Add support for hierarchycal valueset expansion (#2525)

* Add support for hierarchycal valueset expansion

* Add changelog

* Add tests

* Cleanup

* Test fix

* Test fixes

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
     <parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -32,6 +32,17 @@ public class ValueSetExpansionOptions {
 	private boolean myFailOnMissingCodeSystem = true;
 	private int myCount = 1000;
 	private int myOffset = 0;
+	private boolean myIncludeHierarchy;
+	private String myFilter;
+
+	public String getFilter() {
+		return myFilter;
+	}
+
+	public ValueSetExpansionOptions setFilter(String theFilter) {
+		myFilter = theFilter;
+		return this;
+	}
 
 	/**
 	 * The number of codes to return.
@@ -94,6 +105,14 @@ public class ValueSetExpansionOptions {
 		return this;
 	}
 
+	public boolean isIncludeHierarchy() {
+		return myIncludeHierarchy;
+	}
+
+	public void setIncludeHierarchy(boolean theIncludeHierarchy) {
+		myIncludeHierarchy = theIncludeHierarchy;
+	}
+
 	public static ValueSetExpansionOptions forOffsetAndCount(int theOffset, int theCount) {
 		return new ValueSetExpansionOptions()
 			.setOffset(theOffset)

hapi-fhir-bom/pom.xml

@@ -3,14 +3,14 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>ca.uhn.hapi.fhir</groupId>
     <artifactId>hapi-fhir-bom</artifactId>
-    <version>5.4.0-PRE4-SNAPSHOT</version>
+    <version>5.4.0-PRE5-SNAPSHOT</version>
     <packaging>pom</packaging>
 	 <name>HAPI FHIR BOM</name>
 
     <parent>
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-deployable-pom</artifactId>
-      <version>5.4.0-PRE4-SNAPSHOT</version>
+      <version>5.4.0-PRE5-SNAPSHOT</version>
       <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
    </parent>
     

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -78,13 +78,13 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-subscription</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -101,7 +101,7 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-testpage-overlay</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 			<classifier>classes</classifier>
 		</dependency>
 		<dependency>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2525-hierarchical-expansion.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 2525
+title: "A new optional parameter has been added to the `ValueSet/$expand` operation. When provided a value of `true`, the
+  operation will include the concept hierarchy in the expansion response."
+

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-example/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-api/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoValueSet.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.api.dao;
  */
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -28,17 +29,11 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 public interface IFhirResourceDaoValueSet<T extends IBaseResource, CD, CC> extends IFhirResourceDao<T> {
 
-	T expand(IIdType theId, String theFilter, RequestDetails theRequestDetails);
+	T expand(IIdType theId, ValueSetExpansionOptions theOptions, RequestDetails theRequestDetails);
 
-	T expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails);
+	T expand(T theSource, ValueSetExpansionOptions theOptions);
 
-	T expand(T theSource, String theFilter);
+	T expandByIdentifier(String theUri, ValueSetExpansionOptions theOptions);
-
-	T expand(T theSource, String theFilter, int theOffset, int theCount);
-
-	T expandByIdentifier(String theUri, String theFilter);
-
-	T expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount);
 
 	void purgeCaches();
 

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -24,9 +24,9 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
-import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
@@ -40,6 +40,7 @@ import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -51,13 +52,13 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 
+import javax.annotation.Nonnull;
 import javax.annotation.PostConstruct;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.Set;
 
-import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
 import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3.vsValidateCodeOptions;
 import static ca.uhn.fhir.jpa.util.LogicUtil.multiXor;
 import static org.apache.commons.lang3.StringUtils.isBlank;
@@ -104,31 +105,32 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 	}
 
 	@Override
-	public ValueSet expand(IIdType theId, String theFilter, RequestDetails theRequest) {
+	public ValueSet expand(IIdType theId, ValueSetExpansionOptions theOptions, RequestDetails theRequest) {
 		ValueSet source = loadValueSetForExpansion(theId, theRequest);
-		return expand(source, theFilter);
+		return expand(source, theOptions);
 	}
 
 	@Override
-	public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequest) {
+	public ValueSet expand(ValueSet source, ValueSetExpansionOptions theOptions) {
-		throw new UnsupportedOperationException();
-	}
-
-	@Override
-	public ValueSet expand(ValueSet source, String theFilter) {
 		ValueSet retVal = new ValueSet();
 		retVal.setDate(DateTimeDt.withCurrentTime());
 
+
+		String filter = null;
+		if (theOptions != null) {
+			filter = theOptions.getFilter();
+		}
+
 		/*
 		 * Add composed concepts
 		 */
 
 		for (ComposeInclude nextInclude : source.getCompose().getInclude()) {
 			for (ComposeIncludeConcept next : nextInclude.getConcept()) {
-				if (isBlank(theFilter)) {
+				if (isBlank(filter)) {
 					addCompose(retVal, nextInclude.getSystem(), next.getCode(), next.getDisplay());
 				} else {
-					String filter = theFilter.toLowerCase();
+					filter = filter.toLowerCase();
 					if (next.getDisplay().toLowerCase().contains(filter) || next.getCode().toLowerCase().contains(filter)) {
 						addCompose(retVal, nextInclude.getSystem(), next.getCode(), next.getDisplay());
 					}
@@ -141,19 +143,14 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 		 */
 
 		for (CodeSystemConcept next : source.getCodeSystem().getConcept()) {
-			addCompose(theFilter, retVal, source, next);
+			addCompose(filter, retVal, source, next);
 		}
 
 		return retVal;
 	}
 
 	@Override
-	public ValueSet expand(ValueSet source, String theFilter, int theOffset, int theCount) {
+	public ValueSet expandByIdentifier(String theUri, ValueSetExpansionOptions theOptions) {
-		throw new UnsupportedOperationException();
-	}
-
-	@Override
-	public ValueSet expandByIdentifier(String theUri, String theFilter) {
 		if (isBlank(theUri)) {
 			throw new InvalidRequestException("URI must not be blank or missing");
 		}
@@ -173,12 +170,7 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 			source = (ValueSet) ids.getResources(0, 1).get(0);
 		}
 
-		return expand(source, theFilter);
+		return expand(source, theOptions);
-	}
-
-	@Override
-	public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
-		throw new UnsupportedOperationException();
 	}
 
 	@Override
@@ -236,6 +228,7 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 		return null;
 	}
 
+	@Nonnull
 	@Override
 	public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CodingDt theCoding, RequestDetails theRequest) {
 		boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
@@ -294,10 +287,6 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 		// nothing
 	}
 
-	public static String toStringOrNull(IPrimitiveType<String> thePrimitive) {
-		return thePrimitive != null ? thePrimitive.getValue() : null;
-	}
-
 	@Override
 	public IValidationSupport.CodeValidationResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
 																					IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CodingDt theCoding, CodeableConceptDt theCodeableConcept, RequestDetails theRequest) {
@@ -310,4 +299,8 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 		throw new UnsupportedOperationException();
 	}
 
+	public static String toStringOrNull(IPrimitiveType<String> thePrimitive) {
+		return thePrimitive != null ? thePrimitive.getValue() : null;
+	}
+
 }

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

@@ -47,42 +47,21 @@ import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
 public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
 
 	@Override
-	public org.hl7.fhir.dstu3.model.ValueSet expand(IIdType theId, String theFilter, RequestDetails theRequestDetails) {
+	public org.hl7.fhir.dstu3.model.ValueSet expand(IIdType theId, ValueSetExpansionOptions theOptions, RequestDetails theRequestDetails) {
 		org.hl7.fhir.dstu3.model.ValueSet source = read(theId, theRequestDetails);
-		return expand(source, theFilter);
+		return expand(source, theOptions);
 	}
 
 	@Override
-	public org.hl7.fhir.dstu3.model.ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails) {
+	public org.hl7.fhir.dstu3.model.ValueSet expand(org.hl7.fhir.dstu3.model.ValueSet theSource, ValueSetExpansionOptions theOptions) {
-		org.hl7.fhir.dstu3.model.ValueSet source = read(theId, theRequestDetails);
-		return expand(source, theFilter, theOffset, theCount);
-	}
-
-	@Override
-	public org.hl7.fhir.dstu3.model.ValueSet expandByIdentifier(String theUri, String theFilter) {
-		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(null, theUri, theFilter);
-		return ValueSet30_40.convertValueSet(canonicalOutput);
-	}
-
-	@Override
-	public org.hl7.fhir.dstu3.model.ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
-		ValueSetExpansionOptions options = ValueSetExpansionOptions.forOffsetAndCount(theOffset, theCount);
-		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(options, theUri, theFilter);
-		return ValueSet30_40.convertValueSet(canonicalOutput);
-	}
-
-	@Override
-	public org.hl7.fhir.dstu3.model.ValueSet expand(org.hl7.fhir.dstu3.model.ValueSet theSource, String theFilter) {
 		org.hl7.fhir.r4.model.ValueSet canonicalInput = ValueSet30_40.convertValueSet(theSource);
-		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(null, canonicalInput, theFilter);
+		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(theOptions, canonicalInput);
 		return ValueSet30_40.convertValueSet(canonicalOutput);
 	}
 
 	@Override
-	public org.hl7.fhir.dstu3.model.ValueSet expand(org.hl7.fhir.dstu3.model.ValueSet theSource, String theFilter, int theOffset, int theCount) {
+	public org.hl7.fhir.dstu3.model.ValueSet expandByIdentifier(String theUri, ValueSetExpansionOptions theOptions) {
-		ValueSetExpansionOptions options = ValueSetExpansionOptions.forOffsetAndCount(theOffset, theCount);
+		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(theOptions, theUri);
-		org.hl7.fhir.r4.model.ValueSet canonicalInput = ValueSet30_40.convertValueSet(theSource);
-		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(options, canonicalInput, theFilter);
 		return ValueSet30_40.convertValueSet(canonicalOutput);
 	}
 

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

@@ -44,37 +44,20 @@ import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3.vsValidateC
 public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
 
 	@Override
-	public ValueSet expand(IIdType theId, String theFilter, RequestDetails theRequestDetails) {
+	public ValueSet expand(IIdType theId, ValueSetExpansionOptions theOptions, RequestDetails theRequestDetails) {
 		ValueSet source = read(theId, theRequestDetails);
-		return expand(source, theFilter);
+		return expand(source, theOptions);
+	}
+
+
+	@Override
+	public ValueSet expandByIdentifier(String theUri, ValueSetExpansionOptions theOptions) {
+		return myTerminologySvc.expandValueSet(theOptions, theUri);
 	}
 
 	@Override
-	public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails) {
+	public ValueSet expand(ValueSet theSource, ValueSetExpansionOptions theOptions) {
-		ValueSet source = read(theId, theRequestDetails);
+		return myTerminologySvc.expandValueSet(theOptions, theSource);
-		return expand(source, theFilter, theOffset, theCount);
-	}
-
-	@Override
-	public ValueSet expandByIdentifier(String theUri, String theFilter) {
-		return myTerminologySvc.expandValueSet(null, theUri, theFilter);
-	}
-
-	@Override
-	public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
-		ValueSetExpansionOptions options = ValueSetExpansionOptions.forOffsetAndCount(theOffset, theCount);
-		return myTerminologySvc.expandValueSet(options, theUri, theFilter);
-	}
-
-	@Override
-	public ValueSet expand(ValueSet theSource, String theFilter) {
-		return myTerminologySvc.expandValueSet(null, theSource, theFilter);
-	}
-
-	@Override
-	public ValueSet expand(ValueSet theSource, String theFilter, int theOffset, int theCount) {
-		ValueSetExpansionOptions options = ValueSetExpansionOptions.forOffsetAndCount(theOffset, theCount);
-		return myTerminologySvc.expandValueSet(options, theSource, theFilter);
 	}
 
