Merge branch 'master' of https://github.com/jamesagnew/hapi-fhir into…

… jaxrs-sever-evolution

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

@@ -195,7 +195,7 @@ public TemporalPrecisionEnum getPrecision() {
 	 */
 	public TimeZone getTimeZone() {
 		if (myTimeZoneZulu) {
-			return TimeZone.getTimeZone("Z");
+			return TimeZone.getTimeZone("GMT");
 		}
 		return myTimeZone;
 	}

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

@@ -1778,6 +1778,15 @@ public void enteringNewElement(String theNamespaceUri, String theLocalPart) thro
 					push(newState);
 					return;
 				}
+				case CONTAINED_RESOURCES:
+				case CONTAINED_RESOURCE_LIST:
+				case EXTENSION_DECLARED:
+				case PRIMITIVE_XHTML:
+				case PRIMITIVE_XHTML_HL7ORG:
+				case RESOURCE:
+				case RESOURCE_BLOCK:
+				case UNDECL_EXT:
+					break;
 				}
 			}
 

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

@@ -143,6 +143,9 @@ public Object translateQueryParametersIntoServerArgument(RequestDetails theReque
 						uriOrListParam.setValuesAsQueryTokens(ctx, unqualifiedParamName, paramList);
 						retVal.add(next, uriOrListParam);
 						break;
+					case HAS:
+						// Should not happen
+						break;
 					}
 				}
 			}

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

@@ -306,6 +306,7 @@ public static Integer findIdParameterIndex(Method theMethod, FhirContext theCont
 		return index;
 	}
 
+	@SuppressWarnings("GetClassOnAnnotation")
 	public static Integer findParamAnnotationIndex(Method theMethod, Class<?> toFind) {
 		int paramIndex = 0;
 		for (Annotation[] annotations : theMethod.getParameterAnnotations()) {

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

@@ -213,7 +213,7 @@ public boolean incomingServerRequestMatchesMethod(RequestDetails theRequest) {
 					qualifiedNames = processWhitelistAndBlacklist(qualifiedNames, temp.getQualifierWhitelist(), temp.getQualifierBlacklist());
 					methodParamsTemp.addAll(qualifiedNames);
 				}
-				if (!qualifiedParamNames.contains(name) && !qualifiedParamNames.contains(name)) { 
+				if (!qualifiedParamNames.contains(name)) { 
 					methodParamsTemp.add(name);
 				}
 			}

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

@@ -201,7 +201,11 @@ public Date getLowerBoundAsInstant() {
 			case GREATERTHAN_OR_EQUALS:
 				break;
 			case LESSTHAN:
+			case APPROXIMATE:
 			case LESSTHAN_OR_EQUALS:
+			case ENDS_BEFORE:
+			case NOT_EQUAL:
+			case STARTS_AFTER:
 				throw new IllegalStateException("Unvalid lower bound comparator: " + myLowerBound.getPrefix());
 			}
 		}
@@ -229,6 +233,10 @@ public Date getUpperBoundAsInstant() {
 				break;
 			case GREATERTHAN_OR_EQUALS:
 			case GREATERTHAN:
+			case APPROXIMATE:
+			case ENDS_BEFORE:
+			case NOT_EQUAL:
+			case STARTS_AFTER:
 				throw new IllegalStateException("Unvalid upper bound comparator: " + myUpperBound.getPrefix());
 			}
 		}

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

@@ -24,7 +24,24 @@
  */
 
 /**
- * Represents an <b>HTTP 401 Client Unauthorized</b> response, which means that the client needs to provide credentials, or has provided invalid credentials.
+ * Represents an <b>HTTP 401 Client Unauthorized</b> response, which 
+ * means that the client needs to provide credentials, or has 
+ * provided invalid credentials.
+ * <p>
+ * For security failures, you should use
+ * {@link AuthenticationException} if you want to indicate that the
+ * user could not be authenticated (e.g. credential failures), also 
+ * known as an <b>authentication</b> failure. 
+ * You should use {@link ForbiddenOperationException} if you want to 
+ * indicate that the authenticated user does not have permission to
+ * perform the requested operation, also known as an <b>authorization</b>
+ * failure.
+ * </p>
+ * <p>
+ * Note that a complete list of RESTful exceptions is available in the <a href="./package-summary.html">Package
+ * Summary</a>.
+ * </p>
+ 
  */
 @CoverageIgnore
 public class AuthenticationException extends BaseServerResponseException {

