Get history and tags working properly on JPA

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnum.java

@@ -20,7 +20,7 @@ package ca.uhn.fhir.model.api;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.*;
 
 import java.util.Date;
 import java.util.Map;
@@ -46,6 +46,12 @@ public enum ResourceMetadataKeyEnum {
 		public InstantDt get(IResource theResource) {
 			return getInstantFromMetadataOrNullIfNone(theResource.getResourceMetadata(), DELETED_AT);
 		}
+
+		@Override
+		public void put(IResource theResource, Object theObject) {
+			InstantDt obj = (InstantDt) theObject;
+			theResource.getResourceMetadata().put(DELETED_AT, obj);
+		}
 	},
 
 	/**
@@ -61,6 +67,12 @@ public enum ResourceMetadataKeyEnum {
 		public IdDt get(IResource theResource) {
 			return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata(), PREVIOUS_ID);
 		}
+
+		@Override
+		public void put(IResource theResource, Object theObject) {
+			IdDt obj = (IdDt) theObject;
+			theResource.getResourceMetadata().put(PREVIOUS_ID, obj);
+		}
 	},
 
 	/**
@@ -83,6 +95,12 @@ public enum ResourceMetadataKeyEnum {
 		public InstantDt get(IResource theResource) {
 			return getInstantFromMetadataOrNullIfNone(theResource.getResourceMetadata(), PUBLISHED);
 		}
+
+		@Override
+		public void put(IResource theResource, Object theObject) {
+			InstantDt obj = (InstantDt) theObject;
+			theResource.getResourceMetadata().put(PUBLISHED, obj);
+		}
 	},
 
 	
@@ -109,6 +127,12 @@ public enum ResourceMetadataKeyEnum {
 			}
 			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + TAG_LIST.name() + " - Expected " + TagList.class.getCanonicalName());
 		}
+
+		@Override
+		public void put(IResource theResource, Object theObject) {
+			TagList obj = (TagList) theObject;
+			theResource.getResourceMetadata().put(TAG_LIST, obj);
+		}
 	}, 
 	
 	
@@ -128,6 +152,12 @@ public enum ResourceMetadataKeyEnum {
 		public InstantDt get(IResource theResource) {
 			return getInstantFromMetadataOrNullIfNone(theResource.getResourceMetadata(), UPDATED);
 		}
+
+		@Override
+		public void put(IResource theResource, Object theObject) {
+			InstantDt obj = (InstantDt) theObject;
+			theResource.getResourceMetadata().put(UPDATED, obj);
+		}
 	}, 
 	
 	/**
@@ -144,6 +174,12 @@ public enum ResourceMetadataKeyEnum {
 		public IdDt get(IResource theResource) {
 			return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata(), VERSION_ID);
 		}
+
+		@Override
+		public void put(IResource theResource, Object theObject) {
+			IdDt obj = (IdDt) theObject;
+			theResource.getResourceMetadata().put(VERSION_ID, obj);
+		}
 	};
 
 	public abstract Object get(IResource theResource);
@@ -185,5 +221,7 @@ public enum ResourceMetadataKeyEnum {
 		}
 		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected " + InstantDt.class.getCanonicalName());
 	}
+
+	public abstract void put(IResource theResource, Object theObject);
 	
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/TagList.java

@@ -29,7 +29,7 @@ public class TagList extends ArrayList<Tag> {
 	public static final String ELEMENT_NAME = "TagList";
 	public static final String ELEMENT_NAME_LC = ELEMENT_NAME.toLowerCase();
 
-	public Tag addTag(String theTerm, String theLabel, String theScheme) {
+	public Tag addTag(String theScheme, String theTerm, String theLabel) {
 		Tag retVal = new Tag(theTerm, theLabel, theScheme);
 		add(retVal);
 		return retVal;
@@ -38,5 +38,14 @@ public class TagList extends ArrayList<Tag> {
 	public Tag addTag() {
 		return addTag(null, null, null);
 	}
-	
+
+	public Tag getTag(String theScheme, String theTerm) {
+		for (Tag next : this) {
+			if (theScheme.equals(next.getScheme()) && theTerm.equals(next.getTerm())) {
+				return next;
+			}
+		}
+		return null;
+	}
+
 }

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

@@ -48,10 +48,10 @@ import ca.uhn.fhir.rest.server.Constants;
 @DatatypeDef(name = "id")
 public class IdDt extends BasePrimitive<String> {
 
-	private String myUnqualifiedId;
-	private String myValue;
-	private String myUnqualifiedVersionId;
 	private String myResourceType;
+	private String myUnqualifiedId;
+	private String myUnqualifiedVersionId;
+	private String myValue;
 
 	/**
 	 * Create a new empty ID
@@ -71,7 +71,7 @@ public class IdDt extends BasePrimitive<String> {
 			setValue(null);
 		}
 	}
-
+	
 	/**
 	 * Create a new ID using a long
 	 */
@@ -166,6 +166,14 @@ public class IdDt extends BasePrimitive<String> {
 		return myUnqualifiedVersionId;
 	}
 
+	public Long getUnqualifiedVersionIdAsLong() {
+		if (!hasUnqualifiedVersionId()) {
+			return null;
+		}else {
+			return Long.parseLong(getUnqualifiedVersionId());
+		}
+	}
+
 	/**
 	 * Returns the value of this ID. Note that this value may be a fully qualified URL, a relative/partial URL, or a
 	 * simple ID. Use {@link #getUnqualifiedId()} to get just the ID portion.
@@ -182,6 +190,31 @@ public class IdDt extends BasePrimitive<String> {
 		return myValue;
 	}
 
+	public boolean hasUnqualifiedId() {
+		return isNotBlank(getUnqualifiedId());
+	}
+
+	public boolean hasUnqualifiedVersionId() {
+		return isNotBlank(getUnqualifiedVersionId());
+	}
+
+	/**
+	 * Returns <code>true</code> if the unqualified ID is a valid {@link Long} value (in other words, it consists only
+	 * of digits)
+	 */
+	public boolean isValidLong() {
+		String id = getUnqualifiedId();
+		if (StringUtils.isBlank(id)) {
+			return false;
+		}
+		for (int i = 0; i < id.length(); i++) {
+			if (Character.isDigit(id.charAt(i)) == false) {
+				return false;
+			}
+		}
+		return true;
+	}
+
 	/**
 	 * Copies the value from the given IdDt to <code>this</code> IdDt. It is generally not neccesary to use this method
 	 * but it is provided for consistency with the rest of the API.
@@ -254,28 +287,6 @@ public class IdDt extends BasePrimitive<String> {
 		setValue(theValue);
 	}
 
-	@Override
-	public String toString() {
-		return myValue;
-	}
-
-	/**
-	 * Returns <code>true</code> if the unqualified ID is a valid {@link Long} value (in other words, it consists only
-	 * of digits)
-	 */
-	public boolean isValidLong() {
-		String id = getUnqualifiedId();
-		if (StringUtils.isBlank(id)) {
-			return false;
-		}
-		for (int i = 0; i < id.length(); i++) {
-			if (Character.isDigit(id.charAt(i)) == false) {
-				return false;
-			}
-		}
-		return true;
-	}
-
 	/**
 	 * Returns a view of this ID as a fully qualified URL, given a server base and resource name
 	 * (which will only be used if the ID does not already contain those respective parts). Essentially,
@@ -305,4 +316,20 @@ public class IdDt extends BasePrimitive<String> {
 		return retVal.toString();
 	}
 
+	@Override
+	public String toString() {
+		return myValue;
+	}
+
+	public IdDt withoutVersion() {
+		int i = myValue.indexOf(Constants.PARAM_HISTORY);
+		if (i > 1) {
+			return new IdDt(myValue.substring(0, i-1));
+		}else {
+			return this;
+		}
+	}
+
+
+
 }

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

@@ -121,9 +121,11 @@ public class GetTagsMethodBinding extends BaseMethodBinding<TagList> {
 		if (myType != IResource.class) {
 			if (id != null) {
 				if (versionId != null) {
-					retVal = new HttpGetClientInvocation(getResourceName(), id.getValue(), Constants.PARAM_HISTORY, versionId.getValue(), Constants.PARAM_TAGS);
+					retVal = new HttpGetClientInvocation(getResourceName(), id.getUnqualifiedId(), Constants.PARAM_HISTORY, versionId.getValue(), Constants.PARAM_TAGS);
+				} else if (id.hasUnqualifiedVersionId()){
+					retVal = new HttpGetClientInvocation(getResourceName(), id.getUnqualifiedId(), Constants.PARAM_HISTORY, id.getUnqualifiedVersionId(), Constants.PARAM_TAGS);
 				} else {
-					retVal = new HttpGetClientInvocation(getResourceName(), id.getValue(), Constants.PARAM_TAGS);
+					retVal = new HttpGetClientInvocation(getResourceName(), id.getUnqualifiedId(), Constants.PARAM_TAGS);
 				}
 			} else {
 				retVal = new HttpGetClientInvocation(getResourceName(), Constants.PARAM_TAGS);
@@ -192,9 +194,9 @@ public class GetTagsMethodBinding extends BaseMethodBinding<TagList> {
 		if ((myIdParamIndex != null) != (theRequest.getId() != null)) {
 			return false;
 		}
-		if ((myVersionIdParamIndex != null) != (theRequest.getVersionId() != null)) {
+//		if ((myVersionIdParamIndex != null) != (theRequest.getVersionId() != null)) {
-			return false;
+//			return false;
-		}
+//		}
 		return true;
 	}
 