 	@Override
@@ -107,15 +90,5 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
 		return retVal;
 	}
 
-	public static void validateHaveExpansionOrThrowInternalErrorException(IValidationSupport.ValueSetExpansionOutcome theRetVal) {
-		if (theRetVal != null && theRetVal.getValueSet() == null) {
-			throw new InternalErrorException("Unable to expand ValueSet: " + theRetVal.getError());
-		}
-
-		if (theRetVal == null) {
-			throw new InternalErrorException("Unable to expand ValueSet");
-		}
-	}
-
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java

@@ -44,42 +44,21 @@ import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3.vsValidateC
 public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
 
 	@Override
-	public ValueSet expand(IIdType theId, String theFilter, RequestDetails theRequestDetails) {
+	public ValueSet expand(IIdType theId, ValueSetExpansionOptions theOptions, RequestDetails theRequestDetails) {
 		ValueSet source = read(theId, theRequestDetails);
-		return expand(source, theFilter);
+		return expand(source, theOptions);
 	}
 
 	@Override
-	public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails) {
+	public ValueSet expandByIdentifier(String theUri, ValueSetExpansionOptions theOptions) {
-		ValueSet source = read(theId, theRequestDetails);
+		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(theOptions, theUri);
-		return expand(source, theFilter, theOffset, theCount);
-	}
-
-	@Override
-	public ValueSet expandByIdentifier(String theUri, String theFilter) {
-		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(null, theUri, theFilter);
 		return ValueSet40_50.convertValueSet(canonicalOutput);
 	}
 
 	@Override
-	public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
+	public ValueSet expand(ValueSet theSource, ValueSetExpansionOptions theOptions) {
-		ValueSetExpansionOptions options = ValueSetExpansionOptions.forOffsetAndCount(theOffset, theCount);
-		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(options, theUri, theFilter);
-		return ValueSet40_50.convertValueSet(canonicalOutput);
-	}
-
-	@Override
-	public ValueSet expand(ValueSet theSource, String theFilter) {
 		org.hl7.fhir.r4.model.ValueSet canonicalInput = ValueSet40_50.convertValueSet(theSource);
-		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(null, canonicalInput, theFilter);
+		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(theOptions, canonicalInput);
-		return ValueSet40_50.convertValueSet(canonicalOutput);
-	}
-
-	@Override
-	public ValueSet expand(ValueSet theSource, String theFilter, int theOffset, int theCount) {
-		ValueSetExpansionOptions options = ValueSetExpansionOptions.forOffsetAndCount(theOffset, theCount);
-		org.hl7.fhir.r4.model.ValueSet canonicalInput = ValueSet40_50.convertValueSet(theSource);
-		org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(options, canonicalInput, theFilter);
 		return ValueSet40_50.convertValueSet(canonicalOutput);
 	}
 

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

@@ -0,0 +1,47 @@
+package ca.uhn.fhir.jpa.entity;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * 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%
+ */
+
+public interface ITermValueSetConceptView {
+	String getConceptSystemUrl();
+
+	String getConceptCode();
+
+	String getConceptDisplay();
+
+	Long getSourceConceptPid();
+
+	String getSourceConceptDirectParentPids();
+
+	Long getConceptPid();
+
+	Long getDesignationPid();
+
+	String getDesignationUseSystem();
+
+	String getDesignationUseCode();
+
+	String getDesignationUseDisplay();
+
+	String getDesignationVal();
+
+	String getDesignationLang();
+}

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

@@ -388,7 +388,7 @@ public class TermConcept implements Serializable {
 			b.append("NONE");
 		}
 
-		myParentPids = b.toString();
+		setParentPids(b.toString());
 	}
 
 	public TermConcept setParentPids(String theParentPids) {

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

@@ -27,7 +27,21 @@ import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 
 import javax.annotation.Nonnull;
-import javax.persistence.*;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.ForeignKey;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.Lob;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
@@ -60,6 +74,9 @@ public class TermValueSetConcept implements Serializable {
 	@Column(name = "VALUESET_PID", insertable = false, updatable = false, nullable = false)
 	private Long myValueSetPid;
 
+	@Column(name = "INDEX_STATUS", nullable = true)
+	private Long myIndexStatus;
+
 	@Column(name = "VALUESET_ORDER", nullable = false)
 	private int myOrder;
 
@@ -69,6 +86,13 @@ public class TermValueSetConcept implements Serializable {
 	@Transient
 	private String myValueSetName;
 
+	@Column(name = "SOURCE_PID", nullable = true)
+	private Long mySourceConceptPid;
+
+	@Lob
+	@Column(name = "SOURCE_DIRECT_PARENT_PIDS", nullable = true)
+	private String mySourceConceptDirectParentPids;
+
 	@Column(name = "SYSTEM_URL", nullable = false, length = TermCodeSystem.MAX_URL_LENGTH)
 	private String mySystem;
 
@@ -87,6 +111,13 @@ public class TermValueSetConcept implements Serializable {
 	@Transient
 	private transient Integer myHashCode;
 
+	/**
+	 * Constructor
+	 */
+	public TermValueSetConcept() {
+		super();
+	}
+
 	public Long getId() {
 		return myId;
 	}
@@ -219,4 +250,20 @@ public class TermValueSetConcept implements Serializable {
 			.append(myDesignations != null ? ("myDesignations - size=" + myDesignations.size()) : ("myDesignations=(null)"))
 			.toString();
 	}
+
+	public Long getIndexStatus() {
+		return myIndexStatus;
+	}
+
+	public void setIndexStatus(Long theIndexStatus) {
+		myIndexStatus = theIndexStatus;
+	}
+
+	public void setSourceConceptPid(Long theSourceConceptPid) {
+		mySourceConceptPid = theSourceConceptPid;
+	}
+
+	public void setSourceConceptDirectParentPids(String theSourceConceptDirectParentPids) {
+		mySourceConceptDirectParentPids = theSourceConceptDirectParentPids;
+	}
 }

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

@@ -20,16 +20,20 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.io.IOUtils;
 import org.hibernate.annotations.Immutable;
 import org.hibernate.annotations.Subselect;
 
 import javax.persistence.Column;
-import javax.persistence.EmbeddedId;
 import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
 import javax.persistence.Id;
+import javax.persistence.Lob;
+import java.io.IOException;
+import java.io.Reader;
 import java.io.Serializable;
+import java.sql.Clob;
+import java.sql.SQLException;
 
 @Entity
 @Immutable
@@ -45,6 +49,8 @@ import java.io.Serializable;
 		"       vsc.SYSTEM_URL                  AS CONCEPT_SYSTEM_URL, " +
 		"       vsc.CODEVAL                     AS CONCEPT_CODEVAL, " +
 		"       vsc.DISPLAY                     AS CONCEPT_DISPLAY, " +
+		"       vsc.SOURCE_PID                  AS SOURCE_PID, " +
+		"       vsc.SOURCE_DIRECT_PARENT_PIDS   AS SOURCE_DIRECT_PARENT_PIDS, " +
 		"       vscd.PID                        AS DESIGNATION_PID, " +
 		"       vscd.LANG                       AS DESIGNATION_LANG, " +
 		"       vscd.USE_SYSTEM                 AS DESIGNATION_USE_SYSTEM, " +
@@ -54,7 +60,7 @@ import java.io.Serializable;
 		"FROM TRM_VALUESET_CONCEPT vsc " +
 		"LEFT OUTER JOIN TRM_VALUESET_C_DESIGNATION vscd ON vsc.PID = vscd.VALUESET_CONCEPT_PID"
 )
-public class TermValueSetConceptView implements Serializable {
+public class TermValueSetConceptView implements Serializable, ITermValueSetConceptView {
 	private static final long serialVersionUID = 1L;
 
 	@Id
@@ -97,43 +103,76 @@ public class TermValueSetConceptView implements Serializable {
 	@Column(name = "DESIGNATION_VAL", length = TermConceptDesignation.MAX_VAL_LENGTH)
 	private String myDesignationVal;
 
+	@Column(name = "SOURCE_PID", nullable = true)
+	private Long mySourceConceptPid;
 
+	@Lob
+	@Column(name = "SOURCE_DIRECT_PARENT_PIDS", nullable = true)
+	private Clob mySourceConceptDirectParentPids;
+
+	@Override
+	public Long getSourceConceptPid() {
+		return mySourceConceptPid;
+	}
+
+	@Override
+	public String getSourceConceptDirectParentPids() {
+		if (mySourceConceptDirectParentPids != null) {
+			try (Reader characterStream = mySourceConceptDirectParentPids.getCharacterStream()) {
+				return IOUtils.toString(characterStream);
+			} catch (IOException | SQLException e) {
+				throw new InternalErrorException(e);
+			}
+		}
+		return null;
+	}
+
+	@Override
 	public Long getConceptPid() {
 		return myConceptPid;
 	}
 
+	@Override
 	public String getConceptSystemUrl() {
 		return myConceptSystemUrl;
 	}
 
+	@Override
 	public String getConceptCode() {
 		return myConceptCode;
 	}
 
+	@Override
 	public String getConceptDisplay() {
 		return myConceptDisplay;
 	}
 
+	@Override
 	public Long getDesignationPid() {
 		return myDesignationPid;
 	}
 
+	@Override
 	public String getDesignationLang() {
 		return myDesignationLang;
 	}
 
+	@Override
 	public String getDesignationUseSystem() {
 		return myDesignationUseSystem;
 	}
 
+	@Override
 	public String getDesignationUseCode() {
 		return myDesignationUseCode;
 	}
 
+	@Override
 	public String getDesignationUseDisplay() {
 		return myDesignationUseDisplay;
 	}
 
+	@Override
 	public String getDesignationVal() {
 		return myDesignationVal;
 	}

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

@@ -20,18 +20,20 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.io.IOUtils;
 import org.hibernate.annotations.Immutable;
 import org.hibernate.annotations.Subselect;
 
 import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.EmbeddedId;
 import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
 import javax.persistence.Id;
-import javax.persistence.Table;
+import javax.persistence.Lob;
+import java.io.IOException;
+import java.io.Reader;
 import java.io.Serializable;
+import java.sql.Clob;
+import java.sql.SQLException;
 
 @Entity
 @Immutable
@@ -47,6 +49,8 @@ import java.io.Serializable;
 		"       vsc.SYSTEM_URL                  AS CONCEPT_SYSTEM_URL, " +
 		"       vsc.CODEVAL                     AS CONCEPT_CODEVAL, " +
 		"       vsc.DISPLAY                     AS CONCEPT_DISPLAY, " +
+		"       vsc.SOURCE_PID                  AS SOURCE_PID, " +
+		"       vsc.SOURCE_DIRECT_PARENT_PIDS   AS SOURCE_DIRECT_PARENT_PIDS, " +
 		"       vscd.PID                        AS DESIGNATION_PID, " +
 		"       vscd.LANG                       AS DESIGNATION_LANG, " +
 		"       vscd.USE_SYSTEM                 AS DESIGNATION_USE_SYSTEM, " +
@@ -56,7 +60,7 @@ import java.io.Serializable;
 		"FROM TRM_VALUESET_CONCEPT vsc " +
 		"LEFT OUTER JOIN TRM_VALUESET_C_DESIGNATION vscd ON vsc.PID = vscd.VALUESET_CONCEPT_PID"
 )
-public class TermValueSetConceptViewOracle implements Serializable {
+public class TermValueSetConceptViewOracle implements Serializable, ITermValueSetConceptView {
 	private static final long serialVersionUID = 1L;
 
