Add terminology delta operations (#1401)

* Start work on delta operations

* Add changelog

* Some build fixes

* Move upload terminology command to CodeSystem resource

* Updates

* Some test fixes

* Add changelog

* Some test fixes

* More test fixes

* Test fix

* Add additional tests

* Transaction boundary fixes

examples/src/main/java/example/ExampleProviders.java

@@ -48,11 +48,11 @@ public class ExampleServlet extends ca.uhn.fhir.rest.server.RestfulServer {
      */
     List<Object> plainProviders=new ArrayList<Object>();
     plainProviders.add(new PlainProvider());
-    setPlainProviders(plainProviders);
+    registerProviders(plainProviders);
     
     List<IResourceProvider> resourceProviders = new ArrayList<IResourceProvider>();
     // ...add some resource providers...
-    setResourceProviders(resourceProviders);
+	  registerProviders(resourceProviders);
   }
 	
 }

examples/src/main/java/example/ValidatorExamples.java

@@ -264,6 +264,12 @@ public class ValidatorExamples {
 				return null;
 			}
 
+			@Override
+			public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+				// TODO: implement
+				return null;
+			}
+
 			@Override
 			public StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theName) {
 				// TODO: implement

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

@@ -79,7 +79,7 @@ public class FhirContext {
 	private AddProfileTagEnum myAddProfileTagWhenEncoding = AddProfileTagEnum.ONLY_FOR_CUSTOM;
 	private volatile Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinition = Collections.emptyMap();
 	private ArrayList<Class<? extends IBase>> myCustomTypes;
-	private Map<String, Class<? extends IBaseResource>> myDefaultTypeForProfile = new HashMap<String, Class<? extends IBaseResource>>();
+	private Map<String, Class<? extends IBaseResource>> myDefaultTypeForProfile = new HashMap<>();
 	private volatile Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = Collections.emptyMap();
 	private volatile boolean myInitialized;
 	private volatile boolean myInitializing = false;
@@ -90,7 +90,7 @@ public class FhirContext {
 	private volatile INarrativeGenerator myNarrativeGenerator;
 	private volatile IParserErrorHandler myParserErrorHandler = new LenientErrorHandler();
 	private ParserOptions myParserOptions = new ParserOptions();
-	private Set<PerformanceOptionsEnum> myPerformanceOptions = new HashSet<PerformanceOptionsEnum>();
+	private Set<PerformanceOptionsEnum> myPerformanceOptions = new HashSet<>();
 	private Collection<Class<? extends IBaseResource>> myResourceTypesToScan;
 	private volatile IRestfulClientFactory myRestfulClientFactory;
 	private volatile RuntimeChildUndeclaredExtensionDefinition myRuntimeChildUndeclaredExtensionDefinition;
@@ -198,7 +198,7 @@ public class FhirContext {
 	private void ensureCustomTypeList() {
 		myClassToElementDefinition.clear();
 		if (myCustomTypes == null) {
-			myCustomTypes = new ArrayList<Class<? extends IBase>>();
+			myCustomTypes = new ArrayList<>();
 		}
 	}
 
@@ -278,14 +278,6 @@ public class FhirContext {
 		return myNameToElementDefinition.get(theElementName.toLowerCase());
 	}
 
-	/**
-	 * For unit tests only
-	 */
-	int getElementDefinitionCount() {
-		validateInitialized();
-		return myClassToElementDefinition.size();
-	}
-
 	/**
 	 * Returns all element definitions (resources, datatypes, etc.)
 	 */
@@ -741,21 +733,21 @@ public class FhirContext {
 	}
 
 	private BaseRuntimeElementDefinition<?> scanDatatype(Class<? extends IElement> theResourceType) {
-		ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<Class<? extends IElement>>();
+		ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<>();
 		resourceTypes.add(theResourceType);
 		Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> defs = scanResourceTypes(resourceTypes);
 		return defs.get(theResourceType);
 	}
 
 	private RuntimeResourceDefinition scanResourceType(Class<? extends IBaseResource> theResourceType) {
-		ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<Class<? extends IElement>>();
+		ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<>();
 		resourceTypes.add(theResourceType);
 		Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> defs = scanResourceTypes(resourceTypes);
 		return (RuntimeResourceDefinition) defs.get(theResourceType);
 	}
 
 	private synchronized Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> scanResourceTypes(Collection<Class<? extends IElement>> theResourceTypes) {
-		List<Class<? extends IBase>> typesToScan = new ArrayList<Class<? extends IBase>>();
+		List<Class<? extends IBase>> typesToScan = new ArrayList<>();
 		if (theResourceTypes != null) {
 			typesToScan.addAll(theResourceTypes);
 		}
@@ -769,7 +761,7 @@ public class FhirContext {
 			myRuntimeChildUndeclaredExtensionDefinition = scanner.getRuntimeChildUndeclaredExtensionDefinition();
 		}
 
-		Map<String, BaseRuntimeElementDefinition<?>> nameToElementDefinition = new HashMap<String, BaseRuntimeElementDefinition<?>>();
+		Map<String, BaseRuntimeElementDefinition<?>> nameToElementDefinition = new HashMap<>();
 		nameToElementDefinition.putAll(myNameToElementDefinition);
 		for (Entry<String, BaseRuntimeElementDefinition<?>> next : scanner.getNameToElementDefinitions().entrySet()) {
 			if (!nameToElementDefinition.containsKey(next.getKey())) {
@@ -777,7 +769,7 @@ public class FhirContext {
 			}
 		}
 
-		Map<String, RuntimeResourceDefinition> nameToResourceDefinition = new HashMap<String, RuntimeResourceDefinition>();
+		Map<String, RuntimeResourceDefinition> nameToResourceDefinition = new HashMap<>();
 		nameToResourceDefinition.putAll(myNameToResourceDefinition);
 		for (Entry<String, RuntimeResourceDefinition> next : scanner.getNameToResourceDefinition().entrySet()) {
 			if (!nameToResourceDefinition.containsKey(next.getKey())) {
@@ -785,7 +777,7 @@ public class FhirContext {
 			}
 		}
 
-		Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> classToElementDefinition = new HashMap<Class<? extends IBase>, BaseRuntimeElementDefinition<?>>();
+		Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> classToElementDefinition = new HashMap<>();
 		classToElementDefinition.putAll(myClassToElementDefinition);
 		classToElementDefinition.putAll(scanner.getClassToElementDefinitions());
 		for (BaseRuntimeElementDefinition<?> next : classToElementDefinition.values()) {
@@ -798,7 +790,7 @@ public class FhirContext {
 			}
 		}
 
-		Map<String, RuntimeResourceDefinition> idToElementDefinition = new HashMap<String, RuntimeResourceDefinition>();
+		Map<String, RuntimeResourceDefinition> idToElementDefinition = new HashMap<>();
 		idToElementDefinition.putAll(myIdToResourceDefinition);
 		idToElementDefinition.putAll(scanner.getIdToResourceDefinition());
 
@@ -864,9 +856,9 @@ public class FhirContext {
 		if (theResourceTypes == null) {
 			return null;
 		}
-		List<Class<? extends IElement>> resTypes = new ArrayList<Class<? extends IElement>>();
+		List<Class<? extends IElement>> resTypes = new ArrayList<>();
 		for (Class<? extends IBaseResource> next : theResourceTypes) {
-			resTypes.add((Class<? extends IElement>) next);
+			resTypes.add(next);
 		}
 		return resTypes;
 	}
@@ -924,14 +916,14 @@ public class FhirContext {
 	}
 
 	private static Collection<Class<? extends IBaseResource>> toCollection(Class<? extends IBaseResource> theResourceType) {
-		ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<Class<? extends IBaseResource>>(1);
+		ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<>(1);
 		retVal.add(theResourceType);
 		return retVal;
 	}
 
 	@SuppressWarnings("unchecked")
 	private static List<Class<? extends IBaseResource>> toCollection(Class<?>[] theResourceTypes) {
-		ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<Class<? extends IBaseResource>>(1);
+		ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<>(1);
 		for (Class<?> clazz : theResourceTypes) {
 			if (!IResource.class.isAssignableFrom(clazz)) {
 				throw new IllegalArgumentException(clazz.getCanonicalName() + " is not an instance of " + IResource.class.getSimpleName());

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

@@ -21,9 +21,21 @@ package ca.uhn.fhir.context.support;
  */
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.ParametersUtil;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
+import javax.annotation.Nonnull;
+import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /**
  * This interface is a version-independent representation of the
@@ -102,6 +114,68 @@ public interface IContextValidationSupport<EVS_IN, EVS_OUT, SDT, CST, CDCT, IST>
 	 */
 	CodeValidationResult<CDCT, IST> validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay);
 
+	/**
+	 * Look up a code using the system and code value
+	 *
+	 * @param theContext The FHIR context
+	 * @param theSystem  The CodeSystem URL
+	 * @param theCode    The code
+	 */
+	LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode);
+
+	class ConceptDesignation {
+		private String myLanguage;
+		private String myUseSystem;
+		private String myUseCode;
+		private String myUseDisplay;
+		private String myValue;
+
+		public String getLanguage() {
+			return myLanguage;
+		}
+
+		public ConceptDesignation setLanguage(String theLanguage) {
+			myLanguage = theLanguage;
+			return this;
+		}
+
+		public String getUseSystem() {
+			return myUseSystem;
+		}
+
+		public ConceptDesignation setUseSystem(String theUseSystem) {
+			myUseSystem = theUseSystem;
+			return this;
+		}
+
+		public String getUseCode() {
+			return myUseCode;
+		}
+
+		public ConceptDesignation setUseCode(String theUseCode) {
+			myUseCode = theUseCode;
+			return this;
+		}
+
+		public String getUseDisplay() {
+			return myUseDisplay;
+		}
+
+		public ConceptDesignation setUseDisplay(String theUseDisplay) {
+			myUseDisplay = theUseDisplay;
+			return this;
+		}
+
+		public String getValue() {
+			return myValue;
+		}
+
+		public ConceptDesignation setValue(String theValue) {
+			myValue = theValue;
+			return this;
+		}
+	}
+
 	abstract class BaseConceptProperty {
 		private final String myPropertyName;
 
@@ -165,7 +239,7 @@ public interface IContextValidationSupport<EVS_IN, EVS_OUT, SDT, CST, CDCT, IST>
 		}
 	}
 
-	class CodeValidationResult<CDCT, IST> {
+	abstract class CodeValidationResult<CDCT, IST> {
 		private CDCT myDefinition;
 		private String myMessage;
 		private IST mySeverity;
@@ -228,6 +302,190 @@ public interface IContextValidationSupport<EVS_IN, EVS_OUT, SDT, CST, CDCT, IST>
 			return myDefinition != null;
 		}
 
+		public LookupCodeResult asLookupCodeResult(String theSearchedForSystem, String theSearchedForCode) {
+			LookupCodeResult retVal = new LookupCodeResult();
+			retVal.setSearchedForSystem(theSearchedForSystem);
+			retVal.setSearchedForCode(theSearchedForCode);
+			if (isOk()) {
+				retVal.setFound(true);
+				retVal.setCodeDisplay(getDisplay());
+				retVal.setCodeSystemDisplayName(getCodeSystemName());
+				retVal.setCodeSystemVersion(getCodeSystemVersion());
+			}
+			return retVal;
+		}
+
+		protected abstract String getDisplay();
+
+	}
+
+	class LookupCodeResult {
+
+		private String myCodeDisplay;
+		private boolean myCodeIsAbstract;
+		private String myCodeSystemDisplayName;
+		private String myCodeSystemVersion;
+		private boolean myFound;
+		private String mySearchedForCode;
+		private String mySearchedForSystem;
+		private List<IContextValidationSupport.BaseConceptProperty> myProperties;
+		private List<ConceptDesignation> myDesignations;
+
+		/**
+		 * Constructor
+		 */
+		public LookupCodeResult() {
+			super();
+		}
+
+		public List<BaseConceptProperty> getProperties() {
+			if (myProperties == null) {
+				myProperties = new ArrayList<>();
+			}
+			return myProperties;
+		}
+
+		public void setProperties(List<IContextValidationSupport.BaseConceptProperty> theProperties) {
+			myProperties = theProperties;
+		}
+
+		@Nonnull
+		public List<ConceptDesignation> getDesignations() {
+			if (myDesignations == null) {
+				myDesignations = new ArrayList<>();
+			}
+			return myDesignations;
+		}
+
+		public String getCodeDisplay() {
+			return myCodeDisplay;
+		}
+
+		public void setCodeDisplay(String theCodeDisplay) {
+			myCodeDisplay = theCodeDisplay;
+		}
+
+		public String getCodeSystemDisplayName() {
+			return myCodeSystemDisplayName;
+		}
+
+		public void setCodeSystemDisplayName(String theCodeSystemDisplayName) {
+			myCodeSystemDisplayName = theCodeSystemDisplayName;
+		}
+
+		public String getCodeSystemVersion() {
+			return myCodeSystemVersion;
+		}
+
+		public void setCodeSystemVersion(String theCodeSystemVersion) {
+			myCodeSystemVersion = theCodeSystemVersion;
+		}
+
+		public String getSearchedForCode() {
+			return mySearchedForCode;
+		}
+
+		public LookupCodeResult setSearchedForCode(String theSearchedForCode) {
+			mySearchedForCode = theSearchedForCode;
+			return this;
+		}
+
+		public String getSearchedForSystem() {
+			return mySearchedForSystem;
+		}
+
+		public LookupCodeResult setSearchedForSystem(String theSearchedForSystem) {
+			mySearchedForSystem = theSearchedForSystem;
+			return this;
+		}
+
+		public boolean isCodeIsAbstract() {
+			return myCodeIsAbstract;
+		}
+
+		public void setCodeIsAbstract(boolean theCodeIsAbstract) {
+			myCodeIsAbstract = theCodeIsAbstract;
+		}
+
+		public boolean isFound() {
+			return myFound;
+		}
+
+		public LookupCodeResult setFound(boolean theFound) {
+			myFound = theFound;
+			return this;
+		}
+
+		public void throwNotFoundIfAppropriate() {
+			if (isFound() == false) {
+				throw new ResourceNotFoundException("Unable to find code[" + getSearchedForCode() + "] in system[" + getSearchedForSystem() + "]");
+			}
+		}
+
+		public IBaseParameters toParameters(FhirContext theContext, List<? extends IPrimitiveType<String>> theProperties) {
+
+			IBaseParameters retVal = ParametersUtil.newInstance(theContext);
+			if (isNotBlank(getCodeSystemDisplayName())) {
+				ParametersUtil.addParameterToParametersString(theContext, retVal, "name", getCodeSystemDisplayName());
+			}
+			if (isNotBlank(getCodeSystemVersion())) {
+				ParametersUtil.addParameterToParametersString(theContext, retVal, "version", getCodeSystemVersion());
+			}
+			ParametersUtil.addParameterToParametersString(theContext, retVal, "display", getCodeDisplay());
+			ParametersUtil.addParameterToParametersBoolean(theContext, retVal, "abstract", isCodeIsAbstract());
+
+			if (myProperties != null) {
+
+				Set<String> properties = Collections.emptySet();
+				if (theProperties != null) {
+					properties = theProperties
+						.stream()
+						.map(IPrimitiveType::getValueAsString)
+						.collect(Collectors.toSet());
+				}
+
+				for (IContextValidationSupport.BaseConceptProperty next : myProperties) {
+
+					if (!properties.isEmpty()) {
+						if (!properties.contains(next.getPropertyName())) {
+							continue;
+						}
+					}
+
+					IBase property = ParametersUtil.addParameterToParameters(theContext, retVal, "property");
+					ParametersUtil.addPartCode(theContext, property, "code", next.getPropertyName());
+
+					if (next instanceof IContextValidationSupport.StringConceptProperty) {
+						IContextValidationSupport.StringConceptProperty prop = (IContextValidationSupport.StringConceptProperty) next;
+						ParametersUtil.addPartString(theContext, property, "value", prop.getValue());
+					} else if (next instanceof IContextValidationSupport.CodingConceptProperty) {
+						IContextValidationSupport.CodingConceptProperty prop = (IContextValidationSupport.CodingConceptProperty) next;
+						ParametersUtil.addPartCoding(theContext, property, "value", prop.getCodeSystem(), prop.getCode(), prop.getDisplay());
+					} else {
+						throw new IllegalStateException("Don't know how to handle " + next.getClass());
+					}
+				}
+			}
+
+			if (myDesignations != null) {
+				for (ConceptDesignation next : myDesignations) {
+
+					IBase property = ParametersUtil.addParameterToParameters(theContext, retVal, "designation");
+					ParametersUtil.addPartCode(theContext, property, "language", next.getLanguage());
+					ParametersUtil.addPartCoding(theContext, property, "use", next.getUseSystem(), next.getUseCode(), next.getUseDisplay());
+					ParametersUtil.addPartString(theContext, property, "value", next.getValue());
+				}
+			}
+
+			return retVal;
+		}
+
+		public static LookupCodeResult notFound(String theSearchedForSystem, String theSearchedForCode) {
+			return new LookupCodeResult()
+				.setFound(false)
+				.setSearchedForSystem(theSearchedForSystem)
+				.setSearchedForCode(theSearchedForCode);
+		}
 	}
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Operation.java

@@ -54,15 +54,31 @@ public @interface Operation {
 	String name();
 
 	/**
-	 * On a client, this value should be populated with the resource type that the operation applies to. If set to
+	 * This value may be populated with the resource type that the operation applies to. If set to
 	 * {@link IBaseResource} (which is the default) than the operation applies to the server and not to a specific
 	 * resource type.
 	 * <p>
-	 * This value has no effect when used on server implementations.
+	 * This attribute should not be used a resource provider implementing
+	 * <code>IResourceProvider</code> since the type can be inferred from the
+	 * resource provider type.
 	 * </p>
+	 * @see #typeName() may also be used to specify a value as a String
 	 */
 	Class<? extends IBaseResource> type() default IBaseResource.class;
 
+	/**
+	 * This value may be populated with the resource type that the operation applies to. If set to
+	 * {@link IBaseResource} (which is the default) than the operation applies to the server and not to a specific
+	 * resource type.
+	 * <p>
+	 * This attribute should not be used a resource provider implementing
+	 * <code>IResourceProvider</code> since the type can be inferred from the
+	 * resource provider type.
+	 * </p>
+	 * @see #type() may also be used to specify a value for this setting as a class type
+	 */
+	String typeName() default "";
+
 	/**
 	 * If a given operation method is <b><a href="http://en.wikipedia.org/wiki/Idempotence">idempotent</a></b>
 	 * (meaning roughly that it does not modify any data or state on the server)

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

@@ -37,31 +37,30 @@ public class AttachmentUtil {
 	 */
 	@SuppressWarnings("unchecked")
 	public static IPrimitiveType<byte[]> getOrCreateData(FhirContext theContext, ICompositeType theAttachment) {
-		BaseRuntimeChildDefinition entryChild = getChild(theContext, theAttachment, "data");
+		return getOrCreateChild(theContext, theAttachment, "data", "base64Binary");
-		List<IBase> entries = entryChild.getAccessor().getValues(theAttachment);
-		return entries
-			.stream()
-			.map(t -> (IPrimitiveType<byte[]>) t)
-			.findFirst()
-			.orElseGet(() -> {
-				IPrimitiveType<byte[]> binary = newPrimitive(theContext, "base64Binary", null);
-				entryChild.getMutator().setValue(theAttachment, binary);
-				return binary;
-			});
 	}
 
 	@SuppressWarnings("unchecked")
 	public static IPrimitiveType<String> getOrCreateContentType(FhirContext theContext, ICompositeType theAttachment) {
-		BaseRuntimeChildDefinition entryChild = getChild(theContext, theAttachment, "contentType");
+		return getOrCreateChild(theContext, theAttachment, "contentType", "string");
+	}
+
+	public static IPrimitiveType<String> getOrCreateUrl(FhirContext theContext, ICompositeType theAttachment) {
+		return getOrCreateChild(theContext, theAttachment, "url", "uri");
+	}
+
+	@SuppressWarnings("unchecked")
+	private static <T> IPrimitiveType<T> getOrCreateChild(FhirContext theContext, ICompositeType theAttachment, String theChildName, String theChildDatatype) {
+		BaseRuntimeChildDefinition entryChild = getChild(theContext, theAttachment, theChildName);
 		List<IBase> entries = entryChild.getAccessor().getValues(theAttachment);
 		return entries
 			.stream()
-			.map(t -> (IPrimitiveType<String>) t)
+			.map(t -> (IPrimitiveType<T>) t)
 			.findFirst()
 			.orElseGet(() -> {
-				IPrimitiveType<String> string = newPrimitive(theContext, "string", null);
+				IPrimitiveType<String> string = newPrimitive(theContext, theChildDatatype, null);
 				entryChild.getMutator().setValue(theAttachment, string);
-				return string;
+				return (IPrimitiveType<T>) string;
 			});
 	}
 

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

@@ -61,8 +61,8 @@ public class ParametersUtil {
 			List<IBase> valueValues = valueChild.getAccessor().getValues(nextParameter);
 			valueValues
 				.stream()
-				.filter(t->t instanceof IPrimitiveType<?>)
+				.filter(t -> t instanceof IPrimitiveType<?>)
-				.map(t->((IPrimitiveType<?>)t).getValueAsString())
+				.map(t -> ((IPrimitiveType<?>) t).getValueAsString())
 				.filter(StringUtils::isNotBlank)
 				.forEach(retVal::add);
 
@@ -142,9 +142,99 @@ public class ParametersUtil {
 		return value;
 	}
 
+	public static IPrimitiveType<?> createUri(FhirContext theContext, String theValue) {
+		IPrimitiveType<?> value = (IPrimitiveType<?>) theContext.getElementDefinition("uri").newInstance(theValue);
+		return value;
+	}
+
+	public static IPrimitiveType<?> createCode(FhirContext theContext, String theValue) {
+		IPrimitiveType<?> value = (IPrimitiveType<?>) theContext.getElementDefinition("code").newInstance(theValue);
+		return value;
+	}
+
 	public static IBaseParameters newInstance(FhirContext theContext) {
 		Validate.notNull(theContext, "theContext must not be null");
 		return (IBaseParameters) theContext.getResourceDefinition("Parameters").newInstance();
 	}
 