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

@@ -0,0 +1,16 @@
+package ca.uhn.fhir.rest.server;
+
+import java.util.List;
+
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.primitive.InstantDt;
+
+public interface IBundleProvider {
+
+	List<IResource> getResources(int theFromIndex, int theToIndex);
+	
+	int size();
+	
+	InstantDt getPublished();
+	
+}

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

@@ -0,0 +1,5 @@
+package ca.uhn.fhir.rest.server;
+
+public interface IPagingProvider {
+
+}

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

@@ -23,7 +23,6 @@ package ca.uhn.fhir.rest.server;
 import static org.apache.commons.lang3.StringUtils.*;
 
 import java.io.IOException;
-import java.io.StringReader;
 import java.lang.reflect.Method;
 import java.lang.reflect.Modifier;
 import java.util.Arrays;
@@ -567,7 +566,8 @@ public class RestfulServer extends HttpServlet {
 						if (id == null) {
 							throw new InvalidRequestException("Don't know how to handle request path: " + requestPath);
 						}
-						versionId = new IdDt(resourceName + "/" + id.getUnqualifiedId() + "/_history/" + versionString);
+						id = new IdDt(resourceName + "/" + id.getUnqualifiedId() + "/_history/" + versionString);
+						versionId = id;
 					} else {
 						operation = Constants.PARAM_HISTORY;
 					}

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

@@ -156,7 +156,8 @@ public class RestfulServerTesterServlet extends HttpServlet {
 			ctx.setVariable("conf", conformance);
 			ctx.setVariable("base", myServerBase);
 			ctx.setVariable("jsonEncodedConf", myCtx.newJsonParser().encodeResourceToString(conformance));
-
+			addStandardVariables(ctx, theReq.getParameterMap());
+			
 			theResp.setContentType("text/html");
 			theResp.setCharacterEncoding("UTF-8");
 
@@ -167,6 +168,17 @@ public class RestfulServerTesterServlet extends HttpServlet {
 		}
 	}
 
+	private void addStandardVariables(WebContext theCtx, Map<String, String[]> theParameterMap) {
+		addStandardVariable(theCtx, theParameterMap, "configEncoding");
+		addStandardVariable(theCtx, theParameterMap, "configPretty");
+	}
+
+	private void addStandardVariable(WebContext theCtx, Map<String, String[]> theParameterMap, String key) {
+		if (theParameterMap.containsKey(key) && theParameterMap.get(key).length > 0) {
+			theCtx.setVariable(key, theParameterMap.get(key)[0]);
+		}
+	}
+
 	@Override
 	protected void doPost(HttpServletRequest theReq, HttpServletResponse theResp) throws ServletException, IOException {
 		if (DEBUGMODE) {

hapi-fhir-base/src/main/resources/ca/uhn/fhir/rest/server/tester/PublicTester.html

@@ -18,7 +18,7 @@ This file is a Thymeleaf template for the
 		<script type="text/javascript" src="json2.js"></script>
 		<script type="text/javascript" src="minify.json.js"></script>
 	</head>
-	<body>
+	<body onload="selectResourceType();">
 		<table border="0" width="100%">
 			<tr>
 				<td align="left"><img src="hapi_fhir_banner.png"/></td>
@@ -56,17 +56,30 @@ This file is a Thymeleaf template for the
 						<tr>
 							<td class="propertyKeyCell">Encoding</td>
 							<td>
-								<select id="configEncoding">
+								<select id="configEncoding" th:switch="${configEncoding}">
-									<option value="" selected="true">(default)</option>
+									<th:block th:case="'xml'">
-									<option value="xml">XML</option>
+										<option value="">(default)</option>
-									<option value="json">JSON</option>
+										<option value="xml" selected="selected">XML</option>
+										<option value="json">JSON</option>
+									</th:block>
+									<th:block th:case="'json'">
+										<option value="">(default)</option>
+										<option value="xml">XML</option>
+										<option value="json" selected="selected">JSON</option>
+									</th:block>
+									<th:block th:case="*">
+										<option value="" selected="selected">(default)</option>
+										<option value="xml">XML</option>
+										<option value="json">JSON</option>
+									</th:block>
 								</select>
 							</td>
 						</tr>
 						<tr>
 							<td class="propertyKeyCell">Pretty Printing</td>
-							<td>
+							<td th:switch="${configPretty}">
-								<input type="checkbox" id="configPretty" checked="checked"/>
+								<input th:case="'false'" type="checkbox" id="configPretty"/>
+								<input th:case="*" type="checkbox" id="configPretty" checked="checked"/>
 							</td>
 						</tr>
 					</table>
@@ -94,7 +107,24 @@ This file is a Thymeleaf template for the
 							</tr>
 						</table>
 
-						<th:block th:each="resource, resIterStat : ${rest.resource}" th:with="expandoId='resExpando'+${resIterStat.count}">
+						<div class="bodyHeaderBlock">
+							Resources 
+						</div>
+
+						<table border="0" th:id="systemExpando" class="propertyTable">
+							<tr>
+								<td valign="top" class="propertyKeyCell">Select Resource:</td>
+								<td valign="top">
+									<select id="configResource" onchange="selectResourceType();">
+										<th:block th:each="resource, resIterStat : ${rest.resource}">
+											<option th:value="${resource.type.valueAsString}" th:text="${resource.type.valueAsString}"/>
+										</th:block>
+									</select>
+								</td>
+							</tr>
+						</table>
+
+						<div th:each="resource, resIterStat : ${rest.resource}" th:with="expandoId='resExpando'+${resIterStat.count}" th:id="'res' + ${resource.type.valueAsString}" class="resourceTypeContainer" style="display:none;">
 							<div class="bodyHeaderBlock">
 								Resource: <th:block th:text="${resource.type.valueAsString}"/> 
 							</div>
@@ -118,7 +148,7 @@ This file is a Thymeleaf template for the
 									</td>
 								</tr>
 							</table>
-						</th:block>
+						</div>
 					</th:block>
 				</td>
 			</tr>

hapi-fhir-base/src/main/resources/ca/uhn/fhir/rest/server/tester/PublicTester.js

@@ -341,6 +341,15 @@ function newUniqueId() {
     return "uid" + uniqueIdSeed++;
 }
 
+function selectResourceType() {
+	$('.resourceTypeContainer').each(function() {
+		$(this).hide();
+	});
+	var cr = document.getElementById('configResource');
+	var selected = cr.options[cr.selectedIndex].value;
+	$('#res' + selected).show();
+}
+
 /** Show a newly created tester form */
 function showNewForm() {
 	var time = 0;

hapi-fhir-base/src/site/example/java/example/RestfulPatientResourceProviderMore.java

@@ -613,8 +613,8 @@ public Patient readPatient(@IdParam IdDt theId) {
  
   // Create a TagList and place a complete list of the patient's tags inside
   TagList tags = new TagList();
-  tags.addTag("Dog", "Canine Patient", "http://animals"); // TODO: more realistic example
+  tags.addTag("http://animals", "Dog", "Canine Patient"); // TODO: more realistic example
-  tags.addTag("Friendly", "Friendly", "http://personality"); // TODO: more realistic example
+  tags.addTag("http://personality", "Friendly", "Friendly"); // TODO: more realistic example
   
   // The tags are then stored in the Patient resource instance
   retVal.getResourceMetadata().put(ResourceMetadataKeyEnum.TAG_LIST, tags);
@@ -656,8 +656,8 @@ newPatient.addName().addFamily("Jones").addGiven("Frank");
 
 // Populate tags
 TagList tags = new TagList();
-tags.addTag("Dog", "Canine Patient", "http://animals"); // TODO: more realistic example
+tags.addTag("http://animals", "Dog", "Canine Patient"); // TODO: more realistic example
-tags.addTag("Friendly", "Friendly", "http://personality"); // TODO: more realistic example
+tags.addTag("http://personality", "Friendly", "Friendly"); // TODO: more realistic example
 newPatient.getResourceMetadata().put(ResourceMetadataKeyEnum.TAG_LIST, tags);
 
 // ...invoke the create method on the client...

