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

hapi-fhir-base-test-mindeps-server/pom.xml

@@ -25,6 +25,18 @@
 			<artifactId>slf4j-simple</artifactId>
 			<version>1.7.7</version>
 		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>slf4j-simple</artifactId>
+			<version>1.7.7</version>
+		</dependency>
+
+		<!-- Xiaomi phones depend on an old version of this... See #394 -->
+		<dependency>
+		    <groupId>org.apache.commons</groupId>
+		    <artifactId>commons-lang3</artifactId>
+		    <version>3.2</version><!--$NO-MVN-MAN-VER$-->
+		</dependency>
 		
 		<!--
 		Woodstox note: The hapi-fhir-base-testmindeps-client project includes no Woodstox at all, so that we use the

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

@@ -27,6 +27,7 @@ import java.io.Reader;
 import java.io.StringReader;
 import java.io.StringWriter;
 import java.io.Writer;
+import java.lang.reflect.Modifier;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -43,6 +44,7 @@ import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
 import org.hl7.fhir.instance.model.api.IBaseElement;
+import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
 import org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions;
 import org.hl7.fhir.instance.model.api.IBaseMetaType;
@@ -65,7 +67,6 @@ import ca.uhn.fhir.context.RuntimeChildContainedResources;
 import ca.uhn.fhir.context.RuntimeChildNarrativeDefinition;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.Bundle;
-import ca.uhn.fhir.model.api.BundleEntry;
 import ca.uhn.fhir.model.api.IIdentifiableElement;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
@@ -81,6 +82,7 @@ public abstract class BaseParser implements IParser {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
 
 	private ContainedResources myContainedResources;
+
 	private FhirContext myContext;
 	private Set<String> myDontEncodeElements;
 	private boolean myDontEncodeElementsIncludesStars;
@@ -95,7 +97,6 @@ public abstract class BaseParser implements IParser {
 	private boolean myStripVersionsFromReferences = true;
 	private boolean mySummaryMode;
 	private boolean mySuppressNarratives;
-
 	/**
 	 * Constructor
 	 * 
@@ -395,6 +396,51 @@ public abstract class BaseParser implements IParser {
 		return retVal;
 	}
 
+	@SuppressWarnings("unchecked")
+	ChildNameAndDef getChildNameAndDef(BaseRuntimeChildDefinition theChild, IBase theValue) {
+		Class<? extends IBase> type = theValue.getClass();
+		String childName = theChild.getChildNameByDatatype(type);
+		BaseRuntimeElementDefinition<?> childDef = theChild.getChildElementDefinitionByDatatype(type);
+		if (childDef == null) {
+			if (theValue instanceof IBaseExtension) {
+				return null;
+			}
+			
+			/*
+			 * For RI structures Enumeration class, this replaces the child def
+			 * with the "code" one. This is messy, and presumably there is a better
+			 * way..
+			 */
+			BaseRuntimeElementDefinition<?> elementDef = myContext.getElementDefinition(type);
+			if (elementDef.getName().equals("code")) {
+				Class<? extends IBase> type2 = myContext.getElementDefinition("code").getImplementingClass();
+				childDef = theChild.getChildElementDefinitionByDatatype(type2);
+				childName = theChild.getChildNameByDatatype(type2);
+			}
+
+			// See possibly the user has extended a built-in type without
+			// declaring it anywhere, as in XmlParserDstu3Test#testEncodeUndeclaredBlock
+			if (childDef == null) {
+				Class<?> nextSuperType = theValue.getClass();
+				while (IBase.class.isAssignableFrom(nextSuperType) && childDef == null) {
+					if (Modifier.isAbstract(nextSuperType.getModifiers()) == false) {
+						BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition((Class<? extends IBase>) nextSuperType);
+						Class<?> nextChildType = def.getImplementingClass();
+						childDef = theChild.getChildElementDefinitionByDatatype((Class<? extends IBase>) nextChildType);
+						childName = theChild.getChildNameByDatatype((Class<? extends IBase>) nextChildType);
+					}
+					nextSuperType = nextSuperType.getSuperclass();
+				}
+			}
+			
+			if (childDef == null) {
+				throwExceptionForUnknownChildType(theChild, type);
+			}
+		}
+		
+		return new ChildNameAndDef(childName, childDef);
+	}
+
 	protected String getCompositeElementId(IBase theElement) {
 		String elementId = null;
 		if (!(theElement instanceof IBaseResource)) {
@@ -882,6 +928,26 @@ public abstract class BaseParser implements IParser {
 		return false;
 	}
 
+	class ChildNameAndDef {
+
+		private final BaseRuntimeElementDefinition<?> myChildDef;
+		private final String myChildName;
+
+		public ChildNameAndDef(String theChildName, BaseRuntimeElementDefinition<?> theChildDef) {
+			myChildName = theChildName;
+			myChildDef = theChildDef;
+		}
+
+		public BaseRuntimeElementDefinition<?> getChildDef() {
+			return myChildDef;
+		}
+
+		public String getChildName() {
+			return myChildName;
+		}
+
+	}
+
 	protected class CompositeChildElement {
 		private final BaseRuntimeChildDefinition myDef;
 		private final CompositeChildElement myParent;

