Initial changes to support multiple versions for code system.

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

@@ -183,6 +183,24 @@ public interface IValidationSupport {
 		return null;
 	}
 
+	/**
+	 * Validates that the given code exists and if possible returns a display
+	 * name. This method is called to check codes which are found in "example"
+	 * binding fields (e.g. <code>Observation.code</code> in the default profile.
+	 *
+	 * @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
+	 *                                 other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
+	 * @param theOptions               Provides options controlling the validation
+	 * @param theCodeSystem            The code system, e.g. "<code>http://loinc.org</code>"
+	 * @param theCode                  The code, e.g. "<code>1234-5</code>"
+	 * @param theDisplay               The display name, if it should also be validated
+	 * @param theSystemVersion         The code system version.
+	 * @return Returns a validation result object
+	 */
+	default CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl, String theSystemVersion) {
+		return null;
+	}
+
 	/**
 	 * Validates that the given code exists and if possible returns a display
 	 * name. This method is called to check codes which are found in "example"
@@ -212,6 +230,19 @@ public interface IValidationSupport {
 		return null;
 	}
 
+	/**
+	 * Look up a code using the system, system version and code value
+	 *
+	 * @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
+	 *                                 other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
+	 * @param theSystem                The CodeSystem URL
+	 * @param theCode                  The code
+	 * @param theSystemVersion         The CodeSystem version
+	 */
+	default LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theSystemVersion) {
+		return null;
+	}
+
 	/**
 	 * Returns <code>true</code> if the given valueset can be validated by the given
 	 * validation support module

hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java

@@ -227,6 +227,11 @@ public class DaoConfig {
 	 */
 	private boolean myPreloadBlobFromInputStream = false;
 
+	/**
+	 * @since 5.1.0
+	 */
+	private boolean myMultipleCodeSystemVersionsEnabled = false;
+
 	/**
 	 * Constructor
 	 */
@@ -2126,4 +2131,34 @@ public class DaoConfig {
 		myPreloadBlobFromInputStream = thePreloadBlobFromInputStream;
 	}
 
+	/**
+	 * <p>
+	 * This determines whether multiple code system versions will be enabled. If not enabled, existing code systems will be
+	 * deleted when a new version is uploaded.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code false}.
+	 * </p>
+	 *
+	 * @since 5.1.0
+	 */
+	public boolean isMultipleCodeSystemVersionsEnabled() {
+		return myMultipleCodeSystemVersionsEnabled;
+	}
+
+	/**
+	 * <p>
+	 * This determines whether multiple code system versions will be enabled. If not enabled, existing code systems will be
+	 * deleted when a new version is uploaded.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code false}.
+	 * </p>
+	 *
+	 * @since 5.1.0
+	 */
+	public void setMultipleCodeSystemVersionsEnabled(Boolean theMultipleCodeSystemVersionsEnabled) {
+		myMultipleCodeSystemVersionsEnabled = theMultipleCodeSystemVersionsEnabled;
+	}
+
 }

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

@@ -42,6 +42,11 @@ public interface IFhirResourceDaoCodeSystem<T extends IBaseResource, CD, CC> ext
 
 	SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, CD theCodingA, CD theCodingB, RequestDetails theRequestDetails);
 
+	@Nonnull
+	IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CD theCoding, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails);
+
+	SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, CD theCodingA, CD theCodingB, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails);
+
 	class SubsumesResult {
 
 		private final ConceptSubsumptionOutcome myOutcome;

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

@@ -48,6 +48,7 @@ import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.jetbrains.annotations.NotNull;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 
@@ -235,6 +236,12 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 		return null;
 	}
 
+	@NotNull
+	@Override
+	public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CodingDt theCoding, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
+		throw new UnsupportedOperationException();
+	}
+
 	@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());
@@ -280,6 +287,11 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 		return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB);
 	}
 
+	@Override
+	public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, CodingDt theCodingA, CodingDt theCodingB, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
+		throw new UnsupportedOperationException();
+	}
+
 	@Override
 	@PostConstruct
 	public void postConstruct() {

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

@@ -35,9 +35,19 @@ public interface ITermCodeSystemVersionDao extends JpaRepository<TermCodeSystemV
 	@Query("DELETE FROM TermCodeSystemVersion csv WHERE csv.myCodeSystem = :cs")
 	void deleteForCodeSystem(@Param("cs") TermCodeSystem theCodeSystem);
 
+	@Modifying
+	@Query("DELETE FROM TermCodeSystemVersion csv WHERE csv.myId = :pid")
+	void delete(@Param("pid") Long codesystemversion_pid);
+
 	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemPid = :codesystem_pid")
 	List<TermCodeSystemVersion> findByCodeSystemPid(@Param("codesystem_pid") Long theCodeSystemPid);
 
+	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemPid = :codesystem_pid AND cs.myCodeSystemVersionId = :codesystem_version_id")
+	TermCodeSystemVersion findByCodeSystemPidAndVersion(@Param("codesystem_pid") Long theCodeSystemPid, @Param("codesystem_version_id") String theCodeSystemVersionId);
+
+	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemPid = :codesystem_pid AND cs.myCodeSystemVersionId IS NULL")
+	TermCodeSystemVersion findByCodeSystemPidVersionIsNull(@Param("codesystem_pid") Long theCodeSystemPid);
+
 	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResourcePid = :resource_id")
 	List<TermCodeSystemVersion> findByCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);
 

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

@@ -44,6 +44,7 @@ import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.jetbrains.annotations.NotNull;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
@@ -86,9 +87,15 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 		return valueSetIds;
 	}
 
-	@Nonnull
+	@NotNull
 	@Override
 	public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
+		return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
+	}
+
+	@Nonnull
+	@Override
+	public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
 		boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
 		boolean haveCode = theCode != null && theCode.isEmpty() == false;
 		boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
@@ -109,12 +116,16 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 			code = theCode.getValue();
 			system = theSystem.getValue();
 		}
+		String codeSystemVersion = null;
+		if (theVersion != null) {
+			codeSystemVersion = theVersion.getValue();
+		}
 
-		ourLog.debug("Looking up {} / {}", system, code);
+		ourLog.info("Looking up {} / {}, version {}", system, code, codeSystemVersion);
 
 		if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
 			ourLog.debug("Code system {} is supported", system);
-			IValidationSupport.LookupCodeResult result = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
+			IValidationSupport.LookupCodeResult result = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code, codeSystemVersion);
 			if (result != null) {
 				return result;
 			}
@@ -124,6 +135,11 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 		return IValidationSupport.LookupCodeResult.notFound(system, code);
 	}
 
+	@Override
+	public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
+		return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion);
+	}
+
 	@Override
 	public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, RequestDetails theRequestDetails) {
 		return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB);

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

@@ -44,6 +44,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
+import org.jetbrains.annotations.NotNull;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
@@ -81,9 +82,15 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 		return valueSetIds;
 	}
 
-	@Nonnull
+	@NotNull
 	@Override
 	public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
+		return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
+	}
+
+	@Nonnull
+	@Override
+	public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
 		boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
 		boolean haveCode = theCode != null && theCode.isEmpty() == false;
 		boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
@@ -104,13 +111,17 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 			code = theCode.getValue();
 			system = theSystem.getValue();
 		}
+		String codeSystemVersion = null;
+		if (theVersion != null) {
+			codeSystemVersion = theVersion.getValue();
+		}
 