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/client/TagsClientTest.java

@@ -230,6 +230,28 @@ public class TagsClientTest {
 		when(httpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(httpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(ser), Charset.forName("UTF-8")));
 
+		IClient client = ctx.newRestfulClient(IClient.class, "http://foo");
+		TagList response = client.getAllTagsPatientId(new IdDt("Patient", "111", "222"));
+		assertEquals(tagList, response);
+
+		assertEquals(HttpGet.class, capt.getValue().getClass());
+		HttpGet get = (HttpGet) capt.getValue();
+		assertEquals("http://foo/Patient/111/_history/222/_tags", get.getURI().toString());
+	}
+
+	@Test
+	public void testGetAllTagsPatientIdVersionOld() throws Exception {
+
+		TagList tagList = new TagList();
+		tagList.add(new Tag("AAA", "BBB", "CCC"));
+		String ser = ctx.newXmlParser().encodeTagListToString(tagList);
+
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(httpClient.execute(capt.capture())).thenReturn(httpResponse);
+		when(httpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(httpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
+		when(httpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(ser), Charset.forName("UTF-8")));
+
 		IClient client = ctx.newRestfulClient(IClient.class, "http://foo");
 		TagList response = client.getAllTagsPatientIdVersion(new IdDt("111"), new IdDt("222"));
 		assertEquals(tagList, response);

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/ResfulServerMethodTest.java

@@ -1516,8 +1516,11 @@ public class ResfulServerMethodTest {
 
 		@Read()
 		public Patient getResourceById(@IdParam IdDt theId, @VersionIdParam IdDt theVersionId) {
-			Patient retVal = getIdToPatient().get(theId.getValue());
+			Patient retVal = getIdToPatient().get(theId.getUnqualifiedId());
-			retVal.getName().get(0).setText(theVersionId.getValue());
+			List<HumanNameDt> name = retVal.getName();
+			HumanNameDt nameDt = name.get(0);
+			String value = theVersionId.getValue();
+			nameDt.setText(value);
 			return retVal;
 		}
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/TagsServerTest.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.rest.server;
 
+import static org.apache.commons.lang.StringUtils.*;
 import static org.junit.Assert.*;
 
 import java.util.concurrent.TimeUnit;
@@ -25,6 +26,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.api.annotation.TagListParam;
+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.rest.annotation.AddTags;
@@ -58,7 +60,7 @@ public class TagsServerTest {
 	public void testAddTagsById() throws Exception {
 
 		TagList tagList = new TagList();
-		tagList.addTag("term", "label", "scheme");
+		tagList.addTag("scheme", "term", "label");
 
 		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/111/_tags");
 		httpPost.setEntity(new StringEntity(ourCtx.newJsonParser().encodeTagListToString(tagList), ContentType.create(EncodingEnum.JSON.getResourceContentType(), "UTF-8")));
@@ -76,7 +78,7 @@ public class TagsServerTest {
 	public void testAddTagsByIdAndVersion() throws Exception {
 
 		TagList tagList = new TagList();
-		tagList.addTag("term", "label", "scheme");
+		tagList.addTag("scheme", "term", "label");
 
 		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/111/_history/222/_tags");
 		httpPost.setEntity(new StringEntity(ourCtx.newJsonParser().encodeTagListToString(tagList), ContentType.create(EncodingEnum.JSON.getResourceContentType(), "UTF-8")));
@@ -167,11 +169,28 @@ public class TagsServerTest {
 		assertEquals(expected, actual);
 	}
 
+	@Test
+	public void testGetAllTagsObservationIdVersion() throws Exception {
+
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Observation/111/_history/222/_tags");
+		HttpResponse status = ourClient.execute(httpGet);
+
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		ourLog.info("Response was:\n{}", responseContent);
+
+		assertEquals(200, status.getStatusLine().getStatusCode());
+
+		TagList actual = ourCtx.newXmlParser().parseTagList(responseContent);
+		TagList expected = ourProvider.getAllTags();
+		expected.get(0).setTerm("Patient111222");
+		assertEquals(expected, actual);
+	}
+	
 	@Test
 	public void testRemoveTagsById() throws Exception {
 
 		TagList tagList = new TagList();
-		tagList.addTag("term", "label", "scheme");
+		tagList.addTag("scheme", "term", "label");
 
 		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/111/_tags/_delete");
 		httpPost.setEntity(new StringEntity(ourCtx.newJsonParser().encodeTagListToString(tagList), ContentType.create(EncodingEnum.JSON.getResourceContentType(), "UTF-8")));
@@ -189,7 +208,7 @@ public class TagsServerTest {
 	public void testRemoveTagsByIdAndVersion() throws Exception {
 
 		TagList tagList = new TagList();
-		tagList.addTag("term", "label", "scheme");
+		tagList.addTag("scheme", "term", "label");
 
 		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/111/_history/222/_tags/_delete");
 		httpPost.setEntity(new StringEntity(ourCtx.newJsonParser().encodeTagListToString(tagList), ContentType.create(EncodingEnum.JSON.getResourceContentType(), "UTF-8")));
@@ -264,7 +283,7 @@ public class TagsServerTest {
 		@GetTags(type = Patient.class)
 		public TagList getAllTagsPatientId(@IdParam IdDt theId) {
 			TagList tagList = new TagList();
-			tagList.add(new Tag("Patient" + theId.getUnqualifiedId(), "DogLabel", (String) null));
+			tagList.add(new Tag("Patient" + theId.getUnqualifiedId() + defaultString(theId.getUnqualifiedVersionId()), "DogLabel", (String) null));
 			tagList.add(new Tag("AllCat", "CatLabel", "http://cats"));
 			return tagList;
 		}
@@ -277,6 +296,14 @@ public class TagsServerTest {
 			return tagList;
 		}
 
+		@GetTags(type = Observation.class)
+		public TagList getAllTagsObservationIdVersion(@IdParam IdDt theId) {
+			TagList tagList = new TagList();
+			tagList.add(new Tag("Patient" + theId.getUnqualifiedId() + theId.getUnqualifiedVersionId(), "DogLabel", (String) null));
+			tagList.add(new Tag("AllCat", "CatLabel", "http://cats"));
+			return tagList;
+		}
+
 		@DeleteTags(type = Patient.class)
 		public void RemoveTagsPatient(@IdParam IdDt theId, @VersionIdParam IdDt theVersion, @TagListParam TagList theTagList) {
 			ourLastOutcome = "Remove" + theId.getUnqualifiedId() + theVersion.getUnqualifiedVersionId();

hapi-fhir-jpaserver-base/.classpath

@@ -14,6 +14,7 @@
 		</attributes>
 	</classpathentry>
 	<classpathentry excluding="**/*.java" including="**/*.java" kind="src" path="src/main/resources"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/hapi-fhir-base"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

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

@@ -9,8 +9,10 @@ import java.util.Collections;
 import java.util.Comparator;
 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 javax.persistence.EntityManager;
 import javax.persistence.NoResultException;
@@ -34,12 +36,14 @@ import ca.uhn.fhir.jpa.entity.BaseHasResource;
 import ca.uhn.fhir.jpa.entity.BaseTag;
 import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.entity.ResourceHistoryTablePk;
+import ca.uhn.fhir.jpa.entity.ResourceHistoryTag;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
 import ca.uhn.fhir.jpa.entity.ResourceLink;
 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.model.api.IDatatype;
 import ca.uhn.fhir.model.api.IPrimitiveDatatype;
@@ -85,7 +89,14 @@ public abstract class BaseFhirDao {
 		myContext = theContext;
 	}
 
-	private void searchHistoryCurrentVersion(String theResourceName, Long theId, Date theSince, int theLimit, List<HistoryTuple> tuples) {
+	protected DaoConfig getConfig() {
+		return myConfig;
+	}
+
+	@Autowired(required = true)
+	private DaoConfig myConfig;
+
+	private void searchHistoryCurrentVersion(String theResourceName, Long theId, Date theSince, Integer theLimit, List<HistoryTuple> tuples) {
 		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
 		CriteriaQuery<Tuple> cq = builder.createTupleQuery();
 		Root<?> from = cq.from(ResourceTable.class);
@@ -96,20 +107,22 @@ public abstract class BaseFhirDao {
 			Predicate low = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theSince);
 			predicates.add(low);
 		}
-		
+
 		if (theResourceName != null) {
 			predicates.add(builder.equal(from.get("myResourceType"), theResourceName));
 		}
 		if (theId != null) {
 			predicates.add(builder.equal(from.get("myId"), theId));
 		}
-		
+
 		cq.where(builder.and(predicates.toArray(new Predicate[0])));
 
 		cq.orderBy(builder.desc(from.get("myUpdated")));
 		TypedQuery<Tuple> q = myEntityManager.createQuery(cq);
-		if (theLimit > 0) {
+		if (theLimit != null && theLimit < myConfig.getHardSearchLimit()) {
 			q.setMaxResults(theLimit);
+		} else {
+			q.setMaxResults(myConfig.getHardSearchLimit());
 		}
 		for (Tuple next : q.getResultList()) {
 			long id = (Long) next.get(0);
@@ -147,7 +160,7 @@ public abstract class BaseFhirDao {
 		}
 	}
 
-	private void searchHistoryHistory(String theResourceName, Long theId, Date theSince, int theLimit, List<HistoryTuple> tuples) {
+	private void searchHistoryHistory(String theResourceName, Long theId, Date theSince, Integer theLimit, List<HistoryTuple> tuples) {
 		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
 		CriteriaQuery<Tuple> cq = builder.createTupleQuery();
 		Root<?> from = cq.from(ResourceHistoryTable.class);
@@ -158,20 +171,22 @@ public abstract class BaseFhirDao {
 			Predicate low = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theSince);
 			predicates.add(low);
 		}
-		
+
 		if (theResourceName != null) {
 			predicates.add(builder.equal(from.get("myResourceType"), theResourceName));
 		}
 		if (theId != null) {
 			predicates.add(builder.equal(from.get("myId"), theId));
 		}
-		
+
 		cq.where(builder.and(predicates.toArray(new Predicate[0])));
 
 		cq.orderBy(builder.desc(from.get("myUpdated")));
 		TypedQuery<Tuple> q = myEntityManager.createQuery(cq);
-		if (theLimit > 0) {
+		if (theLimit != null && theLimit < myConfig.getHardSearchLimit()) {
 			q.setMaxResults(theLimit);
+		} else {
+			q.setMaxResults(myConfig.getHardSearchLimit());
 		}
 		for (Tuple next : q.getResultList()) {
 			ResourceHistoryTablePk id = (ResourceHistoryTablePk) next.get(0);
@@ -534,13 +549,18 @@ public abstract class BaseFhirDao {
 			for (IFhirResourceDao<?> next : myResourceDaos) {
 				myResourceTypeToDao.put(next.getResourceType(), next);
 			}
+			
+			if (this instanceof IFhirResourceDao<?>) {
+				IFhirResourceDao<?> thiz = (IFhirResourceDao<?>) this;
+				myResourceTypeToDao.put(thiz.getResourceType(), thiz);
+			}
+			
 		}
 