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

@@ -612,13 +612,13 @@ public class JsonParser extends BaseParser implements IParser {
 					}
 				}
 
-				Class<? extends IBase> type = nextValue.getClass();
+				BaseParser.ChildNameAndDef childNameAndDef = super.getChildNameAndDef(nextChild, nextValue);
-
+				if (childNameAndDef == null) {
-				String childName = nextChild.getChildNameByDatatype(type);
+					continue;
-				BaseRuntimeElementDefinition<?> childDef = nextChild.getChildElementDefinitionByDatatype(type);
-				if (childDef == null) {
-					super.throwExceptionForUnknownChildType(nextChild, type);
 				}
+				
+				String childName = childNameAndDef.getChildName();
+				BaseRuntimeElementDefinition<?> childDef = childNameAndDef.getChildDef();
 				boolean primitive = childDef.getChildType() == ChildTypeEnum.PRIMITIVE_DATATYPE;
 
 				if ((childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES || childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCE_LIST) && theContainedResource) {

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

@@ -236,12 +236,6 @@ public class XmlParser extends BaseParser implements IParser {
 
 						break;
 					}
-					case XMLStreamConstants.ATTRIBUTE: {
-						Attribute elem = (Attribute) nextEvent;
-						String name = (elem.getName().getLocalPart());
-						parserState.attributeValue(name, elem.getValue());
-						break;
-					}
 					case XMLStreamConstants.END_DOCUMENT:
 					case XMLStreamConstants.END_ELEMENT: {
 						if (!heldComments.isEmpty()) {
@@ -649,31 +643,14 @@ public class XmlParser extends BaseParser implements IParser {
 						continue;
 					}
 					
-					Class<? extends IBase> type = nextValue.getClass();
+					BaseParser.ChildNameAndDef childNameAndDef = super.getChildNameAndDef(nextChild, nextValue);
-					String childName = nextChild.getChildNameByDatatype(type);
+					if (childNameAndDef == null) {
-					String extensionUrl = nextChild.getExtensionUrl();
-					BaseRuntimeElementDefinition<?> childDef = nextChild.getChildElementDefinitionByDatatype(type);
-					if (childDef == null) {
-						if (nextValue instanceof IBaseExtension) {
 						continue;
 					}
 					
-						/*
+					String childName = childNameAndDef.getChildName();
-						 * For RI structures Enumeration class, this replaces the child def
+					BaseRuntimeElementDefinition<?> childDef = childNameAndDef.getChildDef();
-						 * with the "code" one. This is messy, and presumably there is a better
+					String extensionUrl = nextChild.getExtensionUrl();
-						 * way..
-						 */
-						BaseRuntimeElementDefinition<?> elementDef = myContext.getElementDefinition(type);
-						if (elementDef.getName().equals("code")) {
-							Class type2 = myContext.getElementDefinition("code").getImplementingClass();
-							childDef = nextChild.getChildElementDefinitionByDatatype(type2);
-							childName = nextChild.getChildNameByDatatype(type2);
-						}
-					
-						if (childDef == null) {
-							super.throwExceptionForUnknownChildType(nextChild, type);
-						}
-					}
 					
 					if (nextValue instanceof IBaseExtension && myContext.getVersion().getVersion() == FhirVersionEnum.DSTU1) {
 						// This is called for the Query resource in DSTU1 only

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

@@ -61,6 +61,7 @@ public class XmlUtil {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlUtil.class);
 	private static volatile XMLOutputFactory ourOutputFactory;
 	private static XMLOutputFactory ourFragmentOutputFactory;
+	private static Throwable ourNextException;
 	private static final Map<String, Integer> VALID_ENTITY_NAMES;
 	private static final ExtendedEntityReplacingXmlResolver XML_RESOLVER = new ExtendedEntityReplacingXmlResolver();
 
@@ -1519,6 +1520,8 @@ public class XmlUtil {
 	}
 
 	public static XMLEventReader createXmlReader(Reader reader) throws FactoryConfigurationError, XMLStreamException {
+		throwUnitTestExceptionIfConfiguredToDoSo();
+		
 		XMLInputFactory inputFactory = getOrCreateInputFactory();
 
 		// Now.. create the reader and return it
@@ -1526,7 +1529,19 @@ public class XmlUtil {
 		return er;
 	}
 