-		ourLog.debug("Looking up {} / {}", system, code);
+		ourLog.info("Looking up {} / {}, version {}", system, code, codeSystemVersion);
 
 		if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
 
 			ourLog.debug("Code system {} is supported", system);
-			IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
+			IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code, codeSystemVersion);
 			if (retVal != null) {
 				return retVal;
 			}
@@ -122,6 +133,11 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 
 	}
 
+	@Override
+	public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
+		return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion);
+	}
+
 	@Override
 	public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, RequestDetails theRequestDetails) {
 		return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB);

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

@@ -113,14 +113,17 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
 		ValueSet source = new ValueSet();
 		source.setUrl(theUri);
 
-		source.getCompose().addInclude().addValueSet(theUri);
+//		source.getCompose().addInclude().addValueSet(theUri);
 
 		if (isNotBlank(theFilter)) {
-			ConceptSetComponent include = source.getCompose().addInclude();
+//			ConceptSetComponent include = source.getCompose().addInclude();
-			ConceptSetFilterComponent filter = include.addFilter();
+//			ConceptSetFilterComponent filter = include.addFilter();
+			ConceptSetFilterComponent filter = source.getCompose().addInclude().addValueSet(theUri).addFilter();
 			filter.setProperty("display");
 			filter.setOp(FilterOperator.EQUAL);
 			filter.setValue(theFilter);
+		} else {
+			source.getCompose().addInclude().addValueSet(theUri);
 		}
 
 		ValueSet retVal = doExpand(source);
@@ -148,14 +151,17 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
 		ValueSet source = new ValueSet();
 		source.setUrl(theUri);
 
-		source.getCompose().addInclude().addValueSet(theUri);
+//		source.getCompose().addInclude().addValueSet(theUri);
 
 		if (isNotBlank(theFilter)) {
-			ConceptSetComponent include = source.getCompose().addInclude();
+//			ConceptSetComponent include = source.getCompose().addInclude();
-			ConceptSetFilterComponent filter = include.addFilter();
+//			ConceptSetFilterComponent filter = include.addFilter();
+			ConceptSetFilterComponent filter = source.getCompose().addInclude().addValueSet(theUri).addFilter();
 			filter.setProperty("display");
 			filter.setOp(FilterOperator.EQUAL);
 			filter.setValue(theFilter);
+		} else {
+			source.getCompose().addInclude().addValueSet(theUri);
 		}
 
 		ValueSet retVal = doExpand(source, theOffset, theCount);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java

@@ -45,6 +45,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r5.model.CodeSystem;
 import org.hl7.fhir.r5.model.CodeableConcept;
 import org.hl7.fhir.r5.model.Coding;
+import org.jetbrains.annotations.NotNull;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
@@ -83,9 +84,15 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 		return valueSetIds;
 	}
 
-	@Nonnull
+	@NotNull
 	@Override
 	public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
+		return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
+	}
+
+	@Nonnull
+	@Override
+	public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
 		boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
 		boolean haveCode = theCode != null && theCode.isEmpty() == false;
 		boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
@@ -106,13 +113,17 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 			code = theCode.getValue();
 			system = theSystem.getValue();
 		}
+		String codeSystemVersion = null;
+		if (theVersion != null) {
+			codeSystemVersion = theVersion.getValue();
+		}
 
-		ourLog.info("Looking up {} / {}", system, code);
+		ourLog.info("Looking up {} / {}, version {}", system, code, codeSystemVersion);
 
 		if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
 
 			ourLog.info("Code system {} is supported", system);
-			IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
+			IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code, codeSystemVersion);
 			if (retVal != null) {
 				return retVal;
 			}
@@ -124,6 +135,11 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 
 	}
 
+	@Override
+	public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
+		return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion);
+	}
+
 	@Override
 	public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, RequestDetails theRequestDetails) {
 		return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB);

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

@@ -40,17 +40,21 @@ import javax.persistence.OneToMany;
 import javax.persistence.OneToOne;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
 
 import static org.apache.commons.lang3.StringUtils.length;
 
-@Table(name = "TRM_CODESYSTEM_VER"
+@Table(name = "TRM_CODESYSTEM_VER",
 	// Note, we used to have a constraint named IDX_CSV_RESOURCEPID_AND_VER (don't reuse this)
-)
+	uniqueConstraints = {
+	@UniqueConstraint(name = TermCodeSystemVersion.IDX_CODESYSTEM_AND_VER, columnNames = {"CODESYSTEM_PID", "CS_VERSION_ID"})
+})
 @Entity()
 public class TermCodeSystemVersion implements Serializable {
+	public static final String IDX_CODESYSTEM_AND_VER = "IDX_CODESYSTEM_AND_VER";
 	public static final int MAX_VERSION_LENGTH = 200;
 	private static final long serialVersionUID = 1L;
 	@OneToMany(fetch = FetchType.LAZY, mappedBy = "myCodeSystem")

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

@@ -53,6 +53,7 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
 		@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
 		@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
 		@OperationParam(name = "coding", min = 0, max = 1) Coding theCoding,
+		@OperationParam(name="version", min=0, max=1) StringType theVersion,
 		@OperationParam(name = "property", min = 0, max = OperationParam.MAX_UNLIMITED) List<CodeType> theProperties,
 		RequestDetails theRequestDetails
 	) {
@@ -60,7 +61,7 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
-			IValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
+			IValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theVersion, theRequestDetails);
 			result.throwNotFoundIfAppropriate();
 			return (Parameters) result.toParameters(theRequestDetails.getFhirContext(), theProperties);
 		} catch (FHIRException e) {

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

@@ -55,6 +55,7 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
 			@OperationParam(name="code", min=0, max=1) CodeType theCode, 
 			@OperationParam(name="system", min=0, max=1) UriType theSystem,
 			@OperationParam(name="coding", min=0, max=1) Coding theCoding,
+			@OperationParam(name="version", min=0, max=1) StringType theVersion,
 			@OperationParam(name = "property", min = 0, max = OperationParam.MAX_UNLIMITED) List<CodeType> theProperties,
 			RequestDetails theRequestDetails
 			) {
@@ -62,7 +63,7 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
-			IValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
+			IValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theVersion, theRequestDetails);
 			result.throwNotFoundIfAppropriate();
 			return (Parameters) result.toParameters(theRequestDetails.getFhirContext(), theProperties);
 		} finally {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderCodeSystemR5.java

@@ -55,6 +55,7 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
 			@OperationParam(name="code", min=0, max=1) CodeType theCode, 
 			@OperationParam(name="system", min=0, max=1) UriType theSystem,
 			@OperationParam(name="coding", min=0, max=1) Coding theCoding,
+			@OperationParam(name="version", min=0, max=1) org.hl7.fhir.r4.model.StringType theVersion,
 			@OperationParam(name = "property", min = 0, max = OperationParam.MAX_UNLIMITED) List<CodeType> theProperties,
 			RequestDetails theRequestDetails
 			) {
@@ -62,7 +63,7 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
-			IValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
+			IValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theVersion, theRequestDetails);
 			result.throwNotFoundIfAppropriate();
 			return (Parameters) result.toParameters(theRequestDetails.getFhirContext(), theProperties);
 		} finally {

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

@@ -244,7 +244,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 	@Override
 	public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
-		TermCodeSystemVersion cs = getCurrentCodeSystemVersion(theSystem);
+		TermCodeSystemVersion cs = getCurrentCodeSystemVersionForVersion(theSystem,null);
 		return cs != null;
 	}
 