-		Map<Class<? extends IResource>, IFhirResourceDao<?>> resourceTypeToDao = myResourceTypeToDao;
+		return myResourceTypeToDao.get(theType);
-		return resourceTypeToDao.get(theType);
 	}
 
-	protected ArrayList<IResource> history(String theResourceName, Long theId, Date theSince, int theLimit) {
+	protected ArrayList<IResource> history(String theResourceName, Long theId, Date theSince, Integer theLimit) {
 		List<HistoryTuple> tuples = new ArrayList<HistoryTuple>();
 
 		// Get list of IDs
@@ -564,8 +584,15 @@ public abstract class BaseFhirDao {
 				return theO2.getUpdated().getValue().compareTo(theO1.getUpdated().getValue());
 			}
 		});
-		if (resEntities.size() > theLimit) {
+
-			resEntities = resEntities.subList(0, theLimit);
+		int limit;
+		if (theLimit != null && theLimit < myConfig.getHardSearchLimit()) {
+			limit = theLimit;
+		} else {
+			limit = myConfig.getHardSearchLimit();
+		}
+		if (resEntities.size() > limit) {
+			resEntities = resEntities.subList(0, limit);
 		}
 
 		ArrayList<IResource> retVal = new ArrayList<IResource>();
@@ -588,12 +615,11 @@ public abstract class BaseFhirDao {
 		return new String(out).toUpperCase();
 	}
 
-	
+	protected TagDefinition getTag(String theScheme, String theTerm, String theLabel) {
-	private TagDefinition getTag(String theScheme, String theTerm, String theLabel) {
 		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
 		CriteriaQuery<TagDefinition> cq = builder.createQuery(TagDefinition.class);
 		Root<TagDefinition> from = cq.from(TagDefinition.class);
-		cq.where(builder.and(builder.equal(from.get("myScheme"),theScheme), builder.equal(from.get("myTerm"),theTerm)));
+		cq.where(builder.and(builder.equal(from.get("myScheme"), theScheme), builder.equal(from.get("myTerm"), theTerm)));
 		TypedQuery<TagDefinition> q = myEntityManager.createQuery(cq);
 		try {
 			return q.getSingleResult();
@@ -603,14 +629,14 @@ public abstract class BaseFhirDao {
 			return retVal;
 		}
 	}
-	
+
 	protected void populateResourceIntoEntity(IResource theResource, ResourceTable theEntity) {
 
 		if (theEntity.getPublished().isEmpty()) {
 			theEntity.setPublished(new Date());
 		}
 		theEntity.setUpdated(new Date());
-		
+
 		theEntity.setResourceType(toResourceName(theResource));
 		theEntity.setResource(getContext().newJsonParser().encodeResourceToString(theResource));
 		theEntity.setEncoding(EncodingEnum.JSON);
@@ -618,7 +644,7 @@ public abstract class BaseFhirDao {
 		TagList tagList = (TagList) theResource.getResourceMetadata().get(ResourceMetadataKeyEnum.TAG_LIST);
 		if (tagList != null) {
 			for (Tag next : tagList) {
-				TagDefinition tag = getTag(next.getScheme(), next.getTerm(),next.getLabel());
+				TagDefinition tag = getTag(next.getScheme(), next.getTerm(), next.getLabel());
 				theEntity.addTag(tag);
 			}
 		}
@@ -659,7 +685,11 @@ public abstract class BaseFhirDao {
 	protected String toResourceName(IResource theResource) {
 		return myContext.getResourceDefinition(theResource).getName();
 	}
+	protected String toResourceName(Class<? extends IResource> theResourceType) {
+		return myContext.getResourceDefinition(theResourceType).getName();
+	}
 
+	
 	protected ResourceTable updateEntity(final IResource theResource, ResourceTable entity, boolean theUpdateHistory) {
 		if (entity.getPublished() == null) {
 			entity.setPublished(new Date());
@@ -739,4 +769,66 @@ public abstract class BaseFhirDao {
 		return entity;
 	}
 
+	protected TagList getTags(Class<? extends IResource> theResourceType, IdDt theResourceId) {
+		String resourceName=null;
+		if (theResourceType != null) {
+			resourceName = toResourceName(theResourceType);
+			if (theResourceId != null && theResourceId.hasUnqualifiedVersionId()) {
+				IFhirResourceDao<? extends IResource> dao = getDao(theResourceType);
+				BaseHasResource entity = dao.readEntity(theResourceId);
+				TagList retVal = new TagList();
+				for (BaseTag next : entity.getTags()) {
+					retVal.add(next.getTag().toTag());
+				}
+				return retVal;
+			}
+		}
+		
+		Set<Long> tagIds = new HashSet<Long>();
+		findMatchingTagIds(resourceName, theResourceId, tagIds, ResourceTag.class);
+		findMatchingTagIds(resourceName, theResourceId, tagIds, ResourceHistoryTag.class);
+		if (tagIds.isEmpty()) {
+			return new TagList();
+		}
+		{
+			CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
+			CriteriaQuery<TagDefinition> cq = builder.createQuery(TagDefinition.class);
+			Root<TagDefinition> from = cq.from(TagDefinition.class);
+			cq.where(from.get("myId").in(tagIds));
+			cq.orderBy(builder.asc(from.get("myScheme")), builder.asc(from.get("myTerm")));
+			TypedQuery<TagDefinition> q = myEntityManager.createQuery(cq);
+			q.setMaxResults(getConfig().getHardTagListLimit());
+
+			TagList retVal = new TagList();
+			for (TagDefinition next : q.getResultList()) {
+				retVal.add(next.toTag());
+			}
+
+			return retVal;
+		}
+	}
+
+	private void findMatchingTagIds(String theResourceName, IdDt theResourceId, Set<Long> tagIds, Class<? extends BaseTag> entityClass) {
+		{
+			CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
+			CriteriaQuery<Tuple> cq = builder.createTupleQuery();
+			Root<? extends BaseTag> from = cq.from(entityClass);
+			cq.multiselect(from.get("myTagId").as(Long.class)).distinct(true);
+
+			if (theResourceName != null) {
+				Predicate typePredicate = builder.equal(from.get("myResourceType"), theResourceName);
+				if (theResourceId != null) {
+					cq.where(typePredicate, builder.equal(from.get("myResourceId"), theResourceId.asLong()));
+				} else {
+					cq.where(typePredicate);
+				}
+			}
+
+			TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
+			for (Tuple next : query.getResultList()) {
+				tagIds.add(next.get(0, Long.class));
+			}
+		}
+	}
+
 }

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

@@ -0,0 +1,24 @@
+package ca.uhn.fhir.jpa.dao;
+
+public class DaoConfig {
+
+	private int myHardSearchLimit = 1000;
+	private int myHardTagListLimit = 1000;
+
+	public int getHardSearchLimit() {
+		return myHardSearchLimit;
+	}
+
+	public int getHardTagListLimit() {
+		return myHardTagListLimit;
+	}
+
+	public void setHardSearchLimit(int theHardSearchLimit) {
+		myHardSearchLimit = theHardSearchLimit;
+	}
+
+	public void setHardTagListLimit(int theHardTagListLimit) {
+		myHardTagListLimit = theHardTagListLimit;
+	}
+
+}

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

@@ -33,16 +33,21 @@ import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.jpa.entity.BaseHasResource;
+import ca.uhn.fhir.jpa.entity.BaseTag;
 import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
+import ca.uhn.fhir.jpa.entity.ResourceHistoryTablePk;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
 import ca.uhn.fhir.jpa.entity.ResourceLink;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.jpa.entity.TagDefinition;
 import ca.uhn.fhir.model.api.IPrimitiveDatatype;
 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.dstu.composite.CodingDt;
 import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
 import ca.uhn.fhir.model.dstu.composite.QuantityDt;
@@ -57,6 +62,7 @@ import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 
+@Transactional(propagation = Propagation.REQUIRED)
 public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements IFhirResourceDao<T> {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDao.class);
@@ -70,61 +76,61 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 	private String myResourceName;
 	private Class<T> myResourceType;
 