+	private static void throwUnitTestExceptionIfConfiguredToDoSo() throws FactoryConfigurationError, XMLStreamException {
+		if (ourNextException != null) {
+			if (ourNextException instanceof FactoryConfigurationError) {
+				throw ((FactoryConfigurationError)ourNextException);
+			} else {
+				throw (XMLStreamException)ourNextException;
+			}
+		}
+	}
+
 	public static XMLStreamWriter createXmlStreamWriter(Writer theWriter) throws FactoryConfigurationError, XMLStreamException {
+		throwUnitTestExceptionIfConfiguredToDoSo();
+		
 		XMLOutputFactory outputFactory = getOrCreateOutputFactory();
 		XMLStreamWriter retVal = outputFactory.createXMLStreamWriter(theWriter);
 		return retVal;
@@ -1720,4 +1735,11 @@ public class XmlUtil {
 
 	}
 
+	/**
+	 * FOR UNIT TESTS ONLY - Throw this exception for the next operation
+	 */
+	static void setThrowExceptionForUnitTest(Throwable theException) {
+		ourNextException = theException;
+	}
+
 }

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

@@ -166,7 +166,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 	public List<VersionIndependentConcept> findCodesAbove(String theSystem, String theCode) {
 		TermCodeSystem cs = getCodeSystem(theSystem);
 		if (cs == null) {
-			return Collections.emptyList();
+			return findCodesAboveUsingBuiltInSystems(theSystem, theCode);
 		}
 		TermCodeSystemVersion csv = cs.getCurrentVersion();
 
@@ -198,7 +198,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 	public List<VersionIndependentConcept> findCodesBelow(String theSystem, String theCode) {
 		TermCodeSystem cs = getCodeSystem(theSystem);
 		if (cs == null) {
-			return Collections.emptyList();
+			return findCodesBelowUsingBuiltInSystems(theSystem, theCode);
 		}
 		TermCodeSystemVersion csv = cs.getCurrentVersion();
 
@@ -207,6 +207,24 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		return retVal;
 	}
 
+	/**
+	 * Subclasses may override
+	 * @param theSystem The code system
+	 * @param theCode The code
+	 */
+	protected List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
+		return Collections.emptyList();
+	}
+
+	/**
+	 * Subclasses may override
+	 * @param theSystem The code system
+	 * @param theCode The code
+	 */
+	protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
+		return Collections.emptyList();
+	}
+
 	private TermCodeSystemVersion findCurrentCodeSystemVersionForSystem(String theCodeSystem) {
 		TermCodeSystem cs = getCodeSystem(theCodeSystem);
 		if (cs == null || cs.getCurrentVersion() == null) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java

@@ -78,6 +78,9 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 	@Autowired
 	private ValueSetExpander myValueSetExpander;
 
+	@Autowired
+	private IValidationSupport myValidationSupport;
+	
 	private void addCodeIfNotAlreadyAdded(String system, ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
 		if (addedCodes.add(nextConcept.getCode())) {
 			ValueSetExpansionContainsComponent contains = retVal.addContains();
@@ -87,6 +90,71 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 		}
 	}
 
+	@Override
+	protected List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
+		ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
+		CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
+		if (system != null) {
+			findCodesBelow(system, theSystem, theCode, retVal);
+		}
+		return retVal;
+	}
+
+	private void findCodesBelow(CodeSystem theSystem, String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate) {
+		List<ConceptDefinitionComponent> conceptList = theSystem.getConcept();
+		findCodesBelow(theSystemString, theCode, theListToPopulate, conceptList);
+	}
+
+	private void findCodesBelow(String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate, List<ConceptDefinitionComponent> conceptList) {
+		for (ConceptDefinitionComponent next : conceptList) {
+			if (theCode.equals(next.getCode())) {
+				addAllChildren(theSystemString, next, theListToPopulate);
+			} else {
+				findCodesBelow(theSystemString, theCode, theListToPopulate, next.getConcept());
+			}
+		}
+	}
+
+	private void findCodesAbove(CodeSystem theSystem, String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate) {
+		List<ConceptDefinitionComponent> conceptList = theSystem.getConcept();
+		for (ConceptDefinitionComponent next : conceptList) {
+			addTreeIfItContainsCode(theSystemString, next, theCode, theListToPopulate);
+		}
+	}
+
+	private boolean addTreeIfItContainsCode(String theSystemString, ConceptDefinitionComponent theNext, String theCode, List<VersionIndependentConcept> theListToPopulate) {
+		boolean foundCodeInChild = false;
+		for (ConceptDefinitionComponent nextChild : theNext.getConcept()) {
+			foundCodeInChild |= addTreeIfItContainsCode(theSystemString, nextChild, theCode, theListToPopulate);
+		}
+		
+		if (theCode.equals(theNext.getCode()) || foundCodeInChild) {
+			theListToPopulate.add(new VersionIndependentConcept(theSystemString, theNext.getCode()));
+			return true;
+		}
+		
+		return false;
+	}
+
+	private void addAllChildren(String theSystemString, ConceptDefinitionComponent theCode, List<VersionIndependentConcept> theListToPopulate) {
+		if (isNotBlank(theCode.getCode())) {
+			theListToPopulate.add(new VersionIndependentConcept(theSystemString, theCode.getCode()));
+		}
+		for (ConceptDefinitionComponent nextChild : theCode.getConcept()) {
+			addAllChildren(theSystemString, nextChild, theListToPopulate);
+		}
+	}
+
+	@Override
+	protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
+		ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
+		CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
+		if (system != null) {
+			findCodesAbove(system, theSystem, theCode, retVal);
+		}
+		return retVal;
+	}
+
 	private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
 		bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
 	}