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

@@ -33,6 +33,16 @@
  * </ul>
  * 
  * <p>
+ * For security failures, you should use
+ * {@link AuthenticationException} if you want to indicate that the
+ * user could not be authenticated (e.g. credential failures), also 
+ * known as an <b>authentication</b> failure. 
+ * You should use {@link ForbiddenOperationException} if you want to 
+ * indicate that the authenticated user does not have permission to
+ * perform the requested operation, also known as an <b>authorization</b>
+ * failure.
+ * </p>
+ * <p>
  * Note that a complete list of RESTful exceptions is available in the <a href="./package-summary.html">Package
  * Summary</a>.
  * </p>

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

@@ -110,7 +110,7 @@ private String format(String theResultBody, EncodingEnum theEncodingEnum) {
 						b.append(nextChar);
 						b.append("</span>");
 						inValue = false;
-					} else if (nextChar == '}' || nextChar == '}' || nextChar == ',') {
+					} else if (nextChar == '{' || nextChar == '}' || nextChar == ',') {
 						b.append("<span class='hlControl'>");
 						b.append(nextChar);
 						b.append("</span>");

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleImplConditional.java

@@ -50,6 +50,7 @@ public Verdict applyRule(RestOperationTypeEnum theOperation, RequestDetails theR
 		if (theOperation == myOperationType) {
 			switch (myAppliesTo) {
 			case ALL_RESOURCES:
+			case INSTANCES:
 				break;
 			case TYPES:
 				if (theInputResource == null || !myAppliesToTypes.contains(theInputResource.getClass())) {

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

@@ -109,6 +109,10 @@ public void contextInitialized(ServletContextEvent theSce) {
 				case DSTU3:
 					theSce.getServletContext().setInitParameter(ContextLoader.CONFIG_LOCATION_PARAM, FhirServerConfigDstu3.class.getName());
 					break;
+				case DSTU1:
+				case DSTU2_1:
+				case DSTU2_HL7ORG:
+					break;
 				}
 				cll.contextInitialized(theSce);
 			}

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

@@ -909,12 +909,19 @@ public void reindex(T theResource, ResourceTable theEntity) {
 		updateEntity(theResource, theEntity, null, true, false, theEntity.getUpdatedDate());
 	}
 
+	@Override
+	public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm) {
+		removeTag(theId, theTagType, theScheme, theTerm, null);
+	}
+
 	@Override
 	public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, RequestDetails theRequestDetails) {
 		// Notify interceptors
-		ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theId);
-		notifyInterceptors(RestOperationTypeEnum.DELETE_TAGS, requestDetails);
-
+		if (theRequestDetails != null) {
+			ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theId);
+			notifyInterceptors(RestOperationTypeEnum.DELETE_TAGS, requestDetails);
+		}
+
 		StopWatch w = new StopWatch();
 		BaseHasResource entity = readEntity(theId);
 		if (entity == null) {

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

@@ -447,6 +447,8 @@ private Bundle doTransaction(ServletRequestDetails theRequestDetails, Bundle the
 				entriesToProcess.put(nextRespEntry, outcome.getEntity());
 				break;
 			}
+			case GET:
+				break;
 			}
 		}
 

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

@@ -170,7 +170,9 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	 */
 	void reindex(T theResource, ResourceTable theEntity);
 
-	void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, RequestDetails theRequestDetails);
+	void removeTag(IIdType theId, TagTypeEnum theTagType, String theSystem, String theCode, RequestDetails theRequestDetails);
+
+	void removeTag(IIdType theId, TagTypeEnum theTagType, String theSystem, String theCode);
 
 	IBundleProvider search(Map<String, IQueryParameterType> theParams);
 

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

@@ -26,6 +26,7 @@
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
+import ca.uhn.fhir.jpa.entity.TagTypeEnum;
 import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.method.RequestDetails;
 import ca.uhn.fhir.rest.param.DateRangeParam;
@@ -38,4 +39,5 @@ public interface IFhirResourceDaoPatient<T extends IBaseResource> extends IFhirR
 
 	IBundleProvider patientTypeEverything(HttpServletRequest theServletRequest, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSortSpec, StringAndListParam theContent, StringAndListParam theNarrative, RequestDetails theRequestDetails);
 