-	@Transactional(propagation = Propagation.REQUIRED, readOnly = true)
+	@Override
+	public void addTag(IdDt theId, String theScheme, String theTerm, String theLabel) {
+		BaseHasResource entity = readEntity(theId);
+		if (entity == null) {
+			throw new ResourceNotFoundException(theId);
+		}
+
+		for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
+			if (next.getTag().getScheme().equals(theScheme) && next.getTag().getTerm().equals(theTerm)) {
+				return;
+			}
+		}
+
+		TagDefinition def = getTag(theScheme, theTerm, theLabel);
+		BaseTag newEntity = entity.addTag(def);
+
+		myEntityManager.persist(newEntity);
+		myEntityManager.merge(entity);
+	}
+
 	@Override
 	public MethodOutcome create(final T theResource) {
-
-//		final ResourceTable entity = toEntity(theResource);
-//
-//		entity.setPublished(new Date());
-//		entity.setUpdated(entity.getPublished());
 		ResourceTable entity = new ResourceTable();
 		entity.setResourceType(toResourceName(theResource));
 
-//		final List<ResourceIndexedSearchParamString> stringParams = extractSearchParamStrings(entity, theResource);
+		updateEntity(theResource, entity, false);
-//		final List<ResourceIndexedSearchParamToken> tokenParams = extractSearchParamTokens(entity, theResource);
-//		final List<ResourceIndexedSearchParamNumber> numberParams = extractSearchParamNumber(entity, theResource);
-//		final List<ResourceIndexedSearchParamDate> dateParams = extractSearchParamDates(entity, theResource);
-//		final List<ResourceLink> links = extractResourceLinks(entity, theResource);
-
-//		ourLog.info("Saving links: {}", links);
-
-//		TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
-//		template.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
-//		template.setReadOnly(false);
-//		template.execute(new TransactionCallback<ResourceTable>() {
-//			@Override
-//			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-//				myEntityManager.persist(entity);
-//				for (ResourceIndexedSearchParamString next : stringParams) {
-//					myEntityManager.persist(next);
-//				}
-//				for (ResourceIndexedSearchParamToken next : tokenParams) {
-//					myEntityManager.persist(next);
-//				}
-//				for (ResourceIndexedSearchParamNumber next : numberParams) {
-//					myEntityManager.persist(next);
-//				}
-//				for (ResourceIndexedSearchParamDate next : dateParams) {
-//					myEntityManager.persist(next);
-//				}
-//				for (ResourceLink next : links) {
-//					myEntityManager.persist(next);
-//				}
-				updateEntity(theResource, entity,false);
-//				return entity;
-//			}
-//		});
 
 		MethodOutcome outcome = toMethodOutcome(entity);
 		return outcome;
 	}
 
+	@Override
+	public TagList getAllResourceTags() {
+		return super.getTags(myResourceType, null);
+	}
+
 	public Class<T> getResourceType() {
 		return myResourceType;
 	}
 
-	@Transactional(propagation = Propagation.REQUIRED)
+	@Override
+	public TagList getTags(IdDt theResourceId) {
+		return super.getTags(myResourceType, theResourceId);
+	}
+
+	@Override
+	public List<T> history() {
+		return null;
+	}
+
+	@Override
+	public List<IResource> history(Date theSince, Integer theLimit) {
+		return super.history(myResourceName, null, theSince, theLimit);
+	}
+
 	@Override
 	public List<T> history(IdDt theId) {
 		ArrayList<T> retVal = new ArrayList<T>();
@@ -138,11 +144,11 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 		// myEntityManager.createQuery(criteriaQuery);
 		List<ResourceHistoryTable> results = q.getResultList();
 		for (ResourceHistoryTable next : results) {
-			retVal.add(toResource(myResourceType,next));
+			retVal.add(toResource(myResourceType, next));
 		}
 
 		try {
-			retVal.add(read(theId));
+			retVal.add(read(theId.withoutVersion()));
 		} catch (ResourceNotFoundException e) {
 			// ignore
 		}
@@ -154,20 +160,61 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 		return retVal;
 	}
 
+	@Override
+	public List<IResource> history(Long theId, Date theSince, Integer theLimit) {
+		return super.history(myResourceName, theId, theSince, theLimit);
+	}
+
 	@PostConstruct
 	public void postConstruct() {
 		myResourceName = getContext().getResourceDefinition(myResourceType).getName();
 	}
 
-	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
 	public T read(IdDt theId) {
-		ResourceTable entity = readEntity(theId);
+		BaseHasResource entity = readEntity(theId);
 
-		T retVal = toResource(myResourceType,entity);
+		T retVal = toResource(myResourceType, entity);
 		return retVal;
 	}
 
+	@Override
+	public BaseHasResource readEntity(IdDt theId) {
+		BaseHasResource entity = myEntityManager.find(ResourceTable.class, theId.asLong());
+		if (theId.hasUnqualifiedVersionId()) {
+			if (entity.getVersion() != theId.getUnqualifiedVersionIdAsLong()) {
+				entity = null;
+			}
+		}
+
+		if (entity == null) {
+			if (theId.hasUnqualifiedVersionId()) {
+				entity = myEntityManager.find(ResourceHistoryTable.class, new ResourceHistoryTablePk(myResourceName, theId.asLong(), theId.getUnqualifiedVersionIdAsLong()));
+			}
+			if (entity == null) {
+				throw new ResourceNotFoundException(theId);
+			}
+		}
+		return entity;
+	}
+
+	@Override
+	public void removeTag(IdDt theId, String theScheme, String theTerm) {
+		BaseHasResource entity = readEntity(theId);
+		if (entity == null) {
+			throw new ResourceNotFoundException(theId);
+		}
+
+		for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
+			if (next.getTag().getScheme().equals(theScheme) && next.getTag().getTerm().equals(theTerm)) {
+				myEntityManager.remove(next);
+				entity.getTags().remove(next);
+			}
+		}
+
+		myEntityManager.merge(entity);
+	}
+
 	@Override
 	public List<T> search(Map<String, IQueryParameterType> theParams) {
 		SearchParameterMap map = new SearchParameterMap();
@@ -178,11 +225,6 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 		return search(map);
 	}
 
-	@Override
-	public List<T> history() {
-		return null;
-	}
-	
 	@Override
 	public List<T> search(SearchParameterMap theParams) {
 
@@ -209,23 +251,13 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 
 			List<T> retVal = new ArrayList<T>();
 			for (ResourceTable next : q.getResultList()) {
-				T resource = toResource(myResourceType,next);
+				T resource = toResource(myResourceType, next);
 				retVal.add(resource);
 			}
 			return retVal;
 		}
 	}
 
-	@Override
-	public List<IResource> history(Date theSince, int theLimit) {
-		return super.history(myResourceName, null, theSince, theLimit);
-	}
-
-	@Override
-	public List<IResource> history(Long theId, Date theSince, int theLimit) {
-		return super.history(myResourceName, theId, theSince, theLimit);
-	}
-	
 	@Override
 	public List<T> search(String theParameterName, IQueryParameterType theValue) {
 		return search(Collections.singletonMap(theParameterName, theValue));
@@ -311,27 +343,24 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 		myResourceType = (Class<T>) theTableType;
 	}
 
-	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
 	public MethodOutcome update(final T theResource, final IdDt theId) {
 
-//		TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
+		// TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
-//		ResourceTable savedEntity = template.execute(new TransactionCallback<ResourceTable>() {
+		// ResourceTable savedEntity = template.execute(new TransactionCallback<ResourceTable>() {
-//			@Override
+		// @Override
-//			public ResourceTable doInTransaction(TransactionStatus theStatus) {
+		// public ResourceTable doInTransaction(TransactionStatus theStatus) {
-//				final ResourceTable entity = readEntity(theId);
+		// final ResourceTable entity = readEntity(theId);
-//				return updateEntity(theResource, entity,true);
+		// return updateEntity(theResource, entity,true);
-//			}
+		// }
-//		});
+		// });
 
-		final ResourceTable entity = readEntity(theId);
+		final ResourceTable entity = readEntityLatestVersion(theId);
-		ResourceTable savedEntity = updateEntity(theResource, entity,true);
+		ResourceTable savedEntity = updateEntity(theResource, entity, true);
 
 		return toMethodOutcome(savedEntity);
 	}
 
-	
-
 	private Set<Long> addPredicateDate(Set<Long> thePids, List<IQueryParameterType> theOrParams) {
 		if (theOrParams == null || theOrParams.isEmpty()) {
 			return thePids;
@@ -501,7 +530,7 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 					IdDt dt = new IdDt(resourceId);
 					resourceId = dt.getUnqualifiedId();
 				}
-				
+
 				if (isBlank(ref.getChain())) {
 					Long targetPid = Long.valueOf(resourceId);
 					ourLog.info("Searching for resource link with target PID: {}", targetPid);
@@ -667,7 +696,7 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 		return new HashSet<Long>(q.getResultList());
 	}
 
-	private ResourceTable readEntity(IdDt theId) {
+	private ResourceTable readEntityLatestVersion(IdDt theId) {
 		ResourceTable entity = myEntityManager.find(ResourceTable.class, theId.asLong());
 		if (entity == null) {
 			throw new ResourceNotFoundException(theId);
@@ -709,13 +738,4 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 		}
 	}
 
-	@Override
-	protected IFhirResourceDao<? extends IResource> getDao(Class<? extends IResource> theType) {
-		if (theType.equals(myResourceType)) {
-			return this;
-		}
-		return super.getDao(theType);
-	}
-
-
 }