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

@@ -51,6 +51,7 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
+import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.rest.method.IRequestOperationCallback;
@@ -268,4 +269,12 @@ public abstract class BaseJpaTest {
 		return retVal;
 	}
 
+	public static Set<String> toCodes(List<VersionIndependentConcept> theConcepts) {
+		HashSet<String> retVal = new HashSet<String>();
+		for (VersionIndependentConcept next : theConcepts) {
+			retVal.add(next.getCode());
+		}
+		return retVal;
+	}
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -12,6 +12,7 @@ import org.apache.commons.io.IOUtils;
 import org.hibernate.search.jpa.FullTextEntityManager;
 import org.hibernate.search.jpa.Search;
 import org.hl7.fhir.dstu3.hapi.validation.IValidationSupport;
+import org.hl7.fhir.dstu3.model.AllergyIntolerance;
 import org.hl7.fhir.dstu3.model.Appointment;
 import org.hl7.fhir.dstu3.model.AuditEvent;
 import org.hl7.fhir.dstu3.model.Bundle;
@@ -91,6 +92,9 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	private static JpaValidationSupportChainDstu3 ourJpaValidationSupportChainDstu3;
 	private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
 
+	@Autowired
+	@Qualifier("myAllergyIntoleranceDaoDstu3")
+	protected IFhirResourceDao<AllergyIntolerance> myAllergyIntoleranceDao;
 	@Autowired
 	protected ApplicationContext myAppCtx;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java

@@ -11,6 +11,8 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
 
+import org.hl7.fhir.dstu3.model.AllergyIntolerance;
+import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceStatus;
 import org.hl7.fhir.dstu3.model.AuditEvent;
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
@@ -531,6 +533,92 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 
 	}
 
+	@Test
+	public void testSearchCodeBelowBuiltInCodesystem() {
+		AllergyIntolerance ai1 = new AllergyIntolerance();
+		ai1.setStatus(AllergyIntoleranceStatus.ACTIVE);
+		String id1 = myAllergyIntoleranceDao.create(ai1, mySrd).getId().toUnqualifiedVersionless().getValue();
+		
+		AllergyIntolerance ai2 = new AllergyIntolerance();
+		ai2.setStatus(AllergyIntoleranceStatus.CONFIRMED);
+		String id2 = myAllergyIntoleranceDao.create(ai2, mySrd).getId().toUnqualifiedVersionless().getValue();
+		
+		AllergyIntolerance ai3 = new AllergyIntolerance();
+		ai3.setStatus(AllergyIntoleranceStatus.INACTIVE);
+		String id3 = myAllergyIntoleranceDao.create(ai3, mySrd).getId().toUnqualifiedVersionless().getValue();
+		
+		SearchParameterMap params;
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam("http://hl7.org/fhir/allergy-intolerance-status", AllergyIntoleranceStatus.ACTIVE.toCode()));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id1));
+		
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam("http://hl7.org/fhir/allergy-intolerance-status", AllergyIntoleranceStatus.ACTIVE.toCode()).setModifier(TokenParamModifier.BELOW));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id1, id2));
+
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam("http://hl7.org/fhir/allergy-intolerance-status", AllergyIntoleranceStatus.CONFIRMED.toCode()).setModifier(TokenParamModifier.BELOW));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id2));
+
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam("http://hl7.org/fhir/allergy-intolerance-status", AllergyIntoleranceStatus.CONFIRMED.toCode()));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id2));
+
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam("http://hl7.org/fhir/allergy-intolerance-status", AllergyIntoleranceStatus.ENTEREDINERROR.toCode()));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), empty());
+
+		// Unknown code
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam("http://hl7.org/fhir/allergy-intolerance-status", "fooooo"));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), empty());
+
+		// Unknown system
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam("http://hl7.org/fhir/allergy-intolerance-status222222", "fooooo"));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), empty());
+
+	}
+
+	@Test
+	@Ignore
+	public void testSearchCodeBelowBuiltInCodesystemUnqualified() {
+		AllergyIntolerance ai1 = new AllergyIntolerance();
+		ai1.setStatus(AllergyIntoleranceStatus.ACTIVE);
+		String id1 = myAllergyIntoleranceDao.create(ai1, mySrd).getId().toUnqualifiedVersionless().getValue();
+		
+		AllergyIntolerance ai2 = new AllergyIntolerance();
+		ai2.setStatus(AllergyIntoleranceStatus.CONFIRMED);
+		String id2 = myAllergyIntoleranceDao.create(ai2, mySrd).getId().toUnqualifiedVersionless().getValue();
+		
+		AllergyIntolerance ai3 = new AllergyIntolerance();
+		ai3.setStatus(AllergyIntoleranceStatus.INACTIVE);
+		String id3 = myAllergyIntoleranceDao.create(ai3, mySrd).getId().toUnqualifiedVersionless().getValue();
+		
+		SearchParameterMap params;
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, AllergyIntoleranceStatus.ACTIVE.toCode()));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id1));
+		
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, AllergyIntoleranceStatus.ACTIVE.toCode()).setModifier(TokenParamModifier.BELOW));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id1, id2));
+
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, AllergyIntoleranceStatus.CONFIRMED.toCode()).setModifier(TokenParamModifier.BELOW));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id2));
+
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, AllergyIntoleranceStatus.CONFIRMED.toCode()));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id2));
+
+		params = new SearchParameterMap();
+		params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, AllergyIntoleranceStatus.ENTEREDINERROR.toCode()));
+		assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), empty());
+
+	}
+
+	
 	@Test
 	@Ignore
 	public void testSearchCodeInEmptyValueSet() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplTest.java