+
 }

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

@@ -1046,6 +1046,12 @@ private Predicate createCompositeParamPart(CriteriaBuilder builder, Root<Resourc
 			retVal = createPredicateQuantity(builder, dateJoin, leftValue);
 			break;
 		}
+		case COMPOSITE:
+		case HAS:
+		case NUMBER:
+		case REFERENCE:
+		case URI:
+			break;
 		}
 
 		if (retVal == null) {
@@ -1936,6 +1942,9 @@ private void searchForIdsWithAndOr(SearchParameterMap theParams, DateRangeParam
 							}
 						}
 						break;
+					case HAS: 
+						// should not happen
+						break;
 					}
 				}
 			} 

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

@@ -455,6 +455,9 @@ private Bundle doTransaction(ServletRequestDetails theRequestDetails, Bundle the
 				entriesToProcess.put(nextRespEntry, outcome.getEntity());
 				break;
 			}
+			case GET:
+			case NULL:
+				break;
 			}
 		}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -2592,6 +2592,103 @@ public void testResourceMetaOperation() {
 
 	}
 
+	@Test
+	public void testRemoveTag() {
+
+		String methodName = "testResourceMetaOperation";
+		IIdType id1, id2;
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue(methodName);
+			patient.addName().setFamily("Tester").addGiven("Joe");
+			patient.getMeta().addTag(null, "Dog", "Puppies");
+
+			patient.getMeta().addSecurity().setSystem("seclabel:sys:1").setCode("seclabel:code:1").setDisplay("seclabel:dis:1");
+
+			patient.getMeta().addProfile(("http://profile/1"));
+
+			id1 = myPatientDao.create(patient, mySrd).getId();
+		}
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue(methodName);
+			patient.addName().setFamily("Tester").addGiven("Joe");
+
+			patient.getMeta().addTag("http://foo", "Cat", "Kittens");
+			patient.getMeta().addSecurity().setSystem("seclabel:sys:2").setCode("seclabel:code:2").setDisplay("seclabel:dis:2");
+			patient.getMeta().addProfile("http://profile/2");
+
+			id2 = myPatientDao.create(patient, mySrd).getId();
+		}
+		{
+			Device device = new Device();
+			device.addIdentifier().setSystem("urn:system").setValue(methodName);
+			device.getMeta().addTag("http://foo", "Foo", "Bars");
+			device.getMeta().addSecurity().setSystem("seclabel:sys:3").setCode("seclabel:code:3").setDisplay("seclabel:dis:3");
+			device.getMeta().addProfile("http://profile/3");
+			myDeviceDao.create(device, mySrd);
+		}
+
+		Meta meta;
+
+		meta = myPatientDao.metaGetOperation(Meta.class, mySrd);
+		List<Coding> published = meta.getTag();
+		assertEquals(2, published.size());
+		assertEquals(null, published.get(0).getSystem());
+		assertEquals("Dog", published.get(0).getCode());
+		assertEquals("Puppies", published.get(0).getDisplay());
+		assertEquals("http://foo", published.get(1).getSystem());
+		assertEquals("Cat", published.get(1).getCode());
+		assertEquals("Kittens", published.get(1).getDisplay());
+		List<Coding> secLabels = meta.getSecurity();
+		assertEquals(2, secLabels.size());
+		assertEquals("seclabel:sys:1", secLabels.get(0).getSystemElement().getValue());
+		assertEquals("seclabel:code:1", secLabels.get(0).getCodeElement().getValue());
+		assertEquals("seclabel:dis:1", secLabels.get(0).getDisplayElement().getValue());
+		assertEquals("seclabel:sys:2", secLabels.get(1).getSystemElement().getValue());
+		assertEquals("seclabel:code:2", secLabels.get(1).getCodeElement().getValue());
+		assertEquals("seclabel:dis:2", secLabels.get(1).getDisplayElement().getValue());
+		List<UriType> profiles = meta.getProfile();
+		assertEquals(2, profiles.size());
+		assertEquals("http://profile/1", profiles.get(0).getValue());
+		assertEquals("http://profile/2", profiles.get(1).getValue());
+
+		meta = myPatientDao.metaGetOperation(Meta.class, id2, mySrd);
+		published = meta.getTag();
+		assertEquals(1, published.size());
+		assertEquals("http://foo", published.get(0).getSystem());
+		assertEquals("Cat", published.get(0).getCode());
+		assertEquals("Kittens", published.get(0).getDisplay());
+		secLabels = meta.getSecurity();
+		assertEquals(1, secLabels.size());
+		assertEquals("seclabel:sys:2", secLabels.get(0).getSystemElement().getValue());
+		assertEquals("seclabel:code:2", secLabels.get(0).getCodeElement().getValue());
+		assertEquals("seclabel:dis:2", secLabels.get(0).getDisplayElement().getValue());
+		profiles = meta.getProfile();
+		assertEquals(1, profiles.size());
+		assertEquals("http://profile/2", profiles.get(0).getValue());
+
+		myPatientDao.removeTag(id1, TagTypeEnum.TAG, null, "Dog");
+		myPatientDao.removeTag(id1, TagTypeEnum.SECURITY_LABEL, "seclabel:sys:1", "seclabel:code:1");
+		myPatientDao.removeTag(id1, TagTypeEnum.PROFILE, BaseHapiFhirDao.NS_JPA_PROFILE, "http://profile/1");
+
+		meta = myPatientDao.metaGetOperation(Meta.class, mySrd);
+		published = meta.getTag();
+		assertEquals(1, published.size());
+		assertEquals("http://foo", published.get(0).getSystem());
+		assertEquals("Cat", published.get(0).getCode());
+		assertEquals("Kittens", published.get(0).getDisplay());
+		secLabels = meta.getSecurity();
+		assertEquals(1, secLabels.size());
+		assertEquals("seclabel:sys:2", secLabels.get(0).getSystemElement().getValue());
+		assertEquals("seclabel:code:2", secLabels.get(0).getCodeElement().getValue());
+		assertEquals("seclabel:dis:2", secLabels.get(0).getDisplayElement().getValue());
+		profiles = meta.getProfile();
+		assertEquals(1, profiles.size());
+		assertEquals("http://profile/2", profiles.get(0).getValue());
+
+	}
+
 	@Test
 	public void testReverseIncludes() {
 		String methodName = "testReverseIncludes";