+	@SuppressWarnings("unchecked")
+	public static void addParameterToParametersBoolean(FhirContext theCtx, IBaseParameters theParameters, String theName, boolean theValue) {
+		IPrimitiveType<Boolean> value = (IPrimitiveType<Boolean>) theCtx.getElementDefinition("boolean").newInstance();
+		value.setValue(theValue);
+		addParameterToParameters(theCtx, theParameters, theName, value);
+
+	}
+
+	@SuppressWarnings("unchecked")
+	public static void addParameterToParametersInteger(FhirContext theCtx, IBaseParameters theParameters, String theName, int theValue) {
+		IPrimitiveType<Integer> count = (IPrimitiveType<Integer>) theCtx.getElementDefinition("integer").newInstance();
+		count.setValue(theValue);
+		addParameterToParameters(theCtx, theParameters, theName, count);
+
+	}
+
+	public static void addParameterToParametersReference(FhirContext theCtx, IBaseParameters theParameters, String theName, String theReference) {
+		IBaseReference target = (IBaseReference) theCtx.getElementDefinition("reference").newInstance();
+		target.setReference(theReference);
+		addParameterToParameters(theCtx, theParameters, theName, target);
+	}
+
+	@SuppressWarnings("unchecked")
+	public static void addParameterToParametersString(FhirContext theCtx, IBaseParameters theParameters, String theName, String theValue) {
+		IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("string").newInstance();
+		value.setValue(theValue);
+		addParameterToParameters(theCtx, theParameters, theName, value);
+
+	}
+
+	/**
+	 * Add a parameter with no value (typically because we'll be adding sub-parameters)
+	 */
+	public static IBase addParameterToParameters(FhirContext theContext, IBaseParameters theParameters, String theName) {
+		RuntimeResourceDefinition def = theContext.getResourceDefinition(theParameters);
+		BaseRuntimeChildDefinition paramChild = def.getChildByName("parameter");
+		BaseRuntimeElementCompositeDefinition<?> paramChildElem = (BaseRuntimeElementCompositeDefinition<?>) paramChild.getChildByName("parameter");
+
+		return createParameterRepetition(theContext, theParameters, paramChild, paramChildElem, theName);
+	}
+
+	public static void addPartCode(FhirContext theContext, IBase theParameter, String theName, String theCode) {
+		IPrimitiveType<String> value = (IPrimitiveType<String>) theContext.getElementDefinition("code").newInstance();
+		value.setValue(theCode);
+
+		addPart(theContext, theParameter, theName, value);
+	}
+
+	public static void addPartString(FhirContext theContext, IBase theParameter, String theName, String theValue) {
+		IPrimitiveType<String> value = (IPrimitiveType<String>) theContext.getElementDefinition("string").newInstance();
+		value.setValue(theValue);
+
+		addPart(theContext, theParameter, theName, value);
+	}
+
+	public static void addPartCoding(FhirContext theContext, IBase theParameter, String theName, String theSystem, String theCode, String theDisplay) {
+		IBase coding = theContext.getElementDefinition("coding").newInstance();
+
+		BaseRuntimeElementCompositeDefinition<?> codingDef = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(coding.getClass());
+		codingDef.getChildByName("system").getMutator().addValue(coding, createUri(theContext, theSystem));
+		codingDef.getChildByName("code").getMutator().addValue(coding, createCode(theContext, theCode));
+		codingDef.getChildByName("display").getMutator().addValue(coding, createString(theContext, theDisplay));
+
+		addPart(theContext, theParameter, theName, coding);
+	}
+
+	private static void addPart(FhirContext theContext, IBase theParameter, String theName, IBase theValue) {
+		BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(theParameter.getClass());
+		BaseRuntimeChildDefinition partChild = def.getChildByName("part");
+
+		BaseRuntimeElementCompositeDefinition<?> partChildElem = (BaseRuntimeElementCompositeDefinition<?>) partChild.getChildByName("part");
+		IBase part = partChildElem.newInstance();
+		partChild.getMutator().addValue(theParameter, part);
+
+		IPrimitiveType<String> name = (IPrimitiveType<String>) theContext.getElementDefinition("string").newInstance();
+		name.setValue(theName);
+		partChildElem.getChildByName("name").getMutator().addValue(part, name);
+
+		partChildElem.getChildByName("value[x]").getMutator().addValue(part, theValue);
+	}
 }

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportDstu3.java

@@ -95,6 +95,11 @@ public class LoadingValidationSupportDstu3 implements IValidationSupport {
 		return null;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return null;
+	}
+
 	@Override
 	public StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theName) {
 		return null;

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportR4.java

@@ -102,4 +102,9 @@ public class LoadingValidationSupportR4 implements org.hl7.fhir.r4.hapi.ctx.IVal
 		return null;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return null;
+	}
+
 }

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java

@@ -29,6 +29,7 @@ import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.r4.model.CodeSystem;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
@@ -103,7 +104,7 @@ public class UploadTerminologyCommand extends BaseCommand {
 		ourLog.info("Beginning upload - This may take a while...");
 		IBaseParameters response = client
 			.operation()
-			.onServer()
+			.onType(CodeSystem.class)
 			.named(UPLOAD_EXTERNAL_CODE_SYSTEM)
 			.withParameters(inputParameters)
 			.execute();

hapi-fhir-igpacks/src/main/java/ca/uhn/fhir/igpacks/parser/IgPackValidationSupportDstu3.java

@@ -127,6 +127,11 @@ public class IgPackValidationSupportDstu3 implements IValidationSupport {
 		return null;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return null;
+	}
+
 	@Override
 	public StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theName) {
 		return null;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java

@@ -27,6 +27,7 @@ import java.util.*;
 
 import javax.annotation.PostConstruct;
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import org.apache.commons.codec.binary.StringUtils;
 import org.hl7.fhir.instance.hapi.validation.CachingValidationSupport;
@@ -185,13 +186,13 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
 		return source;
 	}
 
-	private LookupCodeResult lookup(List<ExpansionContains> theContains, String theSystem, String theCode) {
+	private IContextValidationSupport.LookupCodeResult lookup(List<ExpansionContains> theContains, String theSystem, String theCode) {
 		for (ExpansionContains nextCode : theContains) {
 
 			String system = nextCode.getSystem();
 			String code = nextCode.getCode();
 			if (theSystem.equals(system) && theCode.equals(code)) {
-				LookupCodeResult retVal = new LookupCodeResult();
+				IContextValidationSupport.LookupCodeResult retVal = new IContextValidationSupport.LookupCodeResult();
 				retVal.setSearchedForCode(code);
 				retVal.setSearchedForSystem(system);
 				retVal.setFound(true);
@@ -210,7 +211,7 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
 	}
 
 	@Override
-	public LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CodingDt theCoding, RequestDetails theRequest) {
+	public IContextValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CodingDt theCoding, RequestDetails theRequest) {
 		boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
 		boolean haveCode = theCode != null && theCode.isEmpty() == false;
 		boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
@@ -236,13 +237,13 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
 		for (IIdType nextId : valueSetIds) {
 			ValueSet expansion = expand(nextId, null, theRequest);
 			List<ExpansionContains> contains = expansion.getExpansion().getContains();
-			LookupCodeResult result = lookup(contains, system, code);
+			IContextValidationSupport.LookupCodeResult result = lookup(contains, system, code);
 			if (result != null) {
 				return result;
 			}
 		}
 
-		LookupCodeResult retVal = new LookupCodeResult();
+		IContextValidationSupport.LookupCodeResult retVal = new IContextValidationSupport.LookupCodeResult();
 		retVal.setFound(false);
 		retVal.setSearchedForCode(code);
 		retVal.setSearchedForSystem(system);

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

@@ -3,21 +3,15 @@ package ca.uhn.fhir.jpa.dao;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.ParametersUtil;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
 
-import java.util.Collections;
+import javax.annotation.Nonnull;
 import java.util.List;
-import java.util.Set;
-import java.util.stream.Collectors;
-
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /*
  * #%L
@@ -43,7 +37,8 @@ public interface IFhirResourceDaoCodeSystem<T extends IBaseResource, CD, CC> ext
 
 	List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest);
 
-	LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CD theCoding, RequestDetails theRequestDetails);
+	@Nonnull
+	IContextValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CD theCoding, RequestDetails theRequestDetails);
 
 	SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, CD theCodingA, CD theCodingB, RequestDetails theRequestDetails);
 
@@ -72,147 +67,4 @@ public interface IFhirResourceDaoCodeSystem<T extends IBaseResource, CD, CC> ext
 	}
 
 
-	class LookupCodeResult {
-
-		private String myCodeDisplay;
-		private boolean myCodeIsAbstract;
-		private String myCodeSystemDisplayName;
-		private String myCodeSystemVersion;
-		private boolean myFound;
-		private String mySearchedForCode;
-		private String mySearchedForSystem;
-		private List<IContextValidationSupport.BaseConceptProperty> myProperties;
-
-		/**
-		 * Constructor
-		 */
-		public LookupCodeResult() {
-			super();
-		}
-
-		public String getCodeDisplay() {
-			return myCodeDisplay;
-		}
-
-		public void setCodeDisplay(String theCodeDisplay) {
-			myCodeDisplay = theCodeDisplay;
-		}
-
-		public String getCodeSystemDisplayName() {
-			return myCodeSystemDisplayName;
-		}
-
-		public void setCodeSystemDisplayName(String theCodeSystemDisplayName) {
-			myCodeSystemDisplayName = theCodeSystemDisplayName;
-		}
-
-		public String getCodeSystemVersion() {
-			return myCodeSystemVersion;
-		}
-
-		public void setCodeSystemVersion(String theCodeSystemVersion) {
-			myCodeSystemVersion = theCodeSystemVersion;
-		}
-
-		public String getSearchedForCode() {
-			return mySearchedForCode;
-		}
-
-		public void setSearchedForCode(String theSearchedForCode) {
-			mySearchedForCode = theSearchedForCode;
-		}
-
-		public String getSearchedForSystem() {
-			return mySearchedForSystem;
-		}
-
-		public void setSearchedForSystem(String theSearchedForSystem) {
-			mySearchedForSystem = theSearchedForSystem;
-		}
-
-		public boolean isCodeIsAbstract() {
-			return myCodeIsAbstract;
-		}
-
-		public void setCodeIsAbstract(boolean theCodeIsAbstract) {
-			myCodeIsAbstract = theCodeIsAbstract;
-		}
-
-		public boolean isFound() {
-			return myFound;
-		}
-
-		public void setFound(boolean theFound) {
-			myFound = theFound;
-		}
-
-		public void setProperties(List<IContextValidationSupport.BaseConceptProperty> theProperties) {
-			myProperties = theProperties;
-		}
-
-		public void throwNotFoundIfAppropriate() {
-			if (isFound() == false) {
-				throw new ResourceNotFoundException("Unable to find code[" + getSearchedForCode() + "] in system[" + getSearchedForSystem() + "]");
-			}
-		}
-
-		public Parameters toParameters(List<? extends IPrimitiveType<String>> theProperties) {
-			Parameters retVal = new Parameters();
-
-			retVal.addParameter().setName("name").setValue(new StringType(getCodeSystemDisplayName()));
-			if (isNotBlank(getCodeSystemVersion())) {
-				retVal.addParameter().setName("version").setValue(new StringType(getCodeSystemVersion()));
-			}
-			retVal.addParameter().setName("display").setValue(new StringType(getCodeDisplay()));
-			retVal.addParameter().setName("abstract").setValue(new BooleanType(isCodeIsAbstract()));
-
-			if (myProperties != null) {
-
-				Set<String> properties = Collections.emptySet();
-				if (theProperties != null) {
-					properties = theProperties
-						.stream()
-						.map(IPrimitiveType::getValueAsString)
-						.collect(Collectors.toSet());
-				}
-
-				for (IContextValidationSupport.BaseConceptProperty next : myProperties) {
-
-					if (!properties.isEmpty()) {
-						if (!properties.contains(next.getPropertyName())) {
-							continue;
-						}
-					}
-
-					Parameters.ParametersParameterComponent property = retVal.addParameter().setName("property");
-					property
-						.addPart()
-						.setName("code")
-						.setValue(new CodeType(next.getPropertyName()));
-
-					if (next instanceof IContextValidationSupport.StringConceptProperty) {
-						IContextValidationSupport.StringConceptProperty prop = (IContextValidationSupport.StringConceptProperty) next;
-						property
-							.addPart()
-							.setName("value")
-							.setValue(new StringType(prop.getValue()));
-					} else if (next instanceof IContextValidationSupport.CodingConceptProperty) {
-						IContextValidationSupport.CodingConceptProperty prop = (IContextValidationSupport.CodingConceptProperty) next;
-						property
-							.addPart()
-							.setName("value")
-							.setValue(new Coding()
-								.setSystem(prop.getCodeSystem())
-								.setCode(prop.getCode())
-								.setDisplay(prop.getDisplay()));
-					} else {
-						throw new IllegalStateException("Don't know how to handle " + next.getClass());
-					}
-				}
-			}
-
-			return retVal;
-		}
-	}
-
 }

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

@@ -24,8 +24,9 @@ import org.hl7.fhir.instance.model.api.IAnyResource;
 
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum.ResourceMetadataKeySupportingAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 
-final class MetadataKeyResourcePid extends ResourceMetadataKeySupportingAnyResource<Long, Long> {
+public final class MetadataKeyResourcePid extends ResourceMetadataKeySupportingAnyResource<Long, Long> {
 	private static final long serialVersionUID = 1L;
 
 	MetadataKeyResourcePid(String theValue) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java

@@ -20,25 +20,19 @@ package ca.uhn.fhir.jpa.dao.dstu3;
  * #L%
  */
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
-import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
-import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
-import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
-import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport.CodeValidationResult;
+import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
 import org.hl7.fhir.dstu3.model.CodeSystem;
-import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
-import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.IdType;
@@ -52,45 +46,18 @@ import java.util.Date;
 import java.util.List;
 import java.util.Set;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCodeSystemDstu3.class);
 
-	@Autowired
-	private ITermCodeSystemVersionDao myCsvDao;
-
 	@Autowired
 	private ITermCodeSystemDao myCsDao;
 
 	@Autowired
 	private ValidationSupportChain myValidationSupport;
 
-//	private LookupCodeResult lookup(List<ValueSetExpansionContainsComponent> theContains, String theSystem, String theCode) {
-//		for (ValueSetExpansionContainsComponent nextCode : theContains) {
-//
-//			String system = nextCode.getSystem();
-//			String code = nextCode.getCode();
-//			if (theSystem.equals(system) && theCode.equals(code)) {
-//				LookupCodeResult retVal = new LookupCodeResult();
-//				retVal.setSearchedForCode(code);
-//				retVal.setSearchedForSystem(system);
-//				retVal.setFound(true);
-//				if (nextCode.getAbstractElement().getValue() != null) {
-//					retVal.setCodeIsAbstract(nextCode.getAbstractElement().booleanValue());
-//				}
-//				retVal.setCodeDisplay(nextCode.getDisplay());
-//				retVal.setCodeSystemVersion(nextCode.getVersion());
-//				retVal.setCodeSystemDisplayName("Unknown"); // TODO: implement
-//				return retVal;
-//			}
-//
-//		}
-//
-//		return null;
-//	}
-
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
 		List<IIdType> valueSetIds;
@@ -103,7 +70,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 	}
 
 	@Override
-	public LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
+	public IContextValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
 		boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
 		boolean haveCode = theCode != null && theCode.isEmpty() == false;
 		boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
@@ -128,40 +95,15 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 		ourLog.debug("Looking up {} / {}", system, code);
 
 		if (myValidationSupport.isCodeSystemSupported(getContext(), system)) {
-
 			ourLog.debug("Code system {} is supported", system);
-
+			IContextValidationSupport.LookupCodeResult result = myValidationSupport.lookupCode(getContext(), system, code);
-			CodeValidationResult result = myValidationSupport.validateCode(getContext(), system, code, null);
 			if (result != null) {
-				if (result.isOk()) {
+				return result;
-					LookupCodeResult retVal = new LookupCodeResult();
-					retVal.setFound(true);
-					retVal.setSearchedForCode(code);
-					retVal.setSearchedForSystem(system);
-					retVal.setCodeDisplay(result.asConceptDefinition().getDisplay());
-
-					String codeSystemDisplayName = result.getCodeSystemName();
-					if (isBlank(codeSystemDisplayName)) {
-						codeSystemDisplayName = "Unknown";
 			}
-
-					retVal.setCodeSystemDisplayName(codeSystemDisplayName);
-					retVal.setCodeSystemVersion(result.getCodeSystemVersion());
-					retVal.setProperties(result.getProperties());
-
-					return retVal;
-				}
-			}
-
 		}
 
 		// We didn't find it..
-		LookupCodeResult retVal = new LookupCodeResult();
+		return IContextValidationSupport.LookupCodeResult.notFound(system, code);
-		retVal.setFound(false);
-		retVal.setSearchedForCode(code);
-		retVal.setSearchedForSystem(system);
-		return retVal;
-
 	}
 
 	@Override
@@ -182,62 +124,17 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 		}
 	}
 
-	private List<TermConcept> toPersistedConcepts(List<ConceptDefinitionComponent> theConcept, TermCodeSystemVersion theCodeSystemVersion) {
-		ArrayList<TermConcept> retVal = new ArrayList<>();
-
-		for (ConceptDefinitionComponent next : theConcept) {
-			if (isNotBlank(next.getCode())) {
-				TermConcept termConcept = new TermConcept();
-				termConcept.setCode(next.getCode());
-				termConcept.setCodeSystemVersion(theCodeSystemVersion);
-				termConcept.setDisplay(next.getDisplay());
-				termConcept.addChildren(toPersistedConcepts(next.getConcept(), theCodeSystemVersion), RelationshipTypeEnum.ISA);
-				retVal.add(termConcept);
-
-				for (CodeSystem.ConceptDefinitionDesignationComponent designationComponent : next.getDesignation()) {
-					if (isNotBlank(designationComponent.getValue())) {
-						TermConceptDesignation designation = termConcept.addDesignation();
-						designation.setLanguage(designationComponent.hasLanguage() ? designationComponent.getLanguage() : null);
-						if (designationComponent.hasUse()) {
-							designation.setUseSystem(designationComponent.getUse().hasSystem() ? designationComponent.getUse().getSystem() : null);
-							designation.setUseCode(designationComponent.getUse().hasCode() ? designationComponent.getUse().getCode() : null);
-							designation.setUseDisplay(designationComponent.getUse().hasDisplay() ? designationComponent.getUse().getDisplay() : null);
-						}
-						designation.setValue(designationComponent.getValue());
-					}
-				}
-
-				// TODO: DM 2019-07-16 - We should also populate TermConceptProperty entities here.
-			}
-		}
-
-		return retVal;
-	}
-
 	@Override
 	protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 													 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 
-		CodeSystem cs = (CodeSystem) theResource;
+		CodeSystem csDstu3 = (CodeSystem) theResource;
 
-		if (cs != null && isNotBlank(cs.getUrl())) {
+		org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
-			String codeSystemUrl = cs.getUrl();
+		addPidToResource(theEntity, cs);
-			Long codeSystemResourcePid = retVal.getId();
 
-			if (retVal.getDeleted() != null) {
+		myTerminologySvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
-				// deleting
-			} else if (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == null) {
-				ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", retVal.getIdDt().getValue(), cs.getContentElement().getValueAsString());
-
-				TermCodeSystemVersion persCs = new TermCodeSystemVersion();
-				persCs.setResource(retVal);
-				persCs.getConcepts().addAll(toPersistedConcepts(cs.getConcept(), persCs));
-				ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
-				myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, cs.getName(), persCs);
-
-			}
-		}
 
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java

@@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.dao.dstu3;
  * #L%
  */
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
@@ -238,8 +238,8 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
 			}
 			// String code = theCode.getValue();
 			// String system = toStringOrNull(theSystem);
-			LookupCodeResult result = myCodeSystemDao.lookupCode(theCode, theSystem, null, null);
+			IContextValidationSupport.LookupCodeResult result = myCodeSystemDao.lookupCode(theCode, theSystem, null, null);
-			if (result.isFound()) {
+			if (result != null && result.isFound()) {
 				ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult retVal = new ValidateCodeResult(true, "Found code", result.getCodeDisplay());
 				return retVal;
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/JpaValidationSupportDstu3.java

@@ -171,7 +171,7 @@ public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3, Ap
 	@Override
 	@Transactional(value = TxType.SUPPORTS)
 	public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
-		return fetchCodeSystem(theCtx, theSystem) != null;
+		return false;
 	}
 
 	@Override
@@ -193,6 +193,11 @@ public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3, Ap
 		return null;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return null;
+	}
+
 	@Override
 	public StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theName) {
 		return null;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java

@@ -20,14 +20,10 @@ package ca.uhn.fhir.jpa.dao.r4;
  * #L%
  */
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
-import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
-import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
-import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
-import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.util.LogicUtil;
@@ -37,29 +33,25 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.hl7.fhir.r4.hapi.ctx.IValidationSupport.CodeValidationResult;
 import org.hl7.fhir.r4.hapi.validation.ValidationSupportChain;
 import org.hl7.fhir.r4.model.CodeSystem;
-import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
-import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.IdType;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import javax.annotation.Nonnull;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 import java.util.Set;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCodeSystemR4.class);
 
-	@Autowired
-	private ITermCodeSystemVersionDao myCsvDao;
 	@Autowired
 	private ITermCodeSystemDao myCsDao;
 	@Autowired
@@ -76,8 +68,9 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
 		return valueSetIds;
 	}
 
+	@Nonnull
 	@Override
-	public LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
+	public IContextValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
 		boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
 		boolean haveCode = theCode != null && theCode.isEmpty() == false;
 		boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
@@ -104,37 +97,15 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
 		if (myValidationSupport.isCodeSystemSupported(getContext(), system)) {
 
 			ourLog.info("Code system {} is supported", system);
-
+			IContextValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(getContext(), system, code);
-			CodeValidationResult result = myValidationSupport.validateCode(getContext(), system, code, null);
+			if (retVal != null) {
-			if (result != null) {
-				if (result.isOk()) {
-					LookupCodeResult retVal = new LookupCodeResult();
-					retVal.setFound(true);
-					retVal.setSearchedForCode(code);
-					retVal.setSearchedForSystem(system);
-					retVal.setCodeDisplay(result.asConceptDefinition().getDisplay());
-
-					String codeSystemDisplayName = result.getCodeSystemName();
-					if (isBlank(codeSystemDisplayName)) {
-						codeSystemDisplayName = "Unknown";
-					}
-
-					retVal.setCodeSystemDisplayName(codeSystemDisplayName);
-					retVal.setCodeSystemVersion(result.getCodeSystemVersion());
-					retVal.setProperties(result.getProperties());
-
 				return retVal;
 			}
-			}
 
 		}
 
 		// We didn't find it..
-		LookupCodeResult retVal = new LookupCodeResult();
+		return IContextValidationSupport.LookupCodeResult.notFound(system, code);
-		retVal.setFound(false);
-		retVal.setSearchedForCode(code);
-		retVal.setSearchedForSystem(system);
-		return retVal;
 
 	}
 
@@ -156,66 +127,15 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
 		}
 	}
 