@@ -616,6 +616,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	private Boolean expandValueSetHandleIncludeOrExclude(@Nullable ValueSetExpansionOptions theExpansionOptions, IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theIncludeOrExclude, boolean theAdd, AtomicInteger theCodeCounter, int theQueryIndex, VersionIndependentConcept theWantConceptOrNull) {
 
 		String system = theIncludeOrExclude.getSystem();
+		String systemVersion = theIncludeOrExclude.getVersion();
 		boolean hasSystem = isNotBlank(system);
 		boolean hasValueSet = theIncludeOrExclude.getValueSet().size() > 0;
 
@@ -630,7 +631,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 			TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
 			if (cs != null) {
 
-				return expandValueSetHandleIncludeOrExcludeUsingDatabase(theValueSetCodeAccumulator, theAddedCodes, theIncludeOrExclude, theAdd, theCodeCounter, theQueryIndex, theWantConceptOrNull, system, cs);
+				return expandValueSetHandleIncludeOrExcludeUsingDatabase(theValueSetCodeAccumulator, theAddedCodes, theIncludeOrExclude, theAdd, theCodeCounter, theQueryIndex, theWantConceptOrNull, system, cs, systemVersion);
 
 			} else {
 
@@ -671,7 +672,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 								nextSystem = system;
 							}
 
-							LookupCodeResult lookup = myValidationSupport.lookupCode(new ValidationSupportContext(provideValidationSupport()), nextSystem, next.getCode());
+							LookupCodeResult lookup = myValidationSupport.lookupCode(new ValidationSupportContext(provideValidationSupport()), nextSystem, next.getCode(), systemVersion);
 							if (lookup != null && lookup.isFound()) {
 								addOrRemoveCode(theValueSetCodeAccumulator, theAddedCodes, theAdd, nextSystem, next.getCode(), lookup.getCodeDisplay());
 								foundCount++;
@@ -765,7 +766,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	@Nonnull
-	private Boolean expandValueSetHandleIncludeOrExcludeUsingDatabase(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theIncludeOrExclude, boolean theAdd, AtomicInteger theCodeCounter, int theQueryIndex, VersionIndependentConcept theWantConceptOrNull, String theSystem, TermCodeSystem theCs) {
+	private Boolean expandValueSetHandleIncludeOrExcludeUsingDatabase(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theIncludeOrExclude, boolean theAdd, AtomicInteger theCodeCounter, int theQueryIndex, VersionIndependentConcept theWantConceptOrNull, String theSystem, TermCodeSystem theCs, String theSystemVersion) {
 		TermCodeSystemVersion csv = theCs.getCurrentVersion();
 		FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
 
@@ -793,7 +794,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		/*
 		 * Filters
 		 */
-		handleFilters(bool, theSystem, qb, theIncludeOrExclude);
+		handleFilters(bool, theSystem, qb, theIncludeOrExclude, theSystemVersion);
 
 		Query luceneQuery = bool.createQuery();
 
@@ -902,15 +903,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		}
 	}
 
-	private void handleFilters(BooleanJunction<?> theBool, String theSystem, QueryBuilder theQb, ValueSet.ConceptSetComponent theIncludeOrExclude) {
+	private void handleFilters(BooleanJunction<?> theBool, String theSystem, QueryBuilder theQb, ValueSet.ConceptSetComponent theIncludeOrExclude, String theSystemVersion) {
 		if (theIncludeOrExclude.getFilter().size() > 0) {
 			for (ValueSet.ConceptSetFilterComponent nextFilter : theIncludeOrExclude.getFilter()) {
-				handleFilter(theSystem, theQb, theBool, nextFilter);
+				handleFilter(theSystem, theQb, theBool, nextFilter, theSystemVersion);
 			}
 		}
 	}
 
-	private void handleFilter(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void handleFilter(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
 		if (isBlank(theFilter.getValue()) && theFilter.getOp() == null && isBlank(theFilter.getProperty())) {
 			return;
 		}
@@ -926,7 +927,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 				break;
 			case "concept":
 			case "code":
-				handleFilterConceptAndCode(theSystem, theQb, theBool, theFilter);
+				handleFilterConceptAndCode(theSystem, theQb, theBool, theFilter, theSystemVersion);
 				break;
 			case "parent":
 			case "child":
@@ -935,11 +936,11 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 				break;
 			case "ancestor":
 				isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
-				handleFilterLoincAncestor(theSystem, theQb, theBool, theFilter);
+				handleFilterLoincAncestor(theSystem, theQb, theBool, theFilter, theSystemVersion);
 				break;
 			case "descendant":
 				isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
-				handleFilterLoincDescendant(theSystem, theQb, theBool, theFilter);
+				handleFilterLoincDescendant(theSystem, theQb, theBool, theFilter, theSystemVersion);
 				break;
 			case "copyright":
 				isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
@@ -990,8 +991,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		bool.must(textQuery);
 	}
 
-	private void handleFilterConceptAndCode(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void handleFilterConceptAndCode(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
-		TermConcept code = findCode(theSystem, theFilter.getValue())
+		TermConcept code = findCode(theSystem, theFilter.getValue(), theSystemVersion)
 			.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theFilter.getValue()));
 
 		if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
@@ -1036,41 +1037,41 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
-	private void handleFilterLoincAncestor(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void handleFilterLoincAncestor(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
 		switch (theFilter.getOp()) {
 			case EQUAL:
-				addLoincFilterAncestorEqual(theSystem, theQb, theBool, theFilter);
+				addLoincFilterAncestorEqual(theSystem, theQb, theBool, theFilter, theSystemVersion);
 				break;
 			case IN:
-				addLoincFilterAncestorIn(theSystem, theQb, theBool, theFilter);
+				addLoincFilterAncestorIn(theSystem, theQb, theBool, theFilter, theSystemVersion);
 				break;
 			default:
 				throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
 		}
 	}
 
-	private void addLoincFilterAncestorEqual(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void addLoincFilterAncestorEqual(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
-		addLoincFilterAncestorEqual(theSystem, theQb, theBool, theFilter.getProperty(), theFilter.getValue());
+		addLoincFilterAncestorEqual(theSystem, theQb, theBool, theFilter.getProperty(), theFilter.getValue(), theSystemVersion);
 	}
 
-	private void addLoincFilterAncestorEqual(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, String theProperty, String theValue) {
+	private void addLoincFilterAncestorEqual(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, String theProperty, String theValue, String theSystemVersion) {
-		List<Term> terms = getAncestorTerms(theSystem, theProperty, theValue);
+		List<Term> terms = getAncestorTerms(theSystem, theProperty, theValue, theSystemVersion);
 		theBool.must(new TermsQuery(terms));
 	}
 
-	private void addLoincFilterAncestorIn(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void addLoincFilterAncestorIn(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
 		String[] values = theFilter.getValue().split(",");
 		List<Term> terms = new ArrayList<>();
 		for (String value : values) {
-			terms.addAll(getAncestorTerms(theSystem, theFilter.getProperty(), value));
+			terms.addAll(getAncestorTerms(theSystem, theFilter.getProperty(), value, theSystemVersion));
 		}
 		theBool.must(new TermsQuery(terms));
 	}
 
-	private List<Term> getAncestorTerms(String theSystem, String theProperty, String theValue) {
+	private List<Term> getAncestorTerms(String theSystem, String theProperty, String theValue, String theSystemVersion) {
 		List<Term> retVal = new ArrayList<>();
 