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/model/primitive/BaseDateTimeDtDstu2Test.java

@@ -402,7 +402,7 @@ public void testInstantInLocalTimezone() {
 	public void testLargePrecision() {
 		DateTimeDt dt = new DateTimeDt("2014-03-06T22:09:58.9121174+04:30");
 
-		myDateInstantParser.setTimeZone(TimeZone.getTimeZone("Z"));
+		myDateInstantParser.setTimeZone(TimeZone.getTimeZone("GMT"));
 		assertEquals("2014-03-06 17:39:58.912", myDateInstantParser.format(dt.getValue()));
 	}
 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/BaseDateTimeType.java

@@ -307,7 +307,7 @@ public Integer getSecond() {
 	 */
 	public TimeZone getTimeZone() {
 		if (myTimeZoneZulu) {
-			return TimeZone.getTimeZone("Z");
+			return TimeZone.getTimeZone("GMT");
 		}
 		return myTimeZone;
 	}

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

@@ -162,7 +162,7 @@ private String format(String theResultBody, EncodingEnum theEncodingEnum) {
 						b.append(nextChar);
 						b.append("</span>");
 						inValue = false;
-					} else if (nextChar == '}' || nextChar == '}' || nextChar == ',') {
+					} else if (nextChar == '{' || nextChar == '}' || nextChar == ',') {
 						b.append("<span class='hlControl'>");
 						b.append(nextChar);
 						b.append("</span>");
@@ -321,6 +321,9 @@ private IBaseResource loadAndAddConf(HttpServletRequest theServletRequest, final
 			return loadAndAddConfDstu2(theServletRequest, theRequest, theModel);
 		case DSTU3:
 			return loadAndAddConfDstu3(theServletRequest, theRequest, theModel);
+		case DSTU2_1:
+		case DSTU2_HL7ORG:
+			break;
 		}
 		throw new IllegalStateException("Unknown version: " + theRequest.getFhirVersion(myConfig));
 	}

src/changes/changes.xml

@@ -63,6 +63,11 @@
 				of literal ones, meaning that the server will not try to resolve these
 				URLs. Thanks to Eeva Turkka for the suggestion!
 			</action>
+			<action type="add">
+				Add a utility method to JPA server: 
+				<![CDATA[<code>IFhirResourceDao#removeTag(IIdType, TagTypeEnum, String, String)</code>]]>. This allows client code to remove tags
+				from a resource without having a servlet request object in context.
+			</action>
 		</release>
 		<release version="2.3" date="2017-03-18">
 			<action type="add">