-	private List<TermConcept> toPersistedConcepts(List<ConceptDefinitionComponent> theConcept, TermCodeSystemVersion theCodeSystemVersion) {
-		ArrayList<TermConcept> retVal = new ArrayList<>();
-
-		for (ConceptDefinitionComponent next : theConcept) {
-			if (isNotBlank(next.getCode())) {
-				TermConcept termConcept = new TermConcept();
-				termConcept.setCode(next.getCode());
-				termConcept.setCodeSystemVersion(theCodeSystemVersion);
-				termConcept.setDisplay(next.getDisplay());
-				termConcept.addChildren(toPersistedConcepts(next.getConcept(), theCodeSystemVersion), RelationshipTypeEnum.ISA);
-				retVal.add(termConcept);
-
-				for (CodeSystem.ConceptDefinitionDesignationComponent designationComponent : next.getDesignation()) {
-					if (isNotBlank(designationComponent.getValue())) {
-						TermConceptDesignation designation = termConcept.addDesignation();
-						designation.setLanguage(designationComponent.hasLanguage() ? designationComponent.getLanguage() : null);
-						if (designationComponent.hasUse()) {
-							designation.setUseSystem(designationComponent.getUse().hasSystem() ? designationComponent.getUse().getSystem() : null);
-							designation.setUseCode(designationComponent.getUse().hasCode() ? designationComponent.getUse().getCode() : null);
-							designation.setUseDisplay(designationComponent.getUse().hasDisplay() ? designationComponent.getUse().getDisplay() : null);
-						}
-						designation.setValue(designationComponent.getValue());
-					}
-				}
-
-				// TODO: DM 2019-07-16 - We should also populate TermConceptProperty entities here.
-			}
-		}
-
-		return retVal;
-	}
-
 	@Override
 	protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 													 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 
 		CodeSystem cs = (CodeSystem) theResource;
+		addPidToResource(theEntity, theResource);
 
-		if (cs != null && isNotBlank(cs.getUrl())) {
+		myTerminologySvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
-			String codeSystemUrl = cs.getUrl();
-			if (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == null) {
-				ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", retVal.getIdDt().getValue(), cs.getContentElement().getValueAsString());
-
-				Long codeSystemResourcePid = retVal.getId();
-				TermCodeSystemVersion persCs = myCsvDao.findCurrentVersionForCodeSystemResourcePid(codeSystemResourcePid);
-				if (persCs != null) {
-					ourLog.info("Code system version already exists in database");
-				} else {
-
-					persCs = new TermCodeSystemVersion();
-					persCs.setResource(retVal);
-					persCs.getConcepts().addAll(toPersistedConcepts(cs.getConcept(), persCs));
-					ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
-					myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, cs.getName(), persCs);
-
-				}
-
-			}
-		}
 
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java

@@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.dao.r4;
  * #L%
  */
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
@@ -239,7 +239,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
 			}
 			// String code = theCode.getValue();
 			// String system = toStringOrNull(theSystem);
-			LookupCodeResult result = myCodeSystemDao.lookupCode(theCode, theSystem, null, null);
+			IContextValidationSupport.LookupCodeResult result = myCodeSystemDao.lookupCode(theCode, theSystem, null, null);
 			if (result.isFound()) {
 				ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult retVal = new ValidateCodeResult(true, "Found code", result.getCodeDisplay());
 				return retVal;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/JpaValidationSupportR4.java

@@ -173,7 +173,7 @@ public class JpaValidationSupportR4 implements IJpaValidationSupportR4, Applicat
 	@Override
 	@Transactional(value = TxType.SUPPORTS)
 	public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
-		return fetchCodeSystem(theCtx, theSystem) != null;
+		return false;
 	}
 
 	@Override
@@ -195,6 +195,11 @@ public class JpaValidationSupportR4 implements IJpaValidationSupportR4, Applicat
 		return null;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return null;
+	}
+
 	@Override
 	public StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theProfileName) {
 		return null;

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

@@ -63,6 +63,13 @@ public class TermCodeSystem implements Serializable {
 	@Column(name = "CS_NAME", nullable = true, length = MAX_NAME_LENGTH)
 	private String myName;
 
+	/**
+	 * Constructor
+	 */
+	public TermCodeSystem() {
+		super();
+	}
+
 	public String getCodeSystemUri() {
 		return myCodeSystemUri;
 	}

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

@@ -69,6 +69,9 @@ public class TermCodeSystemVersion implements Serializable {
 	@OneToOne(mappedBy = "myCurrentVersion", optional = true)
 	private TermCodeSystem myCodeSystemHavingThisVersionAsCurrentVersionIfAny;
 
+	@Column(name = "CS_DISPLAY", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)
+	private String myCodeSystemDisplayName;
+
 	/**
 	 * Constructor
 	 */
@@ -155,4 +158,14 @@ public class TermCodeSystemVersion implements Serializable {
 		return result;
 	}
 
+	public String getCodeSystemDisplayName() {
+		return myCodeSystemDisplayName;
+	}
+
+	public void setCodeSystemDisplayName(String theCodeSystemDisplayName) {
+		ValidateUtil.isNotTooLongOrThrowIllegalArgument(
+			theCodeSystemDisplayName, MAX_VERSION_LENGTH,
+			"Version ID exceeds maximum length (" + MAX_VERSION_LENGTH + "): " + length(theCodeSystemDisplayName));
+		myCodeSystemDisplayName = theCodeSystemDisplayName;
+	}
 }

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

@@ -111,7 +111,7 @@ public class TermConcept implements Serializable {
 		setCode(theCode);
 	}
 
-	public TermConcept addChild(TermConcept theChild, RelationshipTypeEnum theRelationshipType) {
+	public TermConceptParentChildLink addChild(TermConcept theChild, RelationshipTypeEnum theRelationshipType) {
 		Validate.notNull(theRelationshipType, "theRelationshipType must not be null");
 		TermConceptParentChildLink link = new TermConceptParentChildLink();
 		link.setParent(this);
@@ -120,7 +120,7 @@ public class TermConcept implements Serializable {
 		getChildren().add(link);
 
 		theChild.getParents().add(link);
-		return this;
+		return link;
 	}
 
 	public void addChildren(List<TermConcept> theChildren, RelationshipTypeEnum theRelationshipType) {

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

@@ -66,6 +66,14 @@ public class TermConceptProperty implements Serializable {
 	private String myValue;
 	@Column(name = "PROP_TYPE", nullable = false, length = MAX_PROPTYPE_ENUM_LENGTH)
 	private TermConceptPropertyTypeEnum myType;
+
+	/**
+	 * Constructor
+	 */
+	public TermConceptProperty() {
+		super();
+	}
+
 	/**
 	 * Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
 	 */

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderValueSetDstu2.java

@@ -20,12 +20,8 @@ package ca.uhn.fhir.jpa.provider;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import ca.uhn.fhir.context.support.IContextValidationSupport;
-
-import javax.servlet.http.HttpServletRequest;
-
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
@@ -34,21 +30,27 @@ import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.resource.Parameters;
 import ca.uhn.fhir.model.dstu2.resource.ValueSet;
 import ca.uhn.fhir.model.primitive.*;
-import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 
+import javax.servlet.http.HttpServletRequest;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
 public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDstu2<ValueSet> {
 
 
 	@Operation(name = JpaConstants.OPERATION_EXPAND, idempotent = true)
 	public ValueSet expand(
 		HttpServletRequest theServletRequest,
-			@IdParam(optional=true) IdDt theId,
+		@IdParam(optional = true) IdDt theId,
-			@OperationParam(name="valueSet", min=0, max=1) ValueSet theValueSet,
+		@OperationParam(name = "valueSet", min = 0, max = 1) ValueSet theValueSet,
-			@OperationParam(name="identifier", min=0, max=1) UriDt theIdentifier,
+		@OperationParam(name = "identifier", min = 0, max = 1) UriDt theIdentifier,
-			@OperationParam(name = "filter", min=0, max=1) StringDt theFilter,
+		@OperationParam(name = "filter", min = 0, max = 1) StringDt theFilter,
 		RequestDetails theRequestDetails) {
 
 		boolean haveId = theId != null && theId.hasIdPart();
@@ -79,45 +81,29 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
 		}
 	}
 
-
-	private static boolean moreThanOneTrue(boolean... theBooleans) {
-		boolean haveOne = false;
-		for (boolean next : theBooleans) {
-			if (next) {
-				if (haveOne) {
-					return true;
-				} else {
-					haveOne = true;
-				}
-			}
-		}
-		return false;
-	}
-
-
 	private String toFilterString(StringDt theFilter) {
 		return theFilter != null ? theFilter.getValue() : null;
 	}
 
-	@Operation(name = JpaConstants.OPERATION_LOOKUP, idempotent = true, returnParameters= {
+	@Operation(name = JpaConstants.OPERATION_LOOKUP, idempotent = true, returnParameters = {
-		@OperationParam(name="name", type=StringDt.class, min=1),
+		@OperationParam(name = "name", type = StringDt.class, min = 1),
-		@OperationParam(name="version", type=StringDt.class, min=0),
+		@OperationParam(name = "version", type = StringDt.class, min = 0),
-		@OperationParam(name="display", type=StringDt.class, min=1),
+		@OperationParam(name = "display", type = StringDt.class, min = 1),
-		@OperationParam(name="abstract", type=BooleanDt.class, min=1),
+		@OperationParam(name = "abstract", type = BooleanDt.class, min = 1),
 	})
 	public Parameters lookup(
 		HttpServletRequest theServletRequest,
-			@OperationParam(name="code", min=0, max=1) CodeDt theCode, 
+		@OperationParam(name = "code", min = 0, max = 1) CodeDt theCode,
-			@OperationParam(name="system", min=0, max=1) UriDt theSystem,
+		@OperationParam(name = "system", min = 0, max = 1) UriDt theSystem,
-			@OperationParam(name="coding", min=0, max=1) CodingDt theCoding,
+		@OperationParam(name = "coding", min = 0, max = 1) CodingDt theCoding,
 		RequestDetails theRequestDetails
 	) {
 
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoCodeSystem<ValueSet, CodingDt, CodeableConceptDt> dao = (IFhirResourceDaoCodeSystem<ValueSet, CodingDt, CodeableConceptDt>) getDao();
-			LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
+			IContextValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
-			if (result.isFound()==false) {
+			if (result.isFound() == false) {
 				throw new ResourceNotFoundException("Unable to find code[" + result.getSearchedForCode() + "] in system[" + result.getSearchedForSystem() + "]");
 			}
 			Parameters retVal = new Parameters();
@@ -133,21 +119,20 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
 		}
 	}
 
-	
+	@Operation(name = JpaConstants.OPERATION_VALIDATE_CODE, idempotent = true, returnParameters = {
-	@Operation(name = JpaConstants.OPERATION_VALIDATE_CODE, idempotent = true, returnParameters= {
+		@OperationParam(name = "result", type = BooleanDt.class, min = 1),
-		@OperationParam(name="result", type=BooleanDt.class, min=1),
+		@OperationParam(name = "message", type = StringDt.class),
-		@OperationParam(name="message", type=StringDt.class),
+		@OperationParam(name = "display", type = StringDt.class)
-		@OperationParam(name="display", type=StringDt.class)
 	})
 	public Parameters validateCode(
 		HttpServletRequest theServletRequest,
-			@IdParam(optional=true) IdDt theId, 
+		@IdParam(optional = true) IdDt theId,
-			@OperationParam(name="identifier", min=0, max=1) UriDt theValueSetIdentifier, 
+		@OperationParam(name = "identifier", min = 0, max = 1) UriDt theValueSetIdentifier,
-			@OperationParam(name="code", min=0, max=1) CodeDt theCode, 
+		@OperationParam(name = "code", min = 0, max = 1) CodeDt theCode,
-			@OperationParam(name="system", min=0, max=1) UriDt theSystem,
+		@OperationParam(name = "system", min = 0, max = 1) UriDt theSystem,
-			@OperationParam(name="display", min=0, max=1) StringDt theDisplay,
+		@OperationParam(name = "display", min = 0, max = 1) StringDt theDisplay,
-			@OperationParam(name="coding", min=0, max=1) CodingDt theCoding,
+		@OperationParam(name = "coding", min = 0, max = 1) CodingDt theCoding,
-			@OperationParam(name="codeableConcept", min=0, max=1) CodeableConceptDt theCodeableConcept, 
+		@OperationParam(name = "codeableConcept", min = 0, max = 1) CodeableConceptDt theCodeableConcept,
 		RequestDetails theRequestDetails
 	) {
 
@@ -169,5 +154,19 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
 		}
 	}
 
+	private static boolean moreThanOneTrue(boolean... theBooleans) {
+		boolean haveOne = false;
+		for (boolean next : theBooleans) {
+			if (next) {
+				if (haveOne) {
+					return true;
+				} else {
+					haveOne = true;
+				}
+			}
+		}
+		return false;
+	}
+
 
 }

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

@@ -1,142 +1,19 @@
 package ca.uhn.fhir.jpa.provider;
 
-/*
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
- * #%L
+
- * HAPI FHIR JPA Server
+/**
- * %%
+ * @deprecated TerminologyUploaderProvider
- * Copyright (C) 2014 - 2019 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
  */
+@Deprecated
+public class BaseTerminologyUploaderProvider {
 
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+	// FIXME: remove these before 4.0.0
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc.UploadStatistics;
+	public static final String UPLOAD_EXTERNAL_CODE_SYSTEM = JpaConstants.OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.param.StringParam;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import org.hl7.fhir.r4.model.*;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import javax.servlet.http.HttpServletRequest;
-import java.io.*;
-import java.util.ArrayList;
-import java.util.List;
-
-import static org.apache.commons.lang3.StringUtils.*;
-
-public abstract class BaseTerminologyUploaderProvider extends BaseJpaProvider {
-	public static final String UPLOAD_EXTERNAL_CODE_SYSTEM = "$upload-external-code-system";
-
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseTerminologyUploaderProvider.class);
 	public static final String CONCEPT_COUNT = "conceptCount";
 	public static final String TARGET = "target";
-
+	public static final String SYSTEM = "system";
-	@Autowired
+	public static final String PARENT_CODE = "parentCode";
-	private IHapiTerminologyLoaderSvc myTerminologyLoaderSvc;
+	public static final String VALUE = "value";
-
-	protected Parameters handleUploadExternalCodeSystem(
-		HttpServletRequest theServletRequest,
-		StringParam theCodeSystemUrl,
-		List<StringType> theLocalFile,
-		List<Attachment> thePackage, RequestDetails theRequestDetails
-	) {
-
-		startRequest(theServletRequest);
-
-		if (theLocalFile == null || theLocalFile.size() == 0) {
-			if (thePackage == null || thePackage.size() == 0) {
-				throw new InvalidRequestException("No 'localfile' or 'package' parameter, or package had no data");
-			}
-		}
-
-		try {
-			List<IHapiTerminologyLoaderSvc.FileDescriptor> localFiles = new ArrayList<>();
-			if (theLocalFile != null && theLocalFile.size() > 0) {
-				for (StringType nextLocalFile : theLocalFile) {
-					if (isNotBlank(nextLocalFile.getValue())) {
-						ourLog.info("Reading in local file: {}", nextLocalFile.getValue());
-						File nextFile = new File(nextLocalFile.getValue());
-						if (!nextFile.exists() || !nextFile.isFile()) {
-							throw new InvalidRequestException("Unknown file: " + nextFile.getName());
-						}
-						localFiles.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
-							@Override
-							public String getFilename() {
-								return nextFile.getAbsolutePath();
-							}
-
-							@Override
-							public InputStream getInputStream() {
-								try {
-									return new FileInputStream(nextFile);
-								} catch (FileNotFoundException theE) {
-									throw new InternalErrorException(theE);
-								}
-							}
-						});
-					}
-				}
-			}
-
-			if (thePackage != null) {
-				for (Attachment nextPackage : thePackage) {
-					if (isBlank(nextPackage.getUrl())) {
-						throw new UnprocessableEntityException("Package is missing mandatory url element");
-					}
-
-					localFiles.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
-						@Override
-						public String getFilename() {
-							return nextPackage.getUrl();
-						}
-
-						@Override
-						public InputStream getInputStream() {
-							return new ByteArrayInputStream(nextPackage.getData());
-						}
-					});
-				}
-			}
-
-			String url = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
-			url = defaultString(url);
-
-			UploadStatistics stats;
-			switch(url) {
-				case IHapiTerminologyLoaderSvc.SCT_URI:
-					stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
-					break;
-				case IHapiTerminologyLoaderSvc.LOINC_URI:
-					stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
-					break;
-				case IHapiTerminologyLoaderSvc.IMGTHLA_URI:
-					stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
-					break;
-				default:
-					throw new InvalidRequestException("Unknown URL: " + url);
-			}
-
-			Parameters retVal = new Parameters();
-			retVal.addParameter().setName(CONCEPT_COUNT).setValue(new IntegerType(stats.getConceptCount()));
-			retVal.addParameter().setName(TARGET).setValue(new Reference(stats.getTarget().getValue()));
-			return retVal;
-		} finally {
-			endRequest(theServletRequest);
-		}
-	}
-
 
 }

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

@@ -0,0 +1,261 @@
+package ca.uhn.fhir.jpa.provider;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc.UploadStatistics;
+import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.AttachmentUtil;
+import ca.uhn.fhir.util.ParametersUtil;
+import ca.uhn.fhir.util.ValidateUtil;
+import org.hl7.fhir.convertors.VersionConvertor_30_40;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.ICompositeType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.servlet.http.HttpServletRequest;
+import java.io.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import static org.apache.commons.lang3.StringUtils.*;
+
+public abstract class TerminologyUploaderProvider extends BaseJpaProvider {
+
+	public static final String CONCEPT_COUNT = "conceptCount";
+	public static final String TARGET = "target";
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyUploaderProvider.class);
+	public static final String PARENT_CODE = "parentCode";
+	public static final String VALUE = "value";
+
+	@Autowired
+	private FhirContext myCtx;
+	@Autowired
+	private IHapiTerminologyLoaderSvc myTerminologyLoaderSvc;
+	@Autowired
+	private IHapiTerminologySvc myTerminologySvc;
+
+	/**
+	 * <code>
+	 * $apply-codesystem-delta-add
+	 * </code>
+	 */
+	@Operation(typeName="CodeSystem", name = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD, idempotent = false, returnParameters = {
+	})
+	public IBaseParameters applyCodeSystemDeltaAdd(
+		HttpServletRequest theServletRequest,
+		@OperationParam(name = PARENT_CODE, min = 0, max = 1) IPrimitiveType<String> theParentCode,
+		@OperationParam(name = VALUE, min = 1, max = 1) IBaseResource theValue,
+		RequestDetails theRequestDetails
+	) {
+
+		startRequest(theServletRequest);
+		try {
+
+			CodeSystem value;
+			if (theValue instanceof CodeSystem) {
+				value = (CodeSystem) theValue;
+			} else if (theValue instanceof org.hl7.fhir.dstu3.model.CodeSystem) {
+				value = VersionConvertor_30_40.convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theValue);
+			} else {
+				throw new InvalidRequestException("Value must be present and be a CodeSystem");
+			}
+
+			String system = value.getUrl();
+			String parentCode = theParentCode != null ? theParentCode.getValue() : null;
+
+			AtomicInteger counter = myTerminologySvc.applyDeltaCodesystemsAdd(system, parentCode, value);
+
+			IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
+			ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, "success", true);
+			ParametersUtil.addParameterToParametersInteger(myCtx, retVal, "addedConcepts", counter.get());
+			return retVal;
+
+		} finally {
+			endRequest(theServletRequest);
+		}
+
+	}
+
+
+	/**
+	 * <code>
+	 * $apply-codesystem-delta-remove
+	 * </code>
+	 */
+	@Operation(typeName="CodeSystem", name = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE, idempotent = false, returnParameters = {
+	})
+	public IBaseParameters applyCodeSystemDeltaRemove(
+		HttpServletRequest theServletRequest,
+		@OperationParam(name = VALUE, min = 1, max = 1) IBaseResource theValue,
+		RequestDetails theRequestDetails
+	) {
+
+		startRequest(theServletRequest);
+		try {
+
+			CodeSystem value;
+			if (theValue instanceof CodeSystem) {
+				value = (CodeSystem) theValue;
+			} else if (theValue instanceof org.hl7.fhir.dstu3.model.CodeSystem) {
+				value = VersionConvertor_30_40.convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theValue);
+			} else {
+				throw new InvalidRequestException("Value must be present and be a CodeSystem");
+			}
+
+			String system = value.getUrl();
+
+			AtomicInteger counter = myTerminologySvc.applyDeltaCodesystemsRemove(system, value);
+
+			IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
+			ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, "success", true);
+			ParametersUtil.addParameterToParametersInteger(myCtx, retVal, "removedConcepts", counter.get());
+			return retVal;
+
+		} finally {
+			endRequest(theServletRequest);
+		}
+
+	}
+
+
+	/**
+	 * <code>
+	 * $upload-external-codesystem
+	 * </code>
+	 */
+	@Operation(typeName="CodeSystem", name = JpaConstants.OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM, idempotent = false, returnParameters = {
+//		@OperationParam(name = "conceptCount", type = IntegerType.class, min = 1)
+	})
+	public IBaseParameters uploadExternalCodeSystem(
+		HttpServletRequest theServletRequest,
+		@OperationParam(name = "url", min = 1, typeName = "uri") IPrimitiveType<String> theCodeSystemUrl,
+		@OperationParam(name = "localfile", min = 1, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> theLocalFile,
+		@OperationParam(name = "package", min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> thePackage,
+		RequestDetails theRequestDetails
+	) {
+
+		startRequest(theServletRequest);
+
+		if (theLocalFile == null || theLocalFile.size() == 0) {
+			if (thePackage == null || thePackage.size() == 0) {
+				throw new InvalidRequestException("No 'localfile' or 'package' parameter, or package had no data");
+			}
+			for (ICompositeType next : thePackage) {
+				ValidateUtil.isTrueOrThrowInvalidRequest(myCtx.getElementDefinition(next.getClass()).getName().equals("Attachment"), "Package must be of type Attachment");
+			}
+		}
+
+		try {
+			List<IHapiTerminologyLoaderSvc.FileDescriptor> localFiles = new ArrayList<>();
+			if (theLocalFile != null && theLocalFile.size() > 0) {
+				for (IPrimitiveType<String> nextLocalFile : theLocalFile) {
+					if (isNotBlank(nextLocalFile.getValue())) {
+						ourLog.info("Reading in local file: {}", nextLocalFile.getValue());
+						File nextFile = new File(nextLocalFile.getValue());
+						if (!nextFile.exists() || !nextFile.isFile()) {
+							throw new InvalidRequestException("Unknown file: " + nextFile.getName());
+						}
+						localFiles.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
+							@Override
+							public String getFilename() {
+								return nextFile.getAbsolutePath();
+							}
+
+							@Override
+							public InputStream getInputStream() {
+								try {
+									return new FileInputStream(nextFile);
+								} catch (FileNotFoundException theE) {
+									throw new InternalErrorException(theE);
+								}
+							}
+						});
+					}
+				}
+			}
+
+			if (thePackage != null) {
+				for (ICompositeType nextPackage : thePackage) {
+					final String url = AttachmentUtil.getOrCreateUrl(myCtx, nextPackage).getValueAsString();
+
+					if (isBlank(url)) {
+						throw new UnprocessableEntityException("Package is missing mandatory url element");
+					}
+
+					localFiles.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
+						@Override
+						public String getFilename() {
+							return url;
+						}
+
+						@Override
+						public InputStream getInputStream() {
+							byte[] data = AttachmentUtil.getOrCreateData(myCtx, nextPackage).getValue();
+							return new ByteArrayInputStream(data);
+						}
+					});
+				}
+			}
+
+			String url = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
+			url = defaultString(url);
+
+			UploadStatistics stats;
+			switch (url) {
+				case IHapiTerminologyLoaderSvc.SCT_URI:
+					stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
+					break;
+				case IHapiTerminologyLoaderSvc.LOINC_URI:
+					stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
+					break;
+				case IHapiTerminologyLoaderSvc.IMGTHLA_URI:
+					stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
+					break;
+				default:
+					throw new InvalidRequestException("Unknown URL: " + url);
+			}
+
+			IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
+			ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, "success", true);
+			ParametersUtil.addParameterToParametersInteger(myCtx, retVal, CONCEPT_COUNT, stats.getConceptCount());
+			ParametersUtil.addParameterToParametersReference(myCtx, retVal, TARGET, stats.getTarget().getValue());
+
+			return retVal;
+		} finally {
+			endRequest(theServletRequest);
+		}
+	}
+
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderCodeSystemDstu3.java