 	@Id
@@ -99,43 +103,76 @@ public class TermValueSetConceptViewOracle implements Serializable {
 	@Column(name = "DESIGNATION_VAL", length = TermConceptDesignation.MAX_VAL_LENGTH)
 	private String myDesignationVal;
 
+	@Column(name = "SOURCE_PID", nullable = true)
+	private Long mySourceConceptPid;
 
+	@Lob
+	@Column(name = "SOURCE_DIRECT_PARENT_PIDS", nullable = true)
+	private Clob mySourceConceptDirectParentPids;
+
+	@Override
 	public Long getConceptPid() {
 		return myConceptPid;
 	}
 
+	@Override
 	public String getConceptSystemUrl() {
 		return myConceptSystemUrl;
 	}
 
+	@Override
 	public String getConceptCode() {
 		return myConceptCode;
 	}
 
+	@Override
 	public String getConceptDisplay() {
 		return myConceptDisplay;
 	}
 
+	@Override
+	public Long getSourceConceptPid() {
+		return mySourceConceptPid;
+	}
+
+	@Override
+	public String getSourceConceptDirectParentPids() {
+		if (mySourceConceptDirectParentPids != null) {
+			try (Reader characterStream = mySourceConceptDirectParentPids.getCharacterStream()) {
+				return IOUtils.toString(characterStream);
+			} catch (IOException | SQLException e) {
+				throw new InternalErrorException(e);
+			}
+		}
+		return null;
+	}
+
+	@Override
 	public Long getDesignationPid() {
 		return myDesignationPid;
 	}
 
+	@Override
 	public String getDesignationLang() {
 		return myDesignationLang;
 	}
 
+	@Override
 	public String getDesignationUseSystem() {
 		return myDesignationUseSystem;
 	}
 
+	@Override
 	public String getDesignationUseCode() {
 		return myDesignationUseCode;
 	}
 
+	@Override
 	public String getDesignationUseDisplay() {
 		return myDesignationUseDisplay;
 	}
 
+	@Override
 	public String getDesignationVal() {
 		return myDesignationVal;
 	}

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

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.provider;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
@@ -87,8 +88,11 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
 		}
 	}
 
-	private String toFilterString(StringDt theFilter) {
+	private ValueSetExpansionOptions toFilterString(StringDt theFilter) {
-		return theFilter != null ? theFilter.getValue() : null;
+		if (theFilter != null) {
+			return ValueSetExpansionOptions.forOffsetAndCount(0, 1000).setFilter(theFilter.getValue());
+		}
+		return null;
 	}
 
 	@Operation(name = JpaConstants.OPERATION_LOOKUP, idempotent = true, returnParameters = {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.provider.dstu3;
  */
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
@@ -29,14 +30,24 @@ 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 org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.BooleanType;
+import org.hl7.fhir.dstu3.model.CodeType;
+import org.hl7.fhir.dstu3.model.CodeableConcept;
+import org.hl7.fhir.dstu3.model.Coding;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.IntegerType;
+import org.hl7.fhir.dstu3.model.Parameters;
+import org.hl7.fhir.dstu3.model.StringType;
+import org.hl7.fhir.dstu3.model.UriType;
+import org.hl7.fhir.dstu3.model.ValueSet;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import javax.servlet.http.HttpServletRequest;
 
+import static ca.uhn.fhir.jpa.provider.r4.BaseJpaResourceProviderValueSetR4.createValueSetExpansionOptions;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDstu3<ValueSet> {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaResourceProviderValueSetDstu3.class);
 
 	@Operation(name = JpaConstants.OPERATION_EXPAND, idempotent = true)
 	public ValueSet expand(
@@ -51,6 +62,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
 		@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
 		@OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
 		@OperationParam(name = "count", min = 0, max = 1) IntegerType theCount,
+		@OperationParam(name = JpaConstants.OPERATION_EXPAND_PARAM_INCLUDE_HIERARCHY, min = 0, max = 1, typeName = "boolean") IPrimitiveType<Boolean> theIncludeHierarchy,
 		RequestDetails theRequestDetails) {
 
 		boolean haveId = theId != null && theId.hasIdPart();
@@ -71,56 +83,21 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
 			throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.");
 		}
 
-		int offset = myDaoConfig.getPreExpandValueSetsDefaultOffset();
+		ValueSetExpansionOptions options = createValueSetExpansionOptions(myDaoConfig, theOffset, theCount, theIncludeHierarchy, theFilter);
-		if (theOffset != null && theOffset.hasValue()) {
-			if (theOffset.getValue() >= 0) {
-				offset = theOffset.getValue();
-			} else {
-				throw new InvalidRequestException("offset parameter for $expand operation must be >= 0 when specified. offset: " + theOffset.getValue());
-			}
-		}
-
-		int count = myDaoConfig.getPreExpandValueSetsDefaultCount();
-		if (theCount != null && theCount.hasValue()) {
-			if (theCount.getValue() >= 0) {
-				count = theCount.getValue();
-			} else {
-				throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
-			}
-		}
-		int countMax = myDaoConfig.getPreExpandValueSetsMaxCount();
-		if (count > countMax) {
-			ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
-			count = countMax;
-		}
 
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
-			if (myDaoConfig.isPreExpandValueSets()) {
 			if (haveId) {
-					return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
+				return dao.expand(theId, options, theRequestDetails);
 			} else if (haveIdentifier) {
 				if (haveValueSetVersion) {
-						return dao.expandByIdentifier(url.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
+					return dao.expandByIdentifier(url.getValue() + "|" + theValueSetVersion.getValue(), options);
 				} else {
-						return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter), offset, count);
+					return dao.expandByIdentifier(url.getValue(), options);
 				}
 			} else {
-					return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
+				return dao.expand(theValueSet, options);
-				}
-			} else {
-				if (haveId) {
-					return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
-				} else if (haveIdentifier) {
-					if (haveValueSetVersion) {
-						return dao.expandByIdentifier(url.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter));
-					} else {
-						return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter));
-					}
-				} else {
-					return dao.expand(theValueSet, toFilterString(theFilter));
-				}
 			}
 		} finally {
 			endRequest(theServletRequest);
@@ -128,11 +105,6 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
 	}
 
 
-	private String toFilterString(StringType theFilter) {
-		return theFilter != null ? theFilter.getValue() : null;
-	}
-
-
 	@Operation(name = JpaConstants.OPERATION_VALIDATE_CODE, idempotent = true, returnParameters = {
 		@OperationParam(name = "result", type = BooleanType.class, min = 1),
 		@OperationParam(name = "message", type = StringType.class),

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderValueSetR4.java

@@ -21,6 +21,8 @@ package ca.uhn.fhir.jpa.provider.r4;
  */
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
@@ -29,7 +31,17 @@ 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 org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.CodeType;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.IntegerType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.model.UriType;
+import org.hl7.fhir.r4.model.ValueSet;
 
 import javax.servlet.http.HttpServletRequest;
 
@@ -48,6 +60,7 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
 		@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
 		@OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
 		@OperationParam(name = "count", min = 0, max = 1) IntegerType theCount,
+		@OperationParam(name = JpaConstants.OPERATION_EXPAND_PARAM_INCLUDE_HIERARCHY, min = 0, max = 1, typeName = "boolean") IPrimitiveType<Boolean> theIncludeHierarchy,
 		RequestDetails theRequestDetails) {
 
 		boolean haveId = theId != null && theId.hasIdPart();
@@ -63,69 +76,28 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
 			throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have a url specified, or have a ValueSet specified. Can not combine these options.");
 		}
 
-		int offset = myDaoConfig.getPreExpandValueSetsDefaultOffset();
+		ValueSetExpansionOptions options = createValueSetExpansionOptions(myDaoConfig, theOffset, theCount, theIncludeHierarchy, theFilter);
-		if (theOffset != null && theOffset.hasValue()) {
-			if (theOffset.getValue() >= 0) {
-				offset = theOffset.getValue();
-			} else {
-				throw new InvalidRequestException("offset parameter for $expand operation must be >= 0 when specified. offset: " + theOffset.getValue());
-			}
-		}
-
-		int count = myDaoConfig.getPreExpandValueSetsDefaultCount();
-		if (theCount != null && theCount.hasValue()) {
-			if (theCount.getValue() >= 0) {
-				count = theCount.getValue();
-			} else {
-				throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
-			}
-		}
-		int countMax = myDaoConfig.getPreExpandValueSetsMaxCount();
-		if (count > countMax) {
-			ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
-			count = countMax;
-		}
 
 		startRequest(theServletRequest);
 		try {
+
 			IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
-			if (myDaoConfig.isPreExpandValueSets()) {
 			if (haveId) {
-					return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
+				return dao.expand(theId, options, theRequestDetails);
 			} else if (haveIdentifier) {
 				if (haveValueSetVersion) {
-						return dao.expandByIdentifier(theUrl.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
+					return dao.expandByIdentifier(theUrl.getValue() + "|" + theValueSetVersion.getValue(), options);
 				} else {
-						return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
+					return dao.expandByIdentifier(theUrl.getValue(), options);
 				}
 			} else {
-					return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
+				return dao.expand(theValueSet, options);
-				}
-			} else {
-				if (haveId) {
-					return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
-				} else if (haveIdentifier) {
-					if (haveValueSetVersion) {
-						return dao.expandByIdentifier(theUrl.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter));
-					} else {
-						return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
-					}
-				} else {
-					return dao.expand(theValueSet, toFilterString(theFilter));
-				}
 			}
 		} finally {
 			endRequest(theServletRequest);
 		}
 	}
 
-
-	private String toFilterString(StringType theFilter) {
-		return theFilter != null ? theFilter.getValue() : null;
-	}
-
-
-	@SuppressWarnings("unchecked")
 	@Operation(name = JpaConstants.OPERATION_VALIDATE_CODE, idempotent = true, returnParameters = {
 		@OperationParam(name = "result", type = BooleanType.class, min = 1),
 		@OperationParam(name = "message", type = StringType.class),
@@ -167,6 +139,42 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
 		}
 	}
 