@@ -8,6 +8,7 @@ import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.fail;
 
+import java.util.List;
 import java.util.Set;
 
 import org.hl7.fhir.dstu3.model.CodeSystem;
@@ -102,6 +103,53 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
 
 	}
 
+	@Test
+	public void testFindCodesBelowBuiltInCodeSystem() {
+		List<VersionIndependentConcept> concepts;
+		Set<String> codes;
+
+		concepts = myTermSvc.findCodesBelow("http://hl7.org/fhir/allergy-intolerance-status", "active");
+		codes = toCodes(concepts);
+		assertThat(codes, containsInAnyOrder("active", "confirmed", "unconfirmed"));
+
+		concepts = myTermSvc.findCodesBelow("http://hl7.org/fhir/allergy-intolerance-status", "confirmed");
+		codes = toCodes(concepts);
+		assertThat(codes, containsInAnyOrder("confirmed"));
+
+		// Unknown code
+		concepts = myTermSvc.findCodesBelow("http://hl7.org/fhir/allergy-intolerance-status", "FOO");
+		codes = toCodes(concepts);
+		assertThat(codes, empty());
+
+		// Unknown system
+		concepts = myTermSvc.findCodesBelow("http://hl7.org/fhir/allergy-intolerance-status2222", "FOO");
+		codes = toCodes(concepts);
+		assertThat(codes, empty());
+	}
+
+	@Test
+	public void testFindCodesAboveBuiltInCodeSystem() {
+		List<VersionIndependentConcept> concepts;
+		Set<String> codes;
+
+		concepts = myTermSvc.findCodesAbove("http://hl7.org/fhir/allergy-intolerance-status", "active");
+		codes = toCodes(concepts);
+		assertThat(codes, containsInAnyOrder("active"));
+
+		concepts = myTermSvc.findCodesAbove("http://hl7.org/fhir/allergy-intolerance-status", "confirmed");
+		codes = toCodes(concepts);
+		assertThat(codes, containsInAnyOrder("active", "confirmed"));
+
+		// Unknown code
+		concepts = myTermSvc.findCodesAbove("http://hl7.org/fhir/allergy-intolerance-status", "FOO");
+		codes = toCodes(concepts);
+		assertThat(codes, empty());
+
+		// Unknown system
+		concepts = myTermSvc.findCodesAbove("http://hl7.org/fhir/allergy-intolerance-status2222", "FOO");
+		codes = toCodes(concepts);
+		assertThat(codes, empty());
+	}
 
 	@Test
 	public void testReindexTerminology() {

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/FooMessageHeader.java

@@ -0,0 +1,48 @@
+package ca.uhn.fhir.parser;
+
+import org.hl7.fhir.dstu3.exceptions.FHIRException;
+import org.hl7.fhir.dstu3.model.Identifier;
+import org.hl7.fhir.dstu3.model.MessageHeader;
+import org.hl7.fhir.dstu3.model.MessageHeader.MessageSourceComponent;
+
+import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+
+@ResourceDef(name = "FooMessageHeader")
+public class FooMessageHeader extends MessageHeader {
+
+	private static final long serialVersionUID = 1L;
+
+	@Block()
+	public static class FooMessageSourceComponent extends MessageHeader.MessageSourceComponent {
+
+		private static final long serialVersionUID = 1L;
+		@Child(name = "ext-messageheader-application-id", type = Identifier.class, modifier = true)
+		@Description(shortDefinition = "Message Header Application ID")
+		@Extension(url = "http://foo", definedLocally = false, isModifier = false)
+		private Identifier messageHeaderApplicationId;
+
+		/*
+		 * Get messageHeaderApplicationId
+		 */
+		public Identifier getMessageHeaderApplicationId() throws FHIRException {
+
+			if (messageHeaderApplicationId == null) {
+				messageHeaderApplicationId = new Identifier();
+			}
+			return messageHeaderApplicationId;
+		}
+
+		/*
+		 * Set messageHeaderApplicationId
+		 */
+		public void setmessageHeaderApplicationId(Identifier messageHeaderApplicationId) {
+			this.messageHeaderApplicationId = messageHeaderApplicationId;
+		}
+
+	}
+
+}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java