@@ -20,14 +20,13 @@ package ca.uhn.fhir.jpa.provider.dstu3;
  * #L%
  */
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.exceptions.FHIRException;
 
@@ -36,18 +35,17 @@ import java.util.List;
 
 public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderDstu3<CodeSystem> {
 
-	@SuppressWarnings("unchecked")
+	@Operation(name = JpaConstants.OPERATION_LOOKUP, idempotent = true, returnParameters = {
-	@Operation(name = JpaConstants.OPERATION_LOOKUP, idempotent = true, returnParameters= {
+		@OperationParam(name = "name", type = StringType.class, min = 1),
-		@OperationParam(name="name", type=StringType.class, min=1),
+		@OperationParam(name = "version", type = StringType.class, min = 0),
-		@OperationParam(name="version", type=StringType.class, min=0),
+		@OperationParam(name = "display", type = StringType.class, min = 1),
-		@OperationParam(name="display", type=StringType.class, min=1),
+		@OperationParam(name = "abstract", type = BooleanType.class, min = 1),
-		@OperationParam(name="abstract", type=BooleanType.class, min=1),
 	})
 	public Parameters lookup(
 		HttpServletRequest theServletRequest,
-			@OperationParam(name="code", min=0, max=1) CodeType theCode, 
+		@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
-			@OperationParam(name="system", min=0, max=1) UriType theSystem,
+		@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
-			@OperationParam(name="coding", min=0, max=1) Coding theCoding,
+		@OperationParam(name = "coding", min = 0, max = 1) Coding theCoding,
 		@OperationParam(name = "property", min = 0, max = OperationParam.MAX_UNLIMITED) List<CodeType> theProperties,
 		RequestDetails theRequestDetails
 	) {
@@ -55,10 +53,9 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
-			LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
+			IContextValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
 			result.throwNotFoundIfAppropriate();
-			org.hl7.fhir.r4.model.Parameters parametersR4 = result.toParameters(theProperties);
+			return (Parameters) result.toParameters(theRequestDetails.getFhirContext(), theProperties);
-			return VersionConvertor_30_40.convertParameters(parametersR4);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		} finally {
@@ -70,16 +67,16 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
 	/**
 	 * $subsumes operation
 	 */
-	@Operation(name = JpaConstants.OPERATION_SUBSUMES, idempotent = true, returnParameters= {
+	@Operation(name = JpaConstants.OPERATION_SUBSUMES, idempotent = true, returnParameters = {
-		@OperationParam(name="outcome", type= CodeType.class, min=1),
+		@OperationParam(name = "outcome", type = CodeType.class, min = 1),
 	})
 	public Parameters subsumes(
 		HttpServletRequest theServletRequest,
-		@OperationParam(name="codeA", min=0, max=1) CodeType theCodeA,
+		@OperationParam(name = "codeA", min = 0, max = 1) CodeType theCodeA,
-		@OperationParam(name="codeB", min=0, max=1) CodeType theCodeB,
+		@OperationParam(name = "codeB", min = 0, max = 1) CodeType theCodeB,
-		@OperationParam(name="system", min=0, max=1) UriType theSystem,
+		@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
-		@OperationParam(name="codingA", min=0, max=1) Coding theCodingA,
+		@OperationParam(name = "codingA", min = 0, max = 1) Coding theCodingA,
-		@OperationParam(name="codingB", min=0, max=1) Coding theCodingB,
+		@OperationParam(name = "codingB", min = 0, max = 1) Coding theCodingB,
 		RequestDetails theRequestDetails
 	) {
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3.java

@@ -20,7 +20,8 @@ package ca.uhn.fhir.jpa.provider.dstu3;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.provider.BaseTerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -37,37 +38,10 @@ import javax.servlet.http.HttpServletRequest;
 import java.util.ArrayList;
 import java.util.List;
 
-public class TerminologyUploaderProviderDstu3 extends BaseTerminologyUploaderProvider {
+/**
-
+ * @deprecated Use {@link TerminologyUploaderProvider} instead
-	@Operation(name = UPLOAD_EXTERNAL_CODE_SYSTEM, idempotent = false, returnParameters = {
+ */
-		@OperationParam(name = "conceptCount", type = IntegerType.class, min = 1)
+@Deprecated
-	})
+public class TerminologyUploaderProviderDstu3 extends TerminologyUploaderProvider {
-	public Parameters uploadExternalCodeSystem(
+	// nothing
-		HttpServletRequest theServletRequest,
-		@OperationParam(name = "url", min = 1) StringParam theCodeSystemUrl,
-		@OperationParam(name = "localfile", min = 1, max = OperationParam.MAX_UNLIMITED) List<StringType> theLocalFile,
-		@OperationParam(name = "package", min = 0, max = OperationParam.MAX_UNLIMITED) List<Attachment> thePackage,
-		RequestDetails theRequestDetails
-	) {
-		try {
-			List<org.hl7.fhir.r4.model.StringType> localFile = null;
-			if (theLocalFile != null) {
-				localFile = new ArrayList<>();
-				for (StringType next : theLocalFile) {
-					localFile.add(VersionConvertor_30_40.convertString(next));
-				}
-			}
-			List<org.hl7.fhir.r4.model.Attachment> pkg = null;
-			if (thePackage!=null){
-				pkg = new ArrayList<>();
-				for (Attachment next : thePackage) {
-					pkg.add(VersionConvertor_30_40.convertAttachment(next));
-				}
-			}
-			org.hl7.fhir.r4.model.Parameters retValR4 = handleUploadExternalCodeSystem(theServletRequest, theCodeSystemUrl, localFile, pkg, theRequestDetails);
-			return VersionConvertor_30_40.convertParameters(retValR4);
-		} catch (FHIRException e) {
-			throw new InternalErrorException(e);
-		}
-	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java

@@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.provider.r4;
  * #L%
  */
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
@@ -55,9 +55,9 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
-			LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
+			IContextValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
 			result.throwNotFoundIfAppropriate();
-			return result.toParameters(theProperties);
+			return (Parameters) result.toParameters(theRequestDetails.getFhirContext(), theProperties);
 		} finally {
 			endRequest(theServletRequest);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4.java

@@ -20,7 +20,8 @@ package ca.uhn.fhir.jpa.provider.r4;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.provider.BaseTerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -33,18 +34,9 @@ import org.hl7.fhir.r4.model.StringType;
 import javax.servlet.http.HttpServletRequest;
 import java.util.List;
 
-public class TerminologyUploaderProviderR4 extends BaseTerminologyUploaderProvider {
+/**
-
+ * @deprecated Use {@link TerminologyUploaderProvider} instead
-	@Operation(name = UPLOAD_EXTERNAL_CODE_SYSTEM, idempotent = false, returnParameters = {
+ */
-		@OperationParam(name = "conceptCount", type = IntegerType.class, min = 1)
+public class TerminologyUploaderProviderR4 extends TerminologyUploaderProvider {
-	})
+	// nothing
-	public Parameters uploadExternalCodeSystem(
-		HttpServletRequest theServletRequest,
-		@OperationParam(name = "url", min = 1) StringParam theCodeSystemUrl,
-		@OperationParam(name = "localfile", min = 1, max = OperationParam.MAX_UNLIMITED) List<StringType> theLocalFile,
-		@OperationParam(name = "package", min = 0, max = OperationParam.MAX_UNLIMITED) List<Attachment> thePackage,
-		RequestDetails theRequestDetails
-	) {
-		return handleUploadExternalCodeSystem(theServletRequest, theCodeSystemUrl, theLocalFile, thePackage, theRequestDetails);
-	}
 }

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

@@ -21,10 +21,8 @@ package ca.uhn.fhir.jpa.term;
  */
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.context.support.IContextValidationSupport;
-import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.*;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
-import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.dao.data.*;
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
@@ -78,6 +76,7 @@ import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import javax.annotation.PostConstruct;
 import javax.persistence.EntityManager;
@@ -261,6 +260,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 
 	protected abstract IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource);
 
+	protected void validateCodeSystemForStorage(CodeSystem theCodeSystemResource) {
+		ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theCodeSystemResource.getUrl(), "Can not store a CodeSystem without a valid URL");
+	}
+
 	protected abstract void createOrUpdateConceptMap(ConceptMap theNextConceptMap);
 
 	abstract void createOrUpdateValueSet(ValueSet theValueSet);
@@ -767,9 +770,17 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 
 	@Override
 	public Optional<TermConcept> findCode(String theCodeSystem, String theCode) {
+		/*
+		 * Loading concepts without a transaction causes issues later on some
+		 * platforms (e.g. PSQL) so this transactiontemplate is here to make
+		 * sure that we always call this with an open transaction
+		 */
+		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
+		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_MANDATORY);
+		return txTemplate.execute(t->{
 			TermCodeSystemVersion csv = findCurrentCodeSystemVersionForSystem(theCodeSystem);
-
 			return myConceptDao.findByCodeSystemAndCode(csv, theCode);
+		});
 	}
 
 	@Override
@@ -1036,6 +1047,37 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 
 	}
 
+	/**
+	 * Returns the number of saved concepts
+	 */
+	private int saveOrUpdateConcept(TermConcept theConcept) {
+
+		TermCodeSystemVersion csv = theConcept.getCodeSystemVersion();
+		Optional<TermConcept> existing = myConceptDao.findByCodeSystemAndCode(csv, theConcept.getCode());
+		if (existing.isPresent()) {
+			TermConcept existingConcept = existing.get();
+			boolean haveChanges = false;
+			if (!StringUtils.equals(existingConcept.getDisplay(), theConcept.getDisplay())) {
+				existingConcept.setDisplay(theConcept.getDisplay());
+				haveChanges = true;
+			}
+
+			if (!haveChanges) {
+				return 0;
+			}
+
+			myConceptDao.save(existingConcept);
+			return 1;
+
+		} else {
+			return saveConcept(theConcept);
+		}
+		
+	}
+
+	/**
+	 * Returns the number of saved concepts
+	 */
 	private int saveConcept(TermConcept theConcept) {
 		int retVal = 0;
 
@@ -1124,7 +1166,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 
 	@Override
 	@Transactional(propagation = Propagation.REQUIRED)
-	public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, TermCodeSystemVersion theCodeSystemVersion) {
+	public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion) {
 		ourLog.info("Storing code system");
 
 		ValidateUtil.isTrueOrThrowInvalidRequest(theCodeSystemVersion.getResource() != null, "No resource supplied");
@@ -1170,6 +1212,9 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		}
 		theCodeSystemVersion.setCodeSystem(codeSystem);
 
+		theCodeSystemVersion.setCodeSystemDisplayName(theSystemName);
+		theCodeSystemVersion.setCodeSystemVersionId(theSystemVersionId);
+
 		ourLog.info("Validating all codes in CodeSystem for storage (this can take some time for large sets)");
 
 		// Validate the code system
@@ -1226,8 +1271,9 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 
 		ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
 
-		theCodeSystemVersion.setResource(resource);
+		populateCodeSystemVersionProperties(theCodeSystemVersion, theCodeSystemResource, resource);
-		storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemResource.getName(), theCodeSystemVersion);
+
+		storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemResource.getName(), theCodeSystemResource.getVersion(), theCodeSystemVersion);
 
 		myDeferredConceptMaps.addAll(theConceptMaps);
 		myDeferredValueSets.addAll(theValueSets);
@@ -1235,6 +1281,99 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		return csId;
 	}
 
+	private void populateCodeSystemVersionProperties(TermCodeSystemVersion theCodeSystemVersion, CodeSystem theCodeSystemResource, ResourceTable theResourceTable) {
+		theCodeSystemVersion.setResource(theResourceTable);
+		theCodeSystemVersion.setCodeSystemDisplayName(theCodeSystemResource.getName());
+		theCodeSystemVersion.setCodeSystemVersionId(theCodeSystemResource.getVersion());
+	}
+
+	@Override
+	public void storeNewCodeSystemVersionIfNeeded(CodeSystem theCodeSystem, ResourceTable theResourceEntity) {
+		if (theCodeSystem != null && isNotBlank(theCodeSystem.getUrl())) {
+			String codeSystemUrl = theCodeSystem.getUrl();
+			if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.COMPLETE || theCodeSystem.getContent() == null || theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
+				ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", theResourceEntity.getIdDt().getValue(), theCodeSystem.getContentElement().getValueAsString());
+
+				Long codeSystemResourcePid = IDao.RESOURCE_PID.get(theCodeSystem);
+				TermCodeSystemVersion persCs = myCodeSystemVersionDao.findCurrentVersionForCodeSystemResourcePid(codeSystemResourcePid);
+				if (persCs != null) {
+					ourLog.info("Code system version already exists in database");
+				} else {
+
+					persCs = new TermCodeSystemVersion();
+					populateCodeSystemVersionProperties(persCs, theCodeSystem, theResourceEntity);
+
+					persCs.getConcepts().addAll(toPersistedConcepts(theCodeSystem.getConcept(), persCs));
+					ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
+					storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, theCodeSystem.getName(), theCodeSystem.getVersion(), persCs);
+
+				}
+
+			}
+		}
+	}
+
+	private List<TermConcept> toPersistedConcepts(List<CodeSystem.ConceptDefinitionComponent> theConcept, TermCodeSystemVersion theCodeSystemVersion) {
+		ArrayList<TermConcept> retVal = new ArrayList<>();
+
+		for (CodeSystem.ConceptDefinitionComponent next : theConcept) {
+			if (isNotBlank(next.getCode())) {
+				TermConcept termConcept = toTermConcept(next, theCodeSystemVersion);
+				retVal.add(termConcept);
+			}
+		}
+
+		return retVal;
+	}
+
+	@Nonnull
+	private TermConcept toTermConcept(CodeSystem.ConceptDefinitionComponent theConceptDefinition, TermCodeSystemVersion theCodeSystemVersion) {
+		TermConcept termConcept = new TermConcept();
+		termConcept.setCode(theConceptDefinition.getCode());
+		termConcept.setCodeSystemVersion(theCodeSystemVersion);
+		termConcept.setDisplay(theConceptDefinition.getDisplay());
+		termConcept.addChildren(toPersistedConcepts(theConceptDefinition.getConcept(), theCodeSystemVersion), RelationshipTypeEnum.ISA);
+
+		for (CodeSystem.ConceptDefinitionDesignationComponent designationComponent : theConceptDefinition.getDesignation()) {
+			if (isNotBlank(designationComponent.getValue())) {
+				TermConceptDesignation designation = termConcept.addDesignation();
+				designation.setLanguage(designationComponent.hasLanguage() ? designationComponent.getLanguage() : null);
+				if (designationComponent.hasUse()) {
+					designation.setUseSystem(designationComponent.getUse().hasSystem() ? designationComponent.getUse().getSystem() : null);
+					designation.setUseCode(designationComponent.getUse().hasCode() ? designationComponent.getUse().getCode() : null);
+					designation.setUseDisplay(designationComponent.getUse().hasDisplay() ? designationComponent.getUse().getDisplay() : null);
+				}
+				designation.setValue(designationComponent.getValue());
+			}
+		}
+
+		for (CodeSystem.ConceptPropertyComponent next : theConceptDefinition.getProperty()) {
+			TermConceptProperty property = new TermConceptProperty();
+
+			property.setKey(next.getCode());
+			property.setConcept(termConcept);
+			property.setCodeSystemVersion(theCodeSystemVersion);
+
+			if (next.getValue() instanceof StringType) {
+				property.setType(TermConceptPropertyTypeEnum.STRING);
+				property.setValue(next.getValueStringType().getValue());
+			} else if (next.getValue() instanceof Coding) {
+				Coding nextCoding = next.getValueCoding();
+				property.setType(TermConceptPropertyTypeEnum.CODING);
+				property.setCodeSystem(nextCoding.getSystem());
+				property.setValue(nextCoding.getCode());
+				property.setDisplay(nextCoding.getDisplay());
+			} else if (next.getValue() != null) {
+				// TODO: LOINC has properties of type BOOLEAN that we should handle
+				ourLog.warn("Don't know how to handle properties of type: " + next.getValue().getClass());
+				continue;
+			}
+
+			termConcept.getProperties().add(property);
+		}
+		return termConcept;
+	}
+
 	@Override
 	@Transactional
 	public void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap) {
@@ -1443,6 +1582,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 	}
 
 	@Override
+	@Transactional
 	public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {
 		VersionIndependentConcept conceptA = toConcept(theCodeA, theSystem, theCodingA);
 		VersionIndependentConcept conceptB = toConcept(theCodeB, theSystem, theCodingB);
@@ -1471,6 +1611,136 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		return new IFhirResourceDaoCodeSystem.SubsumesResult(subsumes);
 	}
 
+	@Transactional
+	@Override
+	public AtomicInteger applyDeltaCodesystemsAdd(String theSystem, @Nullable String theParent, CodeSystem theValue) {
+		TermCodeSystem cs = getCodeSystem(theSystem);
+		if (cs == null) {
+			List<CodeSystem.ConceptDefinitionComponent> codes = theValue.getConcept();
+			theValue.setConcept(null);
+			createOrUpdateCodeSystem(theValue);
+			cs = getCodeSystem(theSystem);
+			theValue.setConcept(codes);
+		}
+
+		TermCodeSystemVersion csv = cs.getCurrentVersion();
+
+		AtomicInteger addedCodeCounter = new AtomicInteger(0);
+
+		TermConcept parentCode = null;
+		if (isNotBlank(theParent)) {
+			parentCode = myConceptDao
+				.findByCodeSystemAndCode(csv, theParent)
+				.orElseThrow(() -> new InvalidRequestException("Unknown code [" + theSystem + "|" + theParent + "]"));
+		}
+
+		List<TermConcept> concepts = new ArrayList<>();
+		for (CodeSystem.ConceptDefinitionComponent next : theValue.getConcept()) {
+			TermConcept concept = toTermConcept(next, csv);
+			if (parentCode != null) {
+				parentCode.addChild(concept, RelationshipTypeEnum.ISA);
+			}
+			concepts.add(concept);
+		}
+
+		// The first pass just saves any concepts that were added to the
+		// root of the CodeSystem
+		List<TermConceptParentChildLink> links = new ArrayList<>();
+		for (TermConcept next : concepts) {
+			int addedCount = saveOrUpdateConcept(next);
+			addedCodeCounter.addAndGet(addedCount);
+			extractLinksFromConceptAndChildren(next, links);
+		}
+
+		// This second pass saves any child concepts
+		for (TermConceptParentChildLink next : links) {
+			next.setCodeSystem(csv);
+			int addedCount = saveOrUpdateConcept(next.getChild());
+			addedCodeCounter.addAndGet(addedCount);
+			myConceptParentChildLinkDao.save(next);
+		}
+
+		return addedCodeCounter;
+	}
+
+	@Transactional
+	@Override
+	public AtomicInteger applyDeltaCodesystemsRemove(String theSystem, CodeSystem theValue) {
+		TermCodeSystem cs = getCodeSystem(theSystem);
+		if (cs == null) {
+			throw new InvalidRequestException("Unknown code system: " + theSystem);
+		}
+
+		AtomicInteger removeCounter = new AtomicInteger(0);
+
+		for (CodeSystem.ConceptDefinitionComponent next : theValue.getConcept()) {
+			Optional<TermConcept> conceptOpt = findCode(theSystem, next.getCode());
+			if (conceptOpt.isPresent()) {
+				TermConcept concept = conceptOpt.get();
+				deleteConceptChildrenAndConcept(concept, removeCounter);
+			}
+		}
+
+		return removeCounter;
+	}
+
+	private void deleteConceptChildrenAndConcept(TermConcept theConcept, AtomicInteger theRemoveCounter) {
+		for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
+			deleteConceptChildrenAndConcept(nextChildLink.getChild(), theRemoveCounter);
+			myConceptParentChildLinkDao.delete(nextChildLink);
+		}
+
+		myConceptDesignationDao.deleteAll(theConcept.getDesignations());
+		myConceptPropertyDao.deleteAll(theConcept.getProperties());
+		myConceptDao.delete(theConcept);
+		theRemoveCounter.incrementAndGet();
+	}
+
+	protected IContextValidationSupport.LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
+		return txTemplate.execute(t -> {
+			Optional<TermConcept> codeOpt = findCode(theSystem, theCode);
+			if (codeOpt.isPresent()) {
+				TermConcept code = codeOpt.get();
+
+				IContextValidationSupport.LookupCodeResult result = new IContextValidationSupport.LookupCodeResult();
+				result.setCodeSystemDisplayName(code.getCodeSystemVersion().getCodeSystemDisplayName());
+				result.setCodeSystemVersion(code.getCodeSystemVersion().getCodeSystemVersionId());
+				result.setSearchedForSystem(theSystem);
+				result.setSearchedForCode(theCode);
+				result.setFound(true);
+				result.setCodeDisplay(code.getDisplay());
+
+				for (TermConceptDesignation next : code.getDesignations()) {
+					IContextValidationSupport.ConceptDesignation designation = new IContextValidationSupport.ConceptDesignation();
+					designation.setLanguage(next.getLanguage());
+					designation.setUseSystem(next.getUseSystem());
+					designation.setUseCode(next.getUseCode());
+					designation.setUseDisplay(next.getUseDisplay());
+					designation.setValue(next.getValue());
+					result.getDesignations().add(designation);
+				}
+
+				for (TermConceptProperty next : code.getProperties()) {
+					if (next.getType() == TermConceptPropertyTypeEnum.CODING) {
+						IContextValidationSupport.CodingConceptProperty property = new IContextValidationSupport.CodingConceptProperty(next.getKey(), next.getCodeSystem(), next.getValue(), next.getDisplay());
+						result.getProperties().add(property);
+					} else if (next.getType() == TermConceptPropertyTypeEnum.STRING) {
+						IContextValidationSupport.StringConceptProperty property = new IContextValidationSupport.StringConceptProperty(next.getKey(), next.getValue());
+						result.getProperties().add(property);
+					} else {
+						throw new InternalErrorException("Unknown type: " + next.getType());
+					}
+				}
+
+				return result;
+
+			} else {
+				return null;
+			}
+		});
+	}
+
 	private @Nullable
 	ConceptSubsumptionOutcome testForSubsumption(FullTextEntityManager theEntityManager, TermConcept theLeft, TermConcept theRight, ConceptSubsumptionOutcome theOutput) {
 		QueryBuilder qb = theEntityManager.getSearchFactory().buildQueryBuilder().forEntity(TermConcept.class).get();
@@ -1608,7 +1878,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 				predicates = new ArrayList<>();
 
 				coding = translationQuery.getCoding();
-				String targetCode = null;
+				String targetCode;
 				String targetCodeSystem = null;
 				if (coding.hasCode()) {
 					predicates.add(criteriaBuilder.equal(targetJoin.get("myCode"), coding.getCode()));
@@ -1716,12 +1986,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		return retVal;
 	}
 