+	public static ValueSetExpansionOptions createValueSetExpansionOptions(DaoConfig theDaoConfig, IPrimitiveType<Integer> theOffset, IPrimitiveType<Integer> theCount, IPrimitiveType<Boolean> theIncludeHierarchy, IPrimitiveType<String> theFilter) {
+		int offset = theDaoConfig.getPreExpandValueSetsDefaultOffset();
+		if (theOffset != null && theOffset.hasValue()) {
+			if (theOffset.getValue() >= 0) {
+				offset = theOffset.getValue();
+			} else {
+				throw new InvalidRequestException("offset parameter for $expand operation must be >= 0 when specified. offset: " + theOffset.getValue());
+			}
+		}
+
+		int count = theDaoConfig.getPreExpandValueSetsDefaultCount();
+		if (theCount != null && theCount.hasValue()) {
+			if (theCount.getValue() >= 0) {
+				count = theCount.getValue();
+			} else {
+				throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
+			}
+		}
+		int countMax = theDaoConfig.getPreExpandValueSetsMaxCount();
+		if (count > countMax) {
+			ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
+			count = countMax;
+		}
+
+		ValueSetExpansionOptions options = ValueSetExpansionOptions.forOffsetAndCount(offset, count);
+
+		if (theIncludeHierarchy != null && Boolean.TRUE.equals(theIncludeHierarchy.getValue())) {
+			options.setIncludeHierarchy(true);
+		}
+
+		if (theFilter != null) {
+			options.setFilter(theFilter.getValue());
+		}
+
+		return options;
+	}
 
 	private static boolean moreThanOneTrue(boolean... theBooleans) {
 		boolean haveOne = false;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderValueSetR5.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.provider.r5;
  */
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
@@ -29,14 +30,24 @@ 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 org.hl7.fhir.r5.model.*;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r5.model.BooleanType;
+import org.hl7.fhir.r5.model.CodeType;
+import org.hl7.fhir.r5.model.CodeableConcept;
+import org.hl7.fhir.r5.model.Coding;
+import org.hl7.fhir.r5.model.IdType;
+import org.hl7.fhir.r5.model.IntegerType;
+import org.hl7.fhir.r5.model.Parameters;
+import org.hl7.fhir.r5.model.StringType;
+import org.hl7.fhir.r5.model.UriType;
+import org.hl7.fhir.r5.model.ValueSet;
 
 import javax.servlet.http.HttpServletRequest;
 
+import static ca.uhn.fhir.jpa.provider.r4.BaseJpaResourceProviderValueSetR4.createValueSetExpansionOptions;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<ValueSet> {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaResourceProviderValueSetR5.class);
 
 	@Operation(name = JpaConstants.OPERATION_EXPAND, idempotent = true)
 	public ValueSet expand(
@@ -48,6 +59,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
 		@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
 		@OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
 		@OperationParam(name = "count", min = 0, max = 1) IntegerType theCount,
+		@OperationParam(name = JpaConstants.OPERATION_EXPAND_PARAM_INCLUDE_HIERARCHY, min = 0, max = 1, typeName = "boolean") IPrimitiveType<Boolean> theIncludeHierarchy,
 		RequestDetails theRequestDetails) {
 
 		boolean haveId = theId != null && theId.hasIdPart();
@@ -63,56 +75,21 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
 			throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have a url specified, or have a ValueSet specified. Can not combine these options.");
 		}
 
-		int offset = myDaoConfig.getPreExpandValueSetsDefaultOffset();
+		ValueSetExpansionOptions options = createValueSetExpansionOptions(myDaoConfig, theOffset, theCount, theIncludeHierarchy, theFilter);
-		if (theOffset != null && theOffset.hasValue()) {
-			if (theOffset.getValue() >= 0) {
-				offset = theOffset.getValue();
-			} else {
-				throw new InvalidRequestException("offset parameter for $expand operation must be >= 0 when specified. offset: " + theOffset.getValue());
-			}
-		}
-
-		int count = myDaoConfig.getPreExpandValueSetsDefaultCount();
-		if (theCount != null && theCount.hasValue()) {
-			if (theCount.getValue() >= 0) {
-				count = theCount.getValue();
-			} else {
-				throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
-			}
-		}
-		int countMax = myDaoConfig.getPreExpandValueSetsMaxCount();
-		if (count > countMax) {
-			ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
-			count = countMax;
-		}
 
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
-			if (myDaoConfig.isPreExpandValueSets()) {
 			if (haveId) {
-					return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
+				return dao.expand(theId, options, theRequestDetails);
 			} else if (haveIdentifier) {
 				if (haveValueSetVersion) {
-						return dao.expandByIdentifier(theUrl.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
+					return dao.expandByIdentifier(theUrl.getValue() + "|" + theValueSetVersion.getValue(), options);
 				} else {
-						return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
+					return dao.expandByIdentifier(theUrl.getValue(), options);
 				}
 			} else {
-					return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
+				return dao.expand(theValueSet, options);
-				}
-			} else {
-				if (haveId) {
-					return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
-				} else if (haveIdentifier) {
-					if (haveValueSetVersion) {
-						return dao.expandByIdentifier(theUrl.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter));
-					} else {
-						return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
-					}
-				} else {
-					return dao.expand(theValueSet, toFilterString(theFilter));
-				}
 			}
 		} finally {
 			endRequest(theServletRequest);
@@ -120,12 +97,6 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
 	}
 
 
-	private String toFilterString(StringType theFilter) {
-		return theFilter != null ? theFilter.getValue() : null;
-	}
-
-
-	@SuppressWarnings("unchecked")
 	@Operation(name = JpaConstants.OPERATION_VALIDATE_CODE, idempotent = true, returnParameters = {
 		@OperationParam(name = "result", type = BooleanType.class, min = 1),
 		@OperationParam(name = "message", type = StringType.class),

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

@@ -41,6 +41,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
 import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptViewDao;
 import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptViewOracleDao;
 import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
+import ca.uhn.fhir.jpa.entity.ITermValueSetConceptView;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
@@ -52,8 +53,6 @@ import ca.uhn.fhir.jpa.entity.TermConceptPropertyBinder;
 import ca.uhn.fhir.jpa.entity.TermConceptPropertyTypeEnum;
 import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
-import ca.uhn.fhir.jpa.entity.TermValueSetConceptView;
-import ca.uhn.fhir.jpa.entity.TermValueSetConceptViewOracle;
 import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.sched.HapiJob;
@@ -153,6 +152,7 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -251,19 +251,27 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
 		String code = theConcept.getCode();
 		String display = theConcept.getDisplay();
+		Long sourceConceptPid = theConcept.getId();
+
+		String directParentPids = theConcept
+			.getParents()
+			.stream()
+			.map(t -> t.getParent().getId().toString())
+			.collect(Collectors.joining(" "));
+
 		Collection<TermConceptDesignation> designations = theConcept.getDesignations();
 		if (StringUtils.isNotEmpty(theValueSetIncludeVersion)) {
-			return addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, designations, theAdd, codeSystem + "|" + theValueSetIncludeVersion, code, display);
+			return addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, designations, theAdd, codeSystem + "|" + theValueSetIncludeVersion, code, display, sourceConceptPid, directParentPids);
 		} else {
-			return addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, designations, theAdd, codeSystem, code, display);
+			return addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, designations, theAdd, codeSystem, code, display, sourceConceptPid, directParentPids);
 		}
 	}
 
-	private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, boolean theAdd, String theCodeSystem, String theCodeSystemVersion, String theCode, String theDisplay) {
+	private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, boolean theAdd, String theCodeSystem, String theCodeSystemVersion, String theCode, String theDisplay, Long theSourceConceptPid, String theSourceConceptDirectParentPids) {
 		if (StringUtils.isNotEmpty(theCodeSystemVersion)) {
 			if (isNoneBlank(theCodeSystem, theCode)) {
 				if (theAdd && theAddedCodes.add(theCodeSystem + "|" + theCode)) {
-					theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem + "|" + theCodeSystemVersion, theCode, theDisplay, null);
+					theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem + "|" + theCodeSystemVersion, theCode, theDisplay, null, theSourceConceptPid, theSourceConceptDirectParentPids);
 				}
 
 				if (!theAdd && theAddedCodes.remove(theCodeSystem + "|" + theCode)) {
@@ -272,7 +280,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 			}
 		} else {
 			if (theAdd && theAddedCodes.add(theCodeSystem + "|" + theCode)) {
-				theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem, theCode, theDisplay, null);
+				theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem, theCode, theDisplay, null, theSourceConceptPid, theSourceConceptDirectParentPids);
 			}
 
 			if (!theAdd && theAddedCodes.remove(theCodeSystem + "|" + theCode)) {
@@ -281,10 +289,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		}
 	}
 
-	private boolean addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, Collection<TermConceptDesignation> theDesignations, boolean theAdd, String theCodeSystem, String theCode, String theDisplay) {
+	private boolean addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, Collection<TermConceptDesignation> theDesignations, boolean theAdd, String theCodeSystem, String theCode, String theDisplay, Long theSourceConceptPid, String theSourceConceptDirectParentPids) {
 		if (isNoneBlank(theCodeSystem, theCode)) {
 			if (theAdd && theAddedCodes.add(theCodeSystem + "|" + theCode)) {
-				theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem, theCode, theDisplay, theDesignations);
+				theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem, theCode, theDisplay, theDesignations, theSourceConceptPid, theSourceConceptDirectParentPids);
 				return true;
 			}
 
@@ -353,10 +361,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	@Override
 	@Transactional
 	public List<FhirVersionIndependentConcept> expandValueSetIntoConceptList(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull String theValueSetCanonicalUrl) {
-		String expansionFilter = null;
 		// TODO: DM 2019-09-10 - This is problematic because an incorrect URL that matches ValueSet.id will not be found in the terminology tables but will yield a ValueSet here. Depending on the ValueSet, the expansion may time-out.
 
-		ValueSet expanded = expandValueSet(theExpansionOptions, theValueSetCanonicalUrl, expansionFilter);
+		ValueSet expanded = expandValueSet(theExpansionOptions, theValueSetCanonicalUrl);
 
 		ArrayList<FhirVersionIndependentConcept> retVal = new ArrayList<>();
 		for (ValueSet.ValueSetExpansionContainsComponent nextContains : expanded.getExpansion().getContains()) {
@@ -367,25 +374,23 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 	@Override
 	@Transactional
-	public ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull String theValueSetCanonicalUrl, @Nullable String theExpansionFilter) {
+	public ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull String theValueSetCanonicalUrl) {
 		ValueSet valueSet = fetchCanonicalValueSetFromCompleteContext(theValueSetCanonicalUrl);
 		if (valueSet == null) {
 			throw new ResourceNotFoundException("Unknown ValueSet: " + UrlUtil.escapeUrlParam(theValueSetCanonicalUrl));
 		}
 
-		return expandValueSet(theExpansionOptions, valueSet, theExpansionFilter);
+		return expandValueSet(theExpansionOptions, valueSet);
 	}
 
 	@Override
 	@Transactional(propagation = Propagation.REQUIRED)
 	public ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull ValueSet theValueSetToExpand) {
-		return expandValueSet(theExpansionOptions, theValueSetToExpand, (String) null);
+		String filter = null;
+		if (theExpansionOptions != null) {
+			filter = theExpansionOptions.getFilter();
 		}
-
+		return expandValueSet(theExpansionOptions, theValueSetToExpand, ExpansionFilter.fromFilterString(filter));
-	@Override
-	@Transactional(propagation = Propagation.REQUIRED)
-	public ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull ValueSet theValueSetToExpand, @Nullable String theFilter) {
-		return expandValueSet(theExpansionOptions, theValueSetToExpand, ExpansionFilter.fromFilterString(theFilter));
 	}
 
 	private ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, ValueSet theValueSetToExpand, ExpansionFilter theFilter) {
@@ -395,7 +400,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		int offset = expansionOptions.getOffset();
 		int count = expansionOptions.getCount();
 