-		TermConcept code = findCode(theSystem, theValue)
+		TermConcept code = findCode(theSystem, theValue, theSystemVersion)
 			.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));
 
 		retVal.add(new Term("myParentPids", "" + code.getId()));
@@ -1080,41 +1081,41 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
-	private void handleFilterLoincDescendant(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void handleFilterLoincDescendant(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
 		switch (theFilter.getOp()) {
 			case EQUAL:
-				addLoincFilterDescendantEqual(theSystem, theBool, theFilter);
+				addLoincFilterDescendantEqual(theSystem, theBool, theFilter, theSystemVersion);
 				break;
 			case IN:
-				addLoincFilterDescendantIn(theSystem, theQb, theBool, theFilter);
+				addLoincFilterDescendantIn(theSystem, theQb, theBool, theFilter, theSystemVersion);
 				break;
 			default:
 				throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
 		}
 	}
 
-	private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
-		addLoincFilterDescendantEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue());
+		addLoincFilterDescendantEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue(), theSystemVersion);
 	}
 
-	private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, String theProperty, String theValue) {
+	private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, String theProperty, String theValue, String theSystemVersion) {
-		List<Term> terms = getDescendantTerms(theSystem, theProperty, theValue);
+		List<Term> terms = getDescendantTerms(theSystem, theProperty, theValue, theSystemVersion);
 		theBool.must(new TermsQuery(terms));
 	}
 
-	private void addLoincFilterDescendantIn(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void addLoincFilterDescendantIn(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
 		String[] values = theFilter.getValue().split(",");
 		List<Term> terms = new ArrayList<>();
 		for (String value : values) {
-			terms.addAll(getDescendantTerms(theSystem, theFilter.getProperty(), value));
+			terms.addAll(getDescendantTerms(theSystem, theFilter.getProperty(), value, theSystemVersion));
 		}
 		theBool.must(new TermsQuery(terms));
 	}
 
-	private List<Term> getDescendantTerms(String theSystem, String theProperty, String theValue) {
+	private List<Term> getDescendantTerms(String theSystem, String theProperty, String theValue, String theSystemVersion) {
 		List<Term> retVal = new ArrayList<>();
 
-		TermConcept code = findCode(theSystem, theValue)
+		TermConcept code = findCode(theSystem, theValue, theSystemVersion)
 			.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));
 
 		String[] parentPids = code.getParentPidsAsString().split(" ");
@@ -1363,6 +1364,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 	@Override
 	public Optional<TermConcept> findCode(String theCodeSystem, String theCode) {
+		return findCode(theCodeSystem, theCode, null);
+
+	}
+
+	@Override
+	public Optional<TermConcept> findCode(String theCodeSystem, String theCode, String theVersion) {
 		/*
 		 * Loading concepts without a transaction causes issues later on some
 		 * platforms (e.g. PSQL) so this transactiontemplate is here to make
@@ -1371,7 +1378,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
 		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_MANDATORY);
 		return txTemplate.execute(t -> {
-			TermCodeSystemVersion csv = getCurrentCodeSystemVersion(theCodeSystem);
+			TermCodeSystemVersion csv = getCurrentCodeSystemVersionForVersion(theCodeSystem, theVersion);
 			if (csv == null) {
 				return null;
 			}
@@ -1380,13 +1387,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	@Nullable
-	private TermCodeSystemVersion getCurrentCodeSystemVersion(String theUri) {
+	private TermCodeSystemVersion getCurrentCodeSystemVersionForVersion(String theUri, String theVersion) {
-		TermCodeSystemVersion retVal = myCodeSystemCurrentVersionCache.get(theUri, uri -> myTxTemplate.execute(tx -> {
+		StringBuffer key = new StringBuffer(theUri);
+		if (theVersion != null) {
+			key.append("_").append(theVersion);
+		}
+		TermCodeSystemVersion retVal = myCodeSystemCurrentVersionCache.get(key.toString(), uri -> myTxTemplate.execute(tx -> {
 			TermCodeSystemVersion csv = null;
 			TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(uri);
-			if (cs != null && cs.getCurrentVersion() != null) {
+			if (cs != null) {
+				if (theVersion != null) {
+					csv = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(cs.getPid(), theVersion);
+				} else if (cs.getCurrentVersion() != null) {
 					csv = cs.getCurrentVersion();
 				}
+			}
 			if (csv != null) {
 				return csv;
 			} else {
@@ -1804,19 +1819,28 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	@Override
-	@Transactional
 	public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {
+		return subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, null);
+	}
+
+	@Override
+	@Transactional
+	public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB, IPrimitiveType<String> theSystemVersion) {
 		VersionIndependentConcept conceptA = toConcept(theCodeA, theSystem, theCodingA);
 		VersionIndependentConcept conceptB = toConcept(theCodeB, theSystem, theCodingB);
+		String systemVersion = null;
+		if (theSystemVersion != null) {
+			systemVersion = theSystemVersion.getValue();
+		}
 
 		if (!StringUtils.equals(conceptA.getSystem(), conceptB.getSystem())) {
 			throw new InvalidRequestException("Unable to test subsumption across different code systems");
 		}
 
-		TermConcept codeA = findCode(conceptA.getSystem(), conceptA.getCode())
+		TermConcept codeA = findCode(conceptA.getSystem(), conceptA.getCode(), systemVersion)
 			.orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptA));
 
-		TermConcept codeB = findCode(conceptB.getSystem(), conceptB.getCode())
+		TermConcept codeB = findCode(conceptB.getSystem(), conceptB.getCode(), systemVersion)
 			.orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptB));
 
 		FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
@@ -1835,10 +1859,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 	protected abstract ValueSet toCanonicalValueSet(IBaseResource theValueSet);
 
-	protected IValidationSupport.LookupCodeResult lookupCode(String theSystem, String theCode) {
+	protected IValidationSupport.LookupCodeResult lookupCode(String theSystem, String theCode, String theVersion) {
 		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
 		return txTemplate.execute(t -> {
-			Optional<TermConcept> codeOpt = findCode(theSystem, theCode);
+			Optional<TermConcept> codeOpt = findCode(theSystem, theCode, theVersion);
 			if (codeOpt.isPresent()) {
 				TermConcept code = codeOpt.get();
 
@@ -2107,10 +2131,14 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		return null;
 	}
 
-
 	@CoverageIgnore
 	@Override
 	public IValidationSupport.CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
+		return validateCode(theValidationSupportContext, theOptions, theCodeSystem, theCode, theDisplay, theValueSetUrl, null);
+	}
+
+	@Override
+	public IValidationSupport.CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl, String theSystemVersion) {
 		invokeRunnableForUnitTest();
 
 		if (isNotBlank(theValueSetUrl)) {
@@ -2119,7 +2147,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
 		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
-		Optional<VersionIndependentConcept> codeOpt = txTemplate.execute(t -> findCode(theCodeSystem, theCode).map(c -> new VersionIndependentConcept(theCodeSystem, c.getCode())));
+		Optional<VersionIndependentConcept> codeOpt = txTemplate.execute(t -> findCode(theCodeSystem, theCode, theSystemVersion).map(c -> new VersionIndependentConcept(theCodeSystem, c.getCode())));
 
 		if (codeOpt != null && codeOpt.isPresent()) {
 			VersionIndependentConcept code = codeOpt.get();