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

@@ -15,11 +15,13 @@ import javax.persistence.criteria.CriteriaQuery;
 import javax.persistence.criteria.Predicate;
 import javax.persistence.criteria.Root;
 
+import org.hamcrest.generator.qdox.parser.structs.TagDef;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.jpa.entity.TagDefinition;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
@@ -109,44 +111,13 @@ public class FhirSystemDao extends BaseFhirDao implements IFhirSystemDao {
 	}
 
 	@Override
-	public List<IResource> history(Date theSince, int theLimit) {
+	public List<IResource> history(Date theSince, Integer theLimit) {
 		return super.history(null, null, theSince, theLimit);
 	}
 
 	@Override
 	public TagList getAllTags() {
-		// CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
+		return super.getTags(null, null);
-		// CriteriaQuery<Tuple> cq = builder.createQuery(Tag)
-		// Root<?> from = cq.from(ResourceTable.class);
-		// cq.multiselect(from.get("myId").as(Long.class), from.get("myUpdated").as(Date.class));
-		//
-		// List<Predicate> predicates = new ArrayList<Predicate>();
-		// if (theSince != null) {
-		// Predicate low = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theSince);
-		// predicates.add(low);
-		// }
-		//
-		// if (theResourceName != null) {
-		// predicates.add(builder.equal(from.get("myResourceType"), theResourceName));
-		// }
-		// if (theId != null) {
-		// predicates.add(builder.equal(from.get("myId"), theId));
-		// }
-		//
-		// cq.where(builder.and(predicates.toArray(new Predicate[0])));
-		//
-		// cq.orderBy(builder.desc(from.get("myUpdated")));
-		// TypedQuery<Tuple> q = myEntityManager.createQuery(cq);
-		// if (theLimit > 0) {
-		// q.setMaxResults(theLimit);
-		// }
-		// for (Tuple next : q.getResultList()) {
-		// long id = (Long) next.get(0);
-		// Date updated = (Date) next.get(1);
-		// tuples.add(new HistoryTuple(ResourceTable.class, updated, id));
-		// }
-
-		return null;
 	}
 
 }

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

@@ -5,11 +5,11 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.jpa.entity.BaseHasResource;
 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.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 
@@ -17,6 +17,20 @@ public interface IFhirResourceDao<T extends IResource> {
 
 	MethodOutcome create(T theResource);
 
+	TagList getAllResourceTags();
+
+	Class<T> getResourceType();
+
+	TagList getTags(IdDt theResourceId);
+
+	List<T> history();
+
+	List<IResource> history(Date theDate, Integer theLimit);
+
+	List<T> history(IdDt theId);
+
+	List<IResource> history(Long theId, Date theSince, Integer theLimit);
+
 	/**
 	 * 
 	 * @param theId
@@ -25,28 +39,24 @@ public interface IFhirResourceDao<T extends IResource> {
 	 */
 	T read(IdDt theId);
 
-	MethodOutcome update(T theResource, IdDt theId);
+	BaseHasResource readEntity(IdDt theId);
-
-	List<T> history(IdDt theId);
 
 	List<T> search(Map<String, IQueryParameterType> theParams);
 
-	List<T> search(String theParameterName, IQueryParameterType theValue);
-
 	List<T> search(SearchParameterMap theMap);
 
-	Class<T> getResourceType();
+	List<T> search(String theParameterName, IQueryParameterType theValue);
-
-	Set<Long> searchForIds(String theParameterName, IQueryParameterType theValue);
 
 	Set<Long> searchForIds(Map<String, IQueryParameterType> theParams);
 
+	Set<Long> searchForIds(String theParameterName, IQueryParameterType theValue);
+
 	Set<Long> searchForIdsWithAndOr(Map<String, List<List<IQueryParameterType>>> theMap);
 
-	List<T> history();
+	MethodOutcome update(T theResource, IdDt theId);
 
-	List<IResource> history(Date theDate, Integer theLimit);
+	void removeTag(IdDt theId, String theScheme, String theTerm);
 
-	List<IResource> history(Long theId, Date theSince, Integer theLimit);
+	void addTag(IdDt theId, String theScheme, String theTerm, String theLabel);
 	
 }

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

@@ -11,7 +11,6 @@ import javax.persistence.MappedSuperclass;
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
 
-import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.server.EncodingEnum;
@@ -83,4 +82,6 @@ public abstract class BaseHasResource {
 		myUpdated = theUpdated.getValue();
 	}
 
+	public abstract  BaseTag addTag(TagDefinition theDef);
+
 }

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

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.entity;
 
 import java.io.Serializable;
 
+import javax.persistence.Column;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.MappedSuperclass;
@@ -15,6 +16,9 @@ public class BaseTag implements Serializable {
 	@JoinColumn(name="TAG_ID", nullable=false)
 	private TagDefinition myTag;
 
+	@Column(name="TAG_ID", insertable=false,updatable=false)
+	private Long myTagId;
+	
 	public TagDefinition getTag() {
 		return myTag;
 	}

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

@@ -92,7 +92,16 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 	}
 
 	public void addTag(ResourceTag theTag) {
-		getTags().add(new ResourceHistoryTag(this, theTag.getTag()));
+		ResourceHistoryTag tag = new ResourceHistoryTag(this, theTag.getTag());
+		tag.setResourceType(theTag.getResourceType());
+		getTags().add(tag);
+	}
+
+	@Override
+	public BaseTag addTag(TagDefinition theDef) {
+		ResourceHistoryTag historyTag = new ResourceHistoryTag(this, theDef);
+		getTags().add(historyTag);
+		return historyTag;
 	}
 
 }

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

@@ -10,19 +10,30 @@ public class ResourceHistoryTablePk implements Serializable {
 
 	private static final long serialVersionUID = 1L;
 
-	@Column(name="PID")
+	@Column(name = "PID")
 	private Long myId;
-	
+
-	@Column(name="RES_TYPE", length=30, nullable=false)
+	@Column(name = "RES_TYPE", length = 30, nullable = false)
 	private String myResourceType;
 
-	@Column(name="VERSION", nullable=false)
+	@Column(name = "VERSION", nullable = false)
 	private Long myVersion;
 
+	public ResourceHistoryTablePk() {
+		// nothing
+	}
+
+	public ResourceHistoryTablePk(String theResourceType, Long theResourceId, Long theVersion) {
+		super();
+		myResourceType = theResourceType;
+		myId = theResourceId;
+		myVersion = theVersion;
+	}
+
 	public Long getId() {
 		return myId;
 	}
-	
+
 	public String getResourceType() {
 		return myResourceType;
 	}
@@ -43,5 +54,4 @@ public class ResourceHistoryTablePk implements Serializable {
 		myVersion = theVersion;
 	}
 
-	
 }

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

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.entity;
 
 import java.io.Serializable;
 
+import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
@@ -29,6 +30,32 @@ public class ResourceHistoryTag extends BaseTag implements Serializable {
 	}/*, foreignKey=@ForeignKey(name="FK_HT_RT")*/)
 	private ResourceHistoryTable myResourceHistory;
 
+	@Column(name = "RES_TYPE", length = ResourceTable.RESTYPE_LEN,nullable=false, insertable=false, updatable=false)
+	private String myResourceType;
+
+	@Column(name="PID", insertable=false,updatable=false)
+	private Long myResourceId;
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+
+	public void setResourceType(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+
+	public Long getResourceId() {
+		return myResourceId;
+	}
+
+
+	public void setResourceId(Long theResourceId) {
+		myResourceId = theResourceId;
+	}
+
+
 	public ResourceHistoryTag() {
 	}
 	

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

@@ -28,6 +28,8 @@ import ca.uhn.fhir.rest.server.Constants;
 @Inheritance(strategy = InheritanceType.JOINED)
 @org.hibernate.annotations.Table(appliesTo="HFJ_RESOURCE", indexes= {@Index(name="IDX_RES_DATE", columnNames= {"RES_UPDATED"})})
 public class ResourceTable extends BaseHasResource implements Serializable {
+	static final int RESTYPE_LEN = 30;
+
 	private static final long serialVersionUID = 1L;
 
 	@Column(name = "SP_HAS_LINKS")
@@ -68,7 +70,7 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	@OneToMany(mappedBy = "mySourceResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
 	private Collection<ResourceLink> myResourceLinks;
 
-	@Column(name = "RES_TYPE", length = 30)
+	@Column(name = "RES_TYPE", length = RESTYPE_LEN)
 	private String myResourceType;
 
 	@OneToMany(mappedBy = "myResource", cascade = CascadeType.ALL, fetch = FetchType.EAGER, orphanRemoval = true)
@@ -230,7 +232,10 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		return retVal;
 	}
 
-	public void addTag(TagDefinition theTag) {
+	public ResourceTag addTag(TagDefinition theTag) {
-		getTags().add(new ResourceTag(this, theTag));
+		ResourceTag tag = new ResourceTag(this, theTag);
+		tag.setResourceType(getResourceType());
+		getTags().add(tag);
+		return tag;
 	}
 }