@@ -111,6 +111,29 @@ public class JsonParserDstu3Test {
 		assertThat(output, containsString("\"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">VALUE</div>\""));
 	}
 	
+	
+	@Test
+	public void testEncodeUndeclaredBlock() throws Exception {
+		FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
+		source.getMessageHeaderApplicationId().setValue("APPID");
+		source.setName("NAME");
+		
+		FooMessageHeader header = new FooMessageHeader();
+		header.setSource(source);
+		
+		Bundle bundle = new Bundle();
+		bundle.addEntry().setResource(header);
+		
+      IParser p = ourCtx.newJsonParser();
+      p.setPrettyPrint(true);
+
+      String encode = p.encodeResourceToString(bundle);
+      ourLog.info(encode);
+      
+      assertThat(encode, containsString("\"value\":\"APPID\""));
+	}
+
+
 	/**
 	 * See #344
 	 */

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java

@@ -34,6 +34,7 @@ import org.custommonkey.xmlunit.XMLUnit;
 import org.hamcrest.collection.IsEmptyCollection;
 import org.hamcrest.core.StringContains;
 import org.hamcrest.text.StringContainsInOrder;
+import org.hl7.fhir.dstu3.exceptions.FHIRException;
 import org.hl7.fhir.dstu3.model.Address.AddressUse;
 import org.hl7.fhir.dstu3.model.Address.AddressUseEnumFactory;
 import org.hl7.fhir.dstu3.model.AllergyIntolerance;
@@ -76,6 +77,7 @@ import org.hl7.fhir.dstu3.model.Location;
 import org.hl7.fhir.dstu3.model.Medication;
 import org.hl7.fhir.dstu3.model.MedicationOrder;
 import org.hl7.fhir.dstu3.model.MedicationStatement;
+import org.hl7.fhir.dstu3.model.MessageHeader.MessageSourceComponent;
 import org.hl7.fhir.dstu3.model.Observation;
 import org.hl7.fhir.dstu3.model.Observation.ObservationRelationshipType;
 import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
@@ -119,87 +121,6 @@ public class XmlParserDstu3Test {
 		ourCtx.setNarrativeGenerator(null);
 	}
 
-	/**
-	 * Make sure whitespace is preserved for pre tags
-	 */
-	@Test
-	public void testEncodeDivWithPreNonPrettyPrint() {
-		
-		Patient p = new Patient();
-		p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
-		
-		String output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(p);
-		ourLog.info(output);
-		
-		//@formatter:off
-		assertThat(output, stringContainsInOrder(
-			"<text><div",
-			"<p>A P TAG</p><p>",
-			"<pre>line1\nline2\nline3  <b>BOLD</b></pre>"
-		));
-		//@formatter:on
-		
-	}
-
-	
-	@Test
-	public void testEncodeDivWithPrePrettyPrint() {
-		
-		Patient p = new Patient();
-		p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
-		
-		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
-		ourLog.info(output);
-		
-		//@formatter:off
-		assertThat(output, stringContainsInOrder(
-			"   <text>",
-			"      <div",
-			"         <pre>line1\nline2\nline3  <b>BOLD</b></pre>"
-		));
-		//@formatter:on
-		
-	}
-
-	
-	@Test
-	public void testEncodeContainedWithNonLocalId() throws Exception {
-
-		Patient p = new Patient();
-		p.setId("Patient1");
-		p.setBirthDate(new SimpleDateFormat("yyyy-mm-dd HH:mm:ss").parse("2016-04-15 10:15:30"));
-
-		ProcedureRequest pr = new ProcedureRequest();
-		pr.setId("1234567");
-		pr.setSubject(new Reference(p));
-		pr.setCode(new CodeableConcept().addCoding(new Coding("breastfeeding-readiness-assessment", "Breastfeeding Readiness Assessment", "Breastfeeding Readiness Assessment")));
-//		pr.setReason(new StringType("Single Live Birth"));
-//		pr.setScheduled(new DateType(new Date()));
-		pr.setEncounter(new Reference("Live Birth Encounter"));
-		pr.setPerformer(new Reference("Charge Nurse"));
-		pr.setStatus(ProcedureRequest.ProcedureRequestStatus.PROPOSED);
-		pr.setOrderedOn(new Date());
-		pr.setOrderer(new Reference("CDS System"));
-		pr.setPriority(ProcedureRequest.ProcedureRequestPriority.ROUTINE);
-
-		GuidanceResponse.GuidanceResponseStatus status = GuidanceResponse.GuidanceResponseStatus.SUCCESS;
-
-		//@formatter:off
-		GuidanceResponse gr = new GuidanceResponse()
-				.setRequestId("123")
-				.setModule(new Reference("Evaluate Operation"))
-				.setStatus(status);
-		//@formatter:on
-
-		gr.addAction(new GuidanceResponse.GuidanceResponseActionComponent().setTitle("Action").setResource(new Reference(pr)));
-		gr.getContained().add(p);
-		gr.getContained().add(pr);
-
-		IParser parser = ourCtx.newXmlParser();
-		parser.setPrettyPrint(true);
-		ourLog.info(parser.encodeResourceToString(gr));
-	}
-
 	@Test
 	public void testBundleWithBinary() {
 		//@formatter:off
@@ -231,6 +152,7 @@ public class XmlParserDstu3Test {
 