-	private void verifyNoDuplicates(Collection<TermConcept> theConcepts, Set<String> theCodes) {
+	private static void extractLinksFromConceptAndChildren(TermConcept theConcept, List<TermConceptParentChildLink> theLinks) {
-		for (TermConcept next : theConcepts) {
+		theLinks.addAll(theConcept.getParents());
-			if (!theCodes.add(next.getCode())) {
+		for (TermConceptParentChildLink child : theConcept.getChildren()) {
-				throw new InvalidRequestException("Duplicate code " + next.getCode() + " found in codesystem after checking " + theCodes.size() + " codes");
+			extractLinksFromConceptAndChildren(child.getChild(), theLinks);
-			}
-			verifyNoDuplicates(next.getChildren().stream().map(TermConceptParentChildLink::getChild).collect(Collectors.toList()), theCodes);
 		}
 	}
 
@@ -1775,4 +2043,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 	public static void setForceSaveDeferredAlwaysForUnitTest(boolean theForceSaveDeferredAlwaysForUnitTest) {
 		ourForceSaveDeferredAlwaysForUnitTest = theForceSaveDeferredAlwaysForUnitTest;
 	}
+
+
 }

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

@@ -19,6 +19,9 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionDefinition;
+import org.springframework.transaction.support.TransactionTemplate;
 
 import java.util.ArrayList;
 import java.util.Collections;
@@ -61,6 +64,8 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
 	private IValidationSupport myValidationSupport;
 	@Autowired
 	private IHapiTerminologySvc myTerminologySvc;
+	@Autowired
+	private PlatformTransactionManager myTransactionManager;
 
 	/**
 	 * Constructor
@@ -100,6 +105,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}
+		validateCodeSystemForStorage(theCodeSystemResource);
 		if (isBlank(resourceToStore.getIdElement().getIdPart())) {
 			String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
 			return myCodeSystemResourceDao.update(resourceToStore, matchUrl).getId();
@@ -217,14 +223,14 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
 		return null;
 	}
 
-	@CoverageIgnore
 	@Override
-	public ValueSet fetchValueSet(FhirContext theContext, String theSystem) {
+	public IBaseResource fetchResource(FhirContext theContext, Class theClass, String theUri) {
 		return null;
 	}
 
+	@CoverageIgnore
 	@Override
-	public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
+	public ValueSet fetchValueSet(FhirContext theContext, String theSystem) {
 		return null;
 	}
 
@@ -293,20 +299,30 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
 
 	@CoverageIgnore
 	@Override
-	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+	public IValidationSupport.CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
+		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
+		return txTemplate.execute(t->{
 			Optional<TermConcept> codeOpt = myTerminologySvc.findCode(theCodeSystem, theCode);
 			if (codeOpt.isPresent()) {
 				ConceptDefinitionComponent def = new ConceptDefinitionComponent();
 				TermConcept code = codeOpt.get();
 				def.setCode(code.getCode());
 				def.setDisplay(code.getDisplay());
-			CodeValidationResult retVal = new CodeValidationResult(def);
+				IValidationSupport.CodeValidationResult retVal = new IValidationSupport.CodeValidationResult(def);
 				retVal.setProperties(code.toValidationProperties());
 				retVal.setCodeSystemName(code.getCodeSystemVersion().getCodeSystem().getName());
 				return retVal;
 			}
 
-		return new CodeValidationResult(IssueSeverity.ERROR, "Unknown code {" + theCodeSystem + "}" + theCode);
+			return new IValidationSupport.CodeValidationResult(IssueSeverity.ERROR, "Unknown code {" + theCodeSystem + "}" + theCode);
+		});
+
+	}
+
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return super.lookupCode(theContext, theSystem, theCode);
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.UrlUtil;
+import ca.uhn.fhir.util.ValidateUtil;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
@@ -18,6 +19,9 @@ import org.hl7.fhir.r4.terminologies.ValueSetExpander;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionDefinition;
+import org.springframework.transaction.support.TransactionTemplate;
 
 import java.util.ArrayList;
 import java.util.Collections;
@@ -48,6 +52,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  */
 
 public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements IHapiTerminologySvcR4 {
+
 	@Autowired
 	@Qualifier("myConceptMapDaoR4")
 	private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
@@ -60,7 +65,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
 	@Autowired
 	private IValidationSupport myValidationSupport;
 	@Autowired
-	private IHapiTerminologySvc myTerminologySvc;
+	private PlatformTransactionManager myTransactionManager;
 
 	private void addAllChildren(String theSystemString, ConceptDefinitionComponent theCode, List<VersionIndependentConcept> theListToPopulate) {
 		if (isNotBlank(theCode.getCode())) {
@@ -87,6 +92,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
 
 	@Override
 	protected IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
+		validateCodeSystemForStorage(theCodeSystemResource);
 		if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
 			String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
 			return myCodeSystemResourceDao.update(theCodeSystemResource, matchUrl).getId();
@@ -227,7 +233,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
 
 	@Override
 	public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
-		return myTerminologySvc.supportsSystem(theSystem);
+		return supportsSystem(theSystem);
 	}
 
 	@Override
@@ -237,19 +243,28 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
 
 	@CoverageIgnore
 	@Override
-	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+	public IValidationSupport.CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
-		Optional<TermConcept> codeOpt = myTerminologySvc.findCode(theCodeSystem, theCode);
+		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
+		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
+		return txTemplate.execute(t-> {
+			Optional<TermConcept> codeOpt = findCode(theCodeSystem, theCode);
 			if (codeOpt.isPresent()) {
 				TermConcept code = codeOpt.get();
 				ConceptDefinitionComponent def = new ConceptDefinitionComponent();
 				def.setCode(code.getCode());
 				def.setDisplay(code.getDisplay());
-			CodeValidationResult retVal = new CodeValidationResult(def);
+				IValidationSupport.CodeValidationResult retVal = new IValidationSupport.CodeValidationResult(def);
 				retVal.setProperties(code.toValidationProperties());
 				return retVal;
 			}
 
-		return new CodeValidationResult(IssueSeverity.ERROR, "Unknown code {" + theCodeSystem + "}" + theCode);
+			return new IValidationSupport.CodeValidationResult(IssueSeverity.ERROR, "Unknown code {" + theCodeSystem + "}" + theCode);
+		});
+	}
+
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return super.lookupCode(theContext, theSystem, theCode);
 	}
 
 }

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

@@ -8,12 +8,15 @@ import org.hl7.fhir.instance.model.api.IBaseCoding;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ValueSet;
 
+import javax.annotation.Nullable;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
+import java.util.concurrent.atomic.AtomicInteger;
 
 /*
  * #%L
@@ -76,13 +79,15 @@ public interface IHapiTerminologySvc {
 	 */
 	void setProcessDeferred(boolean theProcessDeferred);
 
-	void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, TermCodeSystemVersion theCodeSytemVersion);
+	void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion);
 
 	/**
 	 * @return Returns the ID of the created/updated code system
 	 */
 	IIdType storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<org.hl7.fhir.r4.model.ValueSet> theValueSets, List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps);
 
+	void storeNewCodeSystemVersionIfNeeded(CodeSystem theCodeSystem, ResourceTable theResourceEntity);
+
 	void deleteConceptMapAndChildren(ResourceTable theResourceTable);
 
 	void deleteValueSetAndChildren(ResourceTable theResourceTable);
@@ -98,4 +103,8 @@ public interface IHapiTerminologySvc {
 	List<TermConceptMapGroupElement> translateWithReverse(TranslationRequest theTranslationRequest);
 
 	IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB);
+
+	AtomicInteger applyDeltaCodesystemsAdd(String theSystem, @Nullable String theParent, CodeSystem theValue);
+
+	AtomicInteger applyDeltaCodesystemsRemove(String theSystem, CodeSystem theDelta);
 }

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

@@ -1,7 +1,7 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
@@ -63,6 +63,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		CodeSystem codeSystem = new CodeSystem();
 		codeSystem.setUrl(URL_MY_CODE_SYSTEM);
 		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
+		codeSystem.setName("ACME Codes");
 		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
 
 		ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
@@ -98,7 +99,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		TermConcept childCA = new TermConcept(cs, "childCA").setDisplay("Child CA");
 		parentC.addChild(childCA, RelationshipTypeEnum.ISA);
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs);
 		return codeSystem;
 	}
 
@@ -129,7 +130,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 			parentB.addChild(childI, RelationshipTypeEnum.ISA);
 		}
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs);
 		return codeSystem;
 	}
 
@@ -165,7 +166,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		TermConcept beagle = new TermConcept(cs, "beagle").setDisplay("Beagle");
 		dogs.addChild(beagle, RelationshipTypeEnum.ISA);
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM,"SYSTEM NAME" , cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM,"SYSTEM NAME", "SYSTEM VERSION" , cs);
 		return codeSystem;
 	}
 
@@ -489,13 +490,17 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		
 		createExternalCsAndLocalVs();
 
+		// We're making sure that a reindex doesn't wipe out all of the
+		// stored codes in the terminology service
 		myResourceReindexingSvc.markAllResourcesForReindexing();
 		myResourceReindexingSvc.forceReindexingPass();
 		myResourceReindexingSvc.forceReindexingPass();
+		myHapiTerminologySvc.saveDeferred();
+		myHapiTerminologySvc.saveDeferred();
+		myHapiTerminologySvc.saveDeferred();
 
-		myHapiTerminologySvc.saveDeferred();
+		IContextValidationSupport.LookupCodeResult lookupResults = myCodeSystemDao.lookupCode(new StringType("childAA"), new StringType(URL_MY_CODE_SYSTEM),null, mySrd);
-		myHapiTerminologySvc.saveDeferred();
+		assertEquals(true, lookupResults.isFound());
-		myHapiTerminologySvc.saveDeferred();
 
 		ValueSet vs = new ValueSet();
 		ConceptSetComponent include = vs.getCompose().addInclude();
@@ -680,11 +685,11 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		cs.setResource(table);
 		TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
 		cs.getConcepts().add(parentA);
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", "SYSTEM VERSION" , cs);
 
 		StringType code = new StringType("ParentA");
 		StringType system = new StringType("http://snomed.info/sct");
-		LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
+		IContextValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
 		assertEquals(true, outcome.isFound());
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -22,6 +22,7 @@ import ca.uhn.fhir.jpa.searchparam.registry.BaseSearchParamRegistry;
 import ca.uhn.fhir.jpa.subscription.module.cache.SubscriptionRegistry;
 import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR4;
@@ -127,6 +128,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Autowired
 	protected ITermCodeSystemDao myTermCodeSystemDao;
 	@Autowired
+	protected ITermConceptParentChildLinkDao myTermConceptParentChildLinkDao;
+	@Autowired
 	protected ITermCodeSystemVersionDao myTermCodeSystemVersionDao;
 	@Autowired
 	@Qualifier("myCompartmentDefinitionDaoR4")
@@ -288,7 +291,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Qualifier("myTaskDaoR4")
 	protected IFhirResourceDao<Task> myTaskDao;
 	@Autowired
-	protected IHapiTerminologySvc myTermSvc;
+	protected IHapiTerminologySvcR4 myTermSvc;
 	@Autowired
 	protected PlatformTransactionManager myTransactionMgr;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java

@@ -1,7 +1,7 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
@@ -96,7 +96,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		TermConcept childCA = new TermConcept(cs, "childCA").setDisplay("Child CA");
 		parentC.addChild(childCA, RelationshipTypeEnum.ISA);
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs);
 		return codeSystem;
 	}
 
@@ -132,7 +132,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		TermConcept beagle = new TermConcept(cs, "beagle").setDisplay("Beagle");
 		dogs.addChild(beagle, RelationshipTypeEnum.ISA);
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs);
 		return codeSystem;
 	}
 
@@ -163,7 +163,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 			parentB.addChild(childI, RelationshipTypeEnum.ISA);
 		}
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs);
 		return codeSystem;
 	}
 
@@ -476,7 +476,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		concept = new TermConcept(cs, "LA9999-7");
 		cs.getConcepts().add(concept);
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs);
 
 		ValueSet valueSet = new ValueSet();
 		valueSet.setUrl(URL_MY_VALUE_SET);
@@ -803,11 +803,11 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		cs.setResource(table);
 		TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
 		cs.getConcepts().add(parentA);
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", "SYSTEM VERSION" , cs);
 
 		StringType code = new StringType("ParentA");
 		StringType system = new StringType("http://snomed.info/sct");
-		LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
+		IContextValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
 		assertEquals(true, outcome.isFound());
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3CodeSystemTest.java

@@ -55,10 +55,12 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
 		assertEquals(("SYSTEM NAME"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
-		assertEquals("display", respParam.getParameter().get(1).getName());
+		assertEquals("version", respParam.getParameter().get(1).getName());
-		assertEquals("Parent A", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals(("SYSTEM VERSION"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
-		assertEquals("abstract", respParam.getParameter().get(2).getName());
+		assertEquals("display", respParam.getParameter().get(2).getName());
-		assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).getValue().booleanValue());
+		assertEquals("Parent A", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
 
 		// With HTTP GET
 		respParam = ourClient
@@ -75,10 +77,12 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
 		assertEquals(("SYSTEM NAME"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
-		assertEquals("display", respParam.getParameter().get(1).getName());
+		assertEquals("version", respParam.getParameter().get(1).getName());
-		assertEquals("Parent A", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("SYSTEM VERSION", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
-		assertEquals("abstract", respParam.getParameter().get(2).getName());
+		assertEquals("display", respParam.getParameter().get(2).getName());
-		assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).getValue().booleanValue());
+		assertEquals("Parent A", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
 
 	}
 
@@ -96,11 +100,13 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 		ourLog.info(resp);
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
-		assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals(("v2 Identifier Type"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
-		assertEquals("display", respParam.getParameter().get(1).getName());
+		assertEquals("version", respParam.getParameter().get(1).getName());
-		assertEquals("Accession ID", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals(("2.8.2"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
-		assertEquals("abstract", respParam.getParameter().get(2).getName());
+		assertEquals("display", respParam.getParameter().get(2).getName());
-		assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).getValue().booleanValue());
+		assertEquals("Accession ID", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
 	}
 
 	@Test
@@ -123,7 +129,6 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 
 	@Test
 	public void testLookupOperationByCodeAndSystemUserDefinedCode() {
-		//@formatter:off
 		Parameters respParam = ourClient
 			.operation()
 			.onType(CodeSystem.class)
@@ -131,13 +136,12 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 			.withParameter(Parameters.class, "code", new CodeType("8450-9"))
 			.andParameter("system", new UriType("http://acme.org"))
 			.execute();
-		//@formatter:on
 
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
-		assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("ACME Codes", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
 		assertEquals("display", respParam.getParameter().get(1).getName());
 		assertEquals(("Systolic blood pressure--expiration"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
 		assertEquals("abstract", respParam.getParameter().get(2).getName());
@@ -164,20 +168,18 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 
 	@Test
 	public void testLookupOperationByCoding() {
-		//@formatter:off
 		Parameters respParam = ourClient
 			.operation()
 			.onType(CodeSystem.class)
 			.named("lookup")
 			.withParameter(Parameters.class, "coding", new Coding().setSystem("http://acme.org").setCode("8450-9"))
 			.execute();
-		//@formatter:on
 
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
-		assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals(("ACME Codes"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
 		assertEquals("display", respParam.getParameter().get(1).getName());
 		assertEquals(("Systolic blood pressure--expiration"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
 		assertEquals("abstract", respParam.getParameter().get(2).getName());
@@ -239,9 +241,7 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 	}
 
 	@Test
-//	@Ignore
 	public void testLookupOperationForBuiltInCode() {
-		//@formatter:off
 		Parameters respParam = ourClient
 			.operation()
 			.onType(CodeSystem.class)
@@ -249,17 +249,18 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 			.withParameter(Parameters.class, "code", new CodeType("M"))
 			.andParameter("system", new UriType("http://hl7.org/fhir/v3/MaritalStatus"))
 			.execute();
-		//@formatter:on
 
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
-		assertEquals("Unknown", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("v3 Code System MaritalStatus", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
-		assertEquals("display", respParam.getParameter().get(1).getName());
+		assertEquals("version", respParam.getParameter().get(1).getName());
-		assertEquals("Married", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("2016-11-11", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
-		assertEquals("abstract", respParam.getParameter().get(2).getName());
+		assertEquals("display", respParam.getParameter().get(2).getName());
-		assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).booleanValue());
+		assertEquals("Married", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).booleanValue());
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java

@@ -126,7 +126,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 			code.addPropertyString("HELLO", "12345-2");
 			cs.getConcepts().add(code);
 
-			myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
+			myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs);
 		});
 	}
 
@@ -233,7 +233,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 
 
 	@Test
-	public void testExpandById() throws IOException {
+	public void testExpandById() {
 		//@formatter:off
 		Parameters respParam = ourClient
 			.operation()
@@ -263,7 +263,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 	}
 
 	@Test
-	public void testExpandByIdWithFilter() throws IOException {
+	public void testExpandByIdWithFilter() {
 
 		//@formatter:off
 		Parameters respParam = ourClient
@@ -350,7 +350,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 	}
 
 	@Test
-	public void testExpandInlineVsAgainstBuiltInCs() throws IOException {
+	public void testExpandInlineVsAgainstBuiltInCs() {
 		createLocalVsPointingAtBuiltInCodeSystem();
 		assertNotNull(myLocalValueSetId);
 
@@ -371,7 +371,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 	}
 
 	@Test
-	public void testExpandInlineVsAgainstExternalCs() throws IOException {
+	public void testExpandInlineVsAgainstExternalCs() {
 		createExternalCsAndLocalVs();
 		assertNotNull(myLocalVs);
 		myLocalVs.setId("");
@@ -446,7 +446,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 	}
 
 	@Test
-	public void testExpandLocalVsAgainstBuiltInCs() throws IOException {
+	public void testExpandLocalVsAgainstBuiltInCs() {
 		createLocalVsPointingAtBuiltInCodeSystem();
 		assertNotNull(myLocalValueSetId);
 
@@ -467,7 +467,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 	}
 
 	@Test
-	public void testExpandLocalVsAgainstExternalCs() throws IOException {
+	public void testExpandLocalVsAgainstExternalCs() {
 		createExternalCsAndLocalVs();
 		assertNotNull(myLocalValueSetId);
 
@@ -491,7 +491,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 	}
 
 	@Test
-	public void testExpandLocalVsCanonicalAgainstExternalCs() throws IOException {
+	public void testExpandLocalVsCanonicalAgainstExternalCs() {
 		createExternalCsAndLocalVs();
 		assertNotNull(myLocalValueSetId);
 
@@ -515,7 +515,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 	}
 
 	@Test
-	public void testExpandLocalVsWithUnknownCode() throws IOException {
+	public void testExpandLocalVsWithUnknownCode() {
 		createExternalCsAndLocalVsWithUnknownCode();
 		assertNotNull(myLocalValueSetId);
 
@@ -636,7 +636,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 		ourLog.info(resp);
 
 		assertEquals("result", respParam.getParameter().get(0).getName());
-		assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue().booleanValue());
+		assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue());
 
 		assertEquals("message", respParam.getParameter().get(1).getName());
 		assertThat(((StringType) respParam.getParameter().get(1).getValue()).getValue(), Matchers.containsStringIgnoringCase("succeeded"));
@@ -664,7 +664,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 		ourLog.info(resp);
 
 		assertEquals("result", respParam.getParameter().get(0).getName());
-		assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue().booleanValue());
+		assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue());
 
 		assertEquals("message", respParam.getParameter().get(1).getName());
 		assertThat(((StringType) respParam.getParameter().get(1).getValue()).getValue(), Matchers.containsStringIgnoringCase("succeeded"));
@@ -682,6 +682,8 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 		CodeSystem codeSystem = new CodeSystem();
 		codeSystem.setUrl(URL_MY_CODE_SYSTEM);
 		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
+		codeSystem.setName("ACME Codes");
+		codeSystem.setVersion("1.2.3.4");
 		IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();
 
 		ResourceTable table = theResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
@@ -707,7 +709,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 		TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
 		cs.getConcepts().add(parentB);
 
-		theTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
+		theTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs);
 		return codeSystem;
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java

@@ -85,7 +85,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 		try {
 			ourClient
 				.operation()
-				.onServer()
+				.onType(CodeSystem.class)
 				.named("upload-external-code-system")
 				.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URI + "FOO"))
 				.andParameter("package", new Attachment().setUrl("foo").setData(packageBytes))
@@ -102,7 +102,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 
 		Parameters respParam = ourClient
 			.operation()
-			.onServer()
+			.onType(CodeSystem.class)
 			.named("upload-external-code-system")
 			.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.LOINC_URI))
 			.andParameter("package", new Attachment().setUrl("file.zip").setData(packageBytes))
@@ -111,7 +111,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);
 