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

@@ -14,21 +14,35 @@ import javax.persistence.Table;
 public class ResourceTag extends BaseTag {
 
 	private static final long serialVersionUID = 1L;
-	
+
-	@GeneratedValue(strategy=GenerationType.AUTO)
+	@GeneratedValue(strategy = GenerationType.AUTO)
 	@Id
 	@Column(name = "PID")
 	private Long myId;
-	
+
-	@ManyToOne(cascade= {})
+	@ManyToOne(cascade = {})
-	@JoinColumn(name = "RES_ID", referencedColumnName="RES_ID")
+	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID")
 	private ResourceTable myResource;
 
+	@Column(name = "RES_TYPE", length = ResourceTable.RESTYPE_LEN,nullable=false)
+	private String myResourceType;
+
+	@Column(name="RES_ID", insertable=false,updatable=false)
+	private Long myResourceId;
+	
+	public Long getResourceId() {
+		return myResourceId;
+	}
+
+	public void setResourceId(Long theResourceId) {
+		myResourceId = theResourceId;
+	}
+
 	public ResourceTag() {
 	}
 
 	public ResourceTag(ResourceTable theResourceTable, TagDefinition theTag) {
-		myResource=theResourceTable;
+		myResource = theResourceTable;
 		setTag(theTag);
 	}
 
@@ -36,8 +50,16 @@ public class ResourceTag extends BaseTag {
 		return myResource;
 	}
 
+	public String getResourceType() {
+		return myResourceType;
+	}
+
 	public void setResource(ResourceTable theResource) {
 		myResource = theResource;
 	}
 
+	public void setResourceType(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
 }

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

@@ -1,15 +1,20 @@
 package ca.uhn.fhir.jpa.entity;
 
 import java.io.Serializable;
+import java.util.Collection;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
+import javax.persistence.OneToMany;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
+import ca.uhn.fhir.model.api.Tag;
+
 @Entity
 @Table(name = "HFJ_TAG_DEF", uniqueConstraints= {@UniqueConstraint(columnNames= {"TAG_SCHEME","TAG_TERM"})})
 //@org.hibernate.annotations.Table(appliesTo="HFJ_TAG", indexes= {@Index(name)})
@@ -17,6 +22,12 @@ public class TagDefinition implements Serializable {
 
 	private static final long serialVersionUID = 1L;
 
+	@OneToMany(cascade= {}, fetch= FetchType.LAZY, mappedBy= "myTag")
+	private Collection<ResourceTag> myResources;
+
+	@OneToMany(cascade= {}, fetch= FetchType.LAZY, mappedBy= "myTag")
+	private Collection<ResourceHistoryTag> myResourceVersions;
+
 	@Id
 	@GeneratedValue(strategy = GenerationType.AUTO)
 	@Column(name = "TAG_ID")
@@ -64,4 +75,8 @@ public class TagDefinition implements Serializable {
 		myTerm = theTerm;
 	}
 
+	public Tag toTag() {
+		return new Tag( getTerm(), getLabel(),getScheme());
+	}
+
 }

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

@@ -10,9 +10,11 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 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.annotation.Count;
 import ca.uhn.fhir.rest.annotation.Create;
+import ca.uhn.fhir.rest.annotation.GetTags;
 import ca.uhn.fhir.rest.annotation.History;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Read;
@@ -25,30 +27,55 @@ import ca.uhn.fhir.rest.server.IResourceProvider;
 
 public class JpaResourceProvider<T extends IResource> implements IResourceProvider {
 
-	private FhirContext myContext=new FhirContext();
+	private FhirContext myContext = new FhirContext();
 	private IFhirResourceDao<T> myDao;
 
 	public JpaResourceProvider() {
-		//nothing
+		// nothing
 	}
 
 	public JpaResourceProvider(IFhirResourceDao<T> theDao) {
-		myDao=theDao;
+		myDao = theDao;
 	}
 
 	@Create
 	public MethodOutcome create(@ResourceParam T theResource) {
 		return myDao.create(theResource);
 	}
-
+	
 	public FhirContext getContext() {
 		return myContext;
 	}
-	
+
 	public IFhirResourceDao<T> getDao() {
 		return myDao;
 	}
 
+	@History
+	public List<IResource> getHistoryForResourceType(@Since Date theDate, @Count Integer theCount) {
+		return myDao.history(theDate, theCount);
+	}
+
+	@History
+	public List<IResource> getHistoryForResourceInstance(@IdParam IdDt theId, @Since Date theDate, @Count Integer theCount) {
+		return myDao.history(theId.asLong(), theDate, theCount);
+	}
+
+	@Override
+	public Class<? extends IResource> getResourceType() {
+		return myDao.getResourceType();
+	}
+
+	@GetTags
+	public TagList getTagsForResourceType() {
+		return myDao.getAllResourceTags();
+	}
+
+	@GetTags
+	public TagList getTagsForResourceInstance(@IdParam IdDt theResourceId) {
+		return myDao.getTags(theResourceId);
+	}
+
 	@History
 	public List<T> history(@IdParam IdDt theId) {
 		return myDao.history(theId);
@@ -58,7 +85,7 @@ public class JpaResourceProvider<T extends IResource> implements IResourceProvid
 	public T read(@IdParam IdDt theId) {
 		return myDao.read(theId);
 	}
-	
+
 	@Search
 	public List<T> search() {
 		return myDao.search(new HashMap<String, IQueryParameterType>());
@@ -74,19 +101,4 @@ public class JpaResourceProvider<T extends IResource> implements IResourceProvid
 		return myDao.update(theResource, theId);
 	}
 
-	@Override
-	public Class<? extends IResource> getResourceType() {
-		return myDao.getResourceType();
-	}
-
-	@History
-	public List<IResource> getHistoryServerWithCriteria(@Since Date theDate, @Count Integer theCount) {
-		return myDao.history(theDate, theCount);
-	}
-
-	@History
-	public List<IResource> getHistoryServerWithCriteria(@IdParam IdDt theId, @Since Date theDate, @Count Integer theCount) {
-		return myDao.history(theId.asLong(), theDate, theCount);
-	}
-
 }

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

@@ -6,9 +6,10 @@ import java.util.List;
 import org.springframework.beans.factory.annotation.Required;
 
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
-import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.rest.annotation.Count;
+import ca.uhn.fhir.rest.annotation.GetTags;
 import ca.uhn.fhir.rest.annotation.History;
 import ca.uhn.fhir.rest.annotation.Since;
 import ca.uhn.fhir.rest.annotation.Transaction;
@@ -38,7 +39,13 @@ public class JpaSystemProvider {
 	}
 
 	@History
-	public List<IResource> getHistoryServerWithCriteria(@Since Date theDate, @Count Integer theCount) {
+	public List<IResource> historyServer(@Since Date theDate, @Count Integer theCount) {
 		return myDao.history(theDate, theCount);
 	}
+	
+	@GetTags
+	public TagList getAllTagsOnServer() {
+		return myDao.getAllTags();
+	}
+	
 }

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

@@ -413,8 +413,8 @@ public class FhirResourceDaoTest {
 		patient.addIdentifier("urn:system", "testTagsWithCreateAndReadAndSearch");
 		patient.addName().addFamily("Tester").addGiven("Joe");
 		TagList tagList = new TagList();
-		tagList.addTag("Dog", "Puppies", null);
+		tagList.addTag(null, "Dog", "Puppies");
-		tagList.addTag("Cat", "Kittens", "http://foo");
+		tagList.addTag("http://foo", "Cat", "Kittens");
 		patient.getResourceMetadata().put(ResourceMetadataKeyEnum.TAG_LIST, tagList);
 
 		MethodOutcome outcome = ourPatientDao.create(patient);
@@ -475,7 +475,7 @@ public class FhirResourceDaoTest {
 
 		Date now2 = new Date();
 
-		Patient retrieved2 = ourPatientDao.read(outcome.getId());
+		Patient retrieved2 = ourPatientDao.read(outcome.getId().withoutVersion());
 
 		assertEquals("2", retrieved2.getId().getUnqualifiedVersionId());
 		assertEquals("002", retrieved2.getIdentifierFirstRep().getValue().getValue());
@@ -490,7 +490,11 @@ public class FhirResourceDaoTest {
 		 */
 
 		List<Patient> history = ourPatientDao.history(outcome.getId());
+
 		assertEquals(2, history.size());
+		assertEquals("1", history.get(0).getId().getUnqualifiedVersionId());
+		assertEquals("2", history.get(1).getId().getUnqualifiedVersionId());
+		assertEquals(published, history.get(0).getResourceMetadata().get(ResourceMetadataKeyEnum.PUBLISHED));
 		assertEquals(published, history.get(0).getResourceMetadata().get(ResourceMetadataKeyEnum.PUBLISHED));
 		assertEquals(updated, history.get(0).getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED));
 		assertEquals("001", history.get(0).getIdentifierFirstRep().getValue().getValue());
@@ -518,7 +522,7 @@ public class FhirResourceDaoTest {
 
 		// Update the name
 		p1.getNameFirstRep().getGivenFirstRep().setValue("testUpdateMaintainsSearchParamsBBB");
-		ourPatientDao.update(p1, p1id);
+		IdDt p1id2 = ourPatientDao.update(p1, p1id).getId();
 
 		ids = ourPatientDao.searchForIds(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsAAA"));
 		assertEquals(0, ids.size());
@@ -526,6 +530,13 @@ public class FhirResourceDaoTest {
 		ids = ourPatientDao.searchForIds(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsBBB"));
 		assertEquals(2, ids.size());
 