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

@@ -284,18 +284,21 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 				ResourcePersistentId codeSystemResourcePid = getCodeSystemResourcePid(theCodeSystem.getIdElement());
 
 				/*
-				 * If this is a not-present codesystem, we don't want to store a new version if one
+				 * If this is a not-present codesystem and codesystem version already exists, we don't want to
-				 * already exists, since that will wipe out the existing concepts. We do create or update
+				 * overwrite the existing version since that will wipe out the existing concepts. We do create
-				 * the TermCodeSystem table though, since that allows the DB to reject changes
+				 * or update the TermCodeSystem table though, since that allows the DB to reject changes that would
-				 * that would result in duplicate CodeSysten.url values.
+				 * result in duplicate CodeSystem.url values.
 				 */
 				if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
-					TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theCodeSystem.getUrl());
+					TermCodeSystem termCodeSystem = myCodeSystemDao.findByCodeSystemUri(theCodeSystem.getUrl());
-					if (codeSystem != null) {
+					if (termCodeSystem != null) {
+						TermCodeSystemVersion codeSystemVersion = getExistingTermCodeSystemVersion(termCodeSystem.getPid(), theCodeSystem.getVersion());
+						if (codeSystemVersion != null) {
 							getOrCreateTermCodeSystem(codeSystemResourcePid, theCodeSystem.getUrl(), theCodeSystem.getUrl(), theResourceEntity);
 							return;
 						}
 					}
+				}
 
 				TermCodeSystemVersion persCs = new TermCodeSystemVersion();
 
@@ -338,22 +341,23 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		ValidateUtil.isTrueOrThrowInvalidRequest(theCodeSystemVersion.getResource() != null, "No resource supplied");
 		ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
 
-		// Grab the existing versions so we can delete them later
+		// Grab the existing version so we can delete it
-		List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourcePid.getIdAsLong());
+		TermCodeSystem existingCodeSystem = myCodeSystemDao.findByCodeSystemUri(theSystemUri);
-
+		TermCodeSystemVersion existing = null;
-		/*
+		if (existingCodeSystem != null) {
-		 * For now we always delete old versions. At some point it would be nice to allow configuration to keep old versions.
+			existing = getExistingTermCodeSystemVersion(existingCodeSystem.getPid(), theSystemVersionId);
-		 */
-
-		for (TermCodeSystemVersion next : existing) {
-			ourLog.info("Deleting old code system version {}", next.getPid());
-			Long codeSystemVersionPid = next.getPid();
-			deleteCodeSystemVersion(codeSystemVersionPid);
 		}
 
-		ourLog.debug("Flushing...");
+		/*
-		myConceptDao.flush();
+		 * Delete version being replaced.
-		ourLog.debug("Done flushing");
+		 */
+
+		if(existing != null) {
+			ourLog.info("Deleting old code system version {}", existing.getPid());
+			Long codeSystemVersionPid = existing.getPid();
+			deleteCodeSystemVersion(codeSystemVersionPid);
+
+		}
 
 		/*
 		 * Do the upload
@@ -408,6 +412,17 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		}
 	}
 
+	private TermCodeSystemVersion getExistingTermCodeSystemVersion(Long theCodeSystemVersionPid, String theCodeSystemVersion) {
+		TermCodeSystemVersion existing;
+		if (theCodeSystemVersion == null) {
+			existing = myCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(theCodeSystemVersionPid);
+		} else {
+			existing = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(theCodeSystemVersionPid, theCodeSystemVersion);
+		}
+
+		return existing;
+	}
+
 	private void deleteCodeSystemVersion(final Long theCodeSystemVersionPid) {
 		ourLog.info(" * Deleting code system version {}", theCodeSystemVersionPid);
 
@@ -457,8 +472,11 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 				myCodeSystemDao.save(codeSystem);
 			}
 
+			myConceptDao.flush();
+
 			ourLog.info(" * Deleting code system version");
-			myCodeSystemVersionDao.deleteById(theCodeSystemVersionPid);
+			myCodeSystemVersionDao.delete(theCodeSystemVersionPid);
+			myCodeSystemVersionDao.flush();
 		});
 
 	}

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

@@ -378,6 +378,10 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
 		try {
 			String loincCsString = IOUtils.toString(BaseTermReadSvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/loinc/loinc.xml"), Charsets.UTF_8);
 			loincCs = FhirContext.forR4().newXmlParser().parseResource(CodeSystem.class, loincCsString);
+			String  codeSystemVersionId = theUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
+			if (codeSystemVersionId != null) {
+				loincCs.setVersion(codeSystemVersionId);
+			}
 		} catch (IOException e) {
 			throw new InternalErrorException("Failed to load loinc.xml", e);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java

@@ -149,7 +149,12 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
 
 	@Override
 	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
-		return super.lookupCode(theSystem, theCode);
+		return super.lookupCode(theSystem, theCode, null);
+	}
+
+	@Override
+	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
+		return super.lookupCode(theSystem, theCode, theVersion);
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR4.java

@@ -89,9 +89,14 @@ public class TermReadSvcR4 extends BaseTermReadSvcImpl implements ITermReadSvcR4
 		return (CodeSystem) theCodeSystem;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
+		return super.lookupCode(theSystem, theCode, theVersion);
+	}
+
 	@Override
 	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
-		return super.lookupCode(theSystem, theCode);
+		return super.lookupCode(theSystem, theCode, null);
 	}
 
 	@Override

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

@@ -73,6 +73,8 @@ public interface ITermReadSvc extends IValidationSupport {
 
 	List<VersionIndependentConcept> expandValueSet(ValueSetExpansionOptions theExpansionOptions, String theValueSet);
 
+	Optional<TermConcept> findCode(String theCodeSystem, String theCode, String theVersion);
+
 	Optional<TermConcept> findCode(String theCodeSystem, String theCode);
 
 	Set<TermConcept> findCodesAbove(Long theCodeSystemResourcePid, Long theCodeSystemResourceVersionPid, String theCode);
@@ -103,6 +105,8 @@ public interface ITermReadSvc extends IValidationSupport {
 
 	IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB);
 
+	IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB, IPrimitiveType<String> theSystemVersion);
+
 	void preExpandDeferredValueSetsToTerminologyTables();
 
 	/**

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

@@ -96,6 +96,9 @@ public enum LoincUploadPropertiesEnum {
 	/*
 	 * OPTIONAL
 	 */
+	// This is the version identifier for the answer list file
+	LOINC_CODESYSTEM_VERSION("loinc.codesystem.version"),
+
 	// This is the version identifier for the answer list file
 	LOINC_ANSWERLIST_VERSION("loinc.answerlist.version"),
 

hapi-fhir-jpaserver-base/src/main/resources/ca/uhn/fhir/jpa/term/loinc/loincupload.properties

@@ -61,6 +61,10 @@ loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersVa
 ### OPTIONAL ###
 ################
 
+# This is the version identifier for the LOINC code system
+## Key may be omitted if only a single version of LOINC is being kept.
+loinc.codesystem.version=2.68
+
 # This is the version identifier for the answer list file
 ## Key may be omitted
 loinc.answerlist.version=Beta.1

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

@@ -521,7 +521,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		myTerminologyDeferredStorageSvc.saveDeferred();
 		myTerminologyDeferredStorageSvc.saveDeferred();
 