 	}
 
+	
 	@Test
 	public void testContainedResourceInExtensionUndeclared() {
 		Patient p = new Patient();
@@ -253,6 +175,7 @@ public class XmlParserDstu3Test {
 		assertEquals("ORG", o.getName());
 	}
 
+	
 	@Test
 	public void testDuration() {
 		Encounter enc = new Encounter();
@@ -1040,6 +963,85 @@ public class XmlParserDstu3Test {
 
 	}
 
+	@Test
+	public void testEncodeContainedWithNonLocalId() throws Exception {
+
+		Patient p = new Patient();
+		p.setId("Patient1");
+		p.setBirthDate(new SimpleDateFormat("yyyy-mm-dd HH:mm:ss").parse("2016-04-15 10:15:30"));
+
+		ProcedureRequest pr = new ProcedureRequest();
+		pr.setId("1234567");
+		pr.setSubject(new Reference(p));
+		pr.setCode(new CodeableConcept().addCoding(new Coding("breastfeeding-readiness-assessment", "Breastfeeding Readiness Assessment", "Breastfeeding Readiness Assessment")));
+//		pr.setReason(new StringType("Single Live Birth"));
+//		pr.setScheduled(new DateType(new Date()));
+		pr.setEncounter(new Reference("Live Birth Encounter"));
+		pr.setPerformer(new Reference("Charge Nurse"));
+		pr.setStatus(ProcedureRequest.ProcedureRequestStatus.PROPOSED);
+		pr.setOrderedOn(new Date());
+		pr.setOrderer(new Reference("CDS System"));
+		pr.setPriority(ProcedureRequest.ProcedureRequestPriority.ROUTINE);
+
+		GuidanceResponse.GuidanceResponseStatus status = GuidanceResponse.GuidanceResponseStatus.SUCCESS;
+
+		//@formatter:off
+		GuidanceResponse gr = new GuidanceResponse()
+				.setRequestId("123")
+				.setModule(new Reference("Evaluate Operation"))
+				.setStatus(status);
+		//@formatter:on
+
+		gr.addAction(new GuidanceResponse.GuidanceResponseActionComponent().setTitle("Action").setResource(new Reference(pr)));
+		gr.getContained().add(p);
+		gr.getContained().add(pr);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setPrettyPrint(true);
+		ourLog.info(parser.encodeResourceToString(gr));
+	}
+
+	/**
+	 * Make sure whitespace is preserved for pre tags
+	 */
+	@Test
+	public void testEncodeDivWithPreNonPrettyPrint() {
+		
+		Patient p = new Patient();
+		p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
+		
+		String output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(p);
+		ourLog.info(output);
+		
+		//@formatter:off
+		assertThat(output, stringContainsInOrder(
+			"<text><div",
+			"<p>A P TAG</p><p>",
+			"<pre>line1\nline2\nline3  <b>BOLD</b></pre>"
+		));
+		//@formatter:on
+		
+	}
+
+	@Test
+	public void testEncodeDivWithPrePrettyPrint() {
+		
+		Patient p = new Patient();
+		p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
+		
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(output);
+		
+		//@formatter:off
+		assertThat(output, stringContainsInOrder(
+			"   <text>",
+			"      <div",
+			"         <pre>line1\nline2\nline3  <b>BOLD</b></pre>"
+		));
+		//@formatter:on
+		
+	}
+
 	@Test
 	public void testEncodeDoesntIncludeUuidId() {
 		Patient p = new Patient();
@@ -1396,6 +1398,27 @@ public class XmlParserDstu3Test {
 		assertThat(encoded, not(containsString("maritalStatus")));
 	}
 