-		assertThat(((IntegerType) respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
+		assertThat(((IntegerType) respParam.getParameter().get(1).getValue()).getValue(), greaterThan(1));
 
 		/*
 		 * Try uploading a second time
@@ -119,7 +119,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 
 		respParam = ourClient
 			.operation()
-			.onServer()
+			.onType(CodeSystem.class)
 			.named("upload-external-code-system")
 			.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.LOINC_URI))
 			.andParameter("package", new Attachment().setUrl("file.zip").setData(packageBytes))
@@ -136,7 +136,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 		try {
 			ourClient
 				.operation()
-				.onServer()
+				.onType(CodeSystem.class)
 				.named("upload-external-code-system")
 				.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URI))
 				.andParameter("package", new Attachment().setData(packageBytes))
@@ -154,7 +154,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 		try {
 			ourClient
 				.operation()
-				.onServer()
+				.onType(CodeSystem.class)
 				.named("upload-external-code-system")
 				.withParameter(Parameters.class, "package", new Attachment().setUrl("foo").setData(packageBytes))
 				.execute();
@@ -170,7 +170,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 		try {
 			ourClient
 				.operation()
-				.onServer()
+				.onType(CodeSystem.class)
 				.named("upload-external-code-system")
 				.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URI))
 				.execute();
@@ -186,7 +186,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 
 		Parameters respParam = ourClient
 			.operation()
-			.onServer()
+			.onType(CodeSystem.class)
 			.named("upload-external-code-system")
 			.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URI))
 			.andParameter("package", new Attachment().setUrl("file.zip").setData(packageBytes))
@@ -195,7 +195,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);
 
-		assertThat(((IntegerType) respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
+		assertThat(((IntegerType) respParam.getParameter().get(1).getValue()).getValue(), greaterThan(1));
 	}
 
 	@Test
@@ -212,7 +212,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 
 		Parameters respParam = ourClient
 			.operation()
-			.onServer()
+			.onType(CodeSystem.class)
 			.named("upload-external-code-system")
 			.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URI))
 			.andParameter("localfile", new StringType(tempFile.getAbsolutePath()))
@@ -221,7 +221,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);
 
-		assertThat(((IntegerType) respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
+		assertThat(((IntegerType) respParam.getParameter().get(1).getValue()).getValue(), greaterThan(1));
 	}
 
 	@AfterClass

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CodeSystemTest.java

@@ -2,6 +2,8 @@ package ca.uhn.fhir.jpa.provider.r4;
 
 import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.TestUtil;
@@ -14,8 +16,8 @@ import org.springframework.transaction.annotation.Transactional;
 
 import java.io.IOException;
 
-import static org.junit.Assert.assertEquals;
+import static org.hamcrest.CoreMatchers.containsString;
-import static org.junit.Assert.fail;
+import static org.junit.Assert.*;
 
 public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test {
 
@@ -45,6 +47,93 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 
 	}
 
+	@Test
+	public void testApplyDeltaAdd() {
+
+		CodeSystem delta = new CodeSystem();
+		delta.setUrl("http://example.com/labCodes");
+		delta.setName("Example Hospital Lab Codes");
+		delta.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		delta.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		delta.setUrl("http://foo");
+		CodeSystem.ConceptDefinitionComponent chem = delta
+			.addConcept()
+			.setCode("CHEM")
+			.setDisplay("Chemistry Tests");
+		chem
+			.addConcept()
+			.setCode("HB")
+			.setDisplay("Hemoglobin");
+		chem
+			.addConcept()
+			.setCode("NEUT")
+			.setDisplay("Neutrophil");
+		CodeSystem.ConceptDefinitionComponent micro = delta
+			.addConcept()
+			.setCode("MICRO")
+			.setDisplay("Microbiology Tests");
+		micro
+			.addConcept()
+			.setCode("C&S")
+			.setDisplay("Culture & Sensitivity");
+
+		LoggingInterceptor interceptor = new LoggingInterceptor(true);
+		ourClient.registerInterceptor(interceptor);
+		Parameters outcome = ourClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD)
+			.withParameter(Parameters.class, TerminologyUploaderProvider.VALUE, delta)
+			.prettyPrint()
+			.execute();
+		ourClient.unregisterInterceptor(interceptor);
+
+		String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
+		ourLog.info(encoded);
+		assertThat(encoded, containsString("\"valueInteger\": 5"));
+	}
+
+	@Test
+	public void testApplyDeltaRemove() {
+		// Create not-present
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://foo");
+		cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		ourClient.create().resource(cs).execute();
+
+		CodeSystem delta = new CodeSystem();
+		delta.setUrl("http://foo");
+		delta
+			.addConcept()
+			.setCode("codeA")
+			.setDisplay("displayA");
+
+		// Add
+		ourClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD)
+			.withParameter(Parameters.class, TerminologyUploaderProvider.VALUE, delta)
+			.prettyPrint()
+			.execute();
+
+		// Remove
+		LoggingInterceptor interceptor = new LoggingInterceptor(true);
+		ourClient.registerInterceptor(interceptor);
+		Parameters outcome = ourClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE)
+			.withParameter(Parameters.class, TerminologyUploaderProvider.VALUE, delta)
+			.prettyPrint()
+			.execute();
+		ourClient.unregisterInterceptor(interceptor);
+
+		String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
+		ourLog.info(encoded);
+		assertThat(encoded, containsString("\"valueInteger\": 1"));
+	}
+
 	@Test
 	public void testLookupOnExternalCode() {
 		ResourceProviderR4ValueSetTest.createExternalCs(myCodeSystemDao, myResourceTableDao, myTermSvc, mySrd);
@@ -61,11 +150,13 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 		ourLog.info(resp);
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
-		assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("SYSTEM NAME", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
-		assertEquals("display", respParam.getParameter().get(1).getName());
+		assertEquals("version", respParam.getParameter().get(1).getName());
-		assertEquals("Parent A", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("SYSTEM VERSION", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
-		assertEquals("abstract", respParam.getParameter().get(2).getName());
+		assertEquals("display", respParam.getParameter().get(2).getName());
-		assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("Parent A", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
 
 		// With HTTP GET
 		respParam = ourClient
@@ -81,11 +172,13 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 		ourLog.info(resp);
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
-		assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals(("SYSTEM NAME"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
-		assertEquals("display", respParam.getParameter().get(1).getName());
+		assertEquals("version", respParam.getParameter().get(1).getName());
-		assertEquals("Parent A", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals(("SYSTEM VERSION"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
-		assertEquals("abstract", respParam.getParameter().get(2).getName());
+		assertEquals("display", respParam.getParameter().get(2).getName());
-		assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("Parent A", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
 
 	}
 
@@ -103,11 +196,13 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 		ourLog.info(resp);
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
-		assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("v2.0203", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
-		assertEquals("display", respParam.getParameter().get(1).getName());
+		assertEquals("version", respParam.getParameter().get(1).getName());
-		assertEquals("Accession ID", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("2.9", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
-		assertEquals("abstract", respParam.getParameter().get(2).getName());
+		assertEquals("display", respParam.getParameter().get(2).getName());
-		assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("Accession ID", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
 	}
 
 	@Test
@@ -140,7 +235,7 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 		ourLog.info(resp);
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
-		assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals(("ACME Codes"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
 		assertEquals("display", respParam.getParameter().get(1).getName());
 		assertEquals(("Systolic blood pressure--expiration"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
 		assertEquals("abstract", respParam.getParameter().get(2).getName());
@@ -176,7 +271,7 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 		ourLog.info(resp);
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
-		assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals(("ACME Codes"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
 		assertEquals("display", respParam.getParameter().get(1).getName());
 		assertEquals(("Systolic blood pressure--expiration"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
 		assertEquals("abstract", respParam.getParameter().get(2).getName());
@@ -245,11 +340,13 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 		ourLog.info(resp);
 
 		assertEquals("name", respParam.getParameter().get(0).getName());
-		assertEquals("Unknown", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("v3.MaritalStatus", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
-		assertEquals("display", respParam.getParameter().get(1).getName());
+		assertEquals("version", respParam.getParameter().get(1).getName());
-		assertEquals("Married", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("2018-08-12", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
-		assertEquals("abstract", respParam.getParameter().get(2).getName());
+		assertEquals("display", respParam.getParameter().get(2).getName());
-		assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).booleanValue());
+		assertEquals("Married", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).booleanValue());
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java

@@ -16,7 +16,6 @@ import org.apache.commons.io.IOUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.client.methods.HttpPost;
-import org.apache.http.client.methods.HttpUriRequest;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -514,7 +513,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
 		ourLog.info(resp);
 
 		assertEquals("result", respParam.getParameter().get(0).getName());
-		assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue().booleanValue());
+		assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue());
 
 		assertEquals("message", respParam.getParameter().get(1).getName());
 		assertThat(((StringType) respParam.getParameter().get(1).getValue()).getValue(), containsStringIgnoringCase("succeeded"));
@@ -603,7 +602,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
 		TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
 		cs.getConcepts().add(parentB);
 
-		theTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
+		theTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs);
 		return codeSystem;
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java

@@ -49,7 +49,7 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
 		try {
 			ourClient
 				.operation()
-				.onServer()
+				.onType(CodeSystem.class)
 				.named("upload-external-code-system")
 				.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URI + "FOO"))
 				.andParameter("package", new Attachment().setUrl("file.zip").setData(packageBytes))
@@ -65,35 +65,31 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
 	public void testUploadLoinc() throws Exception {
 		byte[] packageBytes = TerminologyUploaderProviderDstu3Test.createLoincZip();
 
-		//@formatter:off
 		Parameters respParam = ourClient
 			.operation()
-			.onServer()
+			.onType(CodeSystem.class)
 			.named("upload-external-code-system")
 			.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.LOINC_URI))
 			.andParameter("package", new Attachment().setUrl("file.zip").setData(packageBytes))
 			.execute();
-		//@formatter:on
 
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);
 
-		assertThat(((IntegerType) respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
+		assertThat(((IntegerType) respParam.getParameter().get(1).getValue()).getValue(), greaterThan(1));
-		assertThat(((Reference) respParam.getParameter().get(1).getValue()).getReference(), matchesPattern("CodeSystem\\/[a-zA-Z0-9]+"));
+		assertThat(((Reference) respParam.getParameter().get(2).getValue()).getReference(), matchesPattern("CodeSystem\\/[a-zA-Z0-9]+"));
 
 		/*
 		 * Try uploading a second time
 		 */
 
-		//@formatter:off
 		respParam = ourClient
 			.operation()
-			.onServer()
+			.onType(CodeSystem.class)
 			.named("upload-external-code-system")
 			.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.LOINC_URI))
 			.andParameter("package", new Attachment().setUrl("file.zip").setData(packageBytes))
 			.execute();
-		//@formatter:on
 
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);
@@ -106,7 +102,7 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
 		try {
 			ourClient
 				.operation()
-				.onServer()
+				.onType(CodeSystem.class)
 				.named("upload-external-code-system")
 				.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URI))
 				.execute();
@@ -114,18 +110,16 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
 		} catch (InvalidRequestException e) {
 			assertEquals("HTTP 400 Bad Request: No 'localfile' or 'package' parameter, or package had no data", e.getMessage());
 		}
-		//@formatter:on
 	}
 
 	@Test
 	public void testUploadMissingUrl() throws Exception {
 		byte[] packageBytes = createSctZip();
 
-		//@formatter:off
 		try {
 			ourClient
 				.operation()
-				.onServer()
+				.onType(CodeSystem.class)
 				.named("upload-external-code-system")
 				.withParameter(Parameters.class, "package", new Attachment().setUrl("file.zip").setData(packageBytes))
 				.execute();
@@ -133,27 +127,25 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
 		} catch (InvalidRequestException e) {
 			assertEquals("HTTP 400 Bad Request: Unknown URL: ", e.getMessage());
 		}
-		//@formatter:on
+
 	}
 
 	@Test
 	public void testUploadSct() throws Exception {
 		byte[] packageBytes = createSctZip();
 
-		//@formatter:off
 		Parameters respParam = ourClient
 			.operation()
-			.onServer()
+			.onType(CodeSystem.class)
 			.named("upload-external-code-system")
 			.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URI))
 			.andParameter("package", new Attachment().setUrl("file.zip").setData(packageBytes))
 			.execute();
-		//@formatter:on
 
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);
 
-		assertThat(((IntegerType) respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
+		assertThat(((IntegerType) respParam.getParameter().get(1).getValue()).getValue(), greaterThan(1));
 	}
 
 	@Test
@@ -166,20 +158,18 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
 		fos.write(packageBytes);
 		fos.close();
 
-		//@formatter:off
 		Parameters respParam = ourClient
 			.operation()
-			.onServer()
+			.onType(CodeSystem.class)
 			.named("upload-external-code-system")
 			.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URI))
 			.andParameter("localfile", new StringType(tempFile.getAbsolutePath()))
 			.execute();
-		//@formatter:on
 
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);
 
-		assertThat(((IntegerType) respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
+		assertThat(((IntegerType) respParam.getParameter().get(1).getValue()).getValue(), greaterThan(1));
 	}
 
 	@AfterClass

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/websocket/WebsocketWithSubscriptionIdDstu3Test.java

@@ -52,6 +52,7 @@ public class WebsocketWithSubscriptionIdDstu3Test extends BaseResourceProviderDs
 	@Autowired
 	private SubscriptionTestUtil mySubscriptionTestUtil;
 
+	@Override
 	@After
 	public void after() throws Exception {
 		super.after();
@@ -65,6 +66,7 @@ public class WebsocketWithSubscriptionIdDstu3Test extends BaseResourceProviderDs
 		myWebSocketClient.stop();
 	}
 
+	@Override
 	@Before
 	public void before() throws Exception {
 		super.before();
@@ -117,7 +119,7 @@ public class WebsocketWithSubscriptionIdDstu3Test extends BaseResourceProviderDs
 	}
 
 	@Test
-	public void createObservation() throws Exception {
+	public void createObservation() {
 		Observation observation = new Observation();
 		CodeableConcept codeableConcept = new CodeableConcept();
 		observation.setCode(codeableConcept);
@@ -141,7 +143,7 @@ public class WebsocketWithSubscriptionIdDstu3Test extends BaseResourceProviderDs
 	}
 
 	@Test
-	public void createObservationThatDoesNotMatch() throws Exception {
+	public void createObservationThatDoesNotMatch() {
 		Observation observation = new Observation();
 		CodeableConcept codeableConcept = new CodeableConcept();
 		observation.setCode(codeableConcept);

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

@@ -1,38 +1,22 @@
 package ca.uhn.fhir.jpa.term;
 
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
-import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
-import org.hl7.fhir.r4.model.CodeSystem;
-import org.hl7.fhir.r4.model.ConceptMap;
-import org.hl7.fhir.r4.model.Enumerations;
-import org.hl7.fhir.r4.model.ValueSet;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mockito.ArgumentCaptor;
-import org.mockito.Captor;
 import org.mockito.Mock;
 import org.mockito.junit.MockitoJUnitRunner;
 
 import java.io.IOException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
 
-import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsString;
-import static org.hamcrest.Matchers.empty;
+import static org.junit.Assert.assertThat;
-import static org.junit.Assert.*;
+import static org.junit.Assert.fail;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.Mockito.times;
-import static org.mockito.Mockito.verify;
 
 @RunWith(MockitoJUnitRunner.class)
 public class TerminologyLoaderSvcImgthlaTest {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcIntegrationDstu3Test.java

@@ -1,7 +1,7 @@
 package ca.uhn.fhir.jpa.term;
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
 import ca.uhn.fhir.util.TestUtil;
@@ -134,9 +134,8 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
 		myLoader.loadLoinc(files.getFiles(), mySrd);
 
-		IFhirResourceDaoCodeSystem.LookupCodeResult result = myCodeSystemDao.lookupCode(new StringType("10013-1"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URI), null, mySrd);
+		IContextValidationSupport.LookupCodeResult result = myCodeSystemDao.lookupCode(new StringType("10013-1"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URI), null, mySrd);
-		org.hl7.fhir.r4.model.Parameters parametersR4 = result.toParameters(null);
+		Parameters parameters = (Parameters) result.toParameters(myFhirCtx, null);
-		Parameters parameters = VersionConvertor_30_40.convertParameters(parametersR4);
 
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parameters));
 
@@ -165,9 +164,8 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
 		myLoader.loadLoinc(files.getFiles(), mySrd);
 
-		IFhirResourceDaoCodeSystem.LookupCodeResult result = myCodeSystemDao.lookupCode(new StringType("17788-1"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URI), null, mySrd);
+		IContextValidationSupport.LookupCodeResult result = myCodeSystemDao.lookupCode(new StringType("17788-1"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URI), null, mySrd);
-		org.hl7.fhir.r4.model.Parameters parametersR4 = result.toParameters(null);
+		Parameters parameters = (Parameters) result.toParameters(myFhirCtx, null);
-		Parameters parameters = VersionConvertor_30_40.convertParameters(parametersR4);
 
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parameters));
 
@@ -184,10 +182,9 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
 		myLoader.loadLoinc(files.getFiles(), mySrd);
 
-		IFhirResourceDaoCodeSystem.LookupCodeResult result = myCodeSystemDao.lookupCode(new StringType("10013-1"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URI), null, mySrd);
+		IContextValidationSupport.LookupCodeResult result = myCodeSystemDao.lookupCode(new StringType("10013-1"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URI), null, mySrd);
 		List<? extends IPrimitiveType<String>> properties = Lists.newArrayList(new CodeType("SCALE_TYP"));
-		org.hl7.fhir.r4.model.Parameters parametersR4 = result.toParameters(properties);
+		Parameters parameters = (Parameters) result.toParameters(myFhirCtx, properties);
-		Parameters parameters = VersionConvertor_30_40.convertParameters(parametersR4);
 
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parameters));
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java

@@ -52,6 +52,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		CodeSystem codeSystem = new CodeSystem();
 		codeSystem.setUrl(CS_URL);
 		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
+		codeSystem.setName("SYSTEM NAME");
 		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
 
 		ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
@@ -95,7 +96,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		TermConcept parentB = new TermConcept(cs, "ParentB");
 		cs.getConcepts().add(parentB);
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs);
 
 		return id;
 	}
@@ -114,7 +115,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		TermConcept parentA = new TermConcept(cs, "CS2");
 		cs.getConcepts().add(parentA);
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL_2, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL_2, "SYSTEM NAME", "SYSTEM VERSION" , cs);
 
 		return id;
 	}
@@ -146,7 +147,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 			code.addPropertyString("HELLO", "12345-2");
 			cs.getConcepts().add(code);
 
-			myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
+			myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION" , cs);
 		});
 	}
 
@@ -162,7 +163,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		TermCodeSystemVersion cs = new TermCodeSystemVersion();
 		cs.setResource(table);
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION" , cs);
 
 		// Update
 		cs = new TermCodeSystemVersion();
@@ -171,17 +172,14 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		id = myCodeSystemDao.update(codeSystem, null, true, true, mySrd).getId().toUnqualified();
 		table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
 		cs.setResource(table);
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION" , cs);
 
 		// Try to update to a different resource
 		codeSystem = new CodeSystem();
 		codeSystem.setUrl(CS_URL);
 		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
-		id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
-		table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
-		cs.setResource(table);
 		try {
-			myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
+			myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
 			fail();
 		} catch (UnprocessableEntityException e) {
 			assertThat(e.getMessage(), containsString("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/"));
@@ -585,7 +583,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		child.addChild(parent, RelationshipTypeEnum.ISA);
 
 		try {
-			myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://foo", "SYSTEM NAME", cs);
+			myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://foo", "SYSTEM NAME", "SYSTEM VERSION" , cs);
 			fail();
 		} catch (InvalidRequestException e) {
 			assertEquals("CodeSystem contains circular reference around code parent", e.getMessage());
@@ -708,7 +706,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		runInTransaction(()->{
 			ResourceTable resTable = myEntityManager.find(ResourceTable.class, csId.getIdPartAsLong());
 			version.setResource(resTable);
-			myTermSvc.storeNewCodeSystemVersion(csId.getIdPartAsLong(), cs.getUrl(), "My System", version);
+			myTermSvc.storeNewCodeSystemVersion(csId.getIdPartAsLong(), cs.getUrl(), "My System", "SYSTEM VERSION" , version);
 		});
 
 		org.hl7.fhir.dstu3.model.ValueSet vs = new org.hl7.fhir.dstu3.model.ValueSet();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java

@@ -1,14 +1,22 @@
 package ca.uhn.fhir.jpa.term;
 
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.param.UriParam;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
+import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
 import org.junit.*;
 import org.junit.rules.ExpectedException;
 import org.mockito.Mock;
@@ -18,9 +26,12 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import javax.annotation.Nonnull;
 import java.io.IOException;
 import java.util.List;
 import java.util.Optional;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.stream.Collectors;
 
 import static org.junit.Assert.*;
 import static org.mockito.ArgumentMatchers.*;
@@ -31,13 +42,12 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 	private static final Logger ourLog = LoggerFactory.getLogger(TerminologySvcImplR4Test.class);
 	@Rule
 	public final ExpectedException expectedException = ExpectedException.none();
+	@Mock
+	IValueSetCodeAccumulator myValueSetCodeAccumulator;
 	private IIdType myConceptMapId;
 	private IIdType myExtensionalCsId;
 	private IIdType myExtensionalVsId;
 
-	@Mock
-	IValueSetCodeAccumulator myValueSetCodeAccumulator;
-
 	@Before
 	public void before() {
 		myDaoConfig.setAllowExternalReferences(true);
@@ -53,6 +63,8 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		CodeSystem codeSystem = new CodeSystem();
 		codeSystem.setUrl(CS_URL);
 		codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		codeSystem.setName("SYSTEM NAME");
+		codeSystem.setVersion("SYSTEM VERSION");
 		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
 
 		ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
@@ -95,7 +107,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		TermConcept parentB = new TermConcept(cs, "ParentB");
 		cs.getConcepts().add(parentB);
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs);
 
 		return id;
 	}
@@ -157,6 +169,304 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		});
 	}
 