-		ValueSetExpansionComponentWithConceptAccumulator accumulator = new ValueSetExpansionComponentWithConceptAccumulator(myContext, count);
+		ValueSetExpansionComponentWithConceptAccumulator accumulator = new ValueSetExpansionComponentWithConceptAccumulator(myContext, count, expansionOptions.isIncludeHierarchy());
 		accumulator.setHardExpansionMaximumSize(myDaoConfig.getMaximumExpansionSize());
 		accumulator.setSkipCountRemaining(offset);
 		accumulator.setIdentifier(UUID.randomUUID().toString());
@@ -424,6 +429,11 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 				.setUrl(HapiExtensions.EXT_VALUESET_EXPANSION_MESSAGE)
 				.setValue(new StringType(next));
 		}
+
+		if (expansionOptions.isIncludeHierarchy()) {
+			accumulator.applyHierarchy();
+		}
+
 		return valueSet;
 	}
 
@@ -469,124 +479,14 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		 */
 		String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "valueSetExpandedUsingPreExpansion");
 		theAccumulator.addMessage(msg);
-		if (isOracleDialect()) {
+		expandConcepts(theAccumulator, termValueSet, theFilter, theAdd, isOracleDialect());
-			expandConceptsOracle(theAccumulator, termValueSet, theFilter, theAdd);
-		} else {
-			expandConcepts(theAccumulator, termValueSet, theFilter, theAdd);
-		}
 	}
 
 	private boolean isOracleDialect() {
 		return myHibernatePropertiesProvider.getDialect() instanceof org.hibernate.dialect.Oracle12cDialect;
 	}
 
-	private void expandConceptsOracle(IValueSetConceptAccumulator theAccumulator, TermValueSet theTermValueSet, ExpansionFilter theFilter, boolean theAdd) {
+	private void expandConcepts(IValueSetConceptAccumulator theAccumulator, TermValueSet theTermValueSet, ExpansionFilter theFilter, boolean theAdd, boolean theOracle) {
-		// Literal copy paste from expandConcepts but tailored for Oracle since we can't reliably extend the DAO and hibernate classes
-		Integer offset = theAccumulator.getSkipCountRemaining();
-		offset = ObjectUtils.defaultIfNull(offset, 0);
-		offset = Math.min(offset, theTermValueSet.getTotalConcepts().intValue());
-
-		Integer count = theAccumulator.getCapacityRemaining();
-		count = defaultIfNull(count, myDaoConfig.getMaximumExpansionSize());
-
-		int conceptsExpanded = 0;
-		int designationsExpanded = 0;
-		int toIndex = offset + count;
-
-		Collection<TermValueSetConceptViewOracle> conceptViews;
-		boolean wasFilteredResult = false;
-		String filterDisplayValue = null;
-		if (!theFilter.getFilters().isEmpty() && JpaConstants.VALUESET_FILTER_DISPLAY.equals(theFilter.getFilters().get(0).getProperty()) && theFilter.getFilters().get(0).getOp() == ValueSet.FilterOperator.EQUAL) {
-			filterDisplayValue = lowerCase(theFilter.getFilters().get(0).getValue().replace("%", "[%]"));
-			String displayValue = "%" + lowerCase(filterDisplayValue) + "%";
-			conceptViews = myTermValueSetConceptViewOracleDao.findByTermValueSetId(theTermValueSet.getId(), displayValue);
-			wasFilteredResult = true;
-		} else {
-			// TODO JA HS: I'm pretty sure we are overfetching here.  test says offset 3, count 4, but we are fetching index 3 -> 10 here, grabbing 7 concepts.
-			//Specifically this test testExpandInline_IncludePreExpandedValueSetByUri_FilterOnDisplay_LeftMatch_SelectRange
-			conceptViews = myTermValueSetConceptViewOracleDao.findByTermValueSetId(offset, toIndex, theTermValueSet.getId());
-			theAccumulator.consumeSkipCount(offset);
-			if (theAdd) {
-				theAccumulator.incrementOrDecrementTotalConcepts(true, theTermValueSet.getTotalConcepts().intValue());
-			}
-		}
-
-		if (conceptViews.isEmpty()) {
-			logConceptsExpanded("No concepts to expand. ", theTermValueSet, conceptsExpanded);
-			return;
-		}
-
-		Map<Long, FhirVersionIndependentConcept> pidToConcept = new LinkedHashMap<>();
-		ArrayListMultimap<Long, TermConceptDesignation> pidToDesignations = ArrayListMultimap.create();
-
-		for (TermValueSetConceptViewOracle conceptView : conceptViews) {
-
-			String system = conceptView.getConceptSystemUrl();
-			String code = conceptView.getConceptCode();
-			String display = conceptView.getConceptDisplay();
-
-			//-- this is quick solution, may need to revisit
-			if (!applyFilter(display, filterDisplayValue))
-				continue;
-
-			Long conceptPid = conceptView.getConceptPid();
-			if (!pidToConcept.containsKey(conceptPid)) {
-				FhirVersionIndependentConcept concept = new FhirVersionIndependentConcept(system, code, display);
-				pidToConcept.put(conceptPid, concept);
-			}
-
-			// TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to designations optional.
-			if (conceptView.getDesignationPid() != null) {
-				TermConceptDesignation designation = new TermConceptDesignation();
-				designation.setUseSystem(conceptView.getDesignationUseSystem());
-				designation.setUseCode(conceptView.getDesignationUseCode());
-				designation.setUseDisplay(conceptView.getDesignationUseDisplay());
-				designation.setValue(conceptView.getDesignationVal());
-				designation.setLanguage(conceptView.getDesignationLang());
-				pidToDesignations.put(conceptPid, designation);
-
-				if (++designationsExpanded % 250 == 0) {
-					logDesignationsExpanded("Expansion of designations in progress. ", theTermValueSet, designationsExpanded);
-				}
-			}
-
-			if (++conceptsExpanded % 250 == 0) {
-				logConceptsExpanded("Expansion of concepts in progress. ", theTermValueSet, conceptsExpanded);
-			}
-		}
-
-		for (Long nextPid : pidToConcept.keySet()) {
-			FhirVersionIndependentConcept concept = pidToConcept.get(nextPid);
-			List<TermConceptDesignation> designations = pidToDesignations.get(nextPid);
-			String system = concept.getSystem();
-			String code = concept.getCode();
-			String display = concept.getDisplay();
-
-			if (theAdd) {
-				if (theAccumulator.getCapacityRemaining() != null) {
-					if (theAccumulator.getCapacityRemaining() == 0) {
-						break;
-					}
-				}
-
-				theAccumulator.includeConceptWithDesignations(system, code, display, designations);
-			} else {
-				boolean removed = theAccumulator.excludeConcept(system, code);
-				if (removed) {
-					theAccumulator.incrementOrDecrementTotalConcepts(false, 1);
-				}
-			}
-		}
-
-		if (wasFilteredResult && theAdd) {
-			theAccumulator.incrementOrDecrementTotalConcepts(true, pidToConcept.size());
-		}
-
-		logDesignationsExpanded("Finished expanding designations. ", theTermValueSet, designationsExpanded);
-		logConceptsExpanded("Finished expanding concepts. ", theTermValueSet, conceptsExpanded);
-	}
-
-	private void expandConcepts(IValueSetConceptAccumulator theAccumulator, TermValueSet theTermValueSet, ExpansionFilter theFilter, boolean theAdd) {
 		// NOTE: if you modifiy the logic here, look to `expandConceptsOracle` and see if your new code applies to its copy pasted sibling
 		Integer offset = theAccumulator.getSkipCountRemaining();
 		offset = ObjectUtils.defaultIfNull(offset, 0);
@@ -599,19 +499,26 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		int designationsExpanded = 0;
 		int toIndex = offset + count;
 
-		Collection<TermValueSetConceptView> conceptViews;
+		Collection<? extends ITermValueSetConceptView> conceptViews;
-		Collection<TermValueSetConceptViewOracle> conceptViewsOracle;
 		boolean wasFilteredResult = false;
 		String filterDisplayValue = null;
 		if (!theFilter.getFilters().isEmpty() && JpaConstants.VALUESET_FILTER_DISPLAY.equals(theFilter.getFilters().get(0).getProperty()) && theFilter.getFilters().get(0).getOp() == ValueSet.FilterOperator.EQUAL) {
 			filterDisplayValue = lowerCase(theFilter.getFilters().get(0).getValue().replace("%", "[%]"));
 			String displayValue = "%" + lowerCase(filterDisplayValue) + "%";
+			if (theOracle) {
+				conceptViews = myTermValueSetConceptViewOracleDao.findByTermValueSetId(theTermValueSet.getId(), displayValue);
+			} else {
 				conceptViews = myTermValueSetConceptViewDao.findByTermValueSetId(theTermValueSet.getId(), displayValue);
+			}
 			wasFilteredResult = true;
 		} else {
 			// TODO JA HS: I'm pretty sure we are overfetching here.  test says offset 3, count 4, but we are fetching index 3 -> 10 here, grabbing 7 concepts.
 			//Specifically this test testExpandInline_IncludePreExpandedValueSetByUri_FilterOnDisplay_LeftMatch_SelectRange
+			if (theOracle) {
+				conceptViews = myTermValueSetConceptViewOracleDao.findByTermValueSetId(offset, toIndex, theTermValueSet.getId());
+			} else {
 				conceptViews = myTermValueSetConceptViewDao.findByTermValueSetId(offset, toIndex, theTermValueSet.getId());
+			}
 			theAccumulator.consumeSkipCount(offset);
 			if (theAdd) {
 				theAccumulator.incrementOrDecrementTotalConcepts(true, theTermValueSet.getTotalConcepts().intValue());
@@ -625,8 +532,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 		Map<Long, FhirVersionIndependentConcept> pidToConcept = new LinkedHashMap<>();
 		ArrayListMultimap<Long, TermConceptDesignation> pidToDesignations = ArrayListMultimap.create();
+		Map<Long, Long> pidToSourcePid = new HashMap<>();
+		Map<Long, String> pidToSourceDirectParentPids = new HashMap<>();
 
-		for (TermValueSetConceptView conceptView : conceptViews) {
+		for (ITermValueSetConceptView conceptView : conceptViews) {
 
 			String system = conceptView.getConceptSystemUrl();
 			String code = conceptView.getConceptCode();
@@ -657,6 +566,11 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 				}
 			}
 
+			if (theAccumulator.isTrackingHierarchy()) {
+				pidToSourcePid.put(conceptPid, conceptView.getSourceConceptPid());
+				pidToSourceDirectParentPids.put(conceptPid, conceptView.getSourceConceptDirectParentPids());
+			}
+
 			if (++conceptsExpanded % 250 == 0) {
 				logConceptsExpanded("Expansion of concepts in progress. ", theTermValueSet, conceptsExpanded);
 			}
@@ -676,7 +590,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 					}
 				}
 
-				theAccumulator.includeConceptWithDesignations(system, code, display, designations);
+				Long sourceConceptPid = pidToSourcePid.get(nextPid);
+				String sourceConceptDirectParentPids = pidToSourceDirectParentPids.get(nextPid);
+				theAccumulator.includeConceptWithDesignations(system, code, display, designations, sourceConceptPid, sourceConceptDirectParentPids);
 			} else {
 				boolean removed = theAccumulator.excludeConcept(system, code);
 				if (removed) {
@@ -1158,7 +1074,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 	private void addOrRemoveCode(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, boolean theAdd, String theSystem, String theCode, String theDisplay) {
 		if (theAdd && theAddedCodes.add(theSystem + "|" + theCode)) {
-			theValueSetCodeAccumulator.includeConcept(theSystem, theCode, theDisplay);
+			theValueSetCodeAccumulator.includeConcept(theSystem, theCode, theDisplay, null, null);
 		}
 		if (!theAdd && theAddedCodes.remove(theSystem + "|" + theCode)) {
 			theValueSetCodeAccumulator.excludeConcept(theSystem, theCode);
@@ -1506,7 +1422,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 		if (theInclude.getConcept().isEmpty()) {
 			for (TermConcept next : theVersion.getConcepts()) {
-				addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, theAdd, theSystem, theInclude.getVersion(), next.getCode(), next.getDisplay());
+				addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, theAdd, theSystem, theInclude.getVersion(), next.getCode(), next.getDisplay(), next.getId(), next.getParentPidsAsString());
 			}
 		}
 
