Merge remote-tracking branch 'remotes/origin/feature_20200830_term_multi_version_support' into feature_2020_09_02_term_multi_version_support

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-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -143,6 +143,7 @@ ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownType=Content in resource of
 
 
 ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrlAndVersion=Can not create multiple CodeSystem resources with CodeSystem.url "{0}" and CodeSystem.version "{1}", already have one with resource ID: {2}
 ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
 ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrlAndVersion=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", ConceptMap.version "{1}", already have one with resource ID: {2}
 ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}

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

@@ -43,7 +43,6 @@ import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
-import org.apache.commons.codec.binary.StringUtils;
 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;
@@ -235,6 +234,11 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 		return null;
 	}
 
+	@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 +284,11 @@ 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/HapiFhirResourceDaoCodeSystemUtil.java

@@ -0,0 +1,28 @@
+package ca.uhn.fhir.jpa.dao;
+
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class HapiFhirResourceDaoCodeSystemUtil {
+
+	static public void deleteCodeSystemEntities(ITermCodeSystemDao theCsDao, ITermCodeSystemVersionDao theCsvDao,
+															  ITermDeferredStorageSvc theTermDeferredStorageSvc, String theCodeSystemUrl,
+															  String theCodeSystemVersion) {
+		if (isNotBlank(theCodeSystemUrl)) {
+			TermCodeSystem persCs = theCsDao.findByCodeSystemUri(theCodeSystemUrl);
+			if (persCs != null) {
+				if (theCodeSystemVersion != null) {
+					TermCodeSystemVersion persCsVersion = theCsvDao.findByCodeSystemPidAndVersion(persCs.getPid(), theCodeSystemVersion);
+					theTermDeferredStorageSvc.deleteCodeSystemVersion(persCsVersion);
+				} else {
+					theTermDeferredStorageSvc.deleteCodeSystem(persCs);
+				}
+			}
+		}
+	}
+}

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

@@ -25,7 +25,9 @@ import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
@@ -67,6 +69,8 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 	@Autowired
 	private ITermCodeSystemDao myCsDao;
 	@Autowired
+	private ITermCodeSystemVersionDao myCsvDao;
+	@Autowired
 	private IValidationSupport myValidationSupport;
 	@Autowired
 	private FhirContext myFhirContext;
@@ -89,6 +93,12 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 	@Nonnull
 	@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;
@@ -102,19 +112,24 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 
 		String code;
 		String system;
+		String codeSystemVersion = null;
 		if (haveCoding) {
 			code = theCoding.getCode();
 			system = theCoding.getSystem();
+			codeSystemVersion = theCoding.getVersion();
 		} else {
 			code = theCode.getValue();
 			system = theSystem.getValue();
+			if (theVersion != null) {
+				codeSystemVersion = theVersion.getValue();
+			}
 		}
 
-		ourLog.debug("Looking up {} / {}", system, code);
+		ourLog.debug("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 +139,13 @@ 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) {
+		String codingBVersion = theCodingB != null ? theCodingB.getVersion() : null;
+		String codingAVersion = theCodingA != null ? theCodingA.getVersion() : null;
+		return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, codingAVersion, codingBVersion);
+	}
+
 	@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);
@@ -133,13 +155,9 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 	protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
 		super.preDelete(theResourceToDelete, theEntityToDelete);
 
-		String codeSystemUrl = theResourceToDelete.getUrl();
+		HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
-		if (isNotBlank(codeSystemUrl)) {
+			theResourceToDelete.getVersion());
-			TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
+
-			if (persCs != null) {
-				myTermDeferredStorageSvc.deleteCodeSystