
-						reader = null;
 				} else {
-						reader.unread(firstByte);
+					theParameter.setDescription(desc.shortDefinition());
 				}
-				} catch (IOException e) {
-					BaseOutcomeReturningMethodBinding.ourLog.debug("No content in response, not going to read", e);
-					reader = null;
 			}
-
-				if (reader != null) {
-					IParser parser = ct.newParser(theContext);
-					IResource outcome = parser.parseResource(reader);
-					if (outcome instanceof BaseOperationOutcome) {
-						retVal.setOperationOutcome((BaseOperationOutcome) outcome);
 		}
 	}
 
-			} else {
+	public static Integer findIdParameterIndex(Method theMethod) {
-				BaseOutcomeReturningMethodBinding.ourLog.debug("Ignoring response content of type: {}", theResponseMimeType);
+		return MethodUtil.findParamAnnotationIndex(theMethod, IdParam.class);
-			}
-		}
-		return retVal;
 	}
 
 	public static Integer findParamAnnotationIndex(Method theMethod, Class<?> toFind) {
@@ -416,38 +285,8 @@ public class MethodUtil {
 		return null;
 	}
 
-	public static void extractDescription(SearchParameter theParameter, Annotation[] theAnnotations) {
+	public static Integer findTagListParameterIndex(Method theMethod) {
-		for (Annotation annotation : theAnnotations) {
+		return MethodUtil.findParamAnnotationIndex(theMethod, TagListParam.class);
-			if (annotation instanceof Description) {
-				Description desc = (Description) annotation;
-				if (isNotBlank(desc.formalDefinition())) {
-					theParameter.setDescription(desc.formalDefinition());
-				} else {
-					theParameter.setDescription(desc.shortDefinition());
-				}
-			}
-		}
-	}
-
-	public static IQueryParameterOr<?> singleton(final IQueryParameterType theParam) {
-		return new IQueryParameterOr<IQueryParameterType>() {
-
-			@Override
-			public void setValuesAsQueryTokens(QualifiedParamList theParameters) {
-				if (theParameters.isEmpty()) {
-					return;
-				}
-				if (theParameters.size() > 1) {
-					throw new IllegalArgumentException("Type " + theParam.getClass().getCanonicalName() + " does not support multiple values");
-				}
-				theParam.setValueAsQueryToken(theParameters.getQualifier(), theParameters.get(0));
-			}
-
-			@Override
-			public List<IQueryParameterType> getValuesAsQueryTokens() {
-				return Collections.singletonList(theParam);
-			}
-		};
 	}
 
 	@SuppressWarnings("deprecation")
@@ -455,46 +294,6 @@ public class MethodUtil {
 		return MethodUtil.findParamAnnotationIndex(theMethod, VersionIdParam.class);
 	}
 
-	public static Integer findIdParameterIndex(Method theMethod) {
-		return MethodUtil.findParamAnnotationIndex(theMethod, IdParam.class);
-	}
-
-	public static Integer findTagListParameterIndex(Method theMethod) {
-		return MethodUtil.findParamAnnotationIndex(theMethod, TagListParam.class);
-	}
-
-	/**
-	 * This is a utility method intended provided to help the JPA module.
-	 */
-	public static IQueryParameterAnd<?> parseQueryParams(RuntimeSearchParam theParamDef, String theUnqualifiedParamName, List<QualifiedParamList> theParameters) {
-		QueryParameterAndBinder binder = null;
-		switch (theParamDef.getParamType()) {
-		case COMPOSITE:
-			throw new UnsupportedOperationException();
-		case DATE:
-			binder = new QueryParameterAndBinder(DateAndListParam.class, Collections.<Class<? extends IQueryParameterType>>emptyList());
-			break;
-		case NUMBER:
-			binder = new QueryParameterAndBinder(NumberAndListParam.class, Collections.<Class<? extends IQueryParameterType>>emptyList());
-			break;
-		case QUANTITY:
-			binder = new QueryParameterAndBinder(QuantityAndListParam.class, Collections.<Class<? extends IQueryParameterType>>emptyList());
-			break;
-		case REFERENCE:
-			binder = new QueryParameterAndBinder(ReferenceAndListParam.class, Collections.<Class<? extends IQueryParameterType>>emptyList());
-			break;
-		case STRING:
-			binder = new QueryParameterAndBinder(StringAndListParam.class, Collections.<Class<? extends IQueryParameterType>>emptyList());
-			break;
-		case TOKEN:
-			binder = new QueryParameterAndBinder(TokenAndListParam.class, Collections.<Class<? extends IQueryParameterType>>emptyList());
-			break;
-		}
-		
-		return binder.parse(theUnqualifiedParamName, theParameters);
-	}
-	
-	
 	@SuppressWarnings("unchecked")
 	public static List<IParameter> getResourceParameters(FhirContext theContext, Method theMethod, Object theProvider) {
 		List<IParameter> parameters = new ArrayList<IParameter>();
@@ -612,4 +411,267 @@ public class MethodUtil {
 		return parameters;
 	}
 
+	public static void parseClientRequestResourceHeaders(IdDt theRequestedId, Map<String, List<String>> theHeaders, IBaseResource resource) {
+		List<String> lmHeaders = theHeaders.get(Constants.HEADER_LAST_MODIFIED_LOWERCASE);
+		if (lmHeaders != null && lmHeaders.size() > 0 && StringUtils.isNotBlank(lmHeaders.get(0))) {
+			String headerValue = lmHeaders.get(0);
+			Date headerDateValue;
+			try {
+				headerDateValue = DateUtils.parseDate(headerValue);
+				if (resource instanceof IResource) {
+					InstantDt lmValue = new InstantDt(headerDateValue);
+					((IResource) resource).getResourceMetadata().put(ResourceMetadataKeyEnum.UPDATED, lmValue);
+				} else if (resource instanceof IAnyResource) {
+					((IAnyResource) resource).getMeta().setLastUpdated(headerDateValue);
+				}
+			} catch (Exception e) {
+				ourLog.warn("Unable to parse date string '{}'. Error is: {}", headerValue, e.toString());
+			}
+		}
+
+		List<String> clHeaders = theHeaders.get(Constants.HEADER_CONTENT_LOCATION_LC);
+		if (clHeaders != null && clHeaders.size() > 0 && StringUtils.isNotBlank(clHeaders.get(0))) {
+			String headerValue = clHeaders.get(0);
+			if (isNotBlank(headerValue)) {
+				new IdDt(headerValue).applyTo(resource);
+			}
+		}
+
+		IdDt existing = IdDt.of(resource);
+
+		List<String> eTagHeaders = theHeaders.get(Constants.HEADER_ETAG_LC);
+		String eTagVersion = null;
+		if (eTagHeaders != null && eTagHeaders.size() > 0) {
+			eTagVersion = parseETagValue(eTagHeaders.get(0));
+		}
+		if (isNotBlank(eTagVersion)) {
+			if (existing == null || existing.isEmpty()) {
+				if (theRequestedId != null) {
+					theRequestedId.withVersion(eTagVersion).applyTo(resource);
+				}
+			} else if (existing.hasVersionIdPart() == false) {
+				existing.withVersion(eTagVersion).applyTo(resource);
+			}
+		} else if (existing == null || existing.isEmpty()) {
+			if (theRequestedId != null) {
+				theRequestedId.applyTo(resource);
+			}
+		}
+
+		List<String> categoryHeaders = theHeaders.get(Constants.HEADER_CATEGORY_LC);
+		if (categoryHeaders != null && categoryHeaders.size() > 0 && StringUtils.isNotBlank(categoryHeaders.get(0))) {
+			TagList tagList = new TagList();
+			for (String header : categoryHeaders) {
+				parseTagValue(tagList, header);
+			}
+			if (resource instanceof IResource) {
+				ResourceMetadataKeyEnum.TAG_LIST.put((IResource) resource, tagList);
+			} else if (resource instanceof IAnyResource) {
+				IMetaType meta = ((IAnyResource) resource).getMeta();
+				for (Tag next : tagList) {
+					meta.addTag().setSystem(next.getScheme()).setCode(next.getTerm()).setDisplay(next.getLabel());
+				}
+			}
+		}
+	}
+
+	public static String parseETagValue(String value) {
+		String eTagVersion;
+		value = value.trim();
+		if (value.length() > 1) {
+			if (value.charAt(value.length() - 1) == '"') {
+				if (value.charAt(0) == '"') {
+					eTagVersion = value.substring(1, value.length() - 1);
+				} else if (value.length() > 3 && value.charAt(0) == 'W' && value.charAt(1) == '/' && value.charAt(2) == '"') {
+					eTagVersion = value.substring(3, value.length() - 1);
+				} else {
+					eTagVersion = value;
+				}
+			} else {
+				eTagVersion = value;
+			}
+		} else {
+			eTagVersion = value;
+		}
+		return eTagVersion;
+	}
+
+	/**
+	 * This is a utility method intended provided to help the JPA module.
+	 */
+	public static IQueryParameterAnd<?> parseQueryParams(RuntimeSearchParam theParamDef, String theUnqualifiedParamName, List<QualifiedParamList> theParameters) {
+		QueryParameterAndBinder binder = null;
+		switch (theParamDef.getParamType()) {
+		case COMPOSITE:
+			throw new UnsupportedOperationException();
+		case DATE:
+			binder = new QueryParameterAndBinder(DateAndListParam.class, Collections.<Class<? extends IQueryParameterType>> emptyList());
+			break;
+		case NUMBER:
+			binder = new QueryParameterAndBinder(NumberAndListParam.class, Collections.<Class<? extends IQueryParameterType>> emptyList());
+			break;
+		case QUANTITY:
+			binder = new QueryParameterAndBinder(QuantityAndListParam.class, Collections.<Class<? extends IQueryParameterType>> emptyList());
+			break;
+		case REFERENCE:
+			binder = new QueryParameterAndBinder(ReferenceAndListParam.class, Collections.<Class<? extends IQueryParameterType>> emptyList());
+			break;
+		case STRING:
+			binder = new QueryParameterAndBinder(StringAndListParam.class, Collections.<Class<? extends IQueryParameterType>> emptyList());
+			break;
+		case TOKEN:
+			binder = new QueryParameterAndBinder(TokenAndListParam.class, Collections.<Class<? extends IQueryParameterType>> emptyList());
+			break;
+		}
+
+		return binder.parse(theUnqualifiedParamName, theParameters);
+	}
+
+	public static void parseTagValue(TagList tagList, String nextTagComplete) {
+		StringBuilder next = new StringBuilder(nextTagComplete);
+		parseTagValue(tagList, nextTagComplete, next);
+	}
+
+	private static void parseTagValue(TagList theTagList, String theCompleteHeaderValue, StringBuilder theBuffer) {
+		int firstSemicolon = theBuffer.indexOf(";");
+		int deleteTo;
+		if (firstSemicolon == -1) {
+			firstSemicolon = theBuffer.indexOf(",");
+			if (firstSemicolon == -1) {
+				firstSemicolon = theBuffer.length();
+				deleteTo = theBuffer.length();
+			} else {
+				deleteTo = firstSemicolon;
+			}
+		} else {
+			deleteTo = firstSemicolon + 1;
+		}
+
+		String term = theBuffer.substring(0, firstSemicolon);
+		String scheme = null;
+		String label = null;
+		if (isBlank(term)) {
+			return;
+		}
+
+		theBuffer.delete(0, deleteTo);
+		while (theBuffer.length() > 0 && theBuffer.charAt(0) == ' ') {
+			theBuffer.deleteCharAt(0);
+		}
+
+		while (theBuffer.length() > 0) {
+			boolean foundSomething = false;
+			if (theBuffer.length() > SCHEME.length() && theBuffer.substring(0, SCHEME.length()).equals(SCHEME)) {
+				int closeIdx = theBuffer.indexOf("\"", SCHEME.length());
+				scheme = theBuffer.substring(SCHEME.length(), closeIdx);
+				theBuffer.delete(0, closeIdx + 1);
+				foundSomething = true;
+			}
+			if (theBuffer.length() > LABEL.length() && theBuffer.substring(0, LABEL.length()).equals(LABEL)) {
+				int closeIdx = theBuffer.indexOf("\"", LABEL.length());
+				label = theBuffer.substring(LABEL.length(), closeIdx);
+				theBuffer.delete(0, closeIdx + 1);
+				foundSomething = true;
+			}
+			// TODO: support enc2231-string as described in
+			// http://tools.ietf.org/html/draft-johnston-http-category-header-02
+			// TODO: support multiple tags in one header as described in
+			// http://hl7.org/implement/standards/fhir/http.html#tags
+
+			while (theBuffer.length() > 0 && (theBuffer.charAt(0) == ' ' || theBuffer.charAt(0) == ';')) {
+				theBuffer.deleteCharAt(0);
+			}
+
+			if (!foundSomething) {
+				break;
+			}
+		}
+
+		if (theBuffer.length() > 0 && theBuffer.charAt(0) == ',') {
+			theBuffer.deleteCharAt(0);
+			while (theBuffer.length() > 0 && theBuffer.charAt(0) == ' ') {
+				theBuffer.deleteCharAt(0);
+			}
+			theTagList.add(new Tag(scheme, term, label));
+			parseTagValue(theTagList, theCompleteHeaderValue, theBuffer);
+		} else {
+			theTagList.add(new Tag(scheme, term, label));
+		}
+
+		if (theBuffer.length() > 0) {
+			ourLog.warn("Ignoring extra text at the end of " + Constants.HEADER_CATEGORY + " tag '" + theBuffer.toString() + "' - Complete tag value was: " + theCompleteHeaderValue);
+		}
+
+	}
+
+	public static MethodOutcome process2xxResponse(FhirContext theContext, String theResourceName, int theResponseStatusCode, String theResponseMimeType, Reader theResponseReader, Map<String, List<String>> theHeaders) {
+		List<String> locationHeaders = new ArrayList<String>();
+		List<String> lh = theHeaders.get(Constants.HEADER_LOCATION_LC);
+		if (lh != null) {
+			locationHeaders.addAll(lh);
+		}
+		List<String> clh = theHeaders.get(Constants.HEADER_CONTENT_LOCATION_LC);
+		if (clh != null) {
+			locationHeaders.addAll(clh);
+		}
+
+		MethodOutcome retVal = new MethodOutcome();
+		if (locationHeaders != null && locationHeaders.size() > 0) {
+			String locationHeader = locationHeaders.get(0);
+			BaseOutcomeReturningMethodBinding.parseContentLocation(retVal, theResourceName, locationHeader);
+		}
+		if (theResponseStatusCode != Constants.STATUS_HTTP_204_NO_CONTENT) {
+			EncodingEnum ct = EncodingEnum.forContentType(theResponseMimeType);
+			if (ct != null) {
+				PushbackReader reader = new PushbackReader(theResponseReader);
+
+				try {
+					int firstByte = reader.read();
+					if (firstByte == -1) {
+						BaseOutcomeReturningMethodBinding.ourLog.debug("No content in response, not going to read");
+						reader = null;
+					} else {
+						reader.unread(firstByte);
+					}
+				} catch (IOException e) {
+					BaseOutcomeReturningMethodBinding.ourLog.debug("No content in response, not going to read", e);
+					reader = null;
+				}
+
+				if (reader != null) {
+					IParser parser = ct.newParser(theContext);
+					IResource outcome = parser.parseResource(reader);
+					if (outcome instanceof BaseOperationOutcome) {
+						retVal.setOperationOutcome((BaseOperationOutcome) outcome);
+					}
+				}
+
+			} else {
+				BaseOutcomeReturningMethodBinding.ourLog.debug("Ignoring response content of type: {}", theResponseMimeType);
+			}
+		}
+		return retVal;
+	}
+
+	public static IQueryParameterOr<?> singleton(final IQueryParameterType theParam) {
+		return new IQueryParameterOr<IQueryParameterType>() {
+
+			@Override
+			public List<IQueryParameterType> getValuesAsQueryTokens() {
+				return Collections.singletonList(theParam);
+			}
+
+			@Override
+			public void setValuesAsQueryTokens(QualifiedParamList theParameters) {
+				if (theParameters.isEmpty()) {
+					return;
+				}
+				if (theParameters.size() > 1) {
+					throw new IllegalArgumentException("Type " + theParam.getClass().getCanonicalName() + " does not support multiple values");
+				}
+				theParam.setValueAsQueryToken(theParameters.getQualifier(), theParameters.get(0));
+			}
+		};
+	}
+
 }

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

@@ -111,6 +111,8 @@ public class Constants {
 	public static final int STATUS_HTTP_501_NOT_IMPLEMENTED = 501;
 	public static final String URL_TOKEN_HISTORY = "_history";
 	public static final String URL_TOKEN_METADATA = "metadata";
+	public static final String HEADER_IF_NONE_EXIST = "If-None-Exist";
+	public static final String HEADER_IF_NONE_EXIST_LC = HEADER_IF_NONE_EXIST.toLowerCase();
 
 	static {
 		Map<String, EncodingEnum> valToEncoding = new HashMap<String, EncodingEnum>();

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -24,7 +24,16 @@ ca.uhn.fhir.validation.FhirValidator.noPhlocError=Phloc-schematron library not f
 
 # JPA Messages
 
-ca.uhn.fhir.jpa.dao.BaseFhirSystemDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request.
+ca.uhn.fhir.jpa.dao.BaseFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request.
-ca.uhn.fhir.jpa.dao.BaseFhirSystemDao.transactionOperationWithMultipleMatchFailure=Failed to {0} resource with match URL "{1}" because this search matched {2} resources
+ca.uhn.fhir.jpa.dao.BaseFhirDao.transactionOperationWithMultipleMatchFailure=Failed to {0} resource with match URL "{1}" because this search matched {2} resources
-ca.uhn.fhir.jpa.dao.BaseFhirSystemDao.transactionOperationFailedNoId=Failed to {0} resource in transaction because no ID was provided 
+ca.uhn.fhir.jpa.dao.BaseFhirDao.transactionOperationFailedNoId=Failed to {0} resource in transaction because no ID was provided 
-ca.uhn.fhir.jpa.dao.BaseFhirSystemDao.transactionOperationFailedUnknownId=Failed to {0} resource in transaction because no resource could be found with ID {1} 
+ca.uhn.fhir.jpa.dao.BaseFhirDao.transactionOperationFailedUnknownId=Failed to {0} resource in transaction because no resource could be found with ID {1} 
+
+ca.uhn.fhir.jpa.dao.BaseFhirSystemDao.transactionContainsMultipleWithDuplicateId=Transaction bundle contains multiple resources with ID: {0}
+ca.uhn.fhir.jpa.dao.BaseFhirSystemDao.transactionEntryHasInvalidVerb=Transaction bundle entry has missing or invalid HTTP Verb specified in Bundle.entry.transaction.method. Found value: "{0}" 
+ca.uhn.fhir.jpa.dao.BaseFhirSystemDao.transactionMissingUrl=Unable to perform {0}, no URL provided. 
+ca.uhn.fhir.jpa.dao.BaseFhirSystemDao.transactionInvalidUrl=Unable to perform {0}, URL provided is invalid: {1} 
+
+ca.uhn.fhir.jpa.dao.FhirResourceDao.duplicateCreateForcedId=Can not create entity with ID[{0}], a resource with this ID already exists
+ca.uhn.fhir.jpa.dao.FhirResourceDao.failedToCreateWithClientAssignedNumericId=Can not create entity with ID[{0}], this server does not allow clients to assign numeric IDs
+ca.uhn.fhir.jpa.dao.FhirResourceDao.unableToDeleteNotFound=Unable to find resource matching URL "{0}". Deletion failed.

hapi-fhir-jpaserver-base/.settings/org.eclipse.jdt.core.prefs

@@ -7,9 +7,9 @@ org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nul
 org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.7
+org.eclipse.jdt.core.compiler.compliance=1.6
 org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
@@ -97,4 +97,4 @@ org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
 org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore
 org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
 org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
-org.eclipse.jdt.core.compiler.source=1.7
+org.eclipse.jdt.core.compiler.source=1.6

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

@@ -23,6 +23,8 @@ package ca.uhn.fhir.jpa.dao;
 import static org.apache.commons.lang3.StringUtils.*;
 
 import java.io.UnsupportedEncodingException;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.text.Normalizer;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -48,6 +50,8 @@ import javax.persistence.criteria.Root;
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.utils.URLEncodedUtils;
 import org.hl7.fhir.instance.model.IBaseResource;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
@@ -77,6 +81,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.ResourceTag;
 import ca.uhn.fhir.jpa.entity.TagDefinition;
 import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.model.api.IQueryParameterAnd;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
@@ -87,6 +92,8 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.method.MethodUtil;
+import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -95,15 +102,16 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.FhirTerser;
 
 import com.google.common.base.Function;
+import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Collections2;
 import com.google.common.collect.Lists;
 
 public abstract class BaseFhirDao implements IDao {
 
-	public static final String UCUM_NS = "http://unitsofmeasure.org";
-
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseFhirDao.class);
+
 	private static final Map<FhirVersionEnum, FhirContext> ourRetrievalContexts = new HashMap<FhirVersionEnum, FhirContext>();
+	public static final String UCUM_NS = "http://unitsofmeasure.org";
 
 	@Autowired(required = true)
 	private DaoConfig myConfig;
@@ -114,8 +122,6 @@ public abstract class BaseFhirDao implements IDao {
 	private EntityManager myEntityManager;
 
 	private List<IDaoListener> myListeners = new ArrayList<IDaoListener>();
-	private ISearchParamExtractor mySearchParamExtractor;
-
 	@Autowired
 	private PlatformTransactionManager myPlatformTransactionManager;
 
@@ -124,6 +130,8 @@ public abstract class BaseFhirDao implements IDao {
 
 	private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> myResourceTypeToDao;
 
+	private ISearchParamExtractor mySearchParamExtractor;
+
 	protected void createForcedIdIfNeeded(ResourceTable entity, IdDt id) {
 		if (id.isEmpty() == false && id.hasIdPart()) {
 			if (isValidPid(id)) {
@@ -508,19 +516,6 @@ public abstract class BaseFhirDao implements IDao {
 		return retVal;
 	}
 
-	protected static String normalizeString(String theString) {
-		char[] out = new char[theString.length()];
-		theString = Normalizer.normalize(theString, Normalizer.Form.NFD);
-		int j = 0;
-		for (int i = 0, n = theString.length(); i < n; ++i) {
-			char c = theString.charAt(i);
-			if (c <= '\u007F') {
-				out[j++] = c;
-			}
-		}
-		return new String(out).toUpperCase();
-	}
-
 	protected void notifyWriteCompleted() {
 		for (IDaoListener next : myListeners) {
 			next.writeCompleted();
@@ -579,6 +574,58 @@ public abstract class BaseFhirDao implements IDao {
 
 	}
 
+	protected Set<Long> processMatchUrl(String theMatchUrl, Class<? extends IBaseResource> theResourceType) {
+		RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(theResourceType);
+
+		SearchParameterMap paramMap = translateMatchUrl(theMatchUrl, resourceDef);
+
+		IFhirResourceDao<? extends IResource> dao = getDao(theResourceType);
+		Set<Long> ids = dao.searchForIdsWithAndOr(paramMap);
+
+		return ids;
+	}
+
+	protected SearchParameterMap translateMatchUrl(String theMatchUrl, RuntimeResourceDefinition resourceDef) {
+		SearchParameterMap paramMap = new SearchParameterMap();
+		List<NameValuePair> parameters;
+		try {
+			parameters = URLEncodedUtils.parse(new URI(theMatchUrl), "UTF-8");
+		} catch (URISyntaxException e) {
+			throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Error was: " + e.toString());
+		}
+
+		ArrayListMultimap<String, QualifiedParamList> nameToParamLists = ArrayListMultimap.create();
+		for (NameValuePair next : parameters) {
+			String paramName = next.getName();
+			String qualifier = null;
+			for (int i = 0; i < paramMap.size(); i++) {
+				switch (paramName.charAt(i)) {
+				case '.':
+				case ':':
+					qualifier = paramName.substring(i);
+					paramName = paramName.substring(0, i);
+					i = Integer.MAX_VALUE;
+					break;
+				}
+			}
+
+			QualifiedParamList paramList = QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifier, next.getValue());
+			nameToParamLists.put(paramName, paramList);
+		}
+
+		for (String nextParamName : nameToParamLists.keySet()) {
+			RuntimeSearchParam paramDef = resourceDef.getSearchParam(nextParamName);
+			if (paramDef == null) {
+				throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Resource type " + resourceDef.getName() + " does not have a parameter with name: " + nextParamName);
+			}
+
+			List<QualifiedParamList> paramList = nameToParamLists.get(nextParamName);
+			IQueryParameterAnd<?> param = MethodUtil.parseQueryParams(paramDef, nextParamName, paramList);
+			paramMap.add(nextParamName, param);
+		}
+		return paramMap;
+	}
+
 	@Override
 	public void registerDaoListener(IDaoListener theListener) {
 		Validate.notNull(theListener, "theListener");
@@ -832,7 +879,20 @@ public abstract class BaseFhirDao implements IDao {
 		}
 	}
 
+	protected String translatePidIdToForcedId(Long theId) {
+		ForcedId forcedId = myEntityManager.find(ForcedId.class, theId);
+		if (forcedId != null) {
+			return forcedId.getForcedId();
+		} else {
+			return theId.toString();
+		}
+	}
+
 	protected ResourceTable updateEntity(final IResource theResource, ResourceTable entity, boolean theUpdateHistory, Date theDeletedTimestampOrNull) {
+		return updateEntity(theResource, entity, theUpdateHistory, theDeletedTimestampOrNull, true,true);
+	}
+
+	protected ResourceTable updateEntity(final IResource theResource, ResourceTable entity, boolean theUpdateHistory, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion) {
 		if (entity.getPublished() == null) {
 			entity.setPublished(new Date());
 		}
@@ -849,7 +909,9 @@ public abstract class BaseFhirDao implements IDao {
 			myEntityManager.persist(historyEntry);
 		}
 
+		if (theUpdateVersion) {
 			entity.setVersion(entity.getVersion() + 1);
+		}
 		
 		Collection<ResourceIndexedSearchParamString> paramsString = new ArrayList<ResourceIndexedSearchParamString>(entity.getParamsString());
 		Collection<ResourceIndexedSearchParamToken> paramsToken = new ArrayList<ResourceIndexedSearchParamToken>(entity.getParamsToken());
@@ -858,12 +920,13 @@ public abstract class BaseFhirDao implements IDao {
 		Collection<ResourceIndexedSearchParamDate> paramsDate = new ArrayList<ResourceIndexedSearchParamDate>(entity.getParamsDate());
 		Collection<ResourceLink> resourceLinks = new ArrayList<ResourceLink>(entity.getResourceLinks());
 
-		final List<ResourceIndexedSearchParamString> stringParams;
+		List<ResourceIndexedSearchParamString> stringParams = null;
-		final List<ResourceIndexedSearchParamToken> tokenParams;
+		List<ResourceIndexedSearchParamToken> tokenParams = null;
-		final List<ResourceIndexedSearchParamNumber> numberParams;
+		List<ResourceIndexedSearchParamNumber> numberParams = null;
-		final List<ResourceIndexedSearchParamQuantity> quantityParams;
+		List<ResourceIndexedSearchParamQuantity> quantityParams = null;
-		final List<ResourceIndexedSearchParamDate> dateParams;
+		List<ResourceIndexedSearchParamDate> dateParams = null;
-		final List<ResourceLink> links;
+		List<ResourceLink> links = null;
+
 		if (theDeletedTimestampOrNull != null) {
 
 			stringParams = Collections.emptyList();
@@ -875,7 +938,7 @@ public abstract class BaseFhirDao implements IDao {
 			entity.setDeleted(theDeletedTimestampOrNull);
 			entity.setUpdated(theDeletedTimestampOrNull);
 
-		} else {
+		} else if (thePerformIndexing) {
 
 			stringParams = extractSearchParamStrings(entity, theResource);
 			numberParams = extractSearchParamNumber(entity, theResource);
@@ -893,7 +956,6 @@ public abstract class BaseFhirDao implements IDao {
 
 			links = extractResourceLinks(entity, theResource);
 			populateResourceIntoEntity(theResource, entity);
-
 			entity.setUpdated(new Date());
 			entity.setLanguage(theResource.getLanguage().getValue());
 			entity.setParamsString(stringParams);
@@ -909,6 +971,12 @@ public abstract class BaseFhirDao implements IDao {
 			entity.setResourceLinks(links);
 			entity.setHasLinks(links.isEmpty() == false);
 
+		} else {
+			
+			populateResourceIntoEntity(theResource, entity);
+			entity.setUpdated(new Date());
+			entity.setLanguage(theResource.getLanguage().getValue());
+			
 		}
 
 		if (entity.getId() == null) {
@@ -922,6 +990,8 @@ public abstract class BaseFhirDao implements IDao {
 			entity = myEntityManager.merge(entity);
 		}
 
+		if (thePerformIndexing) {
+
 			if (entity.isParamsStringPopulated()) {
 				for (ResourceIndexedSearchParamString next : paramsString) {
 					myEntityManager.remove(next);
@@ -976,6 +1046,8 @@ public abstract class BaseFhirDao implements IDao {
 				myEntityManager.persist(next);
 			}
 
+		} // if thePerformIndexing
+
 		myEntityManager.flush();
 
 		if (theResource != null) {
@@ -985,4 +1057,17 @@ public abstract class BaseFhirDao implements IDao {
 		return entity;
 	}
 
+	protected static String normalizeString(String theString) {
+		char[] out = new char[theString.length()];
+		theString = Normalizer.normalize(theString, Normalizer.Form.NFD);
+		int j = 0;
+		for (int i = 0, n = theString.length(); i < n; ++i) {
+			char c = theString.charAt(i);
+			if (c <= '\u007F') {
+				out[j++] = c;
+			}
+		}
+		return new String(out).toUpperCase();
+	}
+
 }

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

@@ -20,11 +20,8 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
-import java.net.URI;
-import java.net.URISyntaxException;
 import java.util.Date;
 import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
@@ -36,27 +33,14 @@ import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
 import javax.persistence.criteria.Root;
 
-import org.apache.http.NameValuePair;
-import org.apache.http.client.utils.URLEncodedUtils;
-import org.hl7.fhir.instance.model.IBaseResource;
-
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
-import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.util.StopWatch;
-import ca.uhn.fhir.model.api.IQueryParameterAnd;
-import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
-import ca.uhn.fhir.rest.method.MethodUtil;
-import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.rest.server.IBundleProvider;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 
-import com.google.common.collect.ArrayListMultimap;
-
 public abstract class BaseFhirSystemDao<T> extends BaseFhirDao implements IFhirSystemDao<T> {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseFhirSystemDao.class);
 
@@ -82,53 +66,6 @@ public abstract class BaseFhirSystemDao<T> extends BaseFhirDao implements IFhirS
 		return myEntityManager.find(ResourceTable.class, candidateMatches.iterator().next());
 	}
 
-	protected Set<Long> processMatchUrl(String theMatchUrl, Class<? extends IBaseResource> theResourceType) {
-		RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(theResourceType);
-
-		SearchParameterMap paramMap = new SearchParameterMap();
-		List<NameValuePair> parameters;
-		try {
-			parameters = URLEncodedUtils.parse(new URI(theMatchUrl), "UTF-8");
-		} catch (URISyntaxException e) {
-			throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Error was: " + e.toString());
-		}
-
-		ArrayListMultimap<String, QualifiedParamList> nameToParamLists = ArrayListMultimap.create();
-		for (NameValuePair next : parameters) {
-			String paramName = next.getName();
-			String qualifier = null;
-			for (int i = 0; i < paramMap.size(); i++) {
-				switch (paramName.charAt(i)) {
-				case '.':
-				case ':':
-					qualifier = paramName.substring(i);
-					paramName = paramName.substring(0, i);
-					i = Integer.MAX_VALUE;
-					break;
-				}
-			}
-
-			QualifiedParamList paramList = QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifier, next.getValue());
-			nameToParamLists.put(paramName, paramList);
-		}
-
-		for (String nextParamName : nameToParamLists.keySet()) {
-			RuntimeSearchParam paramDef = resourceDef.getSearchParam(nextParamName);
-			if (paramDef == null) {
-				throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Resource type " + resourceDef.getName() + " does not have a parameter with name: " + nextParamName);
-			}
-
-			List<QualifiedParamList> paramList = nameToParamLists.get(nextParamName);
-			IQueryParameterAnd<?> param = MethodUtil.parseQueryParams(paramDef, nextParamName, paramList);
-			paramMap.add(nextParamName, param);
-		}
-
-		IFhirResourceDao<? extends IResource> dao = getDao(theResourceType);
-		Set<Long> ids = dao.searchForIdsWithAndOr(paramMap);
-
-		return ids;
-	}
-
 	@Override
 	public IBundleProvider history(Date theSince) {
 		StopWatch w = new StopWatch();

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

@@ -0,0 +1,36 @@
+package ca.uhn.fhir.jpa.dao;
+
+import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+
+public class DaoMethodOutcome extends MethodOutcome {
+
+	private ResourceTable myEntity;
+	private IResource myResource;
+
+	public ResourceTable getEntity() {
+		return myEntity;
+	}
+
+	public IResource getResource() {
+		return myResource;
+	}
+
+	@Override
+	public DaoMethodOutcome setCreated(Boolean theCreated) {
+		super.setCreated(theCreated);
+		return this;
+	}
+
+	public DaoMethodOutcome setEntity(ResourceTable theEntity) {
+		myEntity = theEntity;
+		return this;
+	}
+
+	public DaoMethodOutcome setResource(IResource theResource) {
+		myResource = theResource;
+		return this;
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java

@@ -20,229 +20,516 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
+import static org.apache.commons.lang3.StringUtils.*;
+
+import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
+import ca.uhn.fhir.model.dstu2.resource.Bundle.EntryTransactionResponse;
+import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
+import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
+import ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.rest.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.FhirTerser;
 
 public class FhirSystemDaoDstu2 extends BaseFhirSystemDao<Bundle> {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu2.class);
 
+	private UrlParts parseUrl(String theAction, String theUrl) {
+		UrlParts retVal = new UrlParts();
+
+		//@formatter:off
+		/* 
+		 * We assume that the URL passed in is in one of the following forms:
+		 * [Resource Type]?[Search Params]
+		 * [Resource Type]/[Resource ID]
+		 * [Resource Type]/[Resource ID]/_history/[Version ID]
+		 */
+		//@formatter:on
+		int nextStart = 0;
+		boolean nextIsHistory = false;
+
+		for (int idx = 0; idx < theUrl.length(); idx++) {
+			char nextChar = theUrl.charAt(idx);
+			boolean atEnd = (idx + 1) == theUrl.length();
+			if (nextChar == '?' || nextChar == '/' || atEnd) {
+				int endIdx = atEnd ? idx + 1 : idx;
+				String nextSubstring = theUrl.substring(nextStart, endIdx);
+				if (retVal.getResourceType() == null) {
+					retVal.setResourceType(nextSubstring);
+				} else if (retVal.getResourceId() == null) {
+					retVal.setResourceId(nextSubstring);
+				} else if (nextIsHistory) {
+					retVal.setVersionId(nextSubstring);
+				} else {
+					if (nextSubstring.equals(Constants.URL_TOKEN_HISTORY)) {
+						nextIsHistory = true;
+					} else {
+						String msg = getContext().getLocalizer().getMessage(BaseFhirSystemDao.class, "transactionInvalidUrl", theAction, theUrl);
+						throw new InvalidRequestException(msg);
+					}
+				}
+				if (nextChar == '?') {
+					if (theUrl.length() > idx + 1) {
+						retVal.setParams(theUrl.substring(idx + 1, theUrl.length()));
+					}
+					break;
+				}
+				nextStart = idx + 1;
+			}
+		}
+
+		RuntimeResourceDefinition resType = getContext().getResourceDefinition(retVal.getResourceType());
+		IFhirResourceDao<? extends IResource> dao = null;
+		if (resType != null) {
+			dao = getDao(resType.getImplementingClass());
+		}
+		if (dao == null) {
+			String msg = getContext().getLocalizer().getMessage(BaseFhirSystemDao.class, "transactionInvalidUrl", theAction, theUrl);
+			throw new InvalidRequestException(msg);
+		}
+		retVal.setDao(dao);
+
+		if (retVal.getResourceId() == null && retVal.getParams() == null) {
+			String msg = getContext().getLocalizer().getMessage(BaseFhirSystemDao.class, "transactionInvalidUrl", theAction, theUrl);
+			throw new InvalidRequestException(msg);
+		}
+
+		return retVal;
+	}
+
+	@SuppressWarnings("unchecked")
 	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
 	public Bundle transaction(Bundle theResources) {
 		ourLog.info("Beginning transaction with {} resources", theResources.getEntry().size());
 		long start = System.currentTimeMillis();
 
-//		Set<IdDt> allIds = new HashSet<IdDt>();
+		Set<IdDt> allIds = new HashSet<IdDt>();
-//
+		Map<IdDt, IdDt> idSubstitutions = new HashMap<IdDt, IdDt>();
-//		for (int i = 0; i < theResources.size(); i++) {
+		Map<IdDt, DaoMethodOutcome> idToPersistedOutcome = new HashMap<IdDt, DaoMethodOutcome>();
-//			IResource res = theResources.get(i);
-//			if (res.getId().hasIdPart() && !res.getId().hasResourceType()) {
-//				res.setId(new IdDt(toResourceName(res.getClass()), res.getId().getIdPart()));
-//			}
-//
-//			/*
-//			 * Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
-//			 */
-//			if (res.getId().hasResourceType() && res.getId().hasIdPart()) {
-//				IdDt nextId = res.getId().toUnqualifiedVersionless();
-//				if (!allIds.add(nextId)) {
-//					throw new InvalidRequestException("Transaction bundle contains multiple resources with ID: " + nextId);
-//				}
-//			}
-//		}
-//
-//		FhirTerser terser = getContext().newTerser();
-//
-//		int creations = 0;
-//		int updates = 0;
-//
-//		Map<IdDt, IdDt> idConversions = new HashMap<IdDt, IdDt>();
-//
-//		List<ResourceTable> persistedResources = new ArrayList<ResourceTable>();
-//
-//		List<IResource> retVal = new ArrayList<IResource>();
-//		OperationOutcome oo = new OperationOutcome();
-//		retVal.add(oo);
-//
-//		for (int resourceIdx = 0; resourceIdx < theResources.size(); resourceIdx++) {
-//			IResource nextResource = theResources.get(resourceIdx);
-//
-//			IdDt nextId = nextResource.getId();
-//			if (nextId == null) {
-//				nextId = new IdDt();
-//			}
-//
-//			String resourceName = toResourceName(nextResource);
-//			BundleEntryTransactionOperationEnum nextResouceOperationIn = ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(nextResource);
-//			if (nextResouceOperationIn == null && hasValue(ResourceMetadataKeyEnum.DELETED_AT.get(nextResource))) {
-//				nextResouceOperationIn = BundleEntryTransactionOperationEnum.DELETE;
-//			}
-//
-//			String matchUrl = ResourceMetadataKeyEnum.LINK_SEARCH.get(nextResource);
-//			Set<Long> candidateMatches = null;
-//			if (StringUtils.isNotBlank(matchUrl)) {
-//				candidateMatches = processMatchUrl(matchUrl, nextResource.getClass());
-//			}
-//
-//			ResourceTable entity;
-//			if (nextResouceOperationIn == BundleEntryTransactionOperationEnum.CREATE) {
-//				entity = null;
-//			} else if (nextResouceOperationIn == BundleEntryTransactionOperationEnum.UPDATE || nextResouceOperationIn == BundleEntryTransactionOperationEnum.DELETE) {
-//				if (candidateMatches == null || candidateMatches.size() == 0) {
-//					if (nextId == null || StringUtils.isBlank(nextId.getIdPart())) {
-//						throw new InvalidRequestException(getContext().getLocalizer().getMessage(FhirSystemDaoDstu2.class, "transactionOperationFailedNoId", nextResouceOperationIn.name()));
-//					}
-//					entity = tryToLoadEntity(nextId);
-//					if (entity == null) {
-//						if (nextResouceOperationIn == BundleEntryTransactionOperationEnum.UPDATE) {
-//							ourLog.debug("Attempting to UPDATE resource with unknown ID '{}', will CREATE instead", nextId);
-//						} else if (candidateMatches == null) {
-//							throw new InvalidRequestException(getContext().getLocalizer().getMessage(FhirSystemDaoDstu2.class, "transactionOperationFailedUnknownId", nextResouceOperationIn.name(), nextId));
-//						} else {
-//							ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl);
-//							ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(nextResource, BundleEntryTransactionOperationEnum.NOOP);
-//							persistedResources.add(null);
-//							retVal.add(nextResource);
-//							continue;
-//						}
-//					}
-//				} else if (candidateMatches.size() == 1) {
-//					entity = loadFirstEntityFromCandidateMatches(candidateMatches);
-//				} else {
-//					throw new InvalidRequestException(getContext().getLocalizer().getMessage(FhirSystemDaoDstu2.class, "transactionOperationWithMultipleMatchFailure", nextResouceOperationIn.name(), matchUrl, candidateMatches.size()));
-//				}
-//			} else if (nextResouceOperationIn == BundleEntryTransactionOperationEnum.NOOP) {
-//				throw new InvalidRequestException(getContext().getLocalizer().getMessage(FhirSystemDaoDstu2.class, "incomingNoopInTransaction"));
-//			} else if (nextId.isEmpty()) {
-//				entity = null;
-//			} else {
-//				entity = tryToLoadEntity(nextId);
-//			}
-//
-//			BundleEntryTransactionOperationEnum nextResouceOperationOut;
-//			if (entity == null) {
-//				nextResouceOperationOut = BundleEntryTransactionOperationEnum.CREATE;
-//				entity = toEntity(nextResource);
-//				if (nextId.isEmpty() == false && nextId.getIdPart().startsWith("cid:")) {
-//					ourLog.debug("Resource in transaction has ID[{}], will replace with server assigned ID", nextId.getIdPart());
-//				} else if (nextResouceOperationIn == BundleEntryTransactionOperationEnum.CREATE) {
-//					if (nextId.isEmpty() == false) {
-//						ourLog.debug("Resource in transaction has ID[{}] but is marked for CREATE, will ignore ID", nextId.getIdPart());
-//					}
-//					if (candidateMatches != null) {
-//						if (candidateMatches.size() == 1) {
-//							ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl);
-//							BaseHasResource existingEntity = loadFirstEntityFromCandidateMatches(candidateMatches);
-//							IResource existing = (IResource) toResource(existingEntity);
-//							ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(existing, BundleEntryTransactionOperationEnum.NOOP);
-//							persistedResources.add(null);
-//							retVal.add(existing);
-//							continue;
-//						}
-//						if (candidateMatches.size() > 1) {
-//							throw new InvalidRequestException(getContext().getLocalizer().getMessage(FhirSystemDaoDstu2.class, "transactionOperationWithMultipleMatchFailure", BundleEntryTransactionOperationEnum.CREATE.name(), matchUrl, candidateMatches.size()));
-//						}
-//					}
-//				} else {
-//					createForcedIdIfNeeded(entity, nextId);
-//				}
-//				myEntityManager.persist(entity);
-//				if (entity.getForcedId() != null) {
-//					myEntityManager.persist(entity.getForcedId());
-//				}
-//				creations++;
-//				ourLog.info("Resource Type[{}] with ID[{}] does not exist, creating it", resourceName, nextId);
-//			} else {
-//				nextResouceOperationOut = nextResouceOperationIn;
-//				if (nextResouceOperationOut == null) {
-//					nextResouceOperationOut = BundleEntryTransactionOperationEnum.UPDATE;
-//				}
-//				updates++;
-//				ourLog.info("Resource Type[{}] with ID[{}] exists, updating it", resourceName, nextId);
-//			}
-//
-//			persistedResources.add(entity);
-//			retVal.add(nextResource);
-//			ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(nextResource, nextResouceOperationOut);
-//		}
-//
-//		ourLog.info("Flushing transaction to database");
-//		myEntityManager.flush();
-//
-//		for (int i = 0; i < persistedResources.size(); i++) {
-//			ResourceTable entity = persistedResources.get(i);
-//
-//			String resourceName = toResourceName(theResources.get(i));
-//			IdDt nextId = theResources.get(i).getId();
-//
-//			IdDt newId;
-//
-//			if (entity == null) {
-//				newId = retVal.get(i + 1).getId().toUnqualifiedVersionless();
-//			} else {
-//				newId = entity.getIdDt().toUnqualifiedVersionless();
-//			}
-//
-//			if (nextId == null || nextId.isEmpty()) {
-//				ourLog.info("Transaction resource (with no preexisting ID) has been assigned new ID[{}]", nextId, newId);
-//			} else {
-//				if (nextId.toUnqualifiedVersionless().equals(newId)) {
-//					ourLog.info("Transaction resource ID[{}] is being updated", newId);
-//				} else {
-//					if (!nextId.getIdPart().startsWith("#")) {
-//						nextId = new IdDt(resourceName + '/' + nextId.getIdPart());
-//						ourLog.info("Transaction resource ID[{}] has been assigned new ID[{}]", nextId, newId);
-//						idConversions.put(nextId, newId);
-//					}
-//				}
-//			}
-//
-//		}
-//
-//		for (IResource nextResource : theResources) {
-//			List<BaseResourceReferenceDt> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class);
-//			for (BaseResourceReferenceDt nextRef : allRefs) {
-//				IdDt nextId = nextRef.getReference();
-//				if (idConversions.containsKey(nextId)) {
-//					IdDt newId = idConversions.get(nextId);
-//					ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
-//					nextRef.setReference(newId);
-//				} else {
-//					ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
-//				}
-//			}
-//		}
-//
-//		ourLog.info("Re-flushing updated resource references and extracting search criteria");
-//
-//		for (int i = 0; i < theResources.size(); i++) {
-//			IResource resource = theResources.get(i);
-//			ResourceTable table = persistedResources.get(i);
-//			if (table == null) {
-//				continue;
-//			}
-//
-//			InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(resource);
-//			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
-//			if (deletedInstantOrNull == null && ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(resource) == BundleEntryTransactionOperationEnum.DELETE) {
-//				deletedTimestampOrNull = new Date();
-//				ResourceMetadataKeyEnum.DELETED_AT.put(resource, new InstantDt(deletedTimestampOrNull));
-//			}
-//
-//			updateEntity(resource, table, table.getId() != null, deletedTimestampOrNull);
-//		}
-//
-//		long delay = System.currentTimeMillis() - start;
-//		ourLog.info("Transaction completed in {}ms with {} creations and {} updates", new Object[] { delay, creations, updates });
-//
-//		oo.addIssue().setSeverity(IssueSeverityEnum.INFORMATION).setDetails("Transaction completed in " + delay + "ms with " + creations + " creations and " + updates + " updates");
-//
-//		notifyWriteCompleted();
 
-		return null;
+		Bundle response = new Bundle();
+		OperationOutcome oo = new OperationOutcome();
+		response.addEntry().setResource(oo);
+
+		for (int i = 0; i < theResources.getEntry().size(); i++) {
+			Entry nextEntry = theResources.getEntry().get(i);
+			IResource res = nextEntry.getResource();
+			IdDt nextResourceId = null;
+			if (res != null) {
+
+				nextResourceId = res.getId();
+				if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType()) {
+					nextResourceId = new IdDt(toResourceName(res.getClass()), nextResourceId.getIdPart());
+					res.setId(nextResourceId);
 				}
 
+				/*
+				 * Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
+				 */
+				if (nextResourceId.hasResourceType() && nextResourceId.hasIdPart()) {
+					IdDt nextId = nextResourceId.toUnqualifiedVersionless();
+					if (!allIds.add(nextId)) {
+						throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextId));
+					}
+				}
+
+			}
+
+			HTTPVerbEnum verb = nextEntry.getTransaction().getMethodElement().getValueAsEnum();
+			if (verb == null) {
+				throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseFhirSystemDao.class, "transactionEntryHasInvalidVerb", nextEntry.getTransaction().getMethod()));
+			}
+
+			switch (verb) {
+			case POST: {
+				// CREATE
+				@SuppressWarnings("rawtypes")
+				IFhirResourceDao resourceDao = getDao(res.getClass());
+				res.setId(null);
+				DaoMethodOutcome outcome;
+				Entry newEntry = response.addEntry();
+				outcome = resourceDao.create(res, nextEntry.getTransaction().getIfNoneExist(), false);
+				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, newEntry);
+				break;
+			}
+			case DELETE: {
+				// DELETE
+				Entry newEntry = response.addEntry();
+				String url = extractTransactionUrlOrThrowException(nextEntry, verb);
+				UrlParts parts = parseUrl(verb.getCode(), url);
+				if (parts.getResourceId() != null) {
+					parts.getDao().delete(new IdDt(parts.getResourceType(), parts.getResourceId()));
+				} else {
+					parts.getDao().deleteByUrl(parts.getResourceType() + '?' + parts.getParams());
+				}
+
+				newEntry.getTransactionResponse().setStatus(Integer.toString(Constants.STATUS_HTTP_204_NO_CONTENT));
+				break;
+			}
+			case PUT: {
+				// UPDATE
+				@SuppressWarnings("rawtypes")
+				IFhirResourceDao resourceDao = getDao(res.getClass());
+
+				DaoMethodOutcome outcome;
+				Entry newEntry = response.addEntry();
+
+				String url = extractTransactionUrlOrThrowException(nextEntry, verb);
+
+				UrlParts parts = parseUrl(verb.getCode(), url);
+				if (parts.getResourceId() != null) {
+					res.setId(new IdDt(parts.getResourceType(), parts.getResourceId()));
+					outcome = resourceDao.update(res, null, false);
+				} else {
+					res.setId(null);
+					outcome = resourceDao.update(res, parts.getResourceType() + '?' + parts.getParams(), false);
+				}
+
+				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, newEntry);
+				break;
+			}
+			case GET: {
+				// SEARCH/READ/VREAD
+				String url = extractTransactionUrlOrThrowException(nextEntry, verb);
+				UrlParts parts = parseUrl(verb.getCode(), url);
+
+				@SuppressWarnings("rawtypes")
+				IFhirResourceDao resourceDao = parts.getDao();
+
+				if (parts.getResourceId() != null && parts.getParams() == null) {
+					IResource found;
+					if (parts.getVersionId() != null) {
+						found = resourceDao.read(new IdDt(parts.getResourceType(), parts.getResourceId(), parts.getVersionId()));
+					} else {
+						found = resourceDao.read(new IdDt(parts.getResourceType(), parts.getResourceId()));
+					}
+					EntryTransactionResponse resp = response.addEntry().setResource(found).getTransactionResponse();
+					resp.setLocation(found.getId().toUnqualified().getValue());
+					resp.addEtag(found.getId().getVersionIdPart());
+				} else if (parts.getParams() != null) {
+					RuntimeResourceDefinition def = getContext().getResourceDefinition(parts.getDao().getResourceType());
+					SearchParameterMap params = translateMatchUrl(url, def);
+					IBundleProvider bundle = parts.getDao().search(params);
+					
+					Bundle searchBundle = new Bundle();
+					searchBundle.setTotal(bundle.size());
+					
+					int configuredMax = 100; // this should probably be configurable or something
+					if (bundle.size() > configuredMax) {
+						oo.addIssue().setSeverity(IssueSeverityEnum.WARNING).setDetails("Search nested within transaction found more than " + configuredMax + " matches, but paging is not supported in nested transactions");
+					}
+					List<IResource> resourcesToAdd = bundle.getResources(0, Math.min(bundle.size(), configuredMax));
+					for (IResource next : resourcesToAdd) {
+						searchBundle.addEntry().setResource(next);
+					}
+					
+					response.addEntry().setResource(searchBundle);
+				}
+			}
+			}
+
+		}
+
+		FhirTerser terser = getContext().newTerser();
+
+		// int creations = 0;
+		// int updates = 0;
+		//
+		// Map<IdDt, IdDt> idConversions = new HashMap<IdDt, IdDt>();
+		//
+		// List<ResourceTable> persistedResources = new ArrayList<ResourceTable>();
+		//
+		// List<IResource> retVal = new ArrayList<IResource>();
+		// OperationOutcome oo = new OperationOutcome();
+		// retVal.add(oo);
+		//
+		// for (int resourceIdx = 0; resourceIdx < theResources.size(); resourceIdx++) {
+		// IResource nextResource = theResources.get(resourceIdx);
+		//
+		// IdDt nextId = nextResource.getId();
+		// if (nextId == null) {
+		// nextId = new IdDt();
+		// }
+		//
+		// String resourceName = toResourceName(nextResource);
+		// BundleEntryTransactionOperationEnum nextResouceOperationIn =
+		// ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(nextResource);
+		// if (nextResouceOperationIn == null && hasValue(ResourceMetadataKeyEnum.DELETED_AT.get(nextResource))) {
+		// nextResouceOperationIn = BundleEntryTransactionOperationEnum.DELETE;
+		// }
+		//
+		// String matchUrl = ResourceMetadataKeyEnum.LINK_SEARCH.get(nextResource);
+		// Set<Long> candidateMatches = null;
+		// if (StringUtils.isNotBlank(matchUrl)) {
+		// candidateMatches = processMatchUrl(matchUrl, nextResource.getClass());
+		// }
+		//
+		// ResourceTable entity;
+		// if (nextResouceOperationIn == BundleEntryTransactionOperationEnum.CREATE) {
+		// entity = null;
+		// } else if (nextResouceOperationIn == BundleEntryTransactionOperationEnum.UPDATE || nextResouceOperationIn ==
+		// BundleEntryTransactionOperationEnum.DELETE) {
+		// if (candidateMatches == null || candidateMatches.size() == 0) {
+		// if (nextId == null || StringUtils.isBlank(nextId.getIdPart())) {
+		// throw new InvalidRequestException(getContext().getLocalizer().getMessage(FhirSystemDaoDstu2.class,
+		// "transactionOperationFailedNoId", nextResouceOperationIn.name()));
+		// }
+		// entity = tryToLoadEntity(nextId);
+		// if (entity == null) {
+		// if (nextResouceOperationIn == BundleEntryTransactionOperationEnum.UPDATE) {
+		// ourLog.debug("Attempting to UPDATE resource with unknown ID '{}', will CREATE instead", nextId);
+		// } else if (candidateMatches == null) {
+		// throw new InvalidRequestException(getContext().getLocalizer().getMessage(FhirSystemDaoDstu2.class,
+		// "transactionOperationFailedUnknownId", nextResouceOperationIn.name(), nextId));
+		// } else {
+		// ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl);
+		// ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(nextResource,
+		// BundleEntryTransactionOperationEnum.NOOP);
+		// persistedResources.add(null);
+		// retVal.add(nextResource);
+		// continue;
+		// }
+		// }
+		// } else if (candidateMatches.size() == 1) {
+		// entity = loadFirstEntityFromCandidateMatches(candidateMatches);
+		// } else {
+		// throw new InvalidRequestException(getContext().getLocalizer().getMessage(FhirSystemDaoDstu2.class,
+		// "transactionOperationWithMultipleMatchFailure", nextResouceOperationIn.name(), matchUrl,
+		// candidateMatches.size()));
+		// }
+		// } else if (nextResouceOperationIn == BundleEntryTransactionOperationEnum.NOOP) {
+		// throw new InvalidRequestException(getContext().getLocalizer().getMessage(FhirSystemDaoDstu2.class,
+		// "incomingNoopInTransaction"));
+		// } else if (nextId.isEmpty()) {
+		// entity = null;
+		// } else {
+		// entity = tryToLoadEntity(nextId);
+		// }
+		//
+		// BundleEntryTransactionOperationEnum nextResouceOperationOut;
+		// if (entity == null) {
+		// nextResouceOperationOut = BundleEntryTransactionOperationEnum.CREATE;
+		// entity = toEntity(nextResource);
+		// if (nextId.isEmpty() == false && nextId.getIdPart().startsWith("cid:")) {
+		// ourLog.debug("Resource in transaction has ID[{}], will replace with server assigned ID", nextId.getIdPart());
+		// } else if (nextResouceOperationIn == BundleEntryTransactionOperationEnum.CREATE) {
+		// if (nextId.isEmpty() == false) {
+		// ourLog.debug("Resource in transaction has ID[{}] but is marked for CREATE, will ignore ID",
+		// nextId.getIdPart());
+		// }
+		// if (candidateMatches != null) {
+		// if (candidateMatches.size() == 1) {
+		// ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl);
+		// BaseHasResource existingEntity = loadFirstEntityFromCandidateMatches(candidateMatches);
+		// IResource existing = (IResource) toResource(existingEntity);
+		// ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(existing, BundleEntryTransactionOperationEnum.NOOP);
+		// persistedResources.add(null);
+		// retVal.add(existing);
+		// continue;
+		// }
+		// if (candidateMatches.size() > 1) {
+		// throw new InvalidRequestException(getContext().getLocalizer().getMessage(FhirSystemDaoDstu2.class,
+		// "transactionOperationWithMultipleMatchFailure", BundleEntryTransactionOperationEnum.CREATE.name(), matchUrl,
+		// candidateMatches.size()));
+		// }
+		// }
+		// } else {
+		// createForcedIdIfNeeded(entity, nextId);
+		// }
+		// myEntityManager.persist(entity);
+		// if (entity.getForcedId() != null) {
+		// myEntityManager.persist(entity.getForcedId());
+		// }
+		// creations++;
+		// ourLog.info("Resource Type[{}] with ID[{}] does not exist, creating it", resourceName, nextId);
+		// } else {
+		// nextResouceOperationOut = nextResouceOperationIn;
+		// if (nextResouceOperationOut == null) {
+		// nextResouceOperationOut = BundleEntryTransactionOperationEnum.UPDATE;
+		// }
+		// updates++;
+		// ourLog.info("Resource Type[{}] with ID[{}] exists, updating it", resourceName, nextId);
+		// }
+		//
+		// persistedResources.add(entity);
+		// retVal.add(nextResource);
+		// ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(nextResource, nextResouceOperationOut);
+		// }
+		//
+		// ourLog.info("Flushing transaction to database");
+		// myEntityManager.flush();
+		//
+		// for (int i = 0; i < persistedResources.size(); i++) {
+		// ResourceTable entity = persistedResources.get(i);
+		//
+		// String resourceName = toResourceName(theResources.get(i));
+		// IdDt nextId = theResources.get(i).getId();
+		//
+		// IdDt newId;
+		//
+		// if (entity == null) {
+		// newId = retVal.get(i + 1).getId().toUnqualifiedVersionless();
+		// } else {
+		// newId = entity.getIdDt().toUnqualifiedVersionless();
+		// }
+		//
+		// if (nextId == null || nextId.isEmpty()) {
+		// ourLog.info("Transaction resource (with no preexisting ID) has been assigned new ID[{}]", nextId, newId);
+		// } else {
+		// if (nextId.toUnqualifiedVersionless().equals(newId)) {
+		// ourLog.info("Transaction resource ID[{}] is being updated", newId);
+		// } else {
+		// if (!nextId.getIdPart().startsWith("#")) {
+		// nextId = new IdDt(resourceName + '/' + nextId.getIdPart());
+		// ourLog.info("Transaction resource ID[{}] has been assigned new ID[{}]", nextId, newId);
+		// idConversions.put(nextId, newId);
+		// }
+		// }
+		// }
+		//
+		// }
+		//
+		for (DaoMethodOutcome nextOutcome : idToPersistedOutcome.values()) {
+			IResource nextResource = nextOutcome.getResource();
+			if (nextResource == null) {
+				continue;
+			}
+
+			List<BaseResourceReferenceDt> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class);
+			for (BaseResourceReferenceDt nextRef : allRefs) {
+				IdDt nextId = nextRef.getReference();
+				if (idSubstitutions.containsKey(nextId)) {
+					IdDt newId = idSubstitutions.get(nextId);
+					ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
+					nextRef.setReference(newId);
+				} else {
+					ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
+				}
+			}
+
+			InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(nextResource);
+			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
+			updateEntity(nextResource, nextOutcome.getEntity(), false, deletedTimestampOrNull, true, false);
+		}
+		//
+		// ourLog.info("Re-flushing updated resource references and extracting search criteria");
+		//
+		// for (int i = 0; i < theResources.size(); i++) {
+		// IResource resource = theResources.get(i);
+		// ResourceTable table = persistedResources.get(i);
+		// if (table == null) {
+		// continue;
+		// }
+		//
+		// InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(resource);
+		// Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
+		// if (deletedInstantOrNull == null && ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(resource) ==
+		// BundleEntryTransactionOperationEnum.DELETE) {
+		// deletedTimestampOrNull = new Date();
+		// ResourceMetadataKeyEnum.DELETED_AT.put(resource, new InstantDt(deletedTimestampOrNull));
+		// }
+		//
+		// updateEntity(resource, table, table.getId() != null, deletedTimestampOrNull);
+		// }
+
+		long delay = System.currentTimeMillis() - start;
+		ourLog.info("Transaction completed in {}ms", new Object[] { delay });
+
+		oo.addIssue().setSeverity(IssueSeverityEnum.INFORMATION).setDetails("Transaction completed in " + delay + "ms");
+
+		notifyWriteCompleted();
+
+		return response;
+	}
+
+	private void handleTransactionCreateOrUpdateOutcome(Map<IdDt, IdDt> idSubstitutions, Map<IdDt, DaoMethodOutcome> idToPersistedOutcome, IdDt nextResourceId, DaoMethodOutcome outcome, Entry newEntry) {
+		IdDt newId = outcome.getId().toUnqualifiedVersionless();
+		if (newId.equals(nextResourceId) == false) {
+			idSubstitutions.put(nextResourceId, newId);
+		}
+		idToPersistedOutcome.put(newId, outcome);
+		if (outcome.getCreated().booleanValue()) {
+			newEntry.getTransactionResponse().setStatus(Long.toString(Constants.STATUS_HTTP_201_CREATED));
+		} else {
+			newEntry.getTransactionResponse().setStatus(Long.toString(Constants.STATUS_HTTP_200_OK));
+		}
+		newEntry.getTransactionResponse().setLocation(outcome.getId().toUnqualified().getValue());
+		newEntry.getTransactionResponse().addEtag().setValue(outcome.getId().getVersionIdPart());
+	}
+
+	private String extractTransactionUrlOrThrowException(Entry nextEntry, HTTPVerbEnum verb) {
+		String url = nextEntry.getTransaction().getUrl();
+		if (isBlank(url)) {
+			throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseFhirSystemDao.class, "transactionMissingUrl", verb.name()));
+		}
+		return url;
+	}
+
+	private static class UrlParts {
+		private IFhirResourceDao<? extends IResource> myDao;
+		private String myParams;
+		private String myResourceId;
+		private String myResourceType;
+		private String myVersionId;
+
+		public IFhirResourceDao<? extends IResource> getDao() {
+			return myDao;
+		}
+
+		public void setVersionId(String theVersionId) {
+			myVersionId = theVersionId;
+		}
+
+		public String getVersionId() {
+			return myVersionId;
+		}
+
+		public String getParams() {
+			return myParams;
+		}
+
+		public String getResourceId() {
+			return myResourceId;
+		}
+
+		public String getResourceType() {
+			return myResourceType;
+		}
+
+		public void setDao(IFhirResourceDao<? extends IResource> theDao) {
+			myDao = theDao;
+		}
+
+		public void setParams(String theParams) {
+			myParams = theParams;
+		}
+
+		public void setResourceId(String theResourceId) {
+			myResourceId = theResourceId;
+		}
+
+		public void setResourceType(String theResourceType) {
+			myResourceType = theResourceType;
+		}
+	}
 
 }

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

@@ -29,7 +29,6 @@ import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 
@@ -37,9 +36,20 @@ public interface IFhirResourceDao<T extends IResource> extends IDao {
 
 	void addTag(IdDt theId, String theScheme, String theTerm, String theLabel);
 
-	MethodOutcome create(T theResource);
+	DaoMethodOutcome create(T theResource);
 
-	MethodOutcome delete(IdDt theResource);
+	DaoMethodOutcome create(T theResource, String theIfNoneExist);
+
+	/**
+	 * @param thePerformIndexing
+	 *            Use with caution! If you set this to false, you need to manually perform indexing or your resources
+	 *            won't be indexed and searches won't work.
+	 */
+	DaoMethodOutcome create(T theResource, String theIfNoneExist, boolean thePerformIndexing);
+
+	DaoMethodOutcome delete(IdDt theResource);
+
+	DaoMethodOutcome deleteByUrl(String theString);
 
 	TagList getAllResourceTags();
 
@@ -49,7 +59,7 @@ public interface IFhirResourceDao<T extends IResource> extends IDao {
 
 	IBundleProvider history(Date theSince);
 
-	IBundleProvider history(IdDt theId,Date theSince);
+	IBundleProvider history(IdDt theId, Date theSince);
 
 	IBundleProvider history(Long theId, Date theSince);
 
@@ -57,12 +67,20 @@ public interface IFhirResourceDao<T extends IResource> extends IDao {
 	 * 
 	 * @param theId
 	 * @return
-	 * @throws ResourceNotFoundException If the ID is not known to the server
+	 * @throws ResourceNotFoundException
+	 *             If the ID is not known to the server
 	 */
 	T read(IdDt theId);
 
 	BaseHasResource readEntity(IdDt theId);
 
+	/**
+	 * @param theCheckForForcedId
+	 *            If true, this method should fail if the requested ID contains a numeric PID which exists, but is
+	 *            obscured by a "forced ID" so should not exist as far as the outside world is concerned.
+	 */
+	BaseHasResource readEntity(IdDt theId, boolean theCheckForForcedId);
+
 	void removeTag(IdDt theId, String theScheme, String theTerm);
 
 	IBundleProvider search(Map<String, IQueryParameterType> theParams);
@@ -75,15 +93,17 @@ public interface IFhirResourceDao<T extends IResource> extends IDao {
 
 	Set<Long> searchForIds(String theParameterName, IQueryParameterType theValue);
 
-	MethodOutcome update(T theResource, IdDt theId);
-
 	Set<Long> searchForIdsWithAndOr(SearchParameterMap theParams);
 
+	DaoMethodOutcome update(T theResource);
+
+	DaoMethodOutcome update(T theResource, String theMatchUrl);
+
 	/**
-	 * @param theCheckForForcedId If true, this method should fail if the requested ID contains
+	 * @param thePerformIndexing
-	 * a numeric PID which exists, but is obscured by a "forced ID" so should not exist as
+	 *            Use with caution! If you set this to false, you need to manually perform indexing or your resources
-	 * far as the outside world is concerned. 
+	 *            won't be indexed and searches won't work.
 	 */
-	BaseHasResource readEntity(IdDt theId, boolean theCheckForForcedId);
+	DaoMethodOutcome update(T theResource, String theMatchUrl, boolean thePerformIndexing);
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ForcedId.java

@@ -32,9 +32,15 @@ import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
+//@formatter:off
 @Entity()
-@Table(name = "HFJ_FORCED_ID", uniqueConstraints = { @UniqueConstraint(name = "IDX_FORCEDID", columnNames = { "FORCED_ID" }) })
+@Table(name = "HFJ_FORCED_ID", uniqueConstraints = { 
-@NamedQueries(@NamedQuery(name = "Q_GET_FORCED_ID", query = "SELECT f FROM ForcedId f WHERE myForcedId = :ID"))
+	@UniqueConstraint(name = "IDX_FORCEDID", columnNames = { "FORCED_ID" }) 
+})
+@NamedQueries(value= {
+	@NamedQuery(name = "Q_GET_FORCED_ID", query = "SELECT f FROM ForcedId f WHERE myForcedId = :ID")
+})
+//@formatter:on
 public class ForcedId {
 
 	public static final int MAX_FORCED_ID_LENGTH = 100;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/JpaConformanceProviderDstu1.java

@@ -27,6 +27,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.dstu.resource.Conformance;
 import ca.uhn.fhir.model.dstu.resource.Conformance.Rest;
 import ca.uhn.fhir.model.dstu.resource.Conformance.RestResource;
@@ -44,11 +45,11 @@ import javax.servlet.http.HttpServletRequest;
 public class JpaConformanceProviderDstu1 extends ServerConformanceProvider {
 
 	private String myImplementationDescription;
-	private IFhirSystemDao mySystemDao;
+	private IFhirSystemDao<List<IResource>> mySystemDao;
 	private volatile Conformance myCachedValue;
 	private RestfulServer myRestfulServer;
 
-	public JpaConformanceProviderDstu1(RestfulServer theRestfulServer, IFhirSystemDao theSystemDao) {
+	public JpaConformanceProviderDstu1(RestfulServer theRestfulServer, IFhirSystemDao<List<IResource>> theSystemDao) {
 		super(theRestfulServer);
 		myRestfulServer = theRestfulServer;
 		mySystemDao = theSystemDao;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/JpaConformanceProviderDstu2.java

@@ -29,6 +29,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Conformance;
 import ca.uhn.fhir.model.dstu2.resource.Conformance.Rest;
 import ca.uhn.fhir.model.dstu2.resource.Conformance.RestResource;
@@ -44,11 +45,11 @@ import ca.uhn.fhir.util.ExtensionConstants;
 public class JpaConformanceProviderDstu2 extends ServerConformanceProvider {
 
 	private String myImplementationDescription;
-	private IFhirSystemDao mySystemDao;
+	private IFhirSystemDao<Bundle> mySystemDao;
 	private volatile Conformance myCachedValue;
 	private RestfulServer myRestfulServer;
 
-	public JpaConformanceProviderDstu2(RestfulServer theRestfulServer, IFhirSystemDao theSystemDao) {
+	public JpaConformanceProviderDstu2(RestfulServer theRestfulServer, IFhirSystemDao<Bundle> theSystemDao) {
 		super(theRestfulServer);
 		myRestfulServer = theRestfulServer;
 		mySystemDao = theSystemDao;

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

@@ -162,13 +162,12 @@ public class JpaResourceProvider<T extends IResource> extends BaseJpaProvider im
 	public MethodOutcome update(HttpServletRequest theRequest, @ResourceParam T theResource, @IdParam IdDt theId) {
 		startRequest(theRequest);
 		try {
-			return myDao.update(theResource, theId);
+			theResource.setId(theId);
+			return myDao.update(theResource);
 		} catch (ResourceNotFoundException e) {
 			ourLog.info("Can't update resource with ID[" + theId.getValue() + "] because it doesn't exist, going to create it instead");
 			theResource.setId(theId);
-			MethodOutcome retVal = myDao.create(theResource);
+			return myDao.create(theResource);
-			retVal.setCreated(true);
-			return retVal;
 		} finally {
 			endRequest(theRequest);
 		}

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

@@ -1,17 +1,7 @@
 package ca.uhn.fhir.jpa.dao;
 
-import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.*;
-import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.*;
-import static org.hamcrest.Matchers.containsString;
-import static org.hamcrest.Matchers.endsWith;
-import static org.hamcrest.Matchers.greaterThan;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
 
 import java.util.ArrayList;
 import java.util.Date;
@@ -40,6 +30,7 @@ import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
 import ca.uhn.fhir.model.dstu2.composite.PeriodDt;
 import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
 import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Device;
 import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
 import ca.uhn.fhir.model.dstu2.resource.Encounter;
@@ -47,7 +38,9 @@ import ca.uhn.fhir.model.dstu2.resource.Location;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.Organization;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
+import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
 import ca.uhn.fhir.model.dstu2.valueset.QuantityComparatorEnum;
 import ca.uhn.fhir.model.primitive.DateDt;
 import ca.uhn.fhir.model.primitive.DateTimeDt;
@@ -65,8 +58,10 @@ import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenOrListParam;
 import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@@ -84,6 +79,150 @@ public class FhirResourceDaoTest {
 	private static IFhirResourceDao<Organization> ourOrganizationDao;
 	private static IFhirResourceDao<Patient> ourPatientDao;
 
+	@Test
+	public void testCreateDuplicateIdFails() {
+		String methodName = "testCreateDuplocateIdFailsText";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.setId("Patient/" + methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+		try {
+			ourPatientDao.create(p);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertThat(e.getMessage(), containsString("Can not create entity with ID[" + methodName + "], a resource with this ID already exists"));
+		}
+	}
+
+	@Test
+	public void testUpdateByUrl() {
+		String methodName = "testUpdateByUrl";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+		
+		ourPatientDao.update(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		p = ourPatientDao.read(id.toVersionless());
+		assertThat(p.getId().toVersionless().toString(), not(containsString("test")));
+		assertEquals(id.toVersionless(), p.getId().toVersionless());
+		assertNotEquals(id, p.getId());
+		assertThat(p.getId().toString(), endsWith("/_history/2"));
+
+	}
+
+	
+	@Test
+	public void testCreateNumericIdFails() {
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue("testCreateNumericIdFails");
+		p.addName().addFamily("Hello");
+		p.setId("Patient/123");
+		try {
+			ourPatientDao.create(p);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("Can not create entity with ID[123], this server does not allow clients to assign numeric IDs"));
+		}
+	}
+
+	
+	@Test
+	public void testDeleteWithMatchUrl() {
+		String methodName = "testDeleteWithMatchUrl";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		Bundle request = new Bundle();
+		request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		ourPatientDao.deleteByUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		try {
+			ourPatientDao.read(id.toVersionless());
+			fail();
+		} catch (ResourceGoneException e) {
+			// ok
+		}
+
+		try {
+			ourPatientDao.read(new IdDt("Patient/" + methodName));
+			fail();
+		} catch (ResourceNotFoundException e) {
+			// ok
+		}
+
+		IBundleProvider history = ourPatientDao.history(id, null);
+		assertEquals(2, history.size());
+		
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(0, 0).get(0)));
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(0, 0).get(0)).getValue());
+		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(1,1).get(0)));
+		
+	}
+
+	
+	@Test
+	public void testCreateWithIfNoneExist() {
+		String methodName = "testCreateWithIfNoneExist";
+		MethodOutcome results;
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.setId("Patient/" + methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+		results = ourPatientDao.create(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
+		assertEquals(id.getIdPart(), results.getId().getIdPart());
+		assertFalse(results.getCreated().booleanValue());
+
+		// Now create a second one
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName + "DOESNTEXIST");
+		results = ourPatientDao.create(p, "Patient?identifier=urn%3Asystem%7C" + methodName + "DOESNTEXIST");
+		assertNotEquals(id.getIdPart(), results.getId().getIdPart());
+		assertTrue(results.getCreated().booleanValue());
+
+		// Now try to create one with the original match URL and it should fail
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+		try {
+			ourPatientDao.create(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
+			fail();
+		} catch (PreconditionFailedException e) {
+			assertThat(e.getMessage(), containsString("Failed to CREATE"));
+		}
+
+	}
+
 	@Test
 	public void testChoiceParamConcept() {
 		Observation o1 = new Observation();
@@ -216,7 +355,7 @@ public class FhirResourceDaoTest {
 	public void testDatePeriodParamStartAndEnd() {
 		{
 			Encounter enc = new Encounter();
-			enc.addIdentifier().setSystem("testDatePeriodParam").setValue( "03");
+			enc.addIdentifier().setSystem("testDatePeriodParam").setValue("03");
 			enc.getPeriod().getStartElement().setValueAsString("2001-01-02");
 			enc.getPeriod().getEndElement().setValueAsString("2001-01-03");
 			ourEncounterDao.create(enc);
@@ -329,7 +468,7 @@ public class FhirResourceDaoTest {
 		{
 			Patient patient = ourPatientDao.read(id2);
 			patient.addIdentifier().setSystem("ZZZZZZZ").setValue("ZZZZZZZZZ");
-			id2b = ourPatientDao.update(patient, id2).getId();
+			id2b = ourPatientDao.update(patient).getId();
 		}
 		ourLog.info("ID1:{}   ID2:{}   ID2b:{}", new Object[] { id1, id2, id2b });
 
@@ -373,7 +512,7 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testIdParam() {
 		Patient patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system").setValue( "001");
+		patient.addIdentifier().setSystem("urn:system").setValue("001");
 		patient.addName().addFamily("Tester").addGiven("Joe");
 
 		MethodOutcome outcome = ourPatientDao.create(patient);
@@ -484,11 +623,11 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testPersistResourceLink() {
 		Patient patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system").setValue( "testPersistResourceLink01");
+		patient.addIdentifier().setSystem("urn:system").setValue("testPersistResourceLink01");
 		IdDt patientId01 = ourPatientDao.create(patient).getId();
 
 		Patient patient02 = new Patient();
-		patient02.addIdentifier().setSystem("urn:system").setValue( "testPersistResourceLink02");
+		patient02.addIdentifier().setSystem("urn:system").setValue("testPersistResourceLink02");
 		IdDt patientId02 = ourPatientDao.create(patient02).getId();
 
 		Observation obs01 = new Observation();
@@ -524,7 +663,7 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testPersistSearchParamDate() {
 		Patient patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system").setValue( "001");
+		patient.addIdentifier().setSystem("urn:system").setValue("001");
 		patient.setBirthDate(new DateDt("2001-01-01"));
 
 		ourPatientDao.create(patient);
@@ -576,7 +715,7 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testPersistSearchParams() {
 		Patient patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system").setValue( "001testPersistSearchParams");
+		patient.addIdentifier().setSystem("urn:system").setValue("001testPersistSearchParams");
 		patient.getGenderElement().setValueAsEnum(AdministrativeGenderEnum.MALE);
 		patient.addName().addFamily("Tester").addGiven("JoetestPersistSearchParams");
 
@@ -641,20 +780,20 @@ public class FhirResourceDaoTest {
 		assertTrue(patients.size() >= 2);
 	}
 
-	
 	@Test
 	public void testHistoryByForcedId() {
 		IdDt idv1;
 		IdDt idv2;
 		{
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "testHistoryByForcedId");
+			patient.addIdentifier().setSystem("urn:system").setValue("testHistoryByForcedId");
 			patient.addName().addFamily("Tester").addGiven("testHistoryByForcedId");
 			patient.setId("Patient/testHistoryByForcedId");
 			idv1 = ourPatientDao.create(patient).getId();
 
 			patient.addName().addFamily("Tester").addGiven("testHistoryByForcedIdName2");
-			idv2 = ourPatientDao.update(patient, idv1.toUnqualifiedVersionless()).getId();
+			patient.setId(patient.getId().toUnqualifiedVersionless());
+			idv2 = ourPatientDao.update(patient).getId();
 		}
 
 		List<Patient> patients = toList(ourPatientDao.history(idv1.toVersionless(), null));
@@ -676,7 +815,7 @@ public class FhirResourceDaoTest {
 		IdDt id2;
 		{
 			Organization patient = new Organization();
-			patient.addIdentifier().setSystem("urn:system").setValue( "001");
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			id2 = ourOrganizationDao.create(patient).getId();
 		}
 
@@ -769,14 +908,14 @@ public class FhirResourceDaoTest {
 		IdDt id1;
 		{
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "001");
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addFamily("testSearchNameParam01Fam").addGiven("testSearchNameParam01Giv");
 			ResourceMetadataKeyEnum.TITLE.put(patient, "P1TITLE");
 			id1 = ourPatientDao.create(patient).getId();
 		}
 		{
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "002");
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
 			patient.addName().addFamily("testSearchNameParam02Fam").addGiven("testSearchNameParam02Giv");
 			ourPatientDao.create(patient);
 		}
@@ -816,12 +955,12 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testSearchNumberParam() {
 		Encounter e1 = new Encounter();
-		e1.addIdentifier().setSystem("foo").setValue( "testSearchNumberParam01");
+		e1.addIdentifier().setSystem("foo").setValue("testSearchNumberParam01");
 		e1.getLength().setSystem(BaseFhirDao.UCUM_NS).setCode("min").setValue(4.0 * 24 * 60);
 		IdDt id1 = ourEncounterDao.create(e1).getId();
 
 		Encounter e2 = new Encounter();
-		e2.addIdentifier().setSystem("foo").setValue( "testSearchNumberParam02");
+		e2.addIdentifier().setSystem("foo").setValue("testSearchNumberParam02");
 		e2.getLength().setSystem(BaseFhirDao.UCUM_NS).setCode("year").setValue(2.0);
 		IdDt id2 = ourEncounterDao.create(e2).getId();
 		{
@@ -843,13 +982,13 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testSearchResourceLinkWithChain() {
 		Patient patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system").setValue( "testSearchResourceLinkWithChainXX");
+		patient.addIdentifier().setSystem("urn:system").setValue("testSearchResourceLinkWithChainXX");
-		patient.addIdentifier().setSystem("urn:system").setValue( "testSearchResourceLinkWithChain01");
+		patient.addIdentifier().setSystem("urn:system").setValue("testSearchResourceLinkWithChain01");
 		IdDt patientId01 = ourPatientDao.create(patient).getId();
 
 		Patient patient02 = new Patient();
-		patient02.addIdentifier().setSystem("urn:system").setValue( "testSearchResourceLinkWithChainXX");
+		patient02.addIdentifier().setSystem("urn:system").setValue("testSearchResourceLinkWithChainXX");
-		patient02.addIdentifier().setSystem("urn:system").setValue( "testSearchResourceLinkWithChain02");
+		patient02.addIdentifier().setSystem("urn:system").setValue("testSearchResourceLinkWithChain02");
 		IdDt patientId02 = ourPatientDao.create(patient02).getId();
 
 		Observation obs01 = new Observation();
@@ -891,14 +1030,14 @@ public class FhirResourceDaoTest {
 	public void testSearchResourceLinkWithTextLogicalId() {
 		Patient patient = new Patient();
 		patient.setId("testSearchResourceLinkWithTextLogicalId01");
-		patient.addIdentifier().setSystem("urn:system").setValue( "testSearchResourceLinkWithTextLogicalIdXX");
+		patient.addIdentifier().setSystem("urn:system").setValue("testSearchResourceLinkWithTextLogicalIdXX");
-		patient.addIdentifier().setSystem("urn:system").setValue( "testSearchResourceLinkWithTextLogicalId01");
+		patient.addIdentifier().setSystem("urn:system").setValue("testSearchResourceLinkWithTextLogicalId01");
 		IdDt patientId01 = ourPatientDao.create(patient).getId();
 
 		Patient patient02 = new Patient();
 		patient02.setId("testSearchResourceLinkWithTextLogicalId02");
-		patient02.addIdentifier().setSystem("urn:system").setValue( "testSearchResourceLinkWithTextLogicalIdXX");
+		patient02.addIdentifier().setSystem("urn:system").setValue("testSearchResourceLinkWithTextLogicalIdXX");
-		patient02.addIdentifier().setSystem("urn:system").setValue( "testSearchResourceLinkWithTextLogicalId02");
+		patient02.addIdentifier().setSystem("urn:system").setValue("testSearchResourceLinkWithTextLogicalId02");
 		IdDt patientId02 = ourPatientDao.create(patient02).getId();
 
 		Observation obs01 = new Observation();
@@ -981,13 +1120,13 @@ public class FhirResourceDaoTest {
 	public void testSearchStringParam() {
 		{
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "001");
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addFamily("Tester_testSearchStringParam").addGiven("Joe");
 			ourPatientDao.create(patient);
 		}
 		{
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "002");
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
 			patient.addName().addFamily("Tester_testSearchStringParam").addGiven("John");
 			ourPatientDao.create(patient);
 		}
@@ -1009,7 +1148,7 @@ public class FhirResourceDaoTest {
 		{
 			Patient patient = new Patient();
 			patient.getLanguage().setValue("en_CA");
-			patient.addIdentifier().setSystem("urn:system").setValue( "001");
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addFamily("testSearchLanguageParam").addGiven("Joe");
 			id1 = ourPatientDao.create(patient).getId();
 		}
@@ -1017,7 +1156,7 @@ public class FhirResourceDaoTest {
 		{
 			Patient patient = new Patient();
 			patient.getLanguage().setValue("en_US");
-			patient.addIdentifier().setSystem("urn:system").setValue( "002");
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
 			patient.addName().addFamily("testSearchLanguageParam").addGiven("John");
 			id2 = ourPatientDao.create(patient).getId();
 		}
@@ -1048,13 +1187,13 @@ public class FhirResourceDaoTest {
 	public void testSearchStringParamWithNonNormalized() {
 		{
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "001");
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addGiven("testSearchStringParamWithNonNormalized_h\u00F6ra");
 			ourPatientDao.create(patient);
 		}
 		{
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "002");
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
 			patient.addName().addGiven("testSearchStringParamWithNonNormalized_HORA");
 			ourPatientDao.create(patient);
 		}
@@ -1081,7 +1220,7 @@ public class FhirResourceDaoTest {
 		ourPatientDao.create(patient);
 
 		patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system").setValue( "testSearchTokenParam002");
+		patient.addIdentifier().setSystem("urn:system").setValue("testSearchTokenParam002");
 		patient.addName().addFamily("Tester").addGiven("testSearchTokenParam2");
 		ourPatientDao.create(patient);
 
@@ -1147,14 +1286,14 @@ public class FhirResourceDaoTest {
 			IdDt orgId = ourOrganizationDao.create(org).getId();
 
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "001");
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addFamily("Tester_testSearchWithIncludes_P1").addGiven("Joe");
 			patient.getManagingOrganization().setReference(orgId);
 			ourPatientDao.create(patient);
 		}
 		{
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "002");
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
 			patient.addName().addFamily("Tester_testSearchWithIncludes_P2").addGiven("John");
 			ourPatientDao.create(patient);
 		}
@@ -1221,7 +1360,7 @@ public class FhirResourceDaoTest {
 	public void testStoreUtf8Characters() throws Exception {
 		Organization org = new Organization();
 		org.setName("測試醫院");
-		org.addIdentifier().setSystem("urn:system").setValue( "testStoreUtf8Characters_01");
+		org.addIdentifier().setSystem("urn:system").setValue("testStoreUtf8Characters_01");
 		IdDt orgId = ourOrganizationDao.create(org).getId();
 
 		Organization returned = ourOrganizationDao.read(orgId);
@@ -1244,14 +1383,14 @@ public class FhirResourceDaoTest {
 			assertThat(orgId.getValue(), endsWith("Organization/testSearchWithIncludesThatHaveTextId_id1/_history/1"));
 
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "001");
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addFamily("Tester_testSearchWithIncludesThatHaveTextId_P1").addGiven("Joe");
 			patient.getManagingOrganization().setReference(orgId);
 			ourPatientDao.create(patient);
 		}
 		{
 			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue( "002");
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
 			patient.addName().addFamily("Tester_testSearchWithIncludesThatHaveTextId_P2").addGiven("John");
 			ourPatientDao.create(patient);
 		}
@@ -1290,23 +1429,23 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testSort() {
 		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue( "testSort001");
+		p.addIdentifier().setSystem("urn:system").setValue("testSort001");
 		p.addName().addFamily("testSortF1").addGiven("testSortG1");
 		IdDt id1 = ourPatientDao.create(p).getId().toUnqualifiedVersionless();
 
 		// Create out of order
 		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue( "testSort001");
+		p.addIdentifier().setSystem("urn:system").setValue("testSort001");
 		p.addName().addFamily("testSortF3").addGiven("testSortG3");
 		IdDt id3 = ourPatientDao.create(p).getId().toUnqualifiedVersionless();
 
 		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue( "testSort001");
+		p.addIdentifier().setSystem("urn:system").setValue("testSort001");
 		p.addName().addFamily("testSortF2").addGiven("testSortG2");
 		IdDt id2 = ourPatientDao.create(p).getId().toUnqualifiedVersionless();
 
 		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue( "testSort001");
+		p.addIdentifier().setSystem("urn:system").setValue("testSort001");
 		IdDt id4 = ourPatientDao.create(p).getId().toUnqualifiedVersionless();
 
 		SearchParameterMap pm = new SearchParameterMap();
@@ -1367,7 +1506,7 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testTagsWithCreateAndReadAndSearch() {
 		Patient patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system").setValue( "testTagsWithCreateAndReadAndSearch");
+		patient.addIdentifier().setSystem("urn:system").setValue("testTagsWithCreateAndReadAndSearch");
 		patient.addName().addFamily("Tester").addGiven("Joe");
 		TagList tagList = new TagList();
 		tagList.addTag(null, "Dog", "Puppies");
@@ -1458,7 +1597,7 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testUpdateAndGetHistoryResource() throws InterruptedException {
 		Patient patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system").setValue( "001");
+		patient.addIdentifier().setSystem("urn:system").setValue("001");
 		patient.addName().addFamily("Tester").addGiven("Joe");
 
 		MethodOutcome outcome = ourPatientDao.create(patient);
@@ -1477,7 +1616,7 @@ public class FhirResourceDaoTest {
 		Thread.sleep(1000);
 
 		retrieved.getIdentifierFirstRep().setValue("002");
-		MethodOutcome outcome2 = ourPatientDao.update(retrieved, outcome.getId());
+		MethodOutcome outcome2 = ourPatientDao.update(retrieved);
 		assertEquals(outcome.getId().getIdPart(), outcome2.getId().getIdPart());
 		assertNotEquals(outcome.getId().getVersionIdPart(), outcome2.getId().getVersionIdPart());
 
@@ -1521,12 +1660,12 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testUpdateMaintainsSearchParams() throws InterruptedException {
 		Patient p1 = new Patient();
-		p1.addIdentifier().setSystem("urn:system").setValue( "testUpdateMaintainsSearchParamsAAA");
+		p1.addIdentifier().setSystem("urn:system").setValue("testUpdateMaintainsSearchParamsAAA");
 		p1.addName().addFamily("Tester").addGiven("testUpdateMaintainsSearchParamsAAA");
 		IdDt p1id = ourPatientDao.create(p1).getId();
 
 		Patient p2 = new Patient();
-		p2.addIdentifier().setSystem("urn:system").setValue( "testUpdateMaintainsSearchParamsBBB");
+		p2.addIdentifier().setSystem("urn:system").setValue("testUpdateMaintainsSearchParamsBBB");
 		p2.addName().addFamily("Tester").addGiven("testUpdateMaintainsSearchParamsBBB");
 		ourPatientDao.create(p2).getId();
 
@@ -1536,7 +1675,7 @@ public class FhirResourceDaoTest {
 
 		// Update the name
 		p1.getNameFirstRep().getGivenFirstRep().setValue("testUpdateMaintainsSearchParamsBBB");
-		MethodOutcome update2 = ourPatientDao.update(p1, p1id);
+		MethodOutcome update2 = ourPatientDao.update(p1);
 		IdDt p1id2 = update2.getId();
 
 		ids = ourPatientDao.searchForIds(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsAAA"));
@@ -1557,21 +1696,23 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testUpdateRejectsInvalidTypes() throws InterruptedException {
 		Patient p1 = new Patient();
-		p1.addIdentifier().setSystem("urn:system").setValue( "testUpdateRejectsInvalidTypes");
+		p1.addIdentifier().setSystem("urn:system").setValue("testUpdateRejectsInvalidTypes");
 		p1.addName().addFamily("Tester").addGiven("testUpdateRejectsInvalidTypes");
 		IdDt p1id = ourPatientDao.create(p1).getId();
 
 		Organization p2 = new Organization();
 		p2.getNameElement().setValue("testUpdateRejectsInvalidTypes");
 		try {
-			ourOrganizationDao.update(p2, new IdDt("Organization/" + p1id.getIdPart()));
+			p2.setId(new IdDt("Organization/" + p1id.getIdPart()));
+			ourOrganizationDao.update(p2);
 			fail();
 		} catch (UnprocessableEntityException e) {
 			// good
 		}
 
 		try {
-			ourOrganizationDao.update(p2, new IdDt("Patient/" + p1id.getIdPart()));
+			p2.setId(new IdDt("Patient/" + p1id.getIdPart()));
+			ourOrganizationDao.update(p2);
 			fail();
 		} catch (UnprocessableEntityException e) {
 			// good
@@ -1589,7 +1730,7 @@ public class FhirResourceDaoTest {
 		assertEquals("ABABA", p1id.getIdPart());
 
 		Patient p2 = new Patient();
-		p2.addIdentifier().setSystem("urn:system").setValue( "testUpdateRejectsIdWhichPointsToForcedId02");
+		p2.addIdentifier().setSystem("urn:system").setValue("testUpdateRejectsIdWhichPointsToForcedId02");
 		p2.addName().addFamily("Tester").addGiven("testUpdateRejectsIdWhichPointsToForcedId02");
 		IdDt p2id = ourPatientDao.create(p2).getId();
 		long p1longId = p2id.getIdPartAsLong() - 1;
@@ -1602,7 +1743,8 @@ public class FhirResourceDaoTest {
 		}
 
 		try {
-			ourPatientDao.update(p1, new IdDt("Patient/" + p1longId));
+			p1.setId(new IdDt("Patient/" + p1longId));
+			ourPatientDao.update(p1);
 			fail();
 		} catch (ResourceNotFoundException e) {
 			// good
@@ -1613,13 +1755,14 @@ public class FhirResourceDaoTest {
 	@Test
 	public void testReadForcedIdVersionHistory() throws InterruptedException {
 		Patient p1 = new Patient();
-		p1.addIdentifier().setSystem("urn:system").setValue( "testReadVorcedIdVersionHistory01");
+		p1.addIdentifier().setSystem("urn:system").setValue("testReadVorcedIdVersionHistory01");
 		p1.setId("testReadVorcedIdVersionHistory");
 		IdDt p1id = ourPatientDao.create(p1).getId();
 		assertEquals("testReadVorcedIdVersionHistory", p1id.getIdPart());
 
-		p1.addIdentifier().setSystem("urn:system").setValue( "testReadVorcedIdVersionHistory02");
+		p1.addIdentifier().setSystem("urn:system").setValue("testReadVorcedIdVersionHistory02");
-		IdDt p1idv2 = ourPatientDao.update(p1, p1id).getId();
+		p1.setId(p1id);
+		IdDt p1idv2 = ourPatientDao.update(p1).getId();
 		assertEquals("testReadVorcedIdVersionHistory", p1idv2.getIdPart());
 
 		assertNotEquals(p1id.getValue(), p1idv2.getValue());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu1Test.java

@@ -0,0 +1,414 @@
+package ca.uhn.fhir.jpa.dao;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
+
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.List;
+import java.util.Map;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.springframework.context.support.ClassPathXmlApplicationContext;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.TagList;
+import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu.resource.Location;
+import ca.uhn.fhir.model.dstu.resource.Observation;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+
+public class FhirSystemDaoDstu1Test {
+
+	private static ClassPathXmlApplicationContext ourCtx;
+	private static FhirContext ourFhirContext;
+	private static IFhirResourceDao<Location> ourLocationDao;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu1Test.class);
+	private static IFhirResourceDao<Observation> ourObservationDao;
+	private static IFhirResourceDao<Patient> ourPatientDao;
+	private static IFhirSystemDao<List<IResource>> ourSystemDao;
+
+	@Test
+	public void testGetResourceCounts() {
+		Observation obs = new Observation();
+		obs.getName().addCoding().setSystem("urn:system").setCode("testGetResourceCountsO01");
+		ourObservationDao.create(obs);
+
+		Map<String, Long> oldCounts = ourSystemDao.getResourceCounts();
+
+		Patient patient = new Patient();
+		patient.addIdentifier().setSystem("urn:system").setValue("testGetResourceCountsP01");
+		patient.addName().addFamily("Tester").addGiven("Joe");
+		ourPatientDao.create(patient);
+
+		Map<String, Long> newCounts = ourSystemDao.getResourceCounts();
+
+		if (oldCounts.containsKey("Patient")) {
+			assertEquals(oldCounts.get("Patient") + 1, (long) newCounts.get("Patient"));
+		} else {
+			assertEquals(1L, (long) newCounts.get("Patient"));
+		}
+
+		assertEquals((long) oldCounts.get("Observation"), (long) newCounts.get("Observation"));
+
+	}
+
+	@Test
+	public void testHistory() throws Exception {
+		Date start = new Date();
+		Thread.sleep(10);
+
+		Patient patient = new Patient();
+		patient.addIdentifier().setSystem("urn:system").setValue("testHistory");
+		patient.addName().addFamily("Tester").addGiven("Joe");
+		IdDt pid = ourPatientDao.create(patient).getId().toVersionless();
+
+		Thread.sleep(10);
+		patient.setId(pid);
+		IdDt newpid = ourPatientDao.update(patient).getId();
+
+		Thread.sleep(10);
+		patient.setId(pid);
+		IdDt newpid2 = ourPatientDao.update(patient).getId();
+
+		Thread.sleep(10);
+		patient.setId(pid);
+		IdDt newpid3 = ourPatientDao.update(patient).getId();
+
+		IBundleProvider values = ourSystemDao.history(start);
+		assertEquals(4, values.size());
+
+		List<IResource> res = values.getResources(0, 4);
+		assertEquals(newpid3, res.get(0).getId());
+		assertEquals(newpid2, res.get(1).getId());
+		assertEquals(newpid, res.get(2).getId());
+		assertEquals(pid.toUnqualifiedVersionless(), res.get(3).getId().toUnqualifiedVersionless());
+
+		Location loc = new Location();
+		loc.getAddress().addLine("AAA");
+		IdDt lid = ourLocationDao.create(loc).getId();
+
+		Location loc2 = new Location();
+		loc2.getAddress().addLine("AAA");
+		ourLocationDao.create(loc2).getId();
+
+		Thread.sleep(2000);
+
+		values = ourLocationDao.history(start);
+		assertEquals(2, values.size());
+
+		values = ourLocationDao.history(lid.getIdPartAsLong(), start);
+		assertEquals(1, values.size());
+
+	}
+
+	@Test
+	public void testPersistWithSimpleLink() {
+		Patient patient = new Patient();
+		patient.setId(new IdDt("Patient/testPersistWithSimpleLinkP01"));
+		patient.addIdentifier().setSystem("urn:system").setValue("testPersistWithSimpleLinkP01");
+		patient.addName().addFamily("Tester").addGiven("Joe");
+
+		Observation obs = new Observation();
+		obs.getName().addCoding().setSystem("urn:system").setCode("testPersistWithSimpleLinkO01");
+		obs.setSubject(new ResourceReferenceDt("Patient/testPersistWithSimpleLinkP01"));
+
+		ourSystemDao.transaction(Arrays.asList((IResource) patient, obs));
+
+		String patientId = (patient.getId().getIdPart());
+		String obsId = (obs.getId().getIdPart());
+
+		// assertThat(patientId, greaterThan(0L));
+		// assertEquals(patientVersion, 1L);
+		// assertThat(obsId, greaterThan(patientId));
+		// assertEquals(obsVersion, 1L);
+
+		// Try to search
+
+		IBundleProvider obsResults = ourObservationDao.search(Observation.SP_NAME, new IdentifierDt("urn:system", "testPersistWithSimpleLinkO01"));
+		assertEquals(1, obsResults.size());
+
+		IBundleProvider patResults = ourPatientDao.search(Patient.SP_IDENTIFIER, new IdentifierDt("urn:system", "testPersistWithSimpleLinkP01"));
+		assertEquals(1, obsResults.size());
+
+		IdDt foundPatientId = patResults.getResources(0, 1).get(0).getId();
+		ResourceReferenceDt subject = obs.getSubject();
+		assertEquals(foundPatientId.getIdPart(), subject.getReference().getIdPart());
+
+		// Update
+
+		patient = (Patient) patResults.getResources(0, 1).get(0);
+		obs = (Observation) obsResults.getResources(0, 1).get(0);
+		patient.addIdentifier().setSystem("urn:system").setValue("testPersistWithSimpleLinkP02");
+		obs.getName().addCoding().setSystem("urn:system").setCode("testPersistWithSimpleLinkO02");
+
+		ourSystemDao.transaction(Arrays.asList((IResource) patient, obs));
+
+		String patientId2 = (patient.getId().getIdPart());
+		String patientVersion2 = (patient.getId().getVersionIdPart());
+		String obsId2 = (obs.getId().getIdPart());
+		String obsVersion2 = (obs.getId().getVersionIdPart());
+
+		assertEquals(patientId, patientId2);
+		assertEquals(patientVersion2, "2");
+		assertEquals(obsId, obsId2);
+		assertEquals(obsVersion2, "2");
+
+	}
+
+	@Test
+	public void testPersistWithUnknownId() {
+		Observation obs = new Observation();
+		obs.getName().addCoding().setSystem("urn:system").setCode("testPersistWithSimpleLinkO01");
+		obs.setSubject(new ResourceReferenceDt("Patient/999998888888"));
+
+		try {
+			ourSystemDao.transaction(Arrays.asList((IResource) obs));
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("Resource Patient/999998888888 not found, specified in path: Observation.subject"));
+		}
+
+		obs = new Observation();
+		obs.getName().addCoding().setSystem("urn:system").setCode("testPersistWithSimpleLinkO01");
+		obs.setSubject(new ResourceReferenceDt("Patient/1.2.3.4"));
+
+		try {
+			ourSystemDao.transaction(Arrays.asList((IResource) obs));
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("Resource Patient/1.2.3.4 not found, specified in path: Observation.subject"));
+		}
+
+	}
+
+	@Test
+	public void testTagOperationss() throws Exception {
+
+		TagList preSystemTl = ourSystemDao.getAllTags();
+
+		TagList tl1 = new TagList();
+		tl1.addTag("testGetAllTagsScheme1", "testGetAllTagsTerm1", "testGetAllTagsLabel1");
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("foo").setValue("testGetAllTags01");
+		ResourceMetadataKeyEnum.TAG_LIST.put(p1, tl1);
+		ourPatientDao.create(p1);
+
+		TagList tl2 = new TagList();
+		tl2.addTag("testGetAllTagsScheme2", "testGetAllTagsTerm2", "testGetAllTagsLabel2");
+		Observation o1 = new Observation();
+		o1.getName().setText("testGetAllTags02");
+		ResourceMetadataKeyEnum.TAG_LIST.put(o1, tl2);
+		IdDt o1id = ourObservationDao.create(o1).getId();
+		assertTrue(o1id.getVersionIdPart() != null);
+
+		TagList postSystemTl = ourSystemDao.getAllTags();
+		assertEquals(preSystemTl.size() + 2, postSystemTl.size());
+		assertEquals("testGetAllTagsLabel1", postSystemTl.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1").getLabel());
+
+		TagList tags = ourPatientDao.getAllResourceTags();
+		assertEquals("testGetAllTagsLabel1", tags.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1").getLabel());
+		assertNull(tags.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
+
+		TagList tags2 = ourObservationDao.getTags(o1id);
+		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
+		assertEquals("testGetAllTagsLabel2", tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2").getLabel());
+
+		o1.getResourceMetadata().remove(ResourceMetadataKeyEnum.TAG_LIST);
+		o1.setId(o1id);
+		IdDt o1id2 = ourObservationDao.update(o1).getId();
+		assertTrue(o1id2.getVersionIdPart() != null);
+
+		tags2 = ourObservationDao.getTags(o1id);
+		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
+		assertEquals("testGetAllTagsLabel2", tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2").getLabel());
+
+		tags2 = ourObservationDao.getTags(o1id2);
+		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
+		assertNotNull(tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
+
+		/*
+		 * Remove a tag from a version
+		 */
+
+		ourObservationDao.removeTag(o1id2, "testGetAllTagsScheme2", "testGetAllTagsTerm2");
+		tags2 = ourObservationDao.getTags(o1id2);
+		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
+		assertNull(tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
+
+		tags2 = ourObservationDao.getTags(o1id);
+		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
+		assertNotNull(tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
+
+		/*
+		 * Add a tag
+		 */
+		ourObservationDao.addTag(o1id2, "testGetAllTagsScheme3", "testGetAllTagsTerm3", "testGetAllTagsLabel3");
+		tags2 = ourObservationDao.getTags(o1id2);
+		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
+		assertNull(tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
+		assertNotNull(tags2.getTag("testGetAllTagsScheme3", "testGetAllTagsTerm3"));
+		assertEquals("testGetAllTagsLabel3", tags2.getTag("testGetAllTagsScheme3", "testGetAllTagsTerm3").getLabel());
+
+		tags2 = ourObservationDao.getTags(o1id);
+		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
+		assertNotNull(tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
+
+	}
+
+
+	@Test(expected = InvalidRequestException.class)
+	public void testTransactionFailsWithDuplicateIds() {
+		Patient patient1 = new Patient();
+		patient1.setId(new IdDt("Patient/testTransactionFailsWithDusplicateIds"));
+		patient1.addIdentifier().setSystem("urn:system").setValue("testPersistWithSimpleLinkP01");
+
+		Patient patient2 = new Patient();
+		patient2.setId(new IdDt("Patient/testTransactionFailsWithDusplicateIds"));
+		patient2.addIdentifier().setSystem("urn:system").setValue("testPersistWithSimpleLinkP02");
+
+		ourSystemDao.transaction(Arrays.asList((IResource) patient1, patient2));
+	}
+
+	@Test
+ 	public void testTransactionFromBundle() throws Exception {
+
+		InputStream bundleRes = FhirSystemDaoDstu1Test.class.getResourceAsStream("/bundle-dstu1.xml");
+		Bundle bundle = ourFhirContext.newXmlParser().parseBundle(new InputStreamReader(bundleRes));
+		List<IResource> res = bundle.toListOfResources();
+
+		ourSystemDao.transaction(res);
+
+		Patient p1 = (Patient) res.get(0);
+		String id = p1.getId().getValue();
+		ourLog.info("ID: {}", id);
+		assertThat(id, not(equalToIgnoringCase("74635")));
+		assertThat(id, not(equalToIgnoringCase("")));
+	}
+
+
+	/**
+	 * Issue #55
+	 */
+	@Test
+	public void testTransactionWithCidIds() throws Exception {
+		List<IResource> res = new ArrayList<IResource>();
+
+		Patient p1 = new Patient();
+		p1.setId("cid:patient1");
+		p1.addIdentifier().setSystem("system").setValue("testTransactionWithCidIds01");
+		res.add(p1);
+
+		Observation o1 = new Observation();
+		o1.setId("cid:observation1");
+		o1.getIdentifier().setSystem("system").setValue("testTransactionWithCidIds02");
+		o1.setSubject(new ResourceReferenceDt("Patient/cid:patient1"));
+		res.add(o1);
+
+		Observation o2 = new Observation();
+		o2.setId("cid:observation2");
+		o2.getIdentifier().setSystem("system").setValue("testTransactionWithCidIds03");
+		o2.setSubject(new ResourceReferenceDt("Patient/cid:patient1"));
+		res.add(o2);
+
+		ourSystemDao.transaction(res);
+
+		assertTrue(p1.getId().getValue(), p1.getId().getIdPart().matches("^[0-9]+$"));
+		assertTrue(o1.getId().getValue(), o1.getId().getIdPart().matches("^[0-9]+$"));
+		assertTrue(o2.getId().getValue(), o2.getId().getIdPart().matches("^[0-9]+$"));
+
+		assertThat(o1.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
+		assertThat(o2.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
+
+	}
+
+	@Test
+	public void testTransactionWithDelete() throws Exception {
+
+		/*
+		 * Create 3
+		 */
+
+		List<IResource> res;
+		res = new ArrayList<IResource>();
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
+		res.add(p1);
+
+		Patient p2 = new Patient();
+		p2.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
+		res.add(p2);
+
+		Patient p3 = new Patient();
+		p3.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
+		res.add(p3);
+
+		ourSystemDao.transaction(res);
+
+		/*
+		 * Verify
+		 */
+
+		IBundleProvider results = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testTransactionWithDelete"));
+		assertEquals(3, results.size());
+
+		/*
+		 * Now delete 2
+		 */
+
+		res = new ArrayList<IResource>();
+		List<IResource> existing = results.getResources(0, 3);
+
+		p1 = new Patient();
+		p1.setId(existing.get(0).getId());
+		ResourceMetadataKeyEnum.DELETED_AT.put(p1, InstantDt.withCurrentTime());
+		res.add(p1);
+
+		p2 = new Patient();
+		p2.setId(existing.get(1).getId());
+		ResourceMetadataKeyEnum.DELETED_AT.put(p2, InstantDt.withCurrentTime());
+		res.add(p2);
+
+		ourSystemDao.transaction(res);
+
+		/*
+		 * Verify
+		 */
+
+		IBundleProvider results2 = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testTransactionWithDelete"));
+		assertEquals(1, results2.size());
+		List<IResource> existing2 = results2.getResources(0, 1);
+		assertEquals(existing2.get(0).getId(), existing.get(2).getId());
+
+	}
+
+	@AfterClass
+	public static void afterClass() {
+		ourCtx.close();
+	}
+
+	@SuppressWarnings("unchecked")
+	@BeforeClass
+	public static void beforeClass() {
+		ourCtx = new ClassPathXmlApplicationContext("hapi-fhir-server-resourceproviders-dstu1.xml", "fhir-jpabase-spring-test-config.xml");
+		ourFhirContext = ourCtx.getBean(FhirContext.class);
+		ourPatientDao = ourCtx.getBean("myPatientDaoDstu1", IFhirResourceDao.class);
+		ourObservationDao = ourCtx.getBean("myObservationDaoDstu1", IFhirResourceDao.class);
+		ourLocationDao = ourCtx.getBean("myLocationDaoDstu1", IFhirResourceDao.class);
+		ourSystemDao = ourCtx.getBean("mySystemDaoDstu1", IFhirSystemDao.class);
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2Test.java

@@ -0,0 +1,681 @@
+package ca.uhn.fhir.jpa.dao;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
+
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.List;
+import java.util.Map;
+
+import org.hamcrest.Matchers;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.springframework.context.support.ClassPathXmlApplicationContext;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.TagList;
+import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
+import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
+import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu2.resource.Location;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
+import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.valueset.BundleEntryTransactionOperationEnum;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.rest.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+
+public class FhirSystemDaoDstu2Test {
+
+	private static ClassPathXmlApplicationContext ourCtx;
+	private static FhirContext ourFhirContext;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu2Test.class);
+	private static IFhirResourceDao<Patient> ourPatientDao;
+	private static IFhirSystemDao<Bundle> ourSystemDao;
+	private static IFhirResourceDao<Observation> ourObservationDao;
+
+	@Test
+	public void testTransactionCreateMatchUrlWithOneMatch() {
+		String methodName = "testTransactionCreateMatchUrlWithOneMatch";
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.setId("Patient/" + methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+		request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.POST).setIfNoneExist("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		Observation o = new Observation();
+		o.getName().setText("Some Observation");
+		o.getSubject().setReference("Patient/" + methodName);
+		request.addEntry().setResource(o).getTransaction().setMethod(HTTPVerbEnum.POST);
+
+		Bundle resp = ourSystemDao.transaction(request);
+		assertEquals(3, resp.getEntry().size());
+
+		Entry respEntry = resp.getEntry().get(1);
+		assertEquals(Constants.STATUS_HTTP_200_OK + "", respEntry.getTransactionResponse().getStatus());
+		assertThat(respEntry.getTransactionResponse().getLocation(), endsWith("Patient/" + id.getIdPart() + "/_history/1"));
+		assertEquals("1", respEntry.getTransactionResponse().getEtag().get(0).getValue());
+
+		respEntry = resp.getEntry().get(2);
+		assertEquals(Constants.STATUS_HTTP_201_CREATED + "", respEntry.getTransactionResponse().getStatus());
+		assertThat(respEntry.getTransactionResponse().getLocation(), containsString("Observation/"));
+		assertThat(respEntry.getTransactionResponse().getLocation(), endsWith("/_history/1"));
+		assertEquals("1", respEntry.getTransactionResponse().getEtag().get(0).getValue());
+
+		o = (Observation) ourObservationDao.read(new IdDt(respEntry.getTransactionResponse().getLocationElement()));
+		assertEquals(id.toVersionless(), o.getSubject().getReference());
+		assertEquals("1", o.getId().getVersionIdPart());
+
+	}
+
+	
+	@Test
+	public void testTransactionReadAndSearch() {
+		String methodName = "testTransactionReadAndSearch";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.setId("Patient/" + methodName);
+		IdDt idv1 = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got id: {}", idv1);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Family Name");
+		p.setId("Patient/" + methodName);
+		IdDt idv2 = ourPatientDao.update(p).getId();
+		ourLog.info("Updated patient, got id: {}", idv2);
+
+		Bundle request = new Bundle();
+		request.addEntry().getTransaction().setMethod(HTTPVerbEnum.GET).setUrl(idv1.toUnqualifiedVersionless().getValue());
+		request.addEntry().getTransaction().setMethod(HTTPVerbEnum.GET).setUrl(idv1.toUnqualified().getValue());
+		request.addEntry().getTransaction().setMethod(HTTPVerbEnum.GET).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+		
+		Bundle resp = ourSystemDao.transaction(request);
+
+		assertEquals(4, resp.getEntry().size());
+		
+		Entry nextEntry;
+		
+		nextEntry = resp.getEntry().get(1);
+		assertEquals(Patient.class, nextEntry.getResource().getClass());
+		assertEquals(idv2.toUnqualified(), nextEntry.getResource().getId().toUnqualified());
+
+		nextEntry = resp.getEntry().get(2);
+		assertEquals(Patient.class, nextEntry.getResource().getClass());
+		assertEquals(idv1.toUnqualified(), nextEntry.getResource().getId().toUnqualified());
+
+		nextEntry = resp.getEntry().get(3);
+		assertEquals(Bundle.class, nextEntry.getResource().getClass());
+		
+		Bundle respBundle = (Bundle)nextEntry.getResource();
+		assertEquals(1, respBundle.getTotal().intValue());
+	}
+
+	
+	
+	@Test
+	public void testTransactionCreateMatchUrlWithTwoMatch() {
+		String methodName = "testTransactionCreateMatchUrlWithTwoMatch";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		Bundle request = new Bundle();
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+		request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.POST).setIfNoneExist("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		Observation o = new Observation();
+		o.getName().setText("Some Observation");
+		o.getSubject().setReference("Patient/" + methodName);
+		request.addEntry().setResource(o).getTransaction().setMethod(HTTPVerbEnum.POST);
+
+		try {
+			ourSystemDao.transaction(request);
+			fail();
+		} catch (PreconditionFailedException e) {
+			assertThat(e.getMessage(), containsString("with match URL \"Patient"));
+		}
+	}
+
+	@Test
+	public void testTransactionCreateMatchUrlWithZeroMatch() {
+		String methodName = "testTransactionCreateMatchUrlWithZeroMatch";
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+		request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.POST).setIfNoneExist("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		Observation o = new Observation();
+		o.getName().setText("Some Observation");
+		o.getSubject().setReference("Patient/" + methodName);
+		request.addEntry().setResource(o).getTransaction().setMethod(HTTPVerbEnum.POST);
+
+		Bundle resp = ourSystemDao.transaction(request);
+		assertEquals(3, resp.getEntry().size());
+
+		Entry respEntry = resp.getEntry().get(1);
+		assertEquals(Constants.STATUS_HTTP_201_CREATED + "", respEntry.getTransactionResponse().getStatus());
+		String patientId = respEntry.getTransactionResponse().getLocation();
+		assertThat(patientId, not(endsWith("Patient/" + methodName + "/_history/1")));
+		assertThat(patientId, (endsWith("/_history/1")));
+		assertThat(patientId, (containsString("Patient/")));
+		assertEquals("1", respEntry.getTransactionResponse().getEtag().get(0).getValue());
+
+		respEntry = resp.getEntry().get(2);
+		assertEquals(Constants.STATUS_HTTP_201_CREATED + "", respEntry.getTransactionResponse().getStatus());
+		assertThat(respEntry.getTransactionResponse().getLocation(), containsString("Observation/"));
+		assertThat(respEntry.getTransactionResponse().getLocation(), endsWith("/_history/1"));
+		assertEquals("1", respEntry.getTransactionResponse().getEtag().get(0).getValue());
+
+		o = (Observation) ourObservationDao.read(new IdDt(respEntry.getTransactionResponse().getLocationElement()));
+		assertEquals(new IdDt(patientId).toUnqualifiedVersionless(), o.getSubject().getReference());
+	}
+
+	@Test
+	public void testTransactionCreateNoMatchUrl() {
+		String methodName = "testTransactionCreateNoMatchUrl";
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.setId("Patient/" + methodName);
+		request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.POST).setIfNoneExist("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		Bundle resp = ourSystemDao.transaction(request);
+		assertEquals(2, resp.getEntry().size());
+
+		Entry respEntry = resp.getEntry().get(1);
+		assertEquals(Constants.STATUS_HTTP_201_CREATED + "", respEntry.getTransactionResponse().getStatus());
+		String patientId = respEntry.getTransactionResponse().getLocation();
+		assertThat(patientId, not(containsString("test")));
+	}
+
+	@Test
+	public void testTransactionDeleteMatchUrlWithOneMatch() {
+		String methodName = "testTransactionDeleteMatchUrlWithOneMatch";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		Bundle request = new Bundle();
+		request.addEntry().getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		Bundle resp = ourSystemDao.transaction(request);
+		assertEquals(2, resp.getEntry().size());
+
+		Entry nextEntry = resp.getEntry().get(1);
+		assertEquals(Constants.STATUS_HTTP_204_NO_CONTENT + "", nextEntry.getTransactionResponse().getStatus());
+
+		try {
+			ourPatientDao.read(id.toVersionless());
+			fail();
+		} catch (ResourceGoneException e) {
+			// ok
+		}
+
+		try {
+			ourPatientDao.read(new IdDt("Patient/" + methodName));
+			fail();
+		} catch (ResourceNotFoundException e) {
+			// ok
+		}
+
+		IBundleProvider history = ourPatientDao.history(id, null);
+		assertEquals(2, history.size());
+
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(0, 0).get(0)));
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(0, 0).get(0)).getValue());
+		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(1, 1).get(0)));
+
+	}
+
+	@Test
+	public void testTransactionDeleteMatchUrlWithTwoMatch() {
+		String methodName = "testTransactionDeleteMatchUrlWithTwoMatch";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+
+		Bundle request = new Bundle();
+		request.addEntry().getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		try {
+			ourSystemDao.transaction(request);
+			fail();
+		} catch (ResourceNotFoundException e) {
+			assertThat(e.getMessage(), containsString("resource with match URL \"Patient?"));
+		}
+	}
+
+	@Test
+	public void testTransactionDeleteByResourceId() {
+		String methodName = "testTransactionDeleteByResourceId";
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IdDt id1 = ourPatientDao.create(p1).getId();
+		ourLog.info("Created patient, got it: {}", id1);
+
+		Patient p2 = new Patient();
+		p2.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p2.setId("Patient/" + methodName);
+		IdDt id2 = ourPatientDao.create(p2).getId();
+		ourLog.info("Created patient, got it: {}", id2);
+
+		Bundle request = new Bundle();
+
+		request.addEntry().getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient/" + id1.getIdPart());
+		request.addEntry().getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient/" + id2.getIdPart());
+
+		ourPatientDao.read(id1.toVersionless());
+		ourPatientDao.read(id2.toVersionless());
+
+		Bundle resp = ourSystemDao.transaction(request);
+
+		assertEquals(3, resp.getEntry().size());
+		assertEquals("204", resp.getEntry().get(1).getTransactionResponse().getStatus());
+		assertEquals("204", resp.getEntry().get(2).getTransactionResponse().getStatus());
+
+		try {
+			ourPatientDao.read(id1.toVersionless());
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		try {
+			ourPatientDao.read(id2.toVersionless());
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+	}
+
+	@Test
+	public void testTransactionDeleteMatchUrlWithZeroMatch() {
+		String methodName = "testTransactionDeleteMatchUrlWithZeroMatch";
+
+		Bundle request = new Bundle();
+		request.addEntry().getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		try {
+			ourSystemDao.transaction(request);
+			fail();
+		} catch (ResourceNotFoundException e) {
+			assertThat(e.getMessage(), containsString("resource matching URL \"Patient?"));
+		}
+	}
+
+	@Test
+	public void testTransactionDeleteNoMatchUrl() {
+		String methodName = "testTransactionDeleteNoMatchUrl";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.setId("Patient/" + methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		Bundle request = new Bundle();
+		request.addEntry().getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		Bundle res = ourSystemDao.transaction(request);
+		assertEquals(2, res.getEntry().size());
+
+		assertEquals(Constants.STATUS_HTTP_204_NO_CONTENT + "", res.getEntry().get(1).getTransactionResponse().getStatus());
+
+		try {
+			ourPatientDao.read(id.toVersionless());
+			fail();
+		} catch (ResourceGoneException e) {
+			// ok
+		}
+	}
+
+	@Test(expected = InvalidRequestException.class)
+	public void testTransactionFailsWithDuplicateIds() {
+		Bundle request = new Bundle();
+
+		Patient patient1 = new Patient();
+		patient1.setId(new IdDt("Patient/testTransactionFailsWithDusplicateIds"));
+		patient1.addIdentifier().setSystem("urn:system").setValue("testPersistWithSimpleLinkP01");
+		request.addEntry().setResource(patient1).getTransaction().setMethod(HTTPVerbEnum.POST);
+
+		Patient patient2 = new Patient();
+		patient2.setId(new IdDt("Patient/testTransactionFailsWithDusplicateIds"));
+		patient2.addIdentifier().setSystem("urn:system").setValue("testPersistWithSimpleLinkP02");
+		request.addEntry().setResource(patient2).getTransaction().setMethod(HTTPVerbEnum.POST);
+
+		ourSystemDao.transaction(request);
+	}
+
+	@Test
+	public void testTransactionUpdateMatchUrlWithOneMatch() {
+		String methodName = "testTransactionUpdateMatchUrlWithOneMatch";
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+		request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.PUT).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		Observation o = new Observation();
+		o.getName().setText("Some Observation");
+		o.getSubject().setReference("Patient/" + methodName);
+		request.addEntry().setResource(o).getTransaction().setMethod(HTTPVerbEnum.POST);
+
+		Bundle resp = ourSystemDao.transaction(request);
+		assertEquals(3, resp.getEntry().size());
+
+		Entry nextEntry = resp.getEntry().get(1);
+		assertEquals("200", nextEntry.getTransactionResponse().getStatus());
+		assertThat(nextEntry.getTransactionResponse().getLocation(), not(containsString("test")));
+		assertEquals(id.toVersionless(), p.getId().toVersionless());
+		assertNotEquals(id, p.getId());
+		assertThat(p.getId().toString(), endsWith("/_history/2"));
+
+		nextEntry = resp.getEntry().get(1);
+		assertEquals(""+Constants.STATUS_HTTP_200_OK, nextEntry.getTransactionResponse().getStatus());
+		assertThat(nextEntry.getTransactionResponse().getLocation(), not(emptyString()));
+		
+		nextEntry = resp.getEntry().get(2);
+		o = ourObservationDao.read(new IdDt(nextEntry.getTransactionResponse().getLocation()));
+		assertEquals(id.toVersionless(), o.getSubject().getReference());
+
+	}
+
+	@Test
+	public void testTransactionUpdateMatchUrlWithTwoMatch() {
+		String methodName = "testTransactionUpdateMatchUrlWithTwoMatch";
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+		request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.PUT).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		Observation o = new Observation();
+		o.getName().setText("Some Observation");
+		o.getSubject().setReference("Patient/" + methodName);
+		request.addEntry().setResource(o).getTransaction().setMethod(HTTPVerbEnum.POST);
+
+		try {
+			ourSystemDao.transaction(request);
+			fail();
+		} catch (PreconditionFailedException e) {
+			assertThat(e.getMessage(), containsString("with match URL \"Patient"));
+		}
+	}
+
+	@Test
+	public void testTransactionUpdateMatchUrlWithZeroMatch() {
+		String methodName = "testTransactionUpdateMatchUrlWithZeroMatch";
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.addName().addFamily("Hello");
+		IdDt id = ourPatientDao.create(p).getId();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId(id);
+		request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.PUT).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		Observation o = new Observation();
+		o.getName().setText("Some Observation");
+		o.getSubject().setReference(id);
+		request.addEntry().setResource(o).getTransaction().setMethod(HTTPVerbEnum.POST);
+
+		Bundle resp = ourSystemDao.transaction(request);
+		assertEquals(3, resp.getEntry().size());
+
+		Entry nextEntry = resp.getEntry().get(1);
+		assertEquals(Constants.STATUS_HTTP_201_CREATED + "", nextEntry.getTransactionResponse().getStatus());
+
+		assertThat(nextEntry.getTransactionResponse().getLocation(), not(containsString("test")));
+		assertNotEquals(id.toVersionless(), new IdDt(nextEntry.getTransactionResponse().getLocation()).toVersionless());
+
+		assertThat(nextEntry.getTransactionResponse().getLocation(), endsWith("/_history/1"));
+
+		nextEntry = resp.getEntry().get(1);
+		assertEquals(""+Constants.STATUS_HTTP_201_CREATED, nextEntry.getTransactionResponse().getStatus());
+
+		nextEntry = resp.getEntry().get(2);
+		o = ourObservationDao.read(new IdDt(nextEntry.getTransactionResponse().getLocation()));
+		assertEquals(id.toVersionless(), o.getSubject().getReference());
+
+	}
+
+
+	@Test
+	public void testTransactionUpdateNoMatchUrl() {
+		String methodName = "testTransactionUpdateNoMatchUrl";
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.setId("Patient/" + methodName);
+		IdDt id = ourPatientDao.create(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.addName().addFamily("Hello");
+		p.setId("Patient/" + methodName);
+		request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.PUT).setUrl("Patient/"+ id.getIdPart());
+
+		Observation o = new Observation();
+		o.getName().setText("Some Observation");
+		o.getSubject().setReference("Patient/" + methodName);
+		request.addEntry().setResource(o).getTransaction().setMethod(HTTPVerbEnum.POST);
+
+		Bundle resp = ourSystemDao.transaction(request);
+		assertEquals(3, resp.getEntry().size());
+
+		Entry nextEntry = resp.getEntry().get(1);
+		assertEquals("200", nextEntry.getTransactionResponse().getStatus());
+		
+		assertThat(nextEntry.getTransactionResponse().getLocation(), (containsString("test")));
+		assertEquals(id.toVersionless(), new IdDt(nextEntry.getTransactionResponse().getLocation()).toVersionless());
+		assertNotEquals(id, new IdDt(nextEntry.getTransactionResponse().getLocation()));
+		assertThat(nextEntry.getTransactionResponse().getLocation(), endsWith("/_history/2"));
+
+		nextEntry = resp.getEntry().get(2);
+		assertEquals(""+Constants.STATUS_HTTP_201_CREATED, nextEntry.getTransactionResponse().getStatus());
+		
+		o = ourObservationDao.read(new IdDt(resp.getEntry().get(2).getTransactionResponse().getLocation()));
+		assertEquals(id.toVersionless(), o.getSubject().getReference());
+
+	}
+
+	//
+	//
+	// /**
+	// * Issue #55
+	// */
+	// @Test
+	// public void testTransactionWithCidIds() throws Exception {
+	// Bundle request = new Bundle();
+	//
+	// Patient p1 = new Patient();
+	// p1.setId("cid:patient1");
+	// p1.addIdentifier().setSystem("system").setValue("testTransactionWithCidIds01");
+	// res.add(p1);
+	//
+	// Observation o1 = new Observation();
+	// o1.setId("cid:observation1");
+	// o1.getIdentifier().setSystem("system").setValue("testTransactionWithCidIds02");
+	// o1.setSubject(new ResourceReferenceDt("Patient/cid:patient1"));
+	// res.add(o1);
+	//
+	// Observation o2 = new Observation();
+	// o2.setId("cid:observation2");
+	// o2.getIdentifier().setSystem("system").setValue("testTransactionWithCidIds03");
+	// o2.setSubject(new ResourceReferenceDt("Patient/cid:patient1"));
+	// res.add(o2);
+	//
+	// ourSystemDao.transaction(res);
+	//
+	// assertTrue(p1.getId().getValue(), p1.getId().getIdPart().matches("^[0-9]+$"));
+	// assertTrue(o1.getId().getValue(), o1.getId().getIdPart().matches("^[0-9]+$"));
+	// assertTrue(o2.getId().getValue(), o2.getId().getIdPart().matches("^[0-9]+$"));
+	//
+	// assertThat(o1.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
+	// assertThat(o2.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
+	//
+	// }
+	//
+	// @Test
+	// public void testTransactionWithDelete() throws Exception {
+	// Bundle request = new Bundle();
+	//
+	// /*
+	// * Create 3
+	// */
+	//
+	// List<IResource> res;
+	// res = new ArrayList<IResource>();
+	//
+	// Patient p1 = new Patient();
+	// p1.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
+	// res.add(p1);
+	//
+	// Patient p2 = new Patient();
+	// p2.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
+	// res.add(p2);
+	//
+	// Patient p3 = new Patient();
+	// p3.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
+	// res.add(p3);
+	//
+	// ourSystemDao.transaction(res);
+	//
+	// /*
+	// * Verify
+	// */
+	//
+	// IBundleProvider results = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system",
+	// "testTransactionWithDelete"));
+	// assertEquals(3, results.size());
+	//
+	// /*
+	// * Now delete 2
+	// */
+	//
+	// request = new Bundle();
+	// res = new ArrayList<IResource>();
+	// List<IResource> existing = results.getResources(0, 3);
+	//
+	// p1 = new Patient();
+	// p1.setId(existing.get(0).getId());
+	// ResourceMetadataKeyEnum.DELETED_AT.put(p1, InstantDt.withCurrentTime());
+	// res.add(p1);
+	//
+	// p2 = new Patient();
+	// p2.setId(existing.get(1).getId());
+	// ResourceMetadataKeyEnum.DELETED_AT.put(p2, InstantDt.withCurrentTime());
+	// res.add(p2);
+	//
+	// ourSystemDao.transaction(res);
+	//
+	// /*
+	// * Verify
+	// */
+	//
+	// IBundleProvider results2 = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system",
+	// "testTransactionWithDelete"));
+	// assertEquals(1, results2.size());
+	// List<IResource> existing2 = results2.getResources(0, 1);
+	// assertEquals(existing2.get(0).getId(), existing.get(2).getId());
+	//
+	// }
+
+	@AfterClass
+	public static void afterClass() {
+		ourCtx.close();
+	}
+
+	@SuppressWarnings("unchecked")
+	@BeforeClass
+	public static void beforeClass() {
+		ourCtx = new ClassPathXmlApplicationContext("hapi-fhir-server-resourceproviders-dstu2.xml", "fhir-jpabase-spring-test-config.xml");
+		ourFhirContext = ourCtx.getBean(FhirContext.class);
+		assertEquals(FhirVersionEnum.DSTU2, ourFhirContext.getVersion().getVersion());
+		ourPatientDao = ourCtx.getBean("myPatientDaoDstu2", IFhirResourceDao.class);
+		ourObservationDao = ourCtx.getBean("myObservationDaoDstu2", IFhirResourceDao.class);
+		ourSystemDao = ourCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
+	}
+
+}

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

@@ -1,899 +0,0 @@
-package ca.uhn.fhir.jpa.dao;
-
-import static org.hamcrest.Matchers.*;
-import static org.junit.Assert.*;
-
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.List;
-import java.util.Map;
-
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.springframework.context.support.ClassPathXmlApplicationContext;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.Bundle;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
-import ca.uhn.fhir.model.api.TagList;
-import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
-import ca.uhn.fhir.model.dstu.composite.QuantityDt;
-import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
-import ca.uhn.fhir.model.dstu.resource.Location;
-import ca.uhn.fhir.model.dstu.resource.Observation;
-import ca.uhn.fhir.model.dstu.resource.Patient;
-import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.model.primitive.InstantDt;
-import ca.uhn.fhir.model.valueset.BundleEntryTransactionOperationEnum;
-import ca.uhn.fhir.rest.param.TokenParam;
-import ca.uhn.fhir.rest.server.IBundleProvider;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
-
-public class FhirSystemDaoTest {
-
-	private static ClassPathXmlApplicationContext ourCtx;
-	private static FhirContext ourFhirContext;
-	private static IFhirResourceDao<Location> ourLocationDao;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoTest.class);
-	private static IFhirResourceDao<Observation> ourObservationDao;
-	private static IFhirResourceDao<Patient> ourPatientDao;
-	private static IFhirSystemDao<List<IResource>> ourSystemDao;
-
-	@Test
-	public void testGetResourceCounts() {
-		Observation obs = new Observation();
-		obs.getName().addCoding().setSystem("urn:system").setCode("testGetResourceCountsO01");
-		ourObservationDao.create(obs);
-
-		Map<String, Long> oldCounts = ourSystemDao.getResourceCounts();
-
-		Patient patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system").setValue("testGetResourceCountsP01");
-		patient.addName().addFamily("Tester").addGiven("Joe");
-		ourPatientDao.create(patient);
-
-		Map<String, Long> newCounts = ourSystemDao.getResourceCounts();
-
-		if (oldCounts.containsKey("Patient")) {
-			assertEquals(oldCounts.get("Patient") + 1, (long) newCounts.get("Patient"));
-		} else {
-			assertEquals(1L, (long) newCounts.get("Patient"));
-		}
-
-		assertEquals((long) oldCounts.get("Observation"), (long) newCounts.get("Observation"));
-
-	}
-
-	@Test
-	public void testHistory() throws Exception {
-		Date start = new Date();
-		Thread.sleep(10);
-
-		Patient patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system").setValue("testHistory");
-		patient.addName().addFamily("Tester").addGiven("Joe");
-		IdDt pid = ourPatientDao.create(patient).getId().toVersionless();
-
-		Thread.sleep(10);
-		IdDt newpid = ourPatientDao.update(patient, pid).getId();
-
-		Thread.sleep(10);
-		IdDt newpid2 = ourPatientDao.update(patient, pid).getId();
-
-		Thread.sleep(10);
-		IdDt newpid3 = ourPatientDao.update(patient, pid).getId();
-
-		IBundleProvider values = ourSystemDao.history(start);
-		assertEquals(4, values.size());
-
-		List<IResource> res = values.getResources(0, 4);
-		assertEquals(newpid3, res.get(0).getId());
-		assertEquals(newpid2, res.get(1).getId());
-		assertEquals(newpid, res.get(2).getId());
-		assertEquals(pid.toUnqualifiedVersionless(), res.get(3).getId().toUnqualifiedVersionless());
-
-		Location loc = new Location();
-		loc.getAddress().addLine("AAA");
-		IdDt lid = ourLocationDao.create(loc).getId();
-
-		Location loc2 = new Location();
-		loc2.getAddress().addLine("AAA");
-		ourLocationDao.create(loc2).getId();
-
-		Thread.sleep(2000);
-
-		values = ourLocationDao.history(start);
-		assertEquals(2, values.size());
-
-		values = ourLocationDao.history(lid.getIdPartAsLong(), start);
-		assertEquals(1, values.size());
-
-	}
-
-	@Test
-	public void testPersistWithSimpleLink() {
-		Patient patient = new Patient();
-		patient.setId(new IdDt("Patient/testPersistWithSimpleLinkP01"));
-		patient.addIdentifier().setSystem("urn:system").setValue("testPersistWithSimpleLinkP01");
-		patient.addName().addFamily("Tester").addGiven("Joe");
-
-		Observation obs = new Observation();
-		obs.getName().addCoding().setSystem("urn:system").setCode("testPersistWithSimpleLinkO01");
-		obs.setSubject(new ResourceReferenceDt("Patient/testPersistWithSimpleLinkP01"));
-
-		ourSystemDao.transaction(Arrays.asList((IResource) patient, obs));
-
-		String patientId = (patient.getId().getIdPart());
-		String obsId = (obs.getId().getIdPart());
-
-		// assertThat(patientId, greaterThan(0L));
-		// assertEquals(patientVersion, 1L);
-		// assertThat(obsId, greaterThan(patientId));
-		// assertEquals(obsVersion, 1L);
-
-		// Try to search
-
-		IBundleProvider obsResults = ourObservationDao.search(Observation.SP_NAME, new IdentifierDt("urn:system", "testPersistWithSimpleLinkO01"));
-		assertEquals(1, obsResults.size());
-
-		IBundleProvider patResults = ourPatientDao.search(Patient.SP_IDENTIFIER, new IdentifierDt("urn:system", "testPersistWithSimpleLinkP01"));
-		assertEquals(1, obsResults.size());
-
-		IdDt foundPatientId = patResults.getResources(0, 1).get(0).getId();
-		ResourceReferenceDt subject = obs.getSubject();
-		assertEquals(foundPatientId.getIdPart(), subject.getReference().getIdPart());
-
-		// Update
-
-		patient = (Patient) patResults.getResources(0, 1).get(0);
-		obs = (Observation) obsResults.getResources(0, 1).get(0);
-		patient.addIdentifier().setSystem("urn:system").setValue("testPersistWithSimpleLinkP02");
-		obs.getName().addCoding().setSystem("urn:system").setCode("testPersistWithSimpleLinkO02");
-
-		ourSystemDao.transaction(Arrays.asList((IResource) patient, obs));
-
-		String patientId2 = (patient.getId().getIdPart());
-		String patientVersion2 = (patient.getId().getVersionIdPart());
-		String obsId2 = (obs.getId().getIdPart());
-		String obsVersion2 = (obs.getId().getVersionIdPart());
-
-		assertEquals(patientId, patientId2);
-		assertEquals(patientVersion2, "2");
-		assertEquals(obsId, obsId2);
-		assertEquals(obsVersion2, "2");
-
-	}
-
-	@Test
-	public void testPersistWithUnknownId() {
-		Observation obs = new Observation();
-		obs.getName().addCoding().setSystem("urn:system").setCode("testPersistWithSimpleLinkO01");
-		obs.setSubject(new ResourceReferenceDt("Patient/999998888888"));
-
-		try {
-			ourSystemDao.transaction(Arrays.asList((IResource) obs));
-		} catch (InvalidRequestException e) {
-			assertThat(e.getMessage(), containsString("Resource Patient/999998888888 not found, specified in path: Observation.subject"));
-		}
-
-		obs = new Observation();
-		obs.getName().addCoding().setSystem("urn:system").setCode("testPersistWithSimpleLinkO01");
-		obs.setSubject(new ResourceReferenceDt("Patient/1.2.3.4"));
-
-		try {
-			ourSystemDao.transaction(Arrays.asList((IResource) obs));
-		} catch (InvalidRequestException e) {
-			assertThat(e.getMessage(), containsString("Resource Patient/1.2.3.4 not found, specified in path: Observation.subject"));
-		}
-
-	}
-
-	@Test
-	public void testTagOperationss() throws Exception {
-
-		TagList preSystemTl = ourSystemDao.getAllTags();
-
-		TagList tl1 = new TagList();
-		tl1.addTag("testGetAllTagsScheme1", "testGetAllTagsTerm1", "testGetAllTagsLabel1");
-		Patient p1 = new Patient();
-		p1.addIdentifier().setSystem("foo").setValue("testGetAllTags01");
-		ResourceMetadataKeyEnum.TAG_LIST.put(p1, tl1);
-		ourPatientDao.create(p1);
-
-		TagList tl2 = new TagList();
-		tl2.addTag("testGetAllTagsScheme2", "testGetAllTagsTerm2", "testGetAllTagsLabel2");
-		Observation o1 = new Observation();
-		o1.getName().setText("testGetAllTags02");
-		ResourceMetadataKeyEnum.TAG_LIST.put(o1, tl2);
-		IdDt o1id = ourObservationDao.create(o1).getId();
-		assertTrue(o1id.getVersionIdPart() != null);
-
-		TagList postSystemTl = ourSystemDao.getAllTags();
-		assertEquals(preSystemTl.size() + 2, postSystemTl.size());
-		assertEquals("testGetAllTagsLabel1", postSystemTl.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1").getLabel());
-
-		TagList tags = ourPatientDao.getAllResourceTags();
-		assertEquals("testGetAllTagsLabel1", tags.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1").getLabel());
-		assertNull(tags.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
-
-		TagList tags2 = ourObservationDao.getTags(o1id);
-		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
-		assertEquals("testGetAllTagsLabel2", tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2").getLabel());
-
-		o1.getResourceMetadata().remove(ResourceMetadataKeyEnum.TAG_LIST);
-		IdDt o1id2 = ourObservationDao.update(o1, o1id).getId();
-		assertTrue(o1id2.getVersionIdPart() != null);
-
-		tags2 = ourObservationDao.getTags(o1id);
-		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
-		assertEquals("testGetAllTagsLabel2", tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2").getLabel());
-
-		tags2 = ourObservationDao.getTags(o1id2);
-		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
-		assertNotNull(tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
-
-		/*
-		 * Remove a tag from a version
-		 */
-
-		ourObservationDao.removeTag(o1id2, "testGetAllTagsScheme2", "testGetAllTagsTerm2");
-		tags2 = ourObservationDao.getTags(o1id2);
-		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
-		assertNull(tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
-
-		tags2 = ourObservationDao.getTags(o1id);
-		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
-		assertNotNull(tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
-
-		/*
-		 * Add a tag
-		 */
-		ourObservationDao.addTag(o1id2, "testGetAllTagsScheme3", "testGetAllTagsTerm3", "testGetAllTagsLabel3");
-		tags2 = ourObservationDao.getTags(o1id2);
-		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
-		assertNull(tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
-		assertNotNull(tags2.getTag("testGetAllTagsScheme3", "testGetAllTagsTerm3"));
-		assertEquals("testGetAllTagsLabel3", tags2.getTag("testGetAllTagsScheme3", "testGetAllTagsTerm3").getLabel());
-
-		tags2 = ourObservationDao.getTags(o1id);
-		assertNull(tags2.getTag("testGetAllTagsScheme1", "testGetAllTagsTerm1"));
-		assertNotNull(tags2.getTag("testGetAllTagsScheme2", "testGetAllTagsTerm2"));
-
-	}
-
-	@Test
-	public void testTransactionCreateMatchUrlWithOneMatch() {
-		String methodName = "testTransactionCreateMatchUrlWithOneMatch";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.setId("Patient/" + methodName);
-		IdDt id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.CREATE);
-		ResourceMetadataKeyEnum.LINK_SEARCH.put(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		Observation o = new Observation();
-		o.getName().setText("Some Observation");
-		o.getSubject().setReference("Patient/" + methodName);
-
-		List<IResource> resp = ourSystemDao.transaction(Arrays.asList((IResource) p, o));
-		assertEquals(3, resp.size());
-
-		p = (Patient) resp.get(1);
-		assertEquals(BundleEntryTransactionOperationEnum.NOOP, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(p));
-		assertEquals(id, p.getId());
-
-		o = (Observation) resp.get(2);
-		assertEquals(BundleEntryTransactionOperationEnum.CREATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(o));
-		assertEquals(id.toVersionless(), o.getSubject().getReference());
-
-	}
-
-	@Test
-	public void testTransactionCreateMatchUrlWithTwoMatch() {
-		String methodName = "testTransactionCreateMatchUrlWithTwoMatch";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IdDt id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.CREATE);
-		ResourceMetadataKeyEnum.LINK_SEARCH.put(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		Observation o = new Observation();
-		o.getName().setText("Some Observation");
-		o.getSubject().setReference("Patient/" + methodName);
-
-		try {
-			ourSystemDao.transaction(Arrays.asList((IResource) p, o));
-			fail();
-		} catch (InvalidRequestException e) {
-			assertThat(e.getMessage(), containsString("with match URL \"Patient"));
-		}
-	}
-
-	@Test
-	public void testTransactionCreateMatchUrlWithZeroMatch() {
-		String methodName = "testTransactionCreateMatchUrlWithZeroMatch";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.CREATE);
-		ResourceMetadataKeyEnum.LINK_SEARCH.put(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		Observation o = new Observation();
-		o.getName().setText("Some Observation");
-		o.getSubject().setReference("Patient/" + methodName);
-
-		List<IResource> resp = ourSystemDao.transaction(Arrays.asList((IResource) p, o));
-		assertEquals(3, resp.size());
-
-		p = (Patient) resp.get(1);
-		assertEquals(BundleEntryTransactionOperationEnum.CREATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(p));
-		assertThat(p.getId().getIdPart(), not(containsString("test")));
-
-		o = (Observation) resp.get(2);
-		assertEquals(BundleEntryTransactionOperationEnum.CREATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(o));
-		assertEquals(p.getId().toVersionless(), o.getSubject().getReference());
-
-	}
-
-	@Test
-	public void testTransactionCreateNoMatchUrl() {
-		String methodName = "testTransactionCreateNoMatchUrl";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.CREATE);
-
-		List<IResource> resp = ourSystemDao.transaction(Arrays.asList((IResource) p));
-		assertEquals(2, resp.size());
-		p = (Patient) resp.get(1);
-
-		assertEquals(BundleEntryTransactionOperationEnum.CREATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(p));
-		assertThat(p.getId().getIdPart(), not(containsString("test")));
-	}
-
-	@Test
-	public void testTransactionDeleteMatchUrlWithOneMatch() {
-		String methodName = "testTransactionDeleteMatchUrlWithOneMatch";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IdDt id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.DELETE);
-		ResourceMetadataKeyEnum.LINK_SEARCH.put(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		List<IResource> resp = ourSystemDao.transaction(Arrays.asList((IResource) p));
-		assertEquals(2, resp.size());
-
-		p = (Patient) resp.get(1);
-		assertEquals(BundleEntryTransactionOperationEnum.DELETE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(p));
-		assertThat(p.getId().toVersionless().toString(), not(containsString("test")));
-		assertEquals(id.toVersionless(), p.getId().toVersionless());
-		assertNotEquals(id, p.getId());
-		assertThat(p.getId().toString(), endsWith("/_history/2"));
-
-		try {
-			ourPatientDao.read(id.toVersionless());
-			fail();
-		} catch (ResourceGoneException e) {
-			// ok
-		}
-
-		try {
-			ourPatientDao.read(new IdDt("Patient/" + methodName));
-			fail();
-		} catch (ResourceNotFoundException e) {
-			// ok
-		}
-
-	}
-
-	@Test
-	public void testTransactionDeleteMatchUrlWithTwoMatch() {
-		String methodName = "testTransactionDeleteMatchUrlWithTwoMatch";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IdDt id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.DELETE);
-		ResourceMetadataKeyEnum.LINK_SEARCH.put(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		Observation o = new Observation();
-		o.getName().setText("Some Observation");
-		o.getSubject().setReference("Patient/" + methodName);
-
-		try {
-			ourSystemDao.transaction(Arrays.asList((IResource) p, o));
-			fail();
-		} catch (InvalidRequestException e) {
-			assertThat(e.getMessage(), containsString("with match URL \"Patient"));
-		}
-	}
-
-	@Test
-	public void testTransactionDeleteMatchUrlWithZeroMatch() {
-		String methodName = "testTransactionDeleteMatchUrlWithZeroMatch";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName + "ZZZ");
-		p.addName().addFamily("Hello");
-		IdDt id = ourPatientDao.create(p).getId();
-
-		p = new Patient();
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		IdDt id2 = ourPatientDao.create(p).getId();
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.DELETE);
-		ResourceMetadataKeyEnum.LINK_SEARCH.put(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		List<IResource> resp = ourSystemDao.transaction(Arrays.asList((IResource) p));
-		assertEquals(2, resp.size());
-
-		p = (Patient) resp.get(1);
-		assertEquals(BundleEntryTransactionOperationEnum.DELETE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(p));
-		assertThat(p.getId().toVersionless().toString(), (containsString("test")));
-		assertThat(p.getId().toString(), endsWith("/_history/2"));
-		assertEquals(id2.toVersionless(), p.getId().toVersionless());
-		assertNotEquals(id2, p.getId());
-
-		try {
-			ourPatientDao.read(id2.toVersionless());
-			fail();
-		} catch (ResourceGoneException e) {
-			// ok
-		}
-
-		Patient found = ourPatientDao.read(id);
-		assertEquals(id, found.getId());
-
-	}
-
-	@Test
-	public void testTransactionDeleteNoMatchUrl() {
-		String methodName = "testTransactionDeleteNoMatchUrl";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.setId("Patient/" + methodName);
-		IdDt id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.DELETE);
-
-		List<IResource> resp = ourSystemDao.transaction(Arrays.asList((IResource) p));
-		assertEquals(2, resp.size());
-
-		p = (Patient) resp.get(1);
-		assertEquals(BundleEntryTransactionOperationEnum.DELETE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(p));
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get(p).getValue());
-
-		try {
-			ourPatientDao.read(id.toVersionless());
-			fail();
-		} catch (ResourceGoneException e) {
-			// ok
-		}
-	}
-
-	@Test(expected = InvalidRequestException.class)
-	public void testTransactionFailsWithDuplicateIds() {
-		Patient patient1 = new Patient();
-		patient1.setId(new IdDt("Patient/testTransactionFailsWithDusplicateIds"));
-		patient1.addIdentifier().setSystem("urn:system").setValue("testPersistWithSimpleLinkP01");
-
-		Patient patient2 = new Patient();
-		patient2.setId(new IdDt("Patient/testTransactionFailsWithDusplicateIds"));
-		patient2.addIdentifier().setSystem("urn:system").setValue("testPersistWithSimpleLinkP02");
-
-		ourSystemDao.transaction(Arrays.asList((IResource) patient1, patient2));
-	}
-
-//	@Test TODO: re-enable
- 	public void testTransactionFromBundle() throws Exception {
-
-		InputStream bundleRes = FhirSystemDaoTest.class.getResourceAsStream("/bundle.json");
-		Bundle bundle = ourFhirContext.newJsonParser().parseBundle(new InputStreamReader(bundleRes));
-		List<IResource> res = bundle.toListOfResources();
-
-		ourSystemDao.transaction(res);
-
-		Patient p1 = (Patient) res.get(0);
-		String id = p1.getId().getValue();
-		ourLog.info("ID: {}", id);
-		assertThat(id, not(containsString("5556918")));
-		assertThat(id, not(equalToIgnoringCase("")));
-	}
-
-	@Test
-	public void testTransactionUpdateMatchUrlWithOneMatch() {
-		String methodName = "testTransactionUpdateMatchUrlWithOneMatch";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IdDt id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.UPDATE);
-		ResourceMetadataKeyEnum.LINK_SEARCH.put(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		Observation o = new Observation();
-		o.getName().setText("Some Observation");
-		o.getSubject().setReference("Patient/" + methodName);
-
-		List<IResource> resp = ourSystemDao.transaction(Arrays.asList((IResource) p, o));
-		assertEquals(3, resp.size());
-
-		p = (Patient) resp.get(1);
-		assertEquals(BundleEntryTransactionOperationEnum.UPDATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(p));
-		assertThat(p.getId().toVersionless().toString(), not(containsString("test")));
-		assertEquals(id.toVersionless(), p.getId().toVersionless());
-		assertNotEquals(id, p.getId());
-		assertThat(p.getId().toString(), endsWith("/_history/2"));
-
-		o = (Observation) resp.get(2);
-		assertEquals(BundleEntryTransactionOperationEnum.CREATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(o));
-		assertEquals(id.toVersionless(), o.getSubject().getReference());
-
-	}
-
-	@Test
-	public void testTransactionUpdateMatchUrlWithTwoMatch() {
-		String methodName = "testTransactionUpdateMatchUrlWithTwoMatch";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IdDt id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.UPDATE);
-		ResourceMetadataKeyEnum.LINK_SEARCH.put(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		Observation o = new Observation();
-		o.getName().setText("Some Observation");
-		o.getSubject().setReference("Patient/" + methodName);
-
-		try {
-			ourSystemDao.transaction(Arrays.asList((IResource) p, o));
-			fail();
-		} catch (InvalidRequestException e) {
-			assertThat(e.getMessage(), containsString("with match URL \"Patient"));
-		}
-	}
-
-	@Test
-	public void testTransactionUpdateMatchUrlWithZeroMatch() {
-		String methodName = "testTransactionUpdateMatchUrlWithZeroMatch";
-
-		Patient p = new Patient();
-		p.addName().addFamily("Hello");
-		IdDt id = ourPatientDao.create(p).getId();
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId(id);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.UPDATE);
-		ResourceMetadataKeyEnum.LINK_SEARCH.put(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		Observation o = new Observation();
-		o.getName().setText("Some Observation");
-		o.getSubject().setReference(id);
-
-		List<IResource> resp = ourSystemDao.transaction(Arrays.asList((IResource) p, o));
-		assertEquals(3, resp.size());
-
-		p = (Patient) resp.get(1);
-		assertEquals(BundleEntryTransactionOperationEnum.UPDATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(p));
-		assertEquals(id.toVersionless(), p.getId().toVersionless());
-		assertNotEquals(id, p.getId());
-		assertThat(p.getId().toString(), endsWith("/_history/2"));
-
-		o = (Observation) resp.get(2);
-		assertEquals(BundleEntryTransactionOperationEnum.CREATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(o));
-		assertEquals(p.getId().toVersionless(), o.getSubject().getReference());
-
-	}
-
-	@Test
-	public void testTransactionUpdateMatchUrlWithZeroMatchAndNotPreExisting() {
-		String methodName = "testTransactionUpdateMatchUrlWithZeroMatchAndNotPreExisting";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.UPDATE);
-		ResourceMetadataKeyEnum.LINK_SEARCH.put(p, "Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		Observation o = new Observation();
-		o.getName().setText("Some Observation");
-		o.getSubject().setReference("Patient/" + methodName);
-
-		List<IResource> resp = ourSystemDao.transaction(Arrays.asList((IResource) p, o));
-		assertEquals(3, resp.size());
-
-		p = (Patient) resp.get(1);
-		assertEquals(BundleEntryTransactionOperationEnum.CREATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(p));
-		assertThat(p.getId().toVersionless().toString(), containsString("test"));
-		assertThat(p.getId().toString(), endsWith("/_history/1"));
-
-		o = (Observation) resp.get(2);
-		assertEquals(BundleEntryTransactionOperationEnum.CREATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(o));
-		assertEquals(p.getId().toVersionless(), o.getSubject().getReference());
-
-	}
-
-	@Test
-	public void testTransactionUpdateNoMatchUrl() {
-		String methodName = "testTransactionUpdateNoMatchUrl";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.setId("Patient/" + methodName);
-		IdDt id = ourPatientDao.create(p).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.addName().addFamily("Hello");
-		p.setId("Patient/" + methodName);
-		ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.put(p, BundleEntryTransactionOperationEnum.UPDATE);
-
-		Observation o = new Observation();
-		o.getName().setText("Some Observation");
-		o.getSubject().setReference("Patient/" + methodName);
-
-		List<IResource> resp = ourSystemDao.transaction(Arrays.asList((IResource) p, o));
-		assertEquals(3, resp.size());
-
-		p = (Patient) resp.get(1);
-		assertEquals(BundleEntryTransactionOperationEnum.UPDATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(p));
-		assertThat(p.getId().toVersionless().toString(), containsString("test"));
-		assertEquals(id.toVersionless(), p.getId().toVersionless());
-		assertNotEquals(id, p.getId());
-		assertThat(p.getId().toString(), endsWith("/_history/2"));
-
-		o = (Observation) resp.get(2);
-		assertEquals(BundleEntryTransactionOperationEnum.CREATE, ResourceMetadataKeyEnum.ENTRY_TRANSACTION_OPERATION.get(o));
-		assertEquals(id.toVersionless(), o.getSubject().getReference());
-
-	}
-
-	@Test
-	public void testTransactionUpdateNoOperationSpecified() throws Exception {
-		List<IResource> res = new ArrayList<IResource>();
-
-		Patient p1 = new Patient();
-		p1.getId().setValue("testTransactionWithUpdateXXX01");
-		p1.addIdentifier().setSystem("system").setValue("testTransactionWithUpdate01");
-		res.add(p1);
-
-		Observation p2 = new Observation();
-		p2.getId().setValue("testTransactionWithUpdateXXX02");
-		p2.getIdentifier().setSystem("system").setValue("testTransactionWithUpdate02");
-		p2.setSubject(new ResourceReferenceDt("Patient/testTransactionWithUpdateXXX01"));
-		res.add(p2);
-
-		ourSystemDao.transaction(res);
-
-		assertFalse(p1.getId().isEmpty());
-		assertFalse(p2.getId().isEmpty());
-		assertEquals("testTransactionWithUpdateXXX01", p1.getId().getIdPart());
-		assertEquals("testTransactionWithUpdateXXX02", p2.getId().getIdPart());
-		assertNotEquals("testTransactionWithUpdateXXX01", p1.getId().getVersionIdPart());
-		assertNotEquals("testTransactionWithUpdateXXX02", p2.getId().getVersionIdPart());
-		assertEquals(p1.getId().toUnqualified().toVersionless(), p2.getSubject().getReference());
-
-		IdDt p1id = p1.getId().toUnqualified().toVersionless();
-		IdDt p1idWithVer = p1.getId().toUnqualified();
-		IdDt p2id = p2.getId().toUnqualified().toVersionless();
-		IdDt p2idWithVer = p2.getId().toUnqualified();
-
-		/*
-		 * Make some changes
-		 */
-		
-		res = new ArrayList<IResource>();
-
-		p1 = new Patient();
-		p1.getId().setValue("testTransactionWithUpdateXXX01");
-		p1.addIdentifier().setSystem("system").setValue("testTransactionWithUpdate01");
-		p1.addName().addFamily("Name1");
-		res.add(p1);
-
-		p2 = new Observation();
-		p2.getId().setValue("testTransactionWithUpdateXXX02");
-		p2.getIdentifier().setSystem("system").setValue("testTransactionWithUpdate02");
-		p2.setSubject(new ResourceReferenceDt("Patient/testTransactionWithUpdateXXX01"));
-		p2.addReferenceRange().setHigh(new QuantityDt(123L));
-		res.add(p2);
-		
-		List<IResource> results = ourSystemDao.transaction(res);
-
-		assertEquals(p1id, results.get(1).getId().toUnqualified().toVersionless());
-		assertEquals(p2id, results.get(2).getId().toUnqualified().toVersionless());
-		assertNotEquals(p1idWithVer, results.get(1).getId().toUnqualified());
-		assertNotEquals(p2idWithVer, results.get(2).getId().toUnqualified());
-
-	}
-
-	/**
-	 * Issue #55
-	 */
-	@Test
-	public void testTransactionWithCidIds() throws Exception {
-		List<IResource> res = new ArrayList<IResource>();
-
-		Patient p1 = new Patient();
-		p1.setId("cid:patient1");
-		p1.addIdentifier().setSystem("system").setValue("testTransactionWithCidIds01");
-		res.add(p1);
-
-		Observation o1 = new Observation();
-		o1.setId("cid:observation1");
-		o1.getIdentifier().setSystem("system").setValue("testTransactionWithCidIds02");
-		o1.setSubject(new ResourceReferenceDt("Patient/cid:patient1"));
-		res.add(o1);
-
-		Observation o2 = new Observation();
-		o2.setId("cid:observation2");
-		o2.getIdentifier().setSystem("system").setValue("testTransactionWithCidIds03");
-		o2.setSubject(new ResourceReferenceDt("Patient/cid:patient1"));
-		res.add(o2);
-
-		ourSystemDao.transaction(res);
-
-		assertTrue(p1.getId().getValue(), p1.getId().getIdPart().matches("^[0-9]+$"));
-		assertTrue(o1.getId().getValue(), o1.getId().getIdPart().matches("^[0-9]+$"));
-		assertTrue(o2.getId().getValue(), o2.getId().getIdPart().matches("^[0-9]+$"));
-
-		assertThat(o1.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
-		assertThat(o2.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
-
-	}
-
-	@Test
-	public void testTransactionWithDelete() throws Exception {
-
-		/*
-		 * Create 3
-		 */
-
-		List<IResource> res;
-		res = new ArrayList<IResource>();
-
-		Patient p1 = new Patient();
-		p1.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
-		res.add(p1);
-
-		Patient p2 = new Patient();
-		p2.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
-		res.add(p2);
-
-		Patient p3 = new Patient();
-		p3.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
-		res.add(p3);
-
-		ourSystemDao.transaction(res);
-
-		/*
-		 * Verify
-		 */
-
-		IBundleProvider results = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testTransactionWithDelete"));
-		assertEquals(3, results.size());
-
-		/*
-		 * Now delete 2
-		 */
-
-		res = new ArrayList<IResource>();
-		List<IResource> existing = results.getResources(0, 3);
-
-		p1 = new Patient();
-		p1.setId(existing.get(0).getId());
-		ResourceMetadataKeyEnum.DELETED_AT.put(p1, InstantDt.withCurrentTime());
-		res.add(p1);
-
-		p2 = new Patient();
-		p2.setId(existing.get(1).getId());
-		ResourceMetadataKeyEnum.DELETED_AT.put(p2, InstantDt.withCurrentTime());
-		res.add(p2);
-
-		ourSystemDao.transaction(res);
-
-		/*
-		 * Verify
-		 */
-
-		IBundleProvider results2 = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testTransactionWithDelete"));
-		assertEquals(1, results2.size());
-		List<IResource> existing2 = results2.getResources(0, 1);
-		assertEquals(existing2.get(0).getId(), existing.get(2).getId());
-
-	}
-
-	@AfterClass
-	public static void afterClass() {
-		ourCtx.close();
-	}
-
-	@SuppressWarnings("unchecked")
-	@BeforeClass
-	public static void beforeClass() {
-		ourCtx = new ClassPathXmlApplicationContext("hapi-fhir-server-resourceproviders-dstu1.xml", "fhir-jpabase-spring-test-config.xml");
-		ourFhirContext = ourCtx.getBean(FhirContext.class);
-		ourPatientDao = ourCtx.getBean("myPatientDaoDstu1", IFhirResourceDao.class);
-		ourObservationDao = ourCtx.getBean("myObservationDaoDstu1", IFhirResourceDao.class);
-		ourLocationDao = ourCtx.getBean("myLocationDaoDstu1", IFhirResourceDao.class);
-		ourSystemDao = ourCtx.getBean("mySystemDaoDstu1", IFhirSystemDao.class);
-	}
-
-}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -19,7 +19,6 @@ import org.springframework.context.support.ClassPathXmlApplicationContext;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
-import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;

hapi-fhir-structures-dev/src/main/java/ca/uhn/fhir/model/dev/FhirDev.java

@@ -23,12 +23,10 @@ package ca.uhn.fhir.model.dev;
 import java.io.InputStream;
 
 import org.apache.commons.lang3.StringUtils;
-import org.hl7.fhir.instance.model.api.IBaseExtension;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
-import ca.uhn.fhir.model.api.ExtensionDt;
 import ca.uhn.fhir.model.api.IFhirVersion;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.base.composite.BaseContainedDt;

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/GenericClientTestDev.java

@@ -1,74 +0,0 @@
-package ca.uhn.fhir.rest.client;
-
-import static org.junit.Assert.assertEquals;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
-
-import java.io.StringReader;
-import java.nio.charset.Charset;
-
-import org.apache.commons.io.input.ReaderInputStream;
-import org.apache.http.HttpResponse;
-import org.apache.http.ProtocolVersion;
-import org.apache.http.client.HttpClient;
-import org.apache.http.client.methods.HttpUriRequest;
-import org.apache.http.message.BasicHeader;
-import org.apache.http.message.BasicStatusLine;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.mockito.ArgumentCaptor;
-import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.Bundle;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.rest.server.Constants;
-
-public class GenericClientTestDev {
-	private static FhirContext ourCtx;
-	private HttpClient myHttpClient;
-	private HttpResponse myHttpResponse;
-
-
-	@BeforeClass
-	public static void beforeClass() {
-		ourCtx = FhirContext.forDstu2();
-	}
-
-	
-	@Before
-	public void before() {
-		myHttpClient = mock(HttpClient.class, new ReturnsDeepStubs());
-		ourCtx.getRestfulClientFactory().setHttpClient(myHttpClient);
-		ourCtx.getRestfulClientFactory().setServerValidationModeEnum(ServerValidationModeEnum.NEVER);
-		myHttpResponse = mock(HttpResponse.class, new ReturnsDeepStubs());
-	}
-
-	
-	@Test
-	public void testSearchByString() throws Exception {
-		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
-
-		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().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
-
-		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
-
-		//@formatter:off
-		Bundle response = client.search()
-				.forResource("Patient")
-				.where(Patient.NAME.matches().value("james"))
-				.execute();
-		//@formatter:on
-
-		assertEquals("http://example.com/fhir/Patient?name=james", capt.getValue().getURI().toString());
-		assertEquals(Patient.class, response.getEntries().get(0).getResource().getClass());
-
-	}
-
-	
-}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/GenericClientTestDstu2.java

@@ -0,0 +1,212 @@
+package ca.uhn.fhir.rest.client;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.*;
+
+import java.io.IOException;
+import java.io.StringReader;
+import java.nio.charset.Charset;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.input.ReaderInputStream;
+import org.apache.http.HttpResponse;
+import org.apache.http.ProtocolVersion;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpEntityEnclosingRequestBase;
+import org.apache.http.client.methods.HttpUriRequest;
+import org.apache.http.message.BasicHeader;
+import org.apache.http.message.BasicStatusLine;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.mockito.ArgumentCaptor;
+import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.rest.server.EncodingEnum;
+
+public class GenericClientTestDstu2 {
+	private static FhirContext ourCtx;
+	private HttpClient myHttpClient;
+	private HttpResponse myHttpResponse;
+
+
+	@BeforeClass
+	public static void beforeClass() {
+		ourCtx = FhirContext.forDstu2();
+	}
+
+	
+	@Before
+	public void before() {
+		myHttpClient = mock(HttpClient.class, new ReturnsDeepStubs());
+		ourCtx.getRestfulClientFactory().setHttpClient(myHttpClient);
+		ourCtx.getRestfulClientFactory().setServerValidationModeEnum(ServerValidationModeEnum.NEVER);
+		myHttpResponse = mock(HttpResponse.class, new ReturnsDeepStubs());
+	}
+
+	
+	@Test
+	public void testSearchByString() throws Exception {
+		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
+
+		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().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
+		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8")));
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+
+		//@formatter:off
+		Bundle response = client.search()
+				.forResource("Patient")
+				.where(Patient.NAME.matches().value("james"))
+				.execute();
+		//@formatter:on
+
+		assertEquals("http://example.com/fhir/Patient?name=james", capt.getValue().getURI().toString());
+		assertEquals(Patient.class, response.getEntries().get(0).getResource().getClass());
+
+	}
+
+	@Test
+	public void testDeleteConditional() throws Exception {
+		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), Constants.STATUS_HTTP_204_NO_CONTENT, ""));
+//		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_TEXT + "; charset=UTF-8"));
+		when(myHttpResponse.getEntity().getContent()).then(new Answer<ReaderInputStream>() {
+			@Override
+			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				return new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8"));
+			}
+		});
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+
+		int idx = 0;
+		
+		client.delete().resourceById(new IdDt("Patient/123")).execute();
+		assertEquals("DELETE", capt.getAllValues().get(idx).getMethod());
+		assertEquals("http://example.com/fhir/Patient/123", capt.getAllValues().get(idx).getURI().toString());
+		idx++;
+		
+		client.delete().resourceConditionalByUrl("Patient?name=foo").execute();
+		assertEquals("DELETE", capt.getAllValues().get(idx).getMethod());
+		assertEquals("http://example.com/fhir/Patient?name=foo", capt.getAllValues().get(idx).getURI().toString());
+		idx++;
+
+		client.delete().resourceConditionalByType("Patient").where(Patient.NAME.matches().value("foo")).execute();
+		assertEquals("DELETE", capt.getAllValues().get(idx).getMethod());
+		assertEquals("http://example.com/fhir/Patient?name=foo", capt.getAllValues().get(idx).getURI().toString());
+		idx++;
+
+	}
+
+	@Test
+	public void testCreateConditional() throws Exception {
+		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), Constants.STATUS_HTTP_204_NO_CONTENT, ""));
+		when(myHttpResponse.getEntity().getContent()).then(new Answer<ReaderInputStream>() {
+			@Override
+			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				return new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8"));
+			}
+		});
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+
+		int idx = 0;
+		
+		Patient p = new Patient();
+		p.addName().addFamily("FOOFAMILY");
+		
+		client.create().resource(p).conditionalByUrl("Patient?name=foo").execute();
+		assertEquals(1, capt.getAllValues().get(idx).getHeaders(Constants.HEADER_CONTENT_TYPE).length);
+		assertEquals(EncodingEnum.XML.getResourceContentType() + Constants.HEADER_SUFFIX_CT_UTF_8, capt.getAllValues().get(idx).getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue());
+		assertThat(extractBody(capt, idx), containsString("<family value=\"FOOFAMILY\"/>"));
+		assertEquals("http://example.com/fhir/Patient", capt.getAllValues().get(idx).getURI().toString());
+		assertEquals("http://example.com/fhir/Patient?name=foo", capt.getAllValues().get(idx).getFirstHeader(Constants.HEADER_IF_NONE_EXIST).getValue());
+		assertEquals("POST", capt.getAllValues().get(idx).getRequestLine().getMethod());
+		idx++;
+
+		client.create().resource(p).conditional().where(Patient.NAME.matches().value("foo")).execute();
+		assertEquals(1, capt.getAllValues().get(idx).getHeaders(Constants.HEADER_CONTENT_TYPE).length);
+		assertEquals(EncodingEnum.XML.getResourceContentType() + Constants.HEADER_SUFFIX_CT_UTF_8, capt.getAllValues().get(idx).getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue());
+		assertThat(extractBody(capt, idx), containsString("<family value=\"FOOFAMILY\"/>"));
+		assertEquals("http://example.com/fhir/Patient", capt.getAllValues().get(idx).getURI().toString());
+		assertEquals("http://example.com/fhir/Patient?name=foo", capt.getAllValues().get(idx).getFirstHeader(Constants.HEADER_IF_NONE_EXIST).getValue());
+		assertEquals("POST", capt.getAllValues().get(idx).getRequestLine().getMethod());
+		idx++;
+
+	}
+
+
+	@Test
+	public void testUpdateConditional() throws Exception {
+		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), Constants.STATUS_HTTP_204_NO_CONTENT, ""));
+		when(myHttpResponse.getEntity().getContent()).then(new Answer<ReaderInputStream>() {
+			@Override
+			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				return new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8"));
+			}
+		});
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+
+		int idx = 0;
+		
+		Patient p = new Patient();
+		p.addName().addFamily("FOOFAMILY");
+		
+		client.update().resource(p).conditionalByUrl("Patient?name=foo").execute();
+		assertEquals(1, capt.getAllValues().get(idx).getHeaders(Constants.HEADER_CONTENT_TYPE).length);
+		assertEquals(EncodingEnum.XML.getResourceContentType() + Constants.HEADER_SUFFIX_CT_UTF_8, capt.getAllValues().get(idx).getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue());
+		assertThat(extractBody(capt, idx), containsString("<family value=\"FOOFAMILY\"/>"));
+		assertEquals("PUT", capt.getAllValues().get(idx).getRequestLine().getMethod());
+		assertEquals("http://example.com/fhir/Patient?name=foo", capt.getAllValues().get(idx).getURI().toString());
+		idx++;
+
+		client.update().resource(ourCtx.newXmlParser().encodeResourceToString(p)).conditionalByUrl("Patient?name=foo").execute();
+		assertEquals(1, capt.getAllValues().get(idx).getHeaders(Constants.HEADER_CONTENT_TYPE).length);
+		assertEquals(EncodingEnum.XML.getResourceContentType() + Constants.HEADER_SUFFIX_CT_UTF_8, capt.getAllValues().get(idx).getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue());
+		assertThat(extractBody(capt, idx), containsString("<family value=\"FOOFAMILY\"/>"));
+		assertEquals("PUT", capt.getAllValues().get(idx).getRequestLine().getMethod());
+		assertEquals("http://example.com/fhir/Patient?name=foo", capt.getAllValues().get(idx).getURI().toString());
+		idx++;
+
+		client.update().resource(p).conditional().where(Patient.NAME.matches().value("foo")).and(Patient.ADDRESS.matches().value("AAA|BBB")).execute();
+		assertEquals(1, capt.getAllValues().get(idx).getHeaders(Constants.HEADER_CONTENT_TYPE).length);
+		assertEquals(EncodingEnum.XML.getResourceContentType() + Constants.HEADER_SUFFIX_CT_UTF_8, capt.getAllValues().get(idx).getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue());
+		assertThat(extractBody(capt, idx), containsString("<family value=\"FOOFAMILY\"/>"));
+		assertEquals("PUT", capt.getAllValues().get(idx).getRequestLine().getMethod());
+		assertEquals("http://example.com/fhir/Patient?name=foo&address=AAA%5C%7CBBB", capt.getAllValues().get(idx).getURI().toString());
+		idx++;
+
+		client.update().resource(ourCtx.newXmlParser().encodeResourceToString(p)).conditional().where(Patient.NAME.matches().value("foo")).and(Patient.ADDRESS.matches().value("AAA|BBB")).execute();
+		assertEquals(1, capt.getAllValues().get(idx).getHeaders(Constants.HEADER_CONTENT_TYPE).length);
+		assertEquals(EncodingEnum.XML.getResourceContentType() + Constants.HEADER_SUFFIX_CT_UTF_8, capt.getAllValues().get(idx).getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue());
+		assertThat(extractBody(capt, idx), containsString("<family value=\"FOOFAMILY\"/>"));
+		assertEquals("PUT", capt.getAllValues().get(idx).getRequestLine().getMethod());
+		assertEquals("http://example.com/fhir/Patient?name=foo&address=AAA%5C%7CBBB", capt.getAllValues().get(idx).getURI().toString());
+		idx++;
+
+	}
+
+	private String extractBody(ArgumentCaptor<HttpUriRequest> capt, int count) throws IOException {
+		String body = IOUtils.toString(((HttpEntityEnclosingRequestBase) capt.getAllValues().get(count)).getEntity().getContent(), "UTF-8");
+		return body;
+	}
+
+}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/UpdateConditionalTest.java

@@ -0,0 +1,133 @@
+package ca.uhn.fhir.rest.server;
+
+import static org.junit.Assert.*;
+
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.methods.HttpPut;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.TagList;
+import ca.uhn.fhir.model.dstu2.resource.DiagnosticOrder;
+import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
+import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
+import ca.uhn.fhir.model.dstu2.resource.Organization;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.ResourceParam;
+import ca.uhn.fhir.rest.annotation.Update;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.util.PortUtil;
+
+/**
+ * Created by dsotnikov on 2/25/2014.
+ */
+public class UpdateConditionalTest {
+	private static CloseableHttpClient ourClient;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UpdateConditionalTest.class);
+	private static int ourPort;
+	private static Server ourServer;
+
+	@Test
+	public void testUpdate() throws Exception {
+
+		Patient patient = new Patient();
+		patient.addIdentifier().setValue("002");
+
+		HttpPut httpPost = new HttpPut("http://localhost:" + ourPort + "/Patient/001");
+		httpPost.setEntity(new StringEntity(new FhirContext().newXmlParser().encodeResourceToString(patient), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+
+		HttpResponse status = ourClient.execute(httpPost);
+
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		ourLog.info("Response was:\n{}", responseContent);
+
+		OperationOutcome oo = new FhirContext().newXmlParser().parseResource(OperationOutcome.class, responseContent);
+		assertEquals("OODETAILS", oo.getIssueFirstRep().getDetails());
+
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		assertEquals("http://localhost:" + ourPort + "/Patient/001/_history/002", status.getFirstHeader("location").getValue());
+		assertEquals("http://localhost:" + ourPort + "/Patient/001/_history/002", status.getFirstHeader("content-location").getValue());
+
+	}
+	
+	
+	
+	@AfterClass
+	public static void afterClass() throws Exception {
+		ourServer.stop();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		PatientProvider patientProvider = new PatientProvider();
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer();
+		servlet.setResourceProviders(patientProvider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
+	private static String ourLastConditionalUrl;
+		
+	
+	@Before
+	public void before() {
+		ourLastConditionalUrl=null;
+	}
+	
+	public static class PatientProvider implements IResourceProvider {
+
+		@Override
+		public Class<? extends IResource> getResourceType() {
+			return Patient.class;
+		}
+
+		
+		@Update()
+		public MethodOutcome updatePatient(@IdParam IdDt theId, @ResourceParam Patient thePatient) {
+			IdDt id = theId.withVersion(thePatient.getIdentifierFirstRep().getValue());
+			OperationOutcome oo = new OperationOutcome();
+			oo.addIssue().setDetails("OODETAILS");
+			if (theId.getValueAsString().contains("CREATE")) {
+				return new MethodOutcome(id,oo, true);
+			}
+			
+			return new MethodOutcome(id,oo);
+		}
+
+	}
+
+}