@@ -1514,7 +1430,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 			if (!theSystem.equals(theInclude.getSystem()) && isNotBlank(theSystem)) {
 				continue;
 			}
-			addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, theAdd, theSystem, theInclude.getVersion(), next.getCode(), next.getDisplay());
+			addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, theAdd, theSystem, theInclude.getVersion(), next.getCode(), next.getDisplay(), null, null);
 		}
 
 

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

@@ -29,9 +29,9 @@ public interface IValueSetConceptAccumulator {
 
 	void addMessage(String theMessage);
 
-	void includeConcept(String theSystem, String theCode, String theDisplay);
+	void includeConcept(String theSystem, String theCode, String theDisplay, Long theSourceConceptPid, String theSourceConceptDirectParentPids);
 
-	void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, @Nullable Collection<TermConceptDesignation> theDesignations);
+	void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, @Nullable Collection<TermConceptDesignation> theDesignations, Long theSourceConceptPid, String theSourceConceptDirectParentPids);
 
 	/**
 	 * @return Returns <code>true</code> if the code was actually present and was removed
@@ -48,6 +48,10 @@ public interface IValueSetConceptAccumulator {
 		return null;
 	}
 
+	default boolean isTrackingHierarchy() {
+		return true;
+	}
+
 	@Nullable
 	default void consumeSkipCount(int theSkipCountToConsume) {
 		// nothing

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

@@ -66,13 +66,13 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
 	}
 
 	@Override
-	public void includeConcept(String theSystem, String theCode, String theDisplay) {
+	public void includeConcept(String theSystem, String theCode, String theDisplay, Long theSourceConceptPid, String theSourceConceptDirectParentPids) {
-		saveConcept(theSystem, theCode, theDisplay);
+		saveConcept(theSystem, theCode, theDisplay, theSourceConceptPid, theSourceConceptDirectParentPids);
 	}
 
 	@Override
-	public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
+	public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations, Long theSourceConceptPid, String theSourceConceptDirectParentPids) {
-		TermValueSetConcept concept = saveConcept(theSystem, theCode, theDisplay);
+		TermValueSetConcept concept = saveConcept(theSystem, theCode, theDisplay, theSourceConceptPid, theSourceConceptDirectParentPids);
 		if (theDesignations != null) {
 			for (TermConceptDesignation designation : theDesignations) {
 				saveConceptDesignation(concept, designation);
@@ -117,7 +117,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
 		return false;
 	}
 
-	private TermValueSetConcept saveConcept(String theSystem, String theCode, String theDisplay) {
+	private TermValueSetConcept saveConcept(String theSystem, String theCode, String theDisplay, Long theSourceConceptPid, String theSourceConceptDirectParentPids) {
 		ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystem, "ValueSet contains a concept with no system value");
 		ValidateUtil.isNotBlankOrThrowInvalidRequest(theCode, "ValueSet contains a concept with no code value");
 
@@ -135,6 +135,10 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
 		if (isNotBlank(theDisplay)) {
 			concept.setDisplay(theDisplay);
 		}
+
+		concept.setSourceConceptPid(theSourceConceptPid);
+		concept.setSourceConceptDirectParentPids(theSourceConceptDirectParentPids);
+
 		myValueSetConceptDao.save(concept);
 		myValueSetDao.save(myTermValueSet.incrementTotalConcepts());
 

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

@@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.term;
  */
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
 import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
 import ca.uhn.fhir.model.api.annotation.Block;
@@ -32,9 +31,15 @@ import org.hl7.fhir.r4.model.ValueSet;
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 @Block()
 public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.ValueSetExpansionComponent implements IValueSetConceptAccumulator {
@@ -45,25 +50,21 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
 	private List<String> myMessages;
 	private int myAddedConcepts;
 	private Integer myTotalConcepts;
-
+	private Map<Long, ValueSet.ValueSetExpansionContainsComponent> mySourcePidToConcept = new HashMap<>();
-	/**
+	private Map<ValueSet.ValueSetExpansionContainsComponent, String> myConceptToSourceDirectParentPids = new HashMap<>();
-	 * Constructor
+	private boolean myTrackingHierarchy;
-	 *
-	 * @param theDaoConfig Will be used to determine the max capacity for this accumulator
-	 */
-	public ValueSetExpansionComponentWithConceptAccumulator(FhirContext theContext, DaoConfig theDaoConfig) {
-		this(theContext, theDaoConfig.getMaximumExpansionSize());
-	}
 
 	/**
 	 * Constructor
 	 *
 	 * @param theMaxCapacity The maximum number of results this accumulator will accept before throwing
 	 *                       an {@link InternalErrorException}
+	 * @param theTrackingHierarchy
 	 */
-	ValueSetExpansionComponentWithConceptAccumulator(FhirContext theContext, int theMaxCapacity) {
+	ValueSetExpansionComponentWithConceptAccumulator(FhirContext theContext, int theMaxCapacity, boolean theTrackingHierarchy) {
 		myMaxCapacity = theMaxCapacity;
 		myContext = theContext;
+		myTrackingHierarchy = theTrackingHierarchy;
 	}
 
 	@Nonnull
@@ -79,6 +80,11 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
 		return Collections.unmodifiableList(myMessages);
 	}
 
+	@Override
+	public boolean isTrackingHierarchy() {
+		return myTrackingHierarchy;
+	}
+
 	@Override
 	public void addMessage(String theMessage) {
 		if (myMessages == null) {
@@ -88,7 +94,7 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
 	}
 
 	@Override
-	public void includeConcept(String theSystem, String theCode, String theDisplay) {
+	public void includeConcept(String theSystem, String theCode, String theDisplay, Long theSourceConceptPid, String theSourceConceptDirectParentPids) {
 		if (mySkipCountRemaining > 0) {
 			mySkipCountRemaining--;
 			return;
@@ -103,7 +109,7 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
 	}
 
 	@Override
-	public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
+	public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations, Long theSourceConceptPid, String theSourceConceptDirectParentPids) {
 		if (mySkipCountRemaining > 0) {
 			mySkipCountRemaining--;
 			return;
@@ -112,6 +118,14 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
 		incrementConceptsCount();
 
 		ValueSet.ValueSetExpansionContainsComponent contains = this.addContains();
+
+		if (theSourceConceptPid != null) {
+			mySourcePidToConcept.put(theSourceConceptPid, contains);
+		}
+		if (theSourceConceptDirectParentPids != null) {
+			myConceptToSourceDirectParentPids.put(contains, theSourceConceptDirectParentPids);
+		}
+
 		setSystemAndVersion(theSystem, contains);
 		contains.setCode(theCode);
 		contains.setDisplay(theDisplay);
@@ -215,4 +229,29 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
 	public void setHardExpansionMaximumSize(int theHardExpansionMaximumSize) {
 		myHardExpansionMaximumSize = theHardExpansionMaximumSize;
 	}
+
+	public void applyHierarchy() {
+		for (int i = 0; i < this.getContains().size(); i++) {
+			ValueSet.ValueSetExpansionContainsComponent nextContains = this.getContains().get(i);
+
+			String directParentPidsString = myConceptToSourceDirectParentPids.get(nextContains);
+			if (isNotBlank(directParentPidsString)) {
+				List<Long> directParentPids = Arrays.stream(directParentPidsString.split(" ")).map(t -> Long.parseLong(t)).collect(Collectors.toList());
+
+				boolean firstMatch = false;
+				for (Long next : directParentPids) {
+					ValueSet.ValueSetExpansionContainsComponent parentConcept = mySourcePidToConcept.get(next);
+					if (parentConcept != null) {
+						if (!firstMatch) {
+							firstMatch = true;
+							this.getContains().remove(i);
+							i--;
+						}
+
+						parentConcept.addContains(nextContains);
+					}
+				}
+			}
+		}
+	}
 }

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

@@ -58,12 +58,10 @@ import java.util.Set;
  */
 public interface ITermReadSvc extends IValidationSupport {
 
-	ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull String theValueSetCanonicalUrl, @Nullable String theExpansionFilter);
+	ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull String theValueSetCanonicalUrl);
 
 	ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull ValueSet theValueSetToExpand);
 
-	ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull ValueSet theValueSetToExpand, @Nullable String theFilter);
-
 	void expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator);
 
 	/**

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.dstu2;
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
@@ -180,7 +181,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		 * Filter with display name
 		 */
 
-		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
+		expanded = myValueSetDao.expand(myExtensionalVsId, new ValueSetExpansionOptions().setFilter("systolic"), mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off
@@ -193,7 +194,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		 * Filter with code
 		 */
 
-		expanded = myValueSetDao.expand(myExtensionalVsId, ("11378"), mySrd);
+		expanded = myValueSetDao.expand(myExtensionalVsId, new ValueSetExpansionOptions().setFilter("11378"), mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off
@@ -205,7 +206,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 
 	@Test
 	public void testExpandByIdentifier() {
-		ValueSet expanded = myValueSetDao.expandByIdentifier("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", "11378");
+		ValueSet expanded = myValueSetDao.expandByIdentifier("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", new ValueSetExpansionOptions().setFilter("11378"));
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off
@@ -220,7 +221,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 	@Test
 	public void testExpandByValueSet() throws IOException {
 		ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-2.xml");
-		ValueSet expanded = myValueSetDao.expand(toExpand, "11378");
+		ValueSet expanded = myValueSetDao.expand(toExpand, new ValueSetExpansionOptions().setFilter("11378"));
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off

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

@@ -1,16 +1,17 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
-import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
 import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -18,7 +19,6 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.ValidationResult;
 import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
@@ -38,7 +38,6 @@ import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
 import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
@@ -48,21 +47,22 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
 
+import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.containsStringIgnoringCase;
 import static org.hamcrest.Matchers.empty;
 import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.hamcrest.MatcherAssert.assertThat;
 import static org.junit.jupiter.api.Assertions.fail;
 
 public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3TerminologyTest.class);
 	public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
 	public static final String URL_MY_VALUE_SET = "http://example.com/my_value_set";
-
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3TerminologyTest.class);
 	@Autowired
 	private CachingValidationSupport myCachingValidationSupport;
+	@Autowired
+	private ITermDeferredStorageSvc myTermDeferredStorageSvc;
 
 	@AfterEach
 	public void after() {
@@ -155,9 +155,6 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		myTermDeferredStorageSvc.saveAllDeferred();
 	}
 
-	@Autowired
-	private ITermDeferredStorageSvc myTermDeferredStorageSvc;
-
 	private void createExternalCsAndLocalVs() {
 		CodeSystem codeSystem = createExternalCs();
 
@@ -319,7 +316,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 
 		myValueSetDao.create(valueSet, mySrd);
 