-		IValidationSupport.LookupCodeResult lookupResults = myCodeSystemDao.lookupCode(new StringType("childAA"), new StringType(URL_MY_CODE_SYSTEM),null, mySrd);
+		IValidationSupport.LookupCodeResult lookupResults = myCodeSystemDao.lookupCode(new StringType("childAA"), new StringType(URL_MY_CODE_SYSTEM), null,null, mySrd);
 		assertEquals(true, lookupResults.isFound());
 
 		ValueSet vs = new ValueSet();
@@ -711,7 +711,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 
 		StringType code = new StringType("ParentA");
 		StringType system = new StringType("http://snomed.info/sct");
-		IValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
+		IValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null,null, mySrd);
 		assertEquals(true, outcome.isFound());
 	}
 

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

@@ -828,7 +828,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 
 		StringType code = new StringType("ParentA");
 		StringType system = new StringType("http://snomed.info/sct");
-		IValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
+		IValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null,null, mySrd);
 		assertEquals(true, outcome.isFound());
 	}
 

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

@@ -16,6 +16,7 @@ import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.util.ParametersUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
@@ -415,6 +416,51 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
 
 	}
 
+	@Test
+	public void testExpandByValueSetWithFilter() throws IOException {
+		loadAndPersistCodeSystem();
+
+		ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
+
+		Parameters respParam = myClient
+			.operation()
+			.onType(ValueSet.class)
+			.named("expand")
+			.withParameter(Parameters.class, "valueSet", toExpand)
+			.andParameter("filter", new StringType("blood"))
+			.execute();
+		ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
+		ourLog.info(resp);
+		assertThat(resp, stringContainsInOrder(
+			"<code value=\"11378-7\"/>",
+			"<display value=\"Systolic blood pressure at First encounter\"/>"));
+
+	}
+
+	@Test
+	public void testExpandByUrlWithFilter() throws Exception {
+		loadAndPersistCodeSystemAndValueSet();
+
+		Parameters respParam = myClient
+			.operation()
+			.onType(ValueSet.class)
+			.named("expand")
+			.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
+			.andParameter("filter", new StringType("first"))
+			.execute();
+		ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
+		ourLog.info(resp);
+		assertThat(resp, stringContainsInOrder(
+			"<code value=\"11378-7\"/>",
+			"<display value=\"Systolic blood pressure at First encounter\"/>"));
+
+	}
+
+
 	@Test
 	public void testExpandByValueSetWithPreExpansion() throws IOException {
 		myDaoConfig.setPreExpandValueSets(true);

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

@@ -13,7 +13,7 @@ public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
 	public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
 
 	@Test
-	public void testStoreNewCodeSystemVersionForExistingCodeSystem() {
+	public void testStoreNewCodeSystemVersionForExistingCodeSystemNoVersionId() {
 		CodeSystem upload = createCodeSystemWithMoreThan100Concepts();
 
 		// Create CodeSystem resource
@@ -34,15 +34,38 @@ public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
 		assertEquals(125, myTermConceptDao.count());
 	}
 
+	@Test
+	public void testStoreNewCodeSystemVersionForExistingCodeSystemVersionId() {
+		CodeSystem upload = createCodeSystemWithMoreThan100Concepts();
+		upload.setVersion("1");
+
+		// Create CodeSystem resource
+		ResourceTable codeSystemResourceEntity = (ResourceTable) myCodeSystemDao.create(upload, mySrd).getEntity();
+
+		// Update the CodeSystem resource
+		runInTransaction(() -> myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(upload, codeSystemResourceEntity));
+
+		/*
+			Because there are more than 100 concepts in the code system, the first 100 will be persisted immediately and
+			the remaining 25 concepts will be queued up for "deferred save".
+
+			As the CodeSystem was persisted twice, the extra 25 term concepts will be queued twice, each with a different
+			CodeSystem version PID. Only one set of the term concepts should be persisted (i.e. 125 term concepts in total).
+		 */
+		myTerminologyDeferredStorageSvc.setProcessDeferred(true);
+		myTerminologyDeferredStorageSvc.saveDeferred();
+		assertEquals(125, myTermConceptDao.count());
+	}
+
 	private CodeSystem createCodeSystemWithMoreThan100Concepts() {
 		CodeSystem codeSystem = new CodeSystem();
 		codeSystem.setUrl(URL_MY_CODE_SYSTEM);
-		codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
 
 		for (int i = 0; i < 125; i++) {
 			codeSystem.addConcept(new CodeSystem.ConceptDefinitionComponent(new CodeType("codeA " + i)));
 		}
 
+		codeSystem.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
 		return codeSystem;
 
 	}

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

@@ -17,12 +17,10 @@ import ca.uhn.fhir.jpa.term.loinc.LoincTop2000LabResultsUsHandler;
 import ca.uhn.fhir.jpa.term.loinc.LoincUniversalOrderSetHandler;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.ValueSet;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
@@ -342,6 +340,28 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals("13006-2", vs.getCompose().getInclude().get(0).getConcept().get(1).getCode());
 	}
 
+	@Test
+	public void testLoadLoincMultipleVersions() throws IOException {
+
+		// Load LOINC marked as version 2.67
+		addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v267_loincupload.properties");
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+
+		verify(myTermCodeSystemStorageSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		CodeSystem loincCS = mySystemCaptor.getValue();
+		assertEquals("2.67", loincCS.getVersion());
+
+		// Load LOINC marked as version 2.68
+		myFiles = new ZipCollectionBuilder();
+		addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v268_loincupload.properties");
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+
+		verify(myTermCodeSystemStorageSvc, times(2)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		loincCS = mySystemCaptor.getValue();
+		assertEquals("2.68", loincCS.getVersion());
+
+	}
+
 	@Test
 	@Disabled
 	public void testLoadLoincMandatoryFilesOnly() throws IOException {
@@ -382,7 +402,11 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 	}
 
 	public static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
-		theFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+		addLoincMandatoryFilesWithPropertiesFileToZip(theFiles, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+	}
+
+	public static void addLoincMandatoryFilesWithPropertiesFileToZip(ZipCollectionBuilder theFiles, String thePropertiesFile) throws IOException {
+		theFiles.addFileZip("/loinc/", thePropertiesFile);
 		theFiles.addFileZip("/loinc/", LOINC_GROUP_FILE_DEFAULT.getCode());
 		theFiles.addFileZip("/loinc/", LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
 		theFiles.addFileZip("/loinc/", LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcDeltaR4Test.java

@@ -184,7 +184,7 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 		assertEquals(2, outcome.getUpdatedConceptCount());
 
 		runInTransaction(() -> {
-			TermConcept concept = myTermSvc.findCode("http://foo/cs", "ChildAA").orElseThrow(() -> new IllegalStateException());
+			TermConcept concept = myTermSvc.findCode("http://foo/cs", "ChildAA", null).orElseThrow(() -> new IllegalStateException());
 			assertEquals(2, concept.getParents().size());
 			assertThat(concept.getParentPidsAsString(), matchesPattern("^[0-9]+ [0-9]+$"));
 		});

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

@@ -4,11 +4,15 @@ import ca.uhn.fhir.context.support.ConceptValidationOptions;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.jpa.api.model.TranslationRequest;
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptMap;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
 import ca.uhn.fhir.jpa.entity.TermValueSet;
+import ca.uhn.fhir.model.dstu2.valueset.ContentTypeEnum;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.CanonicalType;
@@ -30,9 +34,14 @@ import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.Nonnull;
+import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Optional;
+import java.util.Set;
 