+		// Make sure vreads work
+		p1 = ourPatientDao.read(p1id);
+		assertEquals("testUpdateMaintainsSearchParamsAAA", p1.getNameFirstRep().getGivenAsSingleString());
+
+		p1 = ourPatientDao.read(p1id2);
+		assertEquals("testUpdateMaintainsSearchParamsBBB", p1.getNameFirstRep().getGivenAsSingleString());
+
 	}
 
 	@AfterClass

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

@@ -18,6 +18,8 @@ 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.Device;
@@ -86,6 +88,80 @@ public class FhirSystemDaoTest {
 		values = ourLocationDao.history(lid.asLong(), start, 1000);
 		assertEquals(1, values.size());
 
+	}
+
+	@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("foo", "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.getUnqualifiedVersionId() != 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.getUnqualifiedVersionId() != 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

hapi-fhir-jpaserver-base/src/test/resources/fhir-jpabase-spring-test-config.xml

@@ -13,6 +13,9 @@
 	<context:annotation-config />
 	<context:mbean-server />
 
+	<bean id="myDaoConfig" class="ca.uhn.fhir.jpa.dao.DaoConfig">
+	</bean>
+
 	<bean id="mySystemDao" class="ca.uhn.fhir.jpa.dao.FhirSystemDao">
 	</bean>
 

hapi-fhir-jpaserver-base/src/test/resources/logback-test.xml

@@ -0,0 +1,21 @@
+<configuration>
+
+	<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+		<encoder>
+			<pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n
+			</pattern>
+		</encoder>
+	</appender>
+
+	<logger name="org.eclipse" additivity="false">
+	</logger>
+
+	<logger name="ca.uhn.fhir.rest.client" additivity="false" level="trace">
+		<appender-ref ref="STDOUT" />
+	</logger>
+
+	<root level="info">
+		<appender-ref ref="STDOUT" />
+	</root>
+
+</configuration>

hapi-fhir-jpaserver-test/.classpath

@@ -19,6 +19,8 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry combineaccessrules="false" kind="src" path="/hapi-fhir-base"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/hapi-fhir-jpaserver-base"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

hapi-fhir-jpaserver-test/src/main/java/ca/uhn/fhir/jpa/test/JpaTestApp.java

@@ -17,18 +17,18 @@ public class JpaTestApp {
 	@SuppressWarnings({ "unused", "unchecked" })
 	public static void main(String[] args) throws Exception {
 		
-		ClassPathXmlApplicationContext appCtx = new ClassPathXmlApplicationContext("fhir-spring-test-config.xml");
+//		ClassPathXmlApplicationContext appCtx = new ClassPathXmlApplicationContext("fhir-spring-test-config.xml");
-		
+//		
-		IFhirResourceDao<Patient> patientDao = appCtx.getBean("myPatientDao", IFhirResourceDao.class);
+//		IFhirResourceDao<Patient> patientDao = appCtx.getBean("myPatientDao", IFhirResourceDao.class);
-		PatientResourceProvider patientRp = new PatientResourceProvider();
+//		PatientResourceProvider patientRp = new PatientResourceProvider();
-		patientRp.setDao(patientDao);
+//		patientRp.setDao(patientDao);
-		
+//		
-		IFhirResourceDao<Questionnaire> questionnaireDao = appCtx.getBean("myQuestionnaireDao", IFhirResourceDao.class);
+//		IFhirResourceDao<Questionnaire> questionnaireDao = appCtx.getBean("myQuestionnaireDao", IFhirResourceDao.class);
-		QuestionnaireResourceProvider questionnaireRp = new QuestionnaireResourceProvider();
+//		QuestionnaireResourceProvider questionnaireRp = new QuestionnaireResourceProvider();
-		questionnaireRp.setDao(questionnaireDao);
+//		questionnaireRp.setDao(questionnaireDao);
-		
+//		
-		RestfulServer restServer = new RestfulServer();
+//		RestfulServer restServer = new RestfulServer();
-		restServer.setResourceProviders(patientRp, questionnaireRp);
+//		restServer.setResourceProviders(patientRp, questionnaireRp);
 		
 		int myPort = 8888;
 		Server server = new Server(myPort);
@@ -37,15 +37,16 @@ public class JpaTestApp {
 		proxyHandler.setContextPath("/");
 
 		RestfulServerTesterServlet testerServlet = new RestfulServerTesterServlet();
-		testerServlet.setServerBase("http://localhost:" + myPort + "/fhir/context");
+//		testerServlet.setServerBase("http://localhost:" + myPort + "/fhir/context");
-		// testerServlet.setServerBase("http://fhir.healthintersections.com.au/open");
+		 testerServlet.setServerBase("http://fhir.healthintersections.com.au/open");
 		ServletHolder handler = new ServletHolder();
+		handler.setName("Tester");
 		handler.setServlet(testerServlet);
 		proxyHandler.addServlet(handler, "/fhir/tester/*");
 
-		ServletHolder servletHolder = new ServletHolder();
+//		ServletHolder servletHolder = new ServletHolder();
-		servletHolder.setServlet(restServer);
+//		servletHolder.setServlet(restServer);
-		proxyHandler.addServlet(servletHolder, "/fhir/context/*");
+//		proxyHandler.addServlet(servletHolder, "/fhir/context/*");
 
 		server.setHandler(proxyHandler);
 		server.start();

hapi-fhir-jpaserver-test/src/test/java/ca/uhn/fhir/jpa/test/CompleteResourceProviderTest.java

@@ -13,6 +13,7 @@ import org.springframework.context.support.ClassPathXmlApplicationContext;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu.resource.Observation;
@@ -157,7 +158,7 @@ public class CompleteResourceProviderTest {
 		RestfulServer restServer = new RestfulServer();
 		restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
 
-		int myPort = 8888;
+		int myPort = RandomServerPortProvider.findFreePort();
 		ourServer = new Server(myPort);
 
 		ServletContextHandler proxyHandler = new ServletContextHandler();

hapi-fhir-jpaserver-test/src/test/java/ca/uhn/fhir/jpa/test/SystemTest.java

@@ -16,6 +16,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.provider.JpaSystemProvider;
+import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.dstu.resource.Observation;
@@ -82,7 +83,7 @@ public class SystemTest {
 		restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
 		restServer.setPlainProviders(new JpaSystemProvider(systemDao));
 
-		int myPort = 8888;
+		int myPort = RandomServerPortProvider.findFreePort();
 		ourServer = new Server(myPort);
 
 		ServletContextHandler proxyHandler = new ServletContextHandler();

hapi-fhir-jpaserver-test/src/test/java/ca/uhn/fhir/jpa/testutil/RandomServerPortProvider.java

@@ -0,0 +1,36 @@
+package ca.uhn.fhir.jpa.testutil;
+
+import java.io.IOException;
+import java.net.ServerSocket;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Provides server ports
+ */
+public class RandomServerPortProvider {
+
+	private static List<Integer> ourPorts = new ArrayList<Integer>(); 
+	
+	public static int findFreePort() {
+		ServerSocket server;
+		try {
+			server = new ServerSocket(0);
+			int port = server.getLocalPort();
+			ourPorts.add(port);
+			server.close();
+			Thread.sleep(500);
+			return port;
+		} catch (IOException e) {
+			throw new Error(e);
+		} catch (InterruptedException e) {
+			throw new Error(e);
+		}
+	}
+
+	public static List<Integer> list() {
+		return ourPorts;
+	}
+
+}
+ 

hapi-fhir-jpaserver-test/src/test/resources/fhir-spring-test-config.xml

@@ -13,6 +13,12 @@
 	<context:annotation-config />
 	<context:mbean-server />
 
+	<bean id="myDaoConfig" class="ca.uhn.fhir.jpa.dao.DaoConfig">
+	</bean>
+
+	<bean id="mySystemDao" class="ca.uhn.fhir.jpa.dao.FhirSystemDao">
+	</bean>
+
 	<bean id="myPatientDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
 		<property name="resourceType" value="ca.uhn.fhir.model.dstu.resource.Patient"/>
 	</bean>
@@ -29,9 +35,6 @@
 		<property name="resourceType" value="ca.uhn.fhir.model.dstu.resource.Questionnaire"/>
 	</bean>
 
-	<bean id="mySystemDao" class="ca.uhn.fhir.jpa.dao.FhirSystemDao">
-	</bean>
-
 	<bean id="myPersistenceDataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource" lazy-init="true">
 		<property name="url" value="jdbc:derby:memory:myUnitTestDB;create=true" />
 		<!-- <property name="url" value="jdbc:derby:directory:myUnitTestDB;create=true" />  -->

hapi-fhir-jpaserver-uhnfhirtest/src/main/resources/fhir-spring-uhnfhirtest-config.xml

@@ -15,6 +15,9 @@
 
 	<!-- <import resource="classpath:hapi-jpaserver-springbeans.xml" /> -->
 
+	<bean id="myDaoConfig" class="ca.uhn.fhir.jpa.dao.DaoConfig">
+	</bean>
+
 	<bean id="mySystemDao" class="ca.uhn.fhir.jpa.dao.FhirSystemDao">
 	</bean>