-		ValueSet result = myValueSetDao.expand(valueSet, "");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter(""));
 		logAndValidateValueSet(result);
 
 		assertEquals(4, result.getExpansion().getTotal());
@@ -334,7 +331,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 	public void testExpandWithOpEquals() {
 
 
-		ValueSet result = myValueSetDao.expandByIdentifier("http://hl7.org/fhir/ValueSet/doc-typecodes", "");
+		ValueSet result = myValueSetDao.expandByIdentifier("http://hl7.org/fhir/ValueSet/doc-typecodes", new ValueSetExpansionOptions().setFilter(""));
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result));
 	}
 
@@ -360,7 +357,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 
 		myValueSetDao.create(valueSet, mySrd);
 
-		ValueSet result = myValueSetDao.expand(valueSet, "lab");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter("lab"));
 		logAndValidateValueSet(result);
 
 		assertEquals(1, result.getExpansion().getTotal());
@@ -390,7 +387,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 
 		myValueSetDao.create(valueSet, mySrd);
 
-		ValueSet result = myValueSetDao.expand(valueSet, "hel");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter("hel"));
 		logAndValidateValueSet(result);
 
 		assertEquals(1, result.getExpansion().getTotal());
@@ -408,7 +405,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		valueSet.getCompose().addInclude().setSystem(codeSystem.getUrl());
 		myValueSetDao.create(valueSet, mySrd);
 
-		ValueSet result = myValueSetDao.expand(valueSet, "lab");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter("lab"));
 		logAndValidateValueSet(result);
 
 		assertEquals(1, result.getExpansion().getTotal());
@@ -630,7 +627,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 			.addInclude()
 			.setSystem(codeSystem.getUrl());
 
-		ValueSet result = myValueSetDao.expand(valueSet, "");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter(""));
 		logAndValidateValueSet(result);
 
 		assertEquals(5, result.getExpansion().getTotal());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValueSetTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@@ -155,7 +156,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 		 * Filter with display name
 		 */
 
-		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
+		expanded = myValueSetDao.expand(myExtensionalVsId, new ValueSetExpansionOptions().setFilter("systolic"), mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off
@@ -169,7 +170,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 	@Test
 	@Disabled
 	public void testExpandByIdentifier() {
-		ValueSet expanded = myValueSetDao.expandByIdentifier("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", "11378");
+		ValueSet expanded = myValueSetDao.expandByIdentifier("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", new ValueSetExpansionOptions().setFilter("11378"));
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off
@@ -188,7 +189,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 	@Disabled
 	public void testExpandByValueSet() throws IOException {
 		ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
-		ValueSet expanded = myValueSetDao.expand(toExpand, "11378");
+		ValueSet expanded = myValueSetDao.expand(toExpand, new ValueSetExpansionOptions().setFilter("11378"));
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java

@@ -11,6 +11,7 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
 
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.test.utilities.docker.RequiresDocker;
 import org.hamcrest.Matchers;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -169,7 +170,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
 		ValueSet.ConceptSetComponent include = vs.getCompose().addInclude();
 		include.setSystem(URL_MY_CODE_SYSTEM);
 	
-		ValueSet result = myValueSetDao.expand(vs, "child");
+		ValueSet result = myValueSetDao.expand(vs, new ValueSetExpansionOptions().setFilter("child"));
 				
 		logAndValidateValueSet(result);
 
@@ -187,7 +188,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
 		ValueSet.ConceptSetComponent include = vs.getCompose().addInclude();
 		include.setSystem(URL_MY_CODE_SYSTEM);
 	
-		ValueSet result = myValueSetDao.expand(vs, "chi");
+		ValueSet result = myValueSetDao.expand(vs, new ValueSetExpansionOptions().setFilter("chi"));
 				
 		logAndValidateValueSet(result);
 
@@ -205,7 +206,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
 		ValueSet.ConceptSetComponent include = vs.getCompose().addInclude();
 		include.setSystem(URL_MY_CODE_SYSTEM);
 	
-		ValueSet result = myValueSetDao.expand(vs, "hil");
+		ValueSet result = myValueSetDao.expand(vs, new ValueSetExpansionOptions().setFilter("hil"));
 				
 		logAndValidateValueSet(result);
 

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
@@ -344,7 +345,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 
 		myValueSetDao.create(valueSet, mySrd);
 
-		ValueSet result = myValueSetDao.expand(valueSet, "");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter(""));
 		logAndValidateValueSet(result);
 
 		assertEquals(2, result.getExpansion().getTotal());
@@ -379,7 +380,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 
 		myValueSetDao.create(valueSet, mySrd);
 
-		ValueSet result = myValueSetDao.expand(valueSet, "");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter(""));
 		logAndValidateValueSet(result);
 
 		assertEquals(4, result.getExpansion().getTotal());
@@ -409,7 +410,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 
 		myValueSetDao.create(valueSet, mySrd);
 
-		ValueSet result = myValueSetDao.expand(valueSet, "hel");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter("hel"));
 		logAndValidateValueSet(result);
 
 		assertEquals(1, result.getExpansion().getTotal());
@@ -427,7 +428,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		valueSet.getCompose().addInclude().setSystem(codeSystem.getUrl());
 		myValueSetDao.create(valueSet, mySrd);
 
-		ValueSet result = myValueSetDao.expand(valueSet, "lab");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter("lab"));
 		logAndValidateValueSet(result);
 
 		assertEquals(1, result.getExpansion().getTotal());
@@ -457,7 +458,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 
 		myValueSetDao.create(valueSet, mySrd);
 
-		ValueSet result = myValueSetDao.expand(valueSet, "lab");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter("lab"));
 		logAndValidateValueSet(result);
 
 		assertEquals(1, result.getExpansion().getTotal());
@@ -677,7 +678,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 	public void testExpandWithOpEquals() {
 
 
-		ValueSet result = myValueSetDao.expandByIdentifier("http://hl7.org/fhir/ValueSet/doc-typecodes", "");
+		ValueSet result = myValueSetDao.expandByIdentifier("http://hl7.org/fhir/ValueSet/doc-typecodes", new ValueSetExpansionOptions().setFilter(""));
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result));
 	}
 
@@ -795,7 +796,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 			.addInclude()
 			.setSystem(codeSystem.getUrl());
 
-		ValueSet result = myValueSetDao.expand(valueSet, "");
+		ValueSet result = myValueSetDao.expand(valueSet, new ValueSetExpansionOptions().setFilter(""));
 		logAndValidateValueSet(result);
 
 		assertEquals(5, result.getExpansion().getTotal());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
@@ -258,8 +259,6 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		obs.setEffective(DateTimeType.now());
 		obs.setStatus(ObservationStatus.FINAL);
 
-		OperationOutcome oo;
-
 		// Valid code
 		obs.setValue(new Quantity().setSystem("http://cs").setCode("code1").setValue(123));
 		try {
@@ -1702,7 +1701,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 		myTermReadSvc.preExpandDeferredValueSetsToTerminologyTables();
 
-		ValueSet expansion = myValueSetDao.expand(id, null, 0, 10000, mySrd);
+		ValueSetExpansionOptions options = ValueSetExpansionOptions.forOffsetAndCount(0, 10000);
+		ValueSet expansion = myValueSetDao.expand(id, options, mySrd);
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
 
 		assertEquals(2, expansion.getExpansion().getContains().size());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValueSetTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -221,7 +222,7 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
 		 * Filter with display name
 		 */
 
-		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
+		expanded = myValueSetDao.expand(myExtensionalVsId, new ValueSetExpansionOptions().setFilter("systolic"), mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5ValueSetTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.r5;
 
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
 import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
@@ -226,7 +227,7 @@ public class FhirResourceDaoR5ValueSetTest extends BaseJpaR5Test {
 		 * Filter with display name
 		 */
 
-		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
+		expanded = myValueSetDao.expand(myExtensionalVsId, new ValueSetExpansionOptions().setFilter("systolic"), mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2ValueSetTest.java

@@ -1,21 +1,6 @@
 package ca.uhn.fhir.jpa.provider;
 
-import static org.hamcrest.Matchers.containsString;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
-import static org.hamcrest.Matchers.not;
-import static org.hamcrest.Matchers.stringContainsInOrder;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.junit.jupiter.api.Assertions.fail;
-
-import java.io.IOException;
-
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Disabled;
-import org.junit.jupiter.api.Test;
-import org.springframework.transaction.annotation.Transactional;
-
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.resource.Parameters;
 import ca.uhn.fhir.model.dstu2.resource.ValueSet;
@@ -24,12 +9,25 @@ import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.model.primitive.UriDt;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.util.TestUtil;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.io.IOException;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.stringContainsInOrder;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.fail;
 
 public class ResourceProviderDstu2ValueSetTest extends BaseResourceProviderDstu2Test {
 
-	private IIdType myExtensionalVsId;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu2ValueSetTest.class);
+	private IIdType myExtensionalVsId;
 
 	@BeforeEach
 	@Transactional
@@ -206,7 +204,7 @@ public class ResourceProviderDstu2ValueSetTest extends BaseResourceProviderDstu2
 			.execute();
 		expanded = (ValueSet) respParam.getParameter().get(0).getResource();
 
-		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
+		expanded = myValueSetDao.expand(myExtensionalVsId, new ValueSetExpansionOptions().setFilter("systolic"), mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		assertThat(resp, stringContainsInOrder(

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetNoVerCSNoVerTest.java

@@ -8,9 +8,9 @@ import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
 import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
-import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
 import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -38,6 +38,7 @@ import org.hl7.fhir.r4.model.IntegerType;
 import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.UriType;
+import org.hl7.fhir.r4.model.UrlType;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
@@ -53,12 +54,16 @@ import org.springframework.transaction.support.TransactionTemplate;
 import javax.annotation.Nonnull;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
+import java.util.List;
 import java.util.Optional;
+import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM;
 import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_VALUE_SET;
+import static ca.uhn.fhir.util.HapiExtensions.EXT_VALUESET_EXPANSION_MESSAGE;
 import static org.awaitility.Awaitility.await;
 import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.containsStringIgnoringCase;
 import static org.hamcrest.Matchers.is;
@@ -1037,6 +1042,165 @@ public class ResourceProviderR4ValueSetNoVerCSNoVerTest extends BaseResourceProv
 		testValidateCodeOperationByCodeAndSystemInstanceOnInstance();
 	}
 