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -1880,4 +1889,109 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
 		assertTrue(result.isOk());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
+
+	@Test
+	public void testCreateCodeSystemTwoVersions() {
+		CodeSystem codeSystem = new CodeSystem();
+		codeSystem.setUrl(CS_URL);
+		codeSystem.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		codeSystem
+			.addConcept().setCode("A").setDisplay("Code A");
+		codeSystem
+			.addConcept().setCode("B").setDisplay("Code A");
+
+		codeSystem.setVersion("1");
+
+		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
+
+		Set<TermConcept> codes = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "A");
+		assertThat(toCodes(codes), containsInAnyOrder("A"));
+
+		codes = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "B");
+		assertThat(toCodes(codes), containsInAnyOrder("B"));
+
+		runInTransaction(() -> {
+			List<TermCodeSystemVersion> termCodeSystemVersions = myTermCodeSystemVersionDao.findAll();
+			assertEquals(termCodeSystemVersions.size(), 1);
+			TermCodeSystemVersion termCodeSystemVersion_1 = termCodeSystemVersions.get(0);
+			assertEquals(termCodeSystemVersion_1.getConcepts().size(), 2);
+			Set<TermConcept> termConcepts = new HashSet<>(termCodeSystemVersion_1.getConcepts());
+			assertThat(toCodes(termConcepts), containsInAnyOrder("A", "B"));
+
+			TermCodeSystem termCodeSystem = myTermCodeSystemDao.findByResourcePid(id.getIdPartAsLong());
+			assertEquals("1", termCodeSystem.getCurrentVersion().getCodeSystemVersionId());
+
+		});
+
+		codeSystem.setVersion("2");
+		codeSystem
+			.addConcept().setCode("C").setDisplay("Code C");
+
+		myCodeSystemDao.update(codeSystem, mySrd).getId().toUnqualified();
+		codes = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "C");
+		assertThat(toCodes(codes), containsInAnyOrder("C"));
+
+		runInTransaction(() -> {
+			List<TermCodeSystemVersion> termCodeSystemVersions_updated = myTermCodeSystemVersionDao.findAll();
+			assertEquals(termCodeSystemVersions_updated.size(), 2);
+			TermCodeSystemVersion termCodeSystemVersion_2 = termCodeSystemVersions_updated.get(1);
+			assertEquals(termCodeSystemVersion_2.getConcepts().size(), 3);
+			Set<TermConcept> termConcepts_updated = new HashSet<>(termCodeSystemVersion_2.getConcepts());
+			assertThat(toCodes(termConcepts_updated), containsInAnyOrder("A", "B", "C"));
+
+			TermCodeSystem termCodeSystem = myTermCodeSystemDao.findByResourcePid(id.getIdPartAsLong());
+			assertEquals("2", termCodeSystem.getCurrentVersion().getCodeSystemVersionId());
+		});
+	}
+
+	@Test
+	public void testUpdateCodeSystemContentModeNotPresent() {
+		CodeSystem codeSystem = new CodeSystem();
+		codeSystem.setUrl(CS_URL);
+		codeSystem.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		codeSystem
+			.addConcept().setCode("A").setDisplay("Code A");
+		codeSystem
+			.addConcept().setCode("B").setDisplay("Code A");
+
+		codeSystem.setVersion("1");
+
+		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
+
+		Set<TermConcept> codes = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "A");
+		assertThat(toCodes(codes), containsInAnyOrder("A"));
+
+		codes = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "B");
+		assertThat(toCodes(codes), containsInAnyOrder("B"));
+
+		runInTransaction(() -> {
+			List<TermCodeSystemVersion> termCodeSystemVersions = myTermCodeSystemVersionDao.findAll();
+			assertEquals(termCodeSystemVersions.size(), 1);
+			TermCodeSystemVersion termCodeSystemVersion_1 = termCodeSystemVersions.get(0);
+			assertEquals(termCodeSystemVersion_1.getConcepts().size(), 2);
+			Set<TermConcept> termConcepts = new HashSet<>(termCodeSystemVersion_1.getConcepts());
+			assertThat(toCodes(termConcepts), containsInAnyOrder("A", "B"));
+
+			TermCodeSystem termCodeSystem = myTermCodeSystemDao.findByResourcePid(id.getIdPartAsLong());
+			assertEquals("1", termCodeSystem.getCurrentVersion().getCodeSystemVersionId());
+
+		});
+
+		// Remove concepts and changed ContentMode to NOTPRESENT
+		codeSystem.setConcept(new ArrayList<>());
+		codeSystem.setContent((CodeSystem.CodeSystemContentMode.NOTPRESENT));
+
+		myCodeSystemDao.update(codeSystem, mySrd).getId().toUnqualified();
+		runInTransaction(() -> {
+			List<TermCodeSystemVersion> termCodeSystemVersions_updated = myTermCodeSystemVersionDao.findAll();
+			assertEquals(termCodeSystemVersions_updated.size(), 1);
+			TermCodeSystemVersion termCodeSystemVersion_2 = termCodeSystemVersions_updated.get(0);
+			assertEquals(termCodeSystemVersion_2.getConcepts().size(), 2);
+			Set<TermConcept> termConcepts_updated = new HashSet<>(termCodeSystemVersion_2.getConcepts());
+			assertThat(toCodes(termConcepts_updated), containsInAnyOrder("A", "B"));
+
+			TermCodeSystem termCodeSystem = myTermCodeSystemDao.findByResourcePid(id.getIdPartAsLong());
+			assertEquals("1", termCodeSystem.getCurrentVersion().getCodeSystemVersionId());
+		});
+	}
 }

hapi-fhir-jpaserver-base/src/test/resources/loinc/v267_loincupload.properties

@@ -0,0 +1,87 @@
+#################
+### MANDATORY ###
+#################
+
+# Answer lists (ValueSets of potential answers/values for LOINC "questions")
+## File must be present
+loinc.answerlist.file=AccessoryFiles/AnswerFile/AnswerList.csv
+# Answer list links (connects LOINC observation codes to answer list codes)
+## File must be present
+loinc.answerlist.link.file=AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
+
+# Document ontology
+## File must be present
+loinc.document.ontology.file=AccessoryFiles/DocumentOntology/DocumentOntology.csv
+
+# LOINC codes
+## File must be present
+loinc.file=LoincTable/Loinc.csv
+
+# LOINC hierarchy
+## File must be present
+loinc.hierarchy.file=AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
+
+# IEEE medical device codes
+## File must be present
+loinc.ieee.medical.device.code.mapping.table.file=AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
+
+# Imaging document codes
+## File must be present
+loinc.imaging.document.codes.file=AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
+
+# Part
+## File must be present
+loinc.part.file=AccessoryFiles/PartFile/Part.csv
+
+# Part link
+## File must be present
+loinc.part.link.primary.file=AccessoryFiles/PartFile/LoincPartLink_Primary.csv
+loinc.part.link.supplementary.file=AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv
+
+# Part related code mapping
+## File must be present
+loinc.part.related.code.mapping.file=AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
+
+# RSNA playbook
+## File must be present
+loinc.rsna.playbook.file=AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
+
+# Top 2000 codes - SI
+## File must be present
+loinc.top2000.common.lab.results.si.file=AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
+# Top 2000 codes - US
+## File must be present
+loinc.top2000.common.lab.results.us.file=AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
+
+# Universal lab order ValueSet
+## File must be present
+loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
+
+################
+### OPTIONAL ###
+################
+
+# This is the version identifier for the LOINC code system
+## Key may be omitted if only a single version of LOINC is being kept.
+loinc.codesystem.version=2.67
+
+# This is the version identifier for the answer list file
+## Key may be omitted
+loinc.answerlist.version=Beta.1
+
+# This is the version identifier for uploaded ConceptMap resources
+## Key may be omitted
+loinc.conceptmap.version=Beta.1
+
+# Group
+## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv
+## File may be omitted
+loinc.group.file=AccessoryFiles/GroupFile/Group.csv
+# Group terms
+## Default value if key not provided: AccessoryFiles/GroupFile/GroupLoincTerms.csv
+## File may be omitted
+loinc.group.terms.file=AccessoryFiles/GroupFile/GroupLoincTerms.csv
+# Parent group
+## Default value if key not provided: AccessoryFiles/GroupFile/ParentGroup.csv
+## File may be omitted
+loinc.parent.group.file=AccessoryFiles/GroupFile/ParentGroup.csv