+	@Test
+	public void testEncodeUndeclaredBlock() throws Exception {
+		FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
+		source.getMessageHeaderApplicationId().setValue("APPID");
+		source.setName("NAME");
+		
+		FooMessageHeader header = new FooMessageHeader();
+		header.setSource(source);
+		
+		Bundle bundle = new Bundle();
+		bundle.addEntry().setResource(header);
+		
+      IParser p = ourCtx.newXmlParser();
+      p.setPrettyPrint(true);
+
+      String encode = p.encodeResourceToString(bundle);
+      ourLog.info(encode);
+      
+      assertThat(encode, containsString("<value value=\"APPID\"/>"));
+	}
+
 	@Test
 	public void testEncodeUndeclaredExtensionWithEnumerationContent() {
 		IParser parser = ourCtx.newXmlParser();
@@ -1607,6 +1630,54 @@ public class XmlParserDstu3Test {
 		assertThat(output, containsString("<text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> John <b>SMITH </b>"));
 	}
 
+	@Test
+	public void testExceptionWithoutUrl() {
+		//@formatter:off
+		String input =
+			"<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>" + 
+			"<Patient xmlns=\"http://hl7.org/fhir\">" +
+				"<extension>" + 
+					"<valueString value=\"FOO\">" + 
+				"</extension>" +
+				"<address>" + 
+					"<line value=\"FOO\"/>" + 
+				"</address>" +
+			"</Patient>";
+		//@formatter:on
+
+		try {
+			ourCtx.newXmlParser().parseResource(Patient.class, input);
+			fail();
+		} catch (DataFormatException e) {
+			assertThat(e.toString(), containsString("Extension element has no 'url' attribute"));
+		}
+
+	}
+
+	@Test
+	public void testModifierExceptionWithoutUrl() {
+		//@formatter:off
+		String input =
+			"<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>" + 
+			"<Patient xmlns=\"http://hl7.org/fhir\">" +
+				"<modifierExtension>" + 
+					"<valueString value=\"FOO\">" + 
+				"</modifierExtension>" +
+				"<address>" + 
+					"<line value=\"FOO\"/>" + 
+				"</address>" +
+			"</Patient>";
+		//@formatter:on
+
+		try {
+			ourCtx.newXmlParser().parseResource(Patient.class, input);
+			fail();
+		} catch (DataFormatException e) {
+			assertThat(e.toString(), containsString("Extension element has no 'url' attribute"));
+		}
+
+	}
+
 	@Test
 	public void testMoreExtensions() throws Exception {
 
@@ -2713,6 +2784,7 @@ public class XmlParserDstu3Test {
 		}
 	}
 	
+	
 	/**
 	 * See #339
 	 * 

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/util/XmlUtilDstu3Test.java

@@ -0,0 +1,90 @@
+package ca.uhn.fhir.util;
+
+import static org.junit.Assert.fail;
+
+import javax.xml.parsers.FactoryConfigurationError;
+import javax.xml.stream.XMLStreamException;
+
+import org.hl7.fhir.dstu3.model.Patient;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.parser.DataFormatException;
+
+public class XmlUtilDstu3Test {
+
+	private static FhirContext ourCtx = FhirContext.forDstu3();
+	private Patient myPatient;
+	
+	@After
+	public void after() {
+		XmlUtil.setThrowExceptionForUnitTest(null);
+	}
+	
+	@Before
+	public void before() {
+		myPatient = new Patient();
+		myPatient.setId("1");
+	}
+	
+	@Test
+	public void testParseMalformed() {
+		try {
+			ourCtx.newXmlParser().parseResource("AAAAA");
+			fail();
+		} catch (DataFormatException e) {
+			// good
+		}
+	}
+	
+	public void testXmlFactoryThrowsXmlStreamException() {
+		XmlUtil.setThrowExceptionForUnitTest(new XMLStreamException("FOO"));
+		
+		try {
+			ourCtx.newXmlParser().parseResource("AAAAA");
+			fail();
+		} catch (DataFormatException e) {
+			// good
+		}
+		try {
+			ourCtx.newXmlParser().encodeResourceToString(myPatient);
+			fail();
+		} catch (ConfigurationException e) {
+			// good
+		}
+		try {
+			ourCtx.newXmlParser().encodeBundleToString(new Bundle());
+			fail();
+		} catch (ConfigurationException e) {
+			// good
+		}
+	}
+	
+	public void testXmlFactoryThrowsFactoryConfigurationError() {
+		XmlUtil.setThrowExceptionForUnitTest(new FactoryConfigurationError("FOO"));
+		
+		try {
+			ourCtx.newXmlParser().parseResource("AAAAA");
+			fail();
+		} catch (DataFormatException e) {
+			// good
+		}
+		try {
+			ourCtx.newXmlParser().encodeResourceToString(myPatient);
+			fail();
+		} catch (ConfigurationException e) {
+			// good
+		}
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+	
+}

src/changes/changes.xml

@@ -391,6 +391,10 @@
 				causing issues on some Android phones which come with an older version
 				of this library bundled. Thanks to Paolo Perliti for reporting!
 			</action>
+			<action type="fix">
+				Parser is now better able to handle encoding fields which have been
+				populated with a class that extends the expected class
+			</action>
 		</release>
 		<release version="1.5" date="2016-04-20">
 			<action type="fix" issue="339">