+
+	@Test
+	public void testExpandUsingHierarchy_PreStored_NotPreCalculated() {
+		createLocalCs();
+		createHierarchicalVs();
+
+		myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
+
+		ValueSet expansion;
+
+		// Non-hierarchical
+		myCaptureQueriesListener.clear();
+		expansion = myClient
+			.operation()
+			.onType("ValueSet")
+			.named(JpaConstants.OPERATION_EXPAND)
+			.withParameter(Parameters.class, "url", new UrlType(URL_MY_VALUE_SET))
+			.returnResourceType(ValueSet.class)
+			.execute();
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains()), containsInAnyOrder("A", "AA", "AB", "AAA"));
+		assertEquals(19, myCaptureQueriesListener.getSelectQueries().size());
+		assertEquals("ValueSet \"ValueSet.url[http://example.com/my_value_set]\" has not yet been pre-expanded. Performing in-memory expansion without parameters. Current status: NOT_EXPANDED | The ValueSet is waiting to be picked up and pre-expanded by a scheduled task.", expansion.getMeta().getExtensionString(EXT_VALUESET_EXPANSION_MESSAGE));
+
+		// Hierarchical
+		myCaptureQueriesListener.clear();
+		expansion = myClient
+			.operation()
+			.onType("ValueSet")
+			.named(JpaConstants.OPERATION_EXPAND)
+			.withParameter(Parameters.class, "url", new UrlType(URL_MY_VALUE_SET))
+			.andParameter(JpaConstants.OPERATION_EXPAND_PARAM_INCLUDE_HIERARCHY, new BooleanType("true"))
+			.returnResourceType(ValueSet.class)
+			.execute();
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains()), containsInAnyOrder("A"));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains().get(0).getContains()), containsInAnyOrder("AA", "AB"));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains().get(0).getContains().stream().filter(t->t.getCode().equals("AA")).findFirst().orElseThrow(()->new IllegalArgumentException()).getContains()), containsInAnyOrder("AAA"));
+		assertEquals(16, myCaptureQueriesListener.getSelectQueries().size());
+
+	}
+
+	@Test
+	public void testExpandUsingHierarchy_NotPreStored() {
+		createLocalCs();
+		createHierarchicalVs();
+		myLocalVs.setUrl(null);
+
+		ValueSet expansion;
+
+		// Non-hierarchical
+		myCaptureQueriesListener.clear();
+		expansion = myClient
+			.operation()
+			.onType("ValueSet")
+			.named(JpaConstants.OPERATION_EXPAND)
+			.withParameter(Parameters.class, "valueSet", myLocalVs)
+			.returnResourceType(ValueSet.class)
+			.execute();
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains()), containsInAnyOrder("A", "AA", "AB", "AAA"));
+		assertEquals(15, myCaptureQueriesListener.getSelectQueries().size());
+		assertEquals(null, expansion.getMeta().getExtensionString(EXT_VALUESET_EXPANSION_MESSAGE));
+
+		// Hierarchical
+		myCaptureQueriesListener.clear();
+		expansion = myClient
+			.operation()
+			.onType("ValueSet")
+			.named(JpaConstants.OPERATION_EXPAND)
+			.withParameter(Parameters.class, "valueSet", myLocalVs)
+			.andParameter(JpaConstants.OPERATION_EXPAND_PARAM_INCLUDE_HIERARCHY, new BooleanType("true"))
+			.returnResourceType(ValueSet.class)
+			.execute();
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains()), containsInAnyOrder("A"));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains().get(0).getContains()), containsInAnyOrder("AA", "AB"));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains().get(0).getContains().stream().filter(t->t.getCode().equals("AA")).findFirst().orElseThrow(()->new IllegalArgumentException()).getContains()), containsInAnyOrder("AAA"));
+		assertEquals(14, myCaptureQueriesListener.getSelectQueries().size());
+
+	}
+
+	@Test
+	public void testExpandUsingHierarchy_PreStored_PreCalculated() {
+		createLocalCs();
+		createHierarchicalVs();
+
+		myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
+
+		ValueSet expansion;
+
+		myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
+
+		// Do a warm-up pass to precache anything that can be pre-cached
+		myClient
+			.operation()
+			.onType("ValueSet")
+			.named(JpaConstants.OPERATION_EXPAND)
+			.withParameter(Parameters.class, "url", new UrlType(URL_MY_VALUE_SET))
+			.returnResourceType(ValueSet.class)
+			.execute();
+
+		// Non-hierarchical
+		myCaptureQueriesListener.clear();
+		expansion = myClient
+			.operation()
+			.onType("ValueSet")
+			.named(JpaConstants.OPERATION_EXPAND)
+			.withParameter(Parameters.class, "url", new UrlType(URL_MY_VALUE_SET))
+			.returnResourceType(ValueSet.class)
+			.execute();
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains()), containsInAnyOrder("A", "AA", "AB", "AAA"));
+		assertEquals(3, myCaptureQueriesListener.getSelectQueries().size());
+		assertEquals("ValueSet was expanded using a pre-calculated expansion", expansion.getMeta().getExtensionString(EXT_VALUESET_EXPANSION_MESSAGE));
+
+		// Hierarchical
+		myCaptureQueriesListener.clear();
+		expansion = myClient
+			.operation()
+			.onType("ValueSet")
+			.named(JpaConstants.OPERATION_EXPAND)
+			.withParameter(Parameters.class, "url", new UrlType(URL_MY_VALUE_SET))
+			.andParameter(JpaConstants.OPERATION_EXPAND_PARAM_INCLUDE_HIERARCHY, new BooleanType("true"))
+			.returnResourceType(ValueSet.class)
+			.execute();
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains()), containsInAnyOrder("A"));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains().get(0).getContains()), containsInAnyOrder("AA", "AB"));
+		assertThat(toDirectCodes(expansion.getExpansion().getContains().get(0).getContains().stream().filter(t->t.getCode().equals("AA")).findFirst().orElseThrow(()->new IllegalArgumentException()).getContains()), containsInAnyOrder("AAA"));
+		assertEquals(3, myCaptureQueriesListener.getSelectQueries().size());
+
+	}
+
+	private void createHierarchicalVs() {
+		myLocalVs = new ValueSet();
+		myLocalVs.setUrl(URL_MY_VALUE_SET);
+		myLocalVs
+			.getCompose()
+			.addInclude()
+			.setSystem(URL_MY_CODE_SYSTEM)
+			.addFilter()
+			.setProperty("concept")
+			.setOp(FilterOperator.ISA)
+			.setValue("A");
+		myLocalVs
+			.getCompose()
+			.addInclude()
+			.setSystem(URL_MY_CODE_SYSTEM)
+			.addConcept()
+			.setCode("A");
+	}
+
+	public List<String> toDirectCodes(List<ValueSet.ValueSetExpansionContainsComponent> theContains) {
+		List<String> collect = theContains.stream().map(t -> t.getCode()).collect(Collectors.toList());
+		ourLog.info("Codes: {}", collect);
+		return collect;
+	}
+
 	private void testValidateCodeOperationByCodeAndSystemInstanceOnInstance() throws IOException {
 		String url = ourServerBase +
 			"/ValueSet/" + myLocalValueSetId.getIdPart() + "/$validate-code?system=" +

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

@@ -42,7 +42,7 @@ public class ValueSetConceptAccumulatorTest {
 	@Test
 	public void testIncludeConcept() {
 		for (int i = 0; i < 1000; i++) {
-			myAccumulator.includeConcept("sys", "code", "display");
+			myAccumulator.includeConcept("sys", "code", "display", null, null);
 		}
 		verify(myValueSetConceptDao, times(1000)).save(any());
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4ElasticsearchIT.java

@@ -195,7 +195,7 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest {
 		include.setSystem(CS_URL);
 
 		myTermSvc.expandValueSet(null, vs, myValueSetCodeAccumulator);
-		verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
+		verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection(), nullable(Long.class), nullable(String.class));
 	}
 
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java

@@ -7,7 +7,6 @@ import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
 import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
-import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
 import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
@@ -38,11 +37,10 @@ import java.io.IOException;
 import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
-import java.util.stream.Stream;
 
 import static org.hamcrest.CoreMatchers.containsString;
-import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.CoreMatchers.equalTo;
+import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
@@ -228,7 +226,8 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
 		// ValueSet by ID
 		{
 			myCaptureQueriesListener.clear();
-			ValueSet expandedValueSet = myValueSetDao.expand(vsId, "display value 100", 0, 1000, mySrd);
+			ValueSetExpansionOptions options = ValueSetExpansionOptions.forOffsetAndCount(0, 1000).setFilter("display value 100");
+			ValueSet expandedValueSet = myValueSetDao.expand(vsId, options, mySrd);
 			List<String> codes = expandedValueSet.getExpansion().getContains().stream().map(t -> t.getCode()).collect(Collectors.toList());
 			assertThat(codes.toString(), codes, containsInAnyOrder("code100", "code1000", "code1001", "code1002", "code1003", "code1004"));
 
@@ -953,7 +952,7 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
 		include.setSystem(CS_URL);
 
 		myTermSvc.expandValueSet(null, vs, myValueSetCodeAccumulator);
-		verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
+		verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection(), nullable(Long.class), nullable(String.class));
 	}
 
 	@Test
@@ -1433,5 +1432,4 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
 	}
 
 
-
 }

hapi-fhir-jpaserver-batch/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-cql/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -144,13 +144,13 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-test-utilities</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 			<scope>test</scope>
 		</dependency>
  </dependencies>

hapi-fhir-jpaserver-mdm/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -55,13 +55,13 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-test-utilities</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>

hapi-fhir-jpaserver-migrate/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -87,6 +87,10 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 		version.onTable("HFJ_FORCED_ID").addIndex("20210309.2", "IDX_FORCEID_FID")
 			.unique(false).withColumns("FORCED_ID");
 
+		//-- ValueSet Concept Fulltext Indexing
+		version.onTable("TRM_VALUESET_CONCEPT").addColumn("20210406.1", "INDEX_STATUS").nullable().type(ColumnTypeEnum.LONG);
+		version.onTable("TRM_VALUESET_CONCEPT").addColumn("20210406.2", "SOURCE_DIRECT_PARENT_PIDS").nullable().type(ColumnTypeEnum.CLOB);
+		version.onTable("TRM_VALUESET_CONCEPT").addColumn("20210406.3", "SOURCE_PID").nullable().type(ColumnTypeEnum.LONG);
 	}
 
 	private void init530() {

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -218,6 +218,11 @@ public class JpaConstants {
 	 */
 	public static final String DEFAULT_PARTITION_NAME = "DEFAULT";
 
+	/**
+	 * Parameter for the $expand operation
+	 */
+	public static final String OPERATION_EXPAND_PARAM_INCLUDE_HIERARCHY = "includeHierarchy";
+
 	/**
 	 * Non-instantiable
 	 */

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-subscription/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-utilities/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -164,7 +164,7 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-converter</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 		</dependency>
 
 	</dependencies>

hapi-fhir-server-mdm/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-server/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-samples</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml

@@ -5,7 +5,7 @@
    <parent>
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-deployable-pom</artifactId>
-      <version>5.4.0-PRE4-SNAPSHOT</version>
+      <version>5.4.0-PRE5-SNAPSHOT</version>
       <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
    </parent>
 

hapi-fhir-spring-boot/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-dstu2.1/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-dstu2/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-dstu3/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-hl7org-dstu2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-r4/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-test-utilities/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-testpage-overlay/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-validation-resources-dstu2.1/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-validation-resources-dstu2/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-validation-resources-dstu3/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-validation-resources-r4/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-validation-resources-r5/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-validation/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-tinder-plugin/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -58,37 +58,37 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu3</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-r4</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-r5</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-validation-resources-r4</artifactId>
-			<version>5.4.0-PRE4-SNAPSHOT</version>
+			<version>5.4.0-PRE5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.velocity</groupId>

hapi-tinder-test/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

pom.xml

@@ -6,7 +6,7 @@
 	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir</artifactId>
 	<packaging>pom</packaging>
-	<version>5.4.0-PRE4-SNAPSHOT</version>
+	<version>5.4.0-PRE5-SNAPSHOT</version>
 	<name>HAPI-FHIR</name>
 	<description>An open-source implementation of the FHIR specification in Java.</description>
 	<url>https://hapifhir.io</url>

restful-server-example/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 	

tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 

tests/hapi-fhir-base-test-mindeps-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.4.0-PRE4-SNAPSHOT</version>
+		<version>5.4.0-PRE5-SNAPSHOT</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>