+	@Test
+	public void testApplyCodeSystemDeltaAdd() {
+
+		// Create not-present
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://foo");
+		cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		myCodeSystemDao.create(cs);
+
+		CodeSystem delta = new CodeSystem();
+		delta
+			.addConcept()
+			.setCode("codeA")
+			.setDisplay("displayA");
+		delta
+			.addConcept()
+			.setCode("codeB")
+			.setDisplay("displayB");
+		myTermSvc.applyDeltaCodesystemsAdd("http://foo", null, delta);
+
+		assertEquals(true, myTermSvc.findCode("http://foo", "codeA").isPresent());
+		assertEquals(false, myTermSvc.findCode("http://foo", "codeZZZ").isPresent());
+
+	}
+
+	/**
+	 * This would be a good check, but there is no easy eay to do it...
+	 */
+	@Test
+	@Ignore
+	public void testApplyCodeSystemDeltaAddNotPermittedForNonExternalCodeSystem() {
+
+		// Create not-present
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://foo");
+		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		myCodeSystemDao.create(cs);
+
+		CodeSystem delta = new CodeSystem();
+		delta
+			.addConcept()
+			.setCode("codeA")
+			.setDisplay("displayA");
+		try {
+			myTermSvc.applyDeltaCodesystemsAdd("http://foo", null, delta);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("", e.getMessage());
+		}
+
+	}
+
+	@Test
+	public void testApplyCodeSystemDeltaAddWithoutPreExistingCodeSystem() {
+
+		CodeSystem delta = new CodeSystem();
+		delta.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		delta.setUrl("http://foo");
+		delta.setName("Acme Lab Codes");
+		delta
+			.addConcept()
+			.setCode("CBC")
+			.setDisplay("Complete Blood Count");
+		delta
+			.addConcept()
+			.setCode("URNL")
+			.setDisplay("Routine Urinalysis");
+		myTermSvc.applyDeltaCodesystemsAdd("http://foo", null, delta);
+
+		SearchParameterMap params = new SearchParameterMap();
+		params.setLoadSynchronous(true);
+		params.add(CodeSystem.SP_URL, new UriParam("http://foo"));
+		IBundleProvider searchResult = myCodeSystemDao.search(params, mySrd);
+		assertEquals(1, searchResult.size().intValue());
+		CodeSystem outcome = (CodeSystem) searchResult.getResources(0,1).get(0);
+
+		assertEquals("http://foo", outcome.getUrl());
+		assertEquals("Acme Lab Codes", outcome.getName());
+	}
+
+
+	@Test
+	public void testApplyCodeSystemDeltaAddDuplicatesIgnored() {
+
+		// Add codes
+		CodeSystem delta = new CodeSystem();
+		delta.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		delta.setUrl("http://foo");
+		delta.setName("Acme Lab Codes");
+		delta
+			.addConcept()
+			.setCode("codea")
+			.setDisplay("CODEA0");
+		delta
+			.addConcept()
+			.setCode("codeb")
+			.setDisplay("CODEB0");
+		AtomicInteger outcome = myTermSvc.applyDeltaCodesystemsAdd("http://foo", null, delta);
+		assertEquals(2, outcome.get());
+
+		// Add codes again with different display
+		delta = new CodeSystem();
+		delta.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		delta.setUrl("http://foo");
+		delta.setName("Acme Lab Codes");
+		delta
+			.addConcept()
+			.setCode("codea")
+			.setDisplay("CODEA1");
+		delta
+			.addConcept()
+			.setCode("codeb")
+			.setDisplay("CODEB1");
+		outcome = myTermSvc.applyDeltaCodesystemsAdd("http://foo", null, delta);
+		assertEquals(2, outcome.get());
+
+		// Add codes again with no changes
+		outcome = myTermSvc.applyDeltaCodesystemsAdd("http://foo", null, delta);
+		assertEquals(0, outcome.get());
+	}
+
+
+	@Test
+	public void testApplyCodeSystemDeltaAddAsChild() {
+
+		// Create not-present
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://foo");
+		cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		myCodeSystemDao.create(cs);
+
+		CodeSystem delta = new CodeSystem();
+		delta
+			.addConcept()
+			.setCode("codeA")
+			.setDisplay("displayA");
+		delta
+			.addConcept()
+			.setCode("codeB")
+			.setDisplay("displayB");
+		myTermSvc.applyDeltaCodesystemsAdd("http://foo", null, delta);
+
+		delta = new CodeSystem();
+		CodeSystem.ConceptDefinitionComponent codeAA = delta
+			.addConcept()
+			.setCode("codeAA")
+			.setDisplay("displayAA");
+		codeAA
+			.addConcept()
+			.setCode("codeAAA")
+			.setDisplay("displayAAA");
+		myTermSvc.applyDeltaCodesystemsAdd("http://foo", "codeA", delta);
+
+		assertEquals(true, myTermSvc.findCode("http://foo", "codeAA").isPresent());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMEDBY, myTermSvc.subsumes(toString("codeA"), toString("codeAA"), toString("http://foo"), null, null).getOutcome());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMEDBY, myTermSvc.subsumes(toString("codeA"), toString("codeAAA"), toString("http://foo"), null, null).getOutcome());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMEDBY, myTermSvc.subsumes(toString("codeAA"), toString("codeAAA"), toString("http://foo"), null, null).getOutcome());
+		assertEquals(ConceptSubsumptionOutcome.NOTSUBSUMED, myTermSvc.subsumes(toString("codeB"), toString("codeAA"), toString("http://foo"), null, null).getOutcome());
+
+		runInTransaction(() -> {
+			List<TermConceptParentChildLink> allChildren = myTermConceptParentChildLinkDao.findAll();
+			assertEquals(2, allChildren.size());
+		});
+	}
+
+	@Test
+	public void testApplyCodeSystemDeltaAddWithPropertiesAndDesignations() {
+
+		// Create not-present
+		CodeSystem cs = new CodeSystem();
+		cs.setName("Description of my life");
+		cs.setUrl("http://foo");
+		cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		cs.setVersion("1.2.3");
+		myCodeSystemDao.create(cs);
+
+		CodeSystem delta = new CodeSystem();
+		CodeSystem.ConceptDefinitionComponent concept = delta
+			.addConcept()
+			.setCode("lunch")
+			.setDisplay("I'm having dog food");
+		concept
+			.addDesignation()
+			.setLanguage("fr")
+			.setUse(new Coding("http://sys", "code", "display"))
+			.setValue("Je mange une pomme");
+		concept
+			.addDesignation()
+			.setLanguage("es")
+			.setUse(new Coding("http://sys", "code", "display"))
+			.setValue("Como una pera");
+		concept.addProperty()
+			.setCode("flavour")
+			.setValue(new StringType("Hints of lime"));
+		concept.addProperty()
+			.setCode("useless_sct_code")
+			.setValue(new Coding("http://snomed.info", "1234567", "Choked on large meal (finding)"));
+		myTermSvc.applyDeltaCodesystemsAdd("http://foo", null, delta);
+
+		IContextValidationSupport.LookupCodeResult result = myTermSvc.lookupCode(myFhirCtx, "http://foo", "lunch");
+		assertEquals(true, result.isFound());
+		assertEquals("lunch", result.getSearchedForCode());
+		assertEquals("http://foo", result.getSearchedForSystem());
+
+		Parameters output = (Parameters) result.toParameters(myFhirCtx, null);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
+
+		assertEquals("Description of my life", ((StringType) output.getParameter("name")).getValue());
+		assertEquals("1.2.3", ((StringType) output.getParameter("version")).getValue());
+		assertEquals(false, output.getParameterBool("abstract"));
+
+		List<Parameters.ParametersParameterComponent> designations = output.getParameter().stream().filter(t -> t.getName().equals("designation")).collect(Collectors.toList());
+		assertEquals("language", designations.get(0).getPart().get(0).getName());
+		assertEquals("fr", ((CodeType) designations.get(0).getPart().get(0).getValue()).getValueAsString());
+		assertEquals("use", designations.get(0).getPart().get(1).getName());
+		assertEquals("http://sys", ((Coding) designations.get(0).getPart().get(1).getValue()).getSystem());
+		assertEquals("code", ((Coding) designations.get(0).getPart().get(1).getValue()).getCode());
+		assertEquals("display", ((Coding) designations.get(0).getPart().get(1).getValue()).getDisplay());
+		assertEquals("value", designations.get(0).getPart().get(2).getName());
+		assertEquals("Je mange une pomme", ((StringType) designations.get(0).getPart().get(2).getValue()).getValueAsString());
+
+		List<Parameters.ParametersParameterComponent> properties = output.getParameter().stream().filter(t -> t.getName().equals("property")).collect(Collectors.toList());
+		assertEquals("code", properties.get(0).getPart().get(0).getName());
+		assertEquals("flavour", ((CodeType) properties.get(0).getPart().get(0).getValue()).getValueAsString());
+		assertEquals("value", properties.get(0).getPart().get(1).getName());
+		assertEquals("Hints of lime", ((StringType) properties.get(0).getPart().get(1).getValue()).getValueAsString());
+
+		assertEquals("code", properties.get(1).getPart().get(0).getName());
+		assertEquals("useless_sct_code", ((CodeType) properties.get(1).getPart().get(0).getValue()).getValueAsString());
+		assertEquals("value", properties.get(1).getPart().get(1).getName());
+		assertEquals("http://snomed.info", ((Coding) properties.get(1).getPart().get(1).getValue()).getSystem());
+		assertEquals("1234567", ((Coding) properties.get(1).getPart().get(1).getValue()).getCode());
+		assertEquals("Choked on large meal (finding)", ((Coding) properties.get(1).getPart().get(1).getValue()).getDisplay());
+
+	}
+
+	@Test
+	public void testApplyCodeSystemDeltaRemove() {
+
+		// Create not-present
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://foo");
+		cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		myCodeSystemDao.create(cs);
+
+		CodeSystem delta = new CodeSystem();
+		CodeSystem.ConceptDefinitionComponent codeA = delta
+			.addConcept()
+			.setCode("codeA")
+			.setDisplay("displayA");
+		delta
+			.addConcept()
+			.setCode("codeB")
+			.setDisplay("displayB");
+		CodeSystem.ConceptDefinitionComponent codeAA = codeA
+			.addConcept()
+			.setCode("codeAA")
+			.setDisplay("displayAA");
+		codeAA
+			.addConcept()
+			.setCode("codeAAA")
+			.setDisplay("displayAAA");
+ 		myTermSvc.applyDeltaCodesystemsAdd("http://foo", null, delta);
+
+		// Remove CodeB
+		delta = new CodeSystem();
+		delta
+			.addConcept()
+			.setCode("codeB")
+			.setDisplay("displayB");
+		myTermSvc.applyDeltaCodesystemsRemove("http://foo", delta);
+
+		assertEquals(false, myTermSvc.findCode("http://foo", "codeB").isPresent());
+		assertEquals(true, myTermSvc.findCode("http://foo", "codeA").isPresent());
+		assertEquals(true, myTermSvc.findCode("http://foo", "codeAA").isPresent());
+		assertEquals(true, myTermSvc.findCode("http://foo", "codeAAA").isPresent());
+
+		// Remove CodeA
+		delta = new CodeSystem();
+		delta
+			.addConcept()
+			.setCode("codeA");
+		myTermSvc.applyDeltaCodesystemsRemove("http://foo", delta);
+
+		assertEquals(false, myTermSvc.findCode("http://foo", "codeB").isPresent());
+		assertEquals(false, myTermSvc.findCode("http://foo", "codeA").isPresent());
+		assertEquals(false, myTermSvc.findCode("http://foo", "codeAA").isPresent());
+		assertEquals(false, myTermSvc.findCode("http://foo", "codeAAA").isPresent());
+
+	}
+
+
+	@Nonnull
+	private StringType toString(String theString) {
+		return new StringType(theString);
+	}
+
+
 	@Test
 	public void testCreateConceptMapWithMissingSourceSystem() {
 		ConceptMap conceptMap = new ConceptMap();
@@ -183,7 +493,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 	@Test
 	public void testCreateConceptMapWithVirtualSourceSystem() {
 		ConceptMap conceptMap = createConceptMap();
-		conceptMap.getGroup().forEach(t->t.setSource(null));
+		conceptMap.getGroup().forEach(t -> t.setSource(null));
 		conceptMap.setSource(new CanonicalType("http://hl7.org/fhir/uv/livd/StructureDefinition/loinc-livd"));
 
 		persistConceptMap(conceptMap);
@@ -283,6 +593,17 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		verify(myValueSetCodeAccumulator, times(9)).includeCodeWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
 	}
 
+	@Test
+	public void testValidateCode() {
+		createCodeSystem();
+
+		IValidationSupport.CodeValidationResult validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ParentWithNoChildrenA", null);
+		assertEquals(true, validation.isOk());
+
+		validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ZZZZZZZ", null);
+		assertEquals(false, validation.isOk());
+	}
+
 	@Test
 	public void testStoreTermCodeSystemAndChildren() throws Exception {
 		loadAndPersistCodeSystemWithDesignations();

hapi-fhir-jpaserver-base/src/test/resources/extensional-case-3-cs.xml

@@ -1,5 +1,6 @@
 <CodeSystem xmlns="http://hl7.org/fhir">
 	<url value="http://acme.org" />
+	<name value="ACME Codes" />
 	<concept>
 		<code value="8450-9" />
 		<display value="Systolic blood pressure--expiration" />

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java

@@ -23,6 +23,17 @@ package ca.uhn.fhir.jpa.model.util;
 import ca.uhn.fhir.rest.api.Constants;
 
 public class JpaConstants {
+
+	/**
+	 * Operation name for the $apply-codesystem-delta-add operation
+	 */
+	public static final String OPERATION_APPLY_CODESYSTEM_DELTA_ADD = "$apply-codesystem-delta-add";
+
+	/**
+	 * Operation name for the $apply-codesystem-delta-remove operation
+	 */
+	public static final String OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE = "$apply-codesystem-delta-remove";
+
 	/**
 	 * Operation name for the $expunge operation
 	 */
@@ -158,6 +169,11 @@ public class JpaConstants {
 	 */
 	public static final String OPERATION_BINARY_ACCESS_WRITE = "$binary-access-write";
 
+	/**
+	 * Operation name for the "$upload-external-code-system" operation
+	 */
+	public static final String OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM = "$upload-external-code-system";
+
 	/**
 	 * <p>
 	 * This extension should be of type <code>string</code> and should be

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

@@ -1,7 +1,6 @@
 package ca.uhn.fhirtest.interceptor;
 
 import ca.uhn.fhir.jpa.provider.BaseJpaSystemProvider;
-import ca.uhn.fhir.jpa.provider.BaseTerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
@@ -35,7 +34,9 @@ public class PublicSecurityInterceptor extends AuthorizationInterceptor {
 		if (isBlank(authHeader)) {
 			return new RuleBuilder()
 				.deny().operation().named(BaseJpaSystemProvider.MARK_ALL_RESOURCES_FOR_REINDEXING).onServer().andAllowAllResponses().andThen()
-				.deny().operation().named(BaseTerminologyUploaderProvider.UPLOAD_EXTERNAL_CODE_SYSTEM).onServer().andAllowAllResponses().andThen()
+				.deny().operation().named(JpaConstants.OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM).onServer().andAllowAllResponses().andThen()
+				.deny().operation().named(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD).atAnyLevel().andAllowAllResponses().andThen()
+				.deny().operation().named(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE).atAnyLevel().andAllowAllResponses().andThen()
 				.deny().operation().named(JpaConstants.OPERATION_EXPUNGE).onServer().andAllowAllResponses().andThen()
 				.deny().operation().named(JpaConstants.OPERATION_EXPUNGE).onAnyType().andAllowAllResponses().andThen()
 				.deny().operation().named(JpaConstants.OPERATION_EXPUNGE).onAnyInstance().andAllowAllResponses().andThen()

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseMethodBinding.java

@@ -445,15 +445,6 @@ public abstract class BaseMethodBinding<T> {
 		return theReturnTypeFromMethod.equals(IBaseResource.class) || theReturnTypeFromMethod.equals(IResource.class) || theReturnTypeFromMethod.equals(IAnyResource.class);
 	}
 
-	private static void populateException(BaseServerResponseException theEx, Reader theResponseReader) {
-		try {
-			String responseText = IOUtils.toString(theResponseReader);
-			theEx.setResponseBody(responseText);
-		} catch (IOException e) {
-			ourLog.debug("Failed to read response", e);
-		}
-	}
-
 	private static String toLogString(Class<?> theType) {
 		if (theType == null) {
 			return null;

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

@@ -68,14 +68,15 @@ public class MethodUtil {
 
 	@SuppressWarnings("unchecked")
 	public static List<IParameter> getResourceParameters(final FhirContext theContext, Method theMethod, Object theProvider, RestOperationTypeEnum theRestfulOperationTypeEnum) {
-		List<IParameter> parameters = new ArrayList<IParameter>();
+		List<IParameter> parameters = new ArrayList<>();
 
 		Class<?>[] parameterTypes = theMethod.getParameterTypes();
 		int paramIndex = 0;
 		for (Annotation[] annotations : theMethod.getParameterAnnotations()) {
 
 			IParameter param = null;
-			Class<?> parameterType = parameterTypes[paramIndex];
+			Class<?> declaredParameterType = parameterTypes[paramIndex];
+			Class<?> parameterType = declaredParameterType;
 			Class<? extends java.util.Collection<?>> outerCollectionType = null;
 			Class<? extends java.util.Collection<?>> innerCollectionType = null;
 			if (TagList.class.isAssignableFrom(parameterType)) {
@@ -85,11 +86,13 @@ public class MethodUtil {
 				if (Collection.class.isAssignableFrom(parameterType)) {
 					innerCollectionType = (Class<? extends java.util.Collection<?>>) parameterType;
 					parameterType = ReflectionUtil.getGenericCollectionTypeOfMethodParameter(theMethod, paramIndex);
+					declaredParameterType = parameterType;
 				}
 				if (Collection.class.isAssignableFrom(parameterType)) {
 					outerCollectionType = innerCollectionType;
 					innerCollectionType = (Class<? extends java.util.Collection<?>>) parameterType;
 					parameterType = ReflectionUtil.getGenericCollectionTypeOfMethodParameter(theMethod, paramIndex);
+					declaredParameterType = parameterType;
 				}
 				if (Collection.class.isAssignableFrom(parameterType)) {
 					throw new ConfigurationException("Argument #" + paramIndex + " of Method '" + theMethod.getName() + "' in type '" + theMethod.getDeclaringClass().getCanonicalName()
@@ -223,7 +226,7 @@ public class MethodUtil {
 						param = new OperationParameter(theContext, op.name(), operationParam);
 						if (isNotBlank(operationParam.typeName())) {
 							Class<?> newParameterType = theContext.getElementDefinition(operationParam.typeName()).getImplementingClass();
-							if (!parameterType.isAssignableFrom(newParameterType)) {
+							if (!declaredParameterType.isAssignableFrom(newParameterType)) {
 								throw new ConfigurationException("Non assignable parameter typeName=\"" + operationParam.typeName() + "\" specified on method " + theMethod);
 							}
 							parameterType = newParameterType;

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/OperationMethodBinding.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
+import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
@@ -72,7 +73,7 @@ public class OperationMethodBinding extends BaseResourceReturningMethodBinding {
 	private boolean myManualResponseMode;
 
 	protected OperationMethodBinding(Class<?> theReturnResourceType, Class<? extends IBaseResource> theReturnTypeFromRp, Method theMethod, FhirContext theContext, Object theProvider,
-												boolean theIdempotent, String theOperationName, Class<? extends IBaseResource> theOperationType,
+												boolean theIdempotent, String theOperationName, Class<? extends IBaseResource> theOperationType, String theOperationTypeName,
 												OperationParam[] theReturnParams, BundleTypeEnum theBundleType) {
 		super(theReturnResourceType, theMethod, theContext, theProvider);
 
@@ -99,13 +100,19 @@ public class OperationMethodBinding extends BaseResourceReturningMethodBinding {
 		}
 		myName = theOperationName;
 
+		try {
 			if (theReturnTypeFromRp != null) {
 				setResourceName(theContext.getResourceDefinition(theReturnTypeFromRp).getName());
 			} else if (Modifier.isAbstract(theOperationType.getModifiers()) == false) {
 				setResourceName(theContext.getResourceDefinition(theOperationType).getName());
+			} else if (isNotBlank(theOperationTypeName)) {
+				setResourceName(theContext.getResourceDefinition(theOperationTypeName).getName());
 			} else {
 				setResourceName(null);
 			}
+		} catch (DataFormatException e) {
+			throw new ConfigurationException("Failed to bind method " + theMethod + " - " + e.getMessage(), e);
+		}
 
 		if (theMethod.getReturnType().equals(IBundleProvider.class)) {
 			myReturnType = ReturnTypeEnum.BUNDLE;
@@ -160,7 +167,7 @@ public class OperationMethodBinding extends BaseResourceReturningMethodBinding {
 	 */
 	public OperationMethodBinding(Class<?> theReturnResourceType, Class<? extends IBaseResource> theReturnTypeFromRp, Method theMethod, FhirContext theContext, Object theProvider,
 											Operation theAnnotation) {
-		this(theReturnResourceType, theReturnTypeFromRp, theMethod, theContext, theProvider, theAnnotation.idempotent(), theAnnotation.name(), theAnnotation.type(), theAnnotation.returnParameters(),
+		this(theReturnResourceType, theReturnTypeFromRp, theMethod, theContext, theProvider, theAnnotation.idempotent(), theAnnotation.name(), theAnnotation.type(), theAnnotation.typeName(), theAnnotation.returnParameters(),
 			theAnnotation.bundleType());
 
 		myManualRequestMode = theAnnotation.manualRequest();

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/OperationParameter.java

@@ -187,7 +187,7 @@ public class OperationParameter implements IParameter {
 				mySearchParameterBinding.setType(myContext, theParameterType, theInnerCollectionType, theOuterCollectionType);
 				myConverter = new OperationParamConverter();
 			} else {
-				throw new ConfigurationException("Invalid type for @OperationParam: " + myParameterType.getName());
+				throw new ConfigurationException("Invalid type for @OperationParam on method " + theMethod + ": " + myParameterType.getName());
 			}
 
 		}

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/ValidateMethodBindingDstu2Plus.java

@@ -37,7 +37,7 @@ public class ValidateMethodBindingDstu2Plus extends OperationMethodBinding {
 
 	public ValidateMethodBindingDstu2Plus(Class<?> theReturnResourceType, Class<? extends IBaseResource> theReturnTypeFromRp, Method theMethod, FhirContext theContext, Object theProvider,
 			Validate theAnnotation) {
-		super(theReturnResourceType, theReturnTypeFromRp, theMethod, theContext, theProvider, true, Constants.EXTOP_VALIDATE, theAnnotation.type(), new OperationParam[0], BundleTypeEnum.COLLECTION);
+		super(theReturnResourceType, theReturnTypeFromRp, theMethod, theContext, theProvider, true, Constants.EXTOP_VALIDATE, theAnnotation.type(), null, new OperationParam[0], BundleTypeEnum.COLLECTION);
 
 		List<IParameter> newParams = new ArrayList<IParameter>();
 		int idx = 0;

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/hapi/validation/DefaultProfileValidationSupport.java