hapi-fhir-jpaserver-base/src/test/resources/loinc/v268_loincupload.properties

@@ -0,0 +1,87 @@
+#################
+### MANDATORY ###
+#################
+
+# This is the version identifier for the LOINC code system
+## Key may be omitted if only a single version of LOINC is being kept.
+loinc.codesystem.version=2.68
+
+# Answer lists (ValueSets of potential answers/values for LOINC "questions")
+## File must be present
+loinc.answerlist.file=AccessoryFiles/AnswerFile/AnswerList.csv
+# Answer list links (connects LOINC observation codes to answer list codes)
+## File must be present
+loinc.answerlist.link.file=AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
+
+# Document ontology
+## File must be present
+loinc.document.ontology.file=AccessoryFiles/DocumentOntology/DocumentOntology.csv
+
+# LOINC codes
+## File must be present
+loinc.file=LoincTable/Loinc.csv
+
+# LOINC hierarchy
+## File must be present
+loinc.hierarchy.file=AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
+
+# IEEE medical device codes
+## File must be present
+loinc.ieee.medical.device.code.mapping.table.file=AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
+
+# Imaging document codes
+## File must be present
+loinc.imaging.document.codes.file=AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
+
+# Part
+## File must be present
+loinc.part.file=AccessoryFiles/PartFile/Part.csv
+
+# Part link
+## File must be present
+loinc.part.link.primary.file=AccessoryFiles/PartFile/LoincPartLink_Primary.csv
+loinc.part.link.supplementary.file=AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv
+
+# Part related code mapping
+## File must be present
+loinc.part.related.code.mapping.file=AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
+
+# RSNA playbook
+## File must be present
+loinc.rsna.playbook.file=AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
+
+# Top 2000 codes - SI
+## File must be present
+loinc.top2000.common.lab.results.si.file=AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
+# Top 2000 codes - US
+## File must be present
+loinc.top2000.common.lab.results.us.file=AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
+
+# Universal lab order ValueSet
+## File must be present
+loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
+
+################
+### OPTIONAL ###
+################
+
+# This is the version identifier for the answer list file
+## Key may be omitted
+loinc.answerlist.version=Beta.1
+
+# This is the version identifier for uploaded ConceptMap resources
+## Key may be omitted
+loinc.conceptmap.version=Beta.1
+
+# Group
+## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv
+## File may be omitted
+loinc.group.file=AccessoryFiles/GroupFile/Group.csv
+# Group terms
+## Default value if key not provided: AccessoryFiles/GroupFile/GroupLoincTerms.csv
+## File may be omitted
+loinc.group.terms.file=AccessoryFiles/GroupFile/GroupLoincTerms.csv
+# Parent group
+## Default value if key not provided: AccessoryFiles/GroupFile/ParentGroup.csv
+## File may be omitted
+loinc.parent.group.file=AccessoryFiles/GroupFile/ParentGroup.csv

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/BaseValidationSupportWrapper.java

@@ -58,6 +58,11 @@ public class BaseValidationSupportWrapper extends BaseValidationSupport {
 		return myWrap.validateCode(theValidationSupportContext, theOptions, theCodeSystem, theCode, theDisplay, theValueSetUrl);
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
+		return myWrap.lookupCode(theValidationSupportContext, theSystem, theCode, theVersion);
+	}
+
 	@Override
 	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
 		return myWrap.lookupCode(theValidationSupportContext, theSystem, theCode);

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

@@ -83,6 +83,12 @@ public class CachingValidationSupport extends BaseValidationSupportWrapper imple
 		return loadFromCache(myValidateCodeCache, key, t -> super.validateCode(theValidationSupportContext, theOptions, theCodeSystem, theCode, theDisplay, theValueSetUrl));
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
+		String key = "lookupCode " + theSystem + " " + theCode + " " + theVersion;
+		return loadFromCache(myLookupCodeCache, key, t -> super.lookupCode(theValidationSupportContext, theSystem, theCode, theVersion));
+	}
+
 	@Override
 	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
 		String key = "lookupCode " + theSystem + " " + theCode;

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java

@@ -145,6 +145,12 @@ public class CommonCodeSystemsTerminologyService implements IValidationSupport {
 	}
 
 
+	@Override
+	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
+		// For now Common Code Systems will not be versioned.
+		return lookupCode(theValidationSupportContext, theSystem, theCode);
+	}
+
 	@Override
 	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
 

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/InMemoryTerminologyServerValidationSupport.java

@@ -308,6 +308,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
 			.setMessage(message);
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
+		// TODO: Add support for validating versioned codes as well.
+		return lookupCode(theValidationSupportContext, theSystem, theCode);
+	}
+
 	@Override
 	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
 		return validateCode(theValidationSupportContext, new ConceptValidationOptions(), theSystem, theCode, null, null).asLookupCodeResult(theSystem, theCode);
@@ -470,6 +476,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
 
 			List<VersionIndependentConcept> nextCodeList = new ArrayList<>();
 			String system = nextInclude.getSystem();
+			String systemVersion = nextInclude.getVersion();
 			if (isNotBlank(system)) {
 
 				if (theWantSystem != null && !theWantSystem.equals(system)) {
@@ -492,7 +499,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
 
 					if (theWantCode != null) {
 						if (theValidationSupportContext.getRootValidationSupport().isCodeSystemSupported(theValidationSupportContext, system)) {
-							LookupCodeResult lookup = theValidationSupportContext.getRootValidationSupport().lookupCode(theValidationSupportContext, system, theWantCode);
+							LookupCodeResult lookup = theValidationSupportContext.getRootValidationSupport().lookupCode(theValidationSupportContext, system, theWantCode, systemVersion);
 							if (lookup != null && lookup.isFound()) {
 								CodeSystem.ConceptDefinitionComponent conceptDefinition = new CodeSystem.ConceptDefinitionComponent()
 									.addConcept()

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

@@ -257,6 +257,16 @@ public class ValidationSupportChain implements IValidationSupport {
 		return null;
 	}
 
+	@Override
+	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
+		for (IValidationSupport next : myChain) {
+			if (next.isCodeSystemSupported(theValidationSupportContext, theSystem)) {
+				return next.lookupCode(theValidationSupportContext, theSystem, theCode, theVersion);
+			}
+		}
+		return null;
+	}
+
 	@Override
 	public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
 		for (IValidationSupport next : myChain) {