@@ -276,4 +276,9 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 		return new CodeValidationResult(OperationOutcome.IssueSeverity.WARNING, "Unknown code: " + theCodeSystem + " / " + theCode);
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return validateCode(theContext, theSystem, theCode, null).asLookupCodeResult(theSystem, theCode);
+	}
+
 }

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/hapi/validation/IValidationSupport.java

@@ -100,7 +100,7 @@ public interface IValidationSupport
 	@Override
 	CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay);
 
-	public class CodeValidationResult extends IContextValidationSupport.CodeValidationResult<ConceptDefinitionComponent, OperationOutcome.IssueSeverity> {
+	class CodeValidationResult extends IContextValidationSupport.CodeValidationResult<ConceptDefinitionComponent, OperationOutcome.IssueSeverity> {
 
 		public CodeValidationResult(ConceptDefinitionComponent theNext) {
 			super(theNext);
@@ -114,6 +114,15 @@ public interface IValidationSupport
 			super(severity, message, definition);
 		}
 
+		@Override
+		protected String getDisplay() {
+			String retVal = null;
+			if (isOk()) {
+				retVal = asConceptDefinition().getDisplay();
+			}
+			return retVal;
+		}
+
 	}
 
 }

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/hapi/validation/PrePopulatedValidationSupport.java

@@ -138,4 +138,9 @@ public class PrePopulatedValidationSupport implements IValidationSupport {
 		return null;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return null;
+	}
+
 }

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/hapi/validation/ValidationSupportChain.java

@@ -143,4 +143,15 @@ public class ValidationSupportChain implements IValidationSupport {
 		return myChain.get(0).validateCode(theCtx, theCodeSystem, theCode, theDisplay);
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		for (IValidationSupport next : myChain) {
+			if (next.isCodeSystemSupported(theContext, theSystem)) {
+				return next.lookupCode(theContext, theSystem, theCode);
+			}
+		}
+		return null;
+	}
+
+
 }

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/ctx/DefaultProfileValidationSupport.java

@@ -49,7 +49,7 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
       addConcepts(theInclude, retVal, wantCodes, concepts);
     }
 
-		for (UriType next: theInclude.getValueSet()) {
+    for (UriType next : theInclude.getValueSet()) {
       ValueSet vs = myValueSets.get(defaultString(next.getValueAsString()));
       if (vs != null) {
         for (ConceptSetComponent nextInclude : vs.getCompose().getInclude()) {
@@ -243,16 +243,16 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
     return structureDefinitions;
   }
 
-	private CodeValidationResult testIfConceptIsInList(String theCode, List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive) {
+  private CodeValidationResult testIfConceptIsInList(CodeSystem theCodeSystem, String theCode, List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive) {
     String code = theCode;
     if (theCaseSensitive == false) {
       code = code.toUpperCase();
     }
 
-		return testIfConceptIsInListInner(conceptList, theCaseSensitive, code);
+    return testIfConceptIsInListInner(theCodeSystem, conceptList, theCaseSensitive, code);
   }
 
-	private CodeValidationResult testIfConceptIsInListInner(List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive, String code) {
+  private CodeValidationResult testIfConceptIsInListInner(CodeSystem theCodeSystem, List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive, String code) {
     CodeValidationResult retVal = null;
     for (ConceptDefinitionComponent next : conceptList) {
       String nextCandidate = next.getCode();
@@ -265,12 +265,17 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
       }
 
       // recurse
-			retVal = testIfConceptIsInList(code, next.getConcept(), theCaseSensitive);
+      retVal = testIfConceptIsInList(theCodeSystem, code, next.getConcept(), theCaseSensitive);
       if (retVal != null) {
         break;
       }
     }
 
+    if (retVal != null) {
+      retVal.setCodeSystemName(theCodeSystem.getName());
+      retVal.setCodeSystemVersion(theCodeSystem.getVersion());
+    }
+
     return retVal;
   }
 
@@ -283,7 +288,7 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
         caseSensitive = cs.getCaseSensitive();
       }
 
-			CodeValidationResult retVal = testIfConceptIsInList(theCode, cs.getConcept(), caseSensitive);
+      CodeValidationResult retVal = testIfConceptIsInList(cs, theCode, cs.getConcept(), caseSensitive);
 
       if (retVal != null) {
         return retVal;
@@ -293,6 +298,11 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
     return new CodeValidationResult(IssueSeverity.WARNING, "Unknown code: " + theCodeSystem + " / " + theCode);
   }
 
+  @Override
+  public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+    return validateCode(theContext, theSystem, theCode, null).asLookupCodeResult(theSystem, theCode);
+  }
+
   @Override
   public StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theName) {
     return null;

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/ctx/IValidationSupport.java

@@ -1,18 +1,16 @@
 package org.hl7.fhir.dstu3.hapi.ctx;
 
-import java.util.List;
+import ca.uhn.fhir.context.FhirContext;
-
+import ca.uhn.fhir.context.support.IContextValidationSupport;
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
 import org.hl7.fhir.dstu3.model.StructureDefinition;
 import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 
-import ca.uhn.fhir.context.FhirContext;
+import java.util.List;
-import ca.uhn.fhir.context.support.IContextValidationSupport;
 
 public interface IValidationSupport
   extends ca.uhn.fhir.context.support.IContextValidationSupport<ConceptSetComponent, ValueSetExpansionComponent, StructureDefinition, CodeSystem, ConceptDefinitionComponent, IssueSeverity> {
@@ -20,8 +18,7 @@ public interface IValidationSupport
   /**
    * Expands the given portion of a ValueSet
    *
-	 * @param theInclude
+   * @param theInclude The portion to include
-	 *           The portion to include
    * @return The expansion
    */
   @Override
@@ -36,8 +33,7 @@ public interface IValidationSupport
   /**
    * Fetch a code system by Uri
    *
-   * @param uri
+   * @param uri Canonical Uri of the code system
-   *           Canonical Uri of the code system
    * @return The valueset (must not be null, but can be an empty ValueSet)
    */
   @Override
@@ -46,28 +42,11 @@ public interface IValidationSupport
   /**
    * Fetch a valueset by Uri
    *
-   * @param uri
+   * @param uri Canonical Uri of the ValueSet
-   *           Canonical Uri of the ValueSet
    * @return The valueset (must not be null, but can be an empty ValueSet)
    */
   ValueSet fetchValueSet(FhirContext theContext, String uri);
 
-	/**
-	 * Loads a resource needed by the validation (a StructureDefinition, or a
-	 * ValueSet)
-	 * 
-	 * @param theContext
-	 *           The HAPI FHIR Context object current in use by the validator
-	 * @param theClass
-	 *           The type of the resource to load
-	 * @param theUri
-	 *           The resource URI
-	 * @return Returns the resource, or <code>null</code> if no resource with the
-	 *         given URI can be found
-	 */
-	@Override
-	<T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri);
-
   @Override
   StructureDefinition fetchStructureDefinition(FhirContext theCtx, String theUrl);
 
@@ -75,8 +54,7 @@ public interface IValidationSupport
    * Returns <code>true</code> if codes in the given code system can be expanded
    * or validated
    *
-	 * @param theSystem
+   * @param theSystem The URI for the code system, e.g. <code>"http://loinc.org"</code>
-	 *           The URI for the code system, e.g. <code>"http://loinc.org"</code>
    * @return Returns <code>true</code> if codes in the given code system can be
    * validated
    */
@@ -88,12 +66,9 @@ public interface IValidationSupport
    * name. This method is called to check codes which are found in "example"
    * binding fields (e.g. <code>Observation.code</code> in the default profile.
    *
-	 * @param theCodeSystem
+   * @param theCodeSystem The code system, e.g. "<code>http://loinc.org</code>"
-	 *           The code system, e.g. "<code>http://loinc.org</code>"
+   * @param theCode       The code, e.g. "<code>1234-5</code>"
-	 * @param theCode
+   * @param theDisplay    The display name, if it should also be validated
-	 *           The code, e.g. "<code>1234-5</code>"
-	 * @param theDisplay
-	 *           The display name, if it should also be validated
    * @return Returns a validation result object
    */
   @Override
@@ -102,8 +77,6 @@ public interface IValidationSupport
   /**
    * Generate a snapshot from the given differential profile.
    *
-   * @param theInput
-   * @param theUrl
    * @return Returns null if this module does not know how to handle this request
    */
   StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theName);
@@ -122,6 +95,15 @@ public interface IValidationSupport
       super(severity, message, definition);
     }
 
+    @Override
+    protected String getDisplay() {
+      String retVal = null;
+      if (isOk()) {
+        retVal = asConceptDefinition().getDisplay();
+      }
+      return retVal;
+    }
+
   }
 
 }

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/ctx/DefaultProfileValidationSupport.java

@@ -257,16 +257,16 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
     return structureDefinitions;
   }
 
-  private CodeValidationResult testIfConceptIsInList(String theCode, List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive) {
+  private CodeValidationResult testIfConceptIsInList(CodeSystem theCodeSystem, String theCode, List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive) {
     String code = theCode;
     if (theCaseSensitive == false) {
       code = code.toUpperCase();
     }
 
-    return testIfConceptIsInListInner(conceptList, theCaseSensitive, code);
+    return testIfConceptIsInListInner(theCodeSystem, conceptList, theCaseSensitive, code);
   }
 
-  private CodeValidationResult testIfConceptIsInListInner(List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive, String code) {
+  private CodeValidationResult testIfConceptIsInListInner(CodeSystem theCodeSystem, List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive, String code) {
     CodeValidationResult retVal = null;
     for (ConceptDefinitionComponent next : conceptList) {
       String nextCandidate = next.getCode();
@@ -279,12 +279,17 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
       }
 
       // recurse
-      retVal = testIfConceptIsInList(code, next.getConcept(), theCaseSensitive);
+      retVal = testIfConceptIsInList(theCodeSystem, code, next.getConcept(), theCaseSensitive);
       if (retVal != null) {
         break;
       }
     }
 
+    if (retVal != null) {
+      retVal.setCodeSystemName(theCodeSystem.getName());
+      retVal.setCodeSystemVersion(theCodeSystem.getVersion());
+    }
+
     return retVal;
   }
 
@@ -297,7 +302,7 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
         caseSensitive = cs.getCaseSensitive();
       }
 
-      CodeValidationResult retVal = testIfConceptIsInList(theCode, cs.getConcept(), caseSensitive);
+      CodeValidationResult retVal = testIfConceptIsInList(cs, theCode, cs.getConcept(), caseSensitive);
 
       if (retVal != null) {
         return retVal;
@@ -307,4 +312,9 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
     return new CodeValidationResult(IssueSeverity.WARNING, "Unknown code: " + theCodeSystem + " / " + theCode);
   }
 
+  @Override
+  public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+    return validateCode(theContext, theSystem, theCode, null).asLookupCodeResult(theSystem, theCode);
+  }
+
 }

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/ctx/IValidationSupport.java

@@ -112,6 +112,15 @@ public interface IValidationSupport
       super(severity, message, definition);
     }
 
+    @Override
+    protected String getDisplay() {
+      String retVal = null;
+      if (isOk()) {
+        retVal = asConceptDefinition().getDisplay();
+      }
+      return retVal;
+    }
+
   }
 
 }

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/OperationGenericServer2R4Test.java

@@ -12,6 +12,7 @@ import ca.uhn.fhir.test.utilities.JettyUtil;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
@@ -29,10 +30,11 @@ import org.junit.*;
 
 import javax.servlet.ServletException;
 import java.nio.charset.StandardCharsets;
+import java.util.List;
 import java.util.concurrent.TimeUnit;
 
-import static org.junit.Assert.assertEquals;
+import static org.hamcrest.CoreMatchers.containsString;
-import static org.junit.Assert.fail;
+import static org.junit.Assert.*;
 
 public class OperationGenericServer2R4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(OperationGenericServer2R4Test.class);
@@ -41,6 +43,7 @@ public class OperationGenericServer2R4Test {
 	private static IdType ourLastId;
 	private static Object ourLastParam1;
 	private static Object ourLastParam2;
+	private static Object ourLastParam3;
 	private static Parameters ourLastResourceParam;
 	private int myPort;
 	private Server myServer;
@@ -49,6 +52,7 @@ public class OperationGenericServer2R4Test {
 	public void before() {
 		ourLastParam1 = null;
 		ourLastParam2 = null;
+		ourLastParam3=null;
 		ourLastId = null;
 		ourLastResourceParam = null;
 	}
@@ -112,6 +116,65 @@ public class OperationGenericServer2R4Test {
 
 	}
 
+	@SuppressWarnings("unchecked")
+	@Test
+	public void testDeclarativeStringTypedParameters() throws Exception {
+
+		@SuppressWarnings("unused")
+		class PatientProvider implements IResourceProvider {
+
+			@Override
+			public Class<Patient> getResourceType() {
+				return Patient.class;
+			}
+
+			@Operation(name = "$OP_INSTANCE")
+			public Parameters opInstance(
+				@ResourceParam() IBaseResource theResourceParam,
+				@IdParam IdType theId,
+				@OperationParam(name = "PARAM1", min = 1, typeName = "uri") IPrimitiveType<String> theParam1,
+				@OperationParam(name = "PARAM2", min = 1, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> theParam2,
+				@OperationParam(name = "PARAM3", min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> theParam3
+			) {
+
+				ourLastId = theId;
+				ourLastParam1 = theParam1;
+				ourLastParam2 = theParam2;
+				ourLastParam3 = theParam2;
+				ourLastResourceParam = (Parameters) theResourceParam;
+
+				Parameters retVal = new Parameters();
+				retVal.addParameter().setName("RET1").setValue(new StringType("RETVAL1"));
+				return retVal;
+			}
+
+		}
+
+		PatientProvider provider = new PatientProvider();
+		startServer(provider);
+
+		Parameters p = new Parameters();
+		p.addParameter().setName("PARAM1").setValue(new UriType("PARAM1val"));
+		p.addParameter().setName("PARAM2").setValue(new StringType("PARAM2val"));
+		String inParamsStr = ourCtx.newXmlParser().encodeResourceToString(p);
+
+		HttpPost httpPost = new HttpPost("http://localhost:" + myPort + "/Patient/123/$OP_INSTANCE");
+		httpPost.setEntity(new StringEntity(inParamsStr, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+		try (CloseableHttpResponse status = ourClient.execute(httpPost)) {
+			assertEquals(200, status.getStatusLine().getStatusCode());
+			String response = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(response);
+			status.getEntity().getContent().close();
+
+			UriType param1 = (UriType) ourLastParam1;
+			assertEquals("PARAM1val", param1.getValue());
+
+			List<StringType> param2 = (List<StringType>) ourLastParam2;
+			assertEquals("PARAM2val", param2.get(0).getValue());
+		}
+
+	}
+
 	@Test
 	public void testDeclarativeTypedParametersInvalid() throws Exception {
 
@@ -138,10 +201,71 @@ public class OperationGenericServer2R4Test {
 			fail();
 		} catch (ServletException e) {
 			ConfigurationException ce = (ConfigurationException) e.getCause();
-			assertEquals("Failure scanning class PatientProvider: Non assignable parameter typeName=\"code\" specified on method public org.hl7.fhir.r4.model.Parameters ca.uhn.fhir.rest.server.OperationGenericServer2R4Test$2PatientProvider.opInstance(org.hl7.fhir.instance.model.api.ICompositeType)", ce.getMessage());
+			assertThat(ce.getMessage(), containsString("Failure scanning class PatientProvider: Non assignable parameter typeName=\"code\" specified on method public org.hl7.fhir.r4.model.Parameters ca.uhn.fhir.rest.server.OperationGenericServer2R4Test"));
 		}
 	}
 
+
+	@Test
+	public void testTypeOperationWithTypeDeclaredByName() throws Exception {
+
+		@SuppressWarnings("unused")
+		class PlainProvider {
+
+			@Operation(name = "$OP_INSTANCE", typeName = "Patient", idempotent = true)
+			public Parameters opInstance(
+				@ResourceParam() IBaseResource theResourceParam,
+				@IdParam IdType theId
+			) {
+
+				ourLastId = theId;
+
+				Parameters retVal = new Parameters();
+				retVal.addParameter().setName("RET1").setValue(new StringType("RETVAL1"));
+				return retVal;
+			}
+
+		}
+
+		PlainProvider provider = new PlainProvider();
+		startServer(provider);
+
+		HttpGet httpPost = new HttpGet("http://localhost:" + myPort + "/Patient/123/$OP_INSTANCE");
+		try (CloseableHttpResponse status = ourClient.execute(httpPost)) {
+			assertEquals(200, status.getStatusLine().getStatusCode());
+			String response = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(response);
+			status.getEntity().getContent().close();
+
+			assertEquals("123", ourLastId.getIdPart());
+		}
+
+	}
+
+	@Test
+	public void testTypeOperationWithInvalidType() throws Exception {
+
+		@SuppressWarnings("unused")
+		class PlainProvider {
+
+			@Operation(name = "$OP_INSTANCE", typeName = "FOO", idempotent = true)
+			public Parameters opInstance() {
+				return null;
+			}
+
+		}
+
+		PlainProvider provider = new PlainProvider();
+		try {
+			startServer(provider);
+			fail();
+		} catch (ServletException e) {
+			Throwable cause = e.getRootCause();
+			assertEquals("Failure scanning class PlainProvider: Failed to bind method public org.hl7.fhir.r4.model.Parameters ca.uhn.fhir.rest.server.OperationGenericServer2R4Test$2PlainProvider.opInstance() - Unknown resource name \"FOO\" (this name is not known in FHIR version \"R4\")", cause.getMessage());
+		}
+	}
+
+
 	private void startServer(Object theProvider) throws Exception {
 		myServer = new Server(0);
 

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/OperationServerR4Test.java

@@ -915,7 +915,7 @@ public class OperationServerR4Test {
 		}
 
 		@Operation(name= "$manualResponseWithPrimitiveParam", idempotent = true, global = true, manualResponse = true)
-		public void binaryAccess(
+		public void manualResponseWithPrimitiveParam(
 			@IdParam IIdType theResourceId,
 			@OperationParam(name="path", min = 1, max = 1) IPrimitiveType<String> thePath,
 			ServletRequestDetails theRequestDetails,

hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/CachingValidationSupport.java

@@ -70,6 +70,11 @@ public class CachingValidationSupport implements IValidationSupport {
 		return myWrap.validateCode(theContext, theCodeSystem, theCode, theDisplay);
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return myWrap.lookupCode(theContext, theSystem, theCode);
+	}
+
 	@Override
 	public StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theName) {
 		return myWrap.generateSnapshot(theInput, theUrl, theName);

hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/PrePopulatedValidationSupport.java

@@ -185,6 +185,11 @@ public class PrePopulatedValidationSupport implements IValidationSupport {
     return null;
   }
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return null;
+	}
+
 	@Override
 	public StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theName) {
 		return null;

hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/SnapshotGeneratingValidationSupport.java

@@ -3,8 +3,6 @@ package org.hl7.fhir.dstu3.hapi.validation;
 import ca.uhn.fhir.context.*;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import org.apache.commons.lang3.Validate;
-import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.dstu3.conformance.ProfileUtilities;
 import org.hl7.fhir.dstu3.context.IWorkerContext;
 import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
@@ -13,6 +11,8 @@ import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.ElementDefinition;
 import org.hl7.fhir.dstu3.model.StructureDefinition;
 import org.hl7.fhir.dstu3.model.ValueSet;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 
 import java.util.ArrayList;
@@ -95,6 +95,11 @@ public class SnapshotGeneratingValidationSupport implements IValidationSupport {
 		return null;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return null;
+	}
+
 	private class MyProfileKnowledgeWorker implements ProfileUtilities.ProfileKnowledgeProvider {
 		@Override
 		public boolean isDatatype(String typeSimple) {

hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/ValidationSupportChain.java

@@ -170,6 +170,16 @@ public class ValidationSupportChain implements IValidationSupport {
 		return myChain.get(0).validateCode(theCtx, theCodeSystem, theCode, theDisplay);
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		for (IValidationSupport next : myChain) {
+			if (next.isCodeSystemSupported(theContext, theSystem)) {
+				return next.lookupCode(theContext, theSystem, theCode);
+			}
+		}
+		return null;
+	}
+
 	@Override
 	public StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theProfileName) {
 		StructureDefinition outcome = null;

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/CachingValidationSupport.java

@@ -75,4 +75,9 @@ public class CachingValidationSupport implements IValidationSupport {
 	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
 		return myWrap.validateCode(theContext, theCodeSystem, theCode, theDisplay);
 	}
+
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return myWrap.lookupCode(theContext, theSystem, theCode);
+	}
 }

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/PrePopulatedValidationSupport.java

@@ -192,4 +192,9 @@ public class PrePopulatedValidationSupport implements IValidationSupport {
 		return null;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return null;
+	}
+
 }

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/SnapshotGeneratingValidationSupport.java

@@ -96,6 +96,11 @@ public class SnapshotGeneratingValidationSupport implements IValidationSupport {
 		return null;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		return null;
+	}
+
 	private class MyProfileKnowledgeWorker implements ProfileUtilities.ProfileKnowledgeProvider {
 		@Override
 		public boolean isDatatype(String typeSimple) {

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/ValidationSupportChain.java

@@ -159,6 +159,16 @@ public class ValidationSupportChain implements IValidationSupport {
 		return myChain.get(0).validateCode(theCtx, theCodeSystem, theCode, theDisplay);
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
+		for (IValidationSupport next : myChain) {
+			if (next.isCodeSystemSupported(theContext, theSystem)) {
+				return next.lookupCode(theContext, theSystem, theCode);
+			}
+		}
+		return null;
+	}
+
 	@Override
 	public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
 		ArrayList<StructureDefinition> retVal = new ArrayList<>();

src/changes/changes.xml

@@ -52,6 +52,14 @@
 				the user has not explicitly configured a preference.
 				]]>
 			</action>
+			<action type="change">
+				<![CDATA[
+				<b>Breaking Change</b>:
+				The JPA $upload-external-code-system operation has been moved from being a
+				server level operation (i.e. called on the root of the server) to being
+				a type level operation (i.e. called on the CodeSystem type).
+				]]>
+			</action>
 		<action type="add">
 				A new interceptor called
 				<![CDATA[<code>ConsentInterceptor</code>]]> has been added. This interceptor allows
@@ -340,6 +348,12 @@
 				a narrative on an untitled DiagnosticReport were fixed. Thanks to GitHub
 				user @navyflower for reporting!
 			</action>
+			<action type="add">
+				A new attribute has been added to the @Operation annotation called 
+				<![CDATA[<code>typeName</code>]]>. This annotation can be used to specify a 
+				type for an operation declared on a plain provider without needing to use 
+				a specific version of the FHIR structures.
+			</action>
 		</release>
 		<release version="3.8.0" date="2019-05-30" description="Hippo">
 			<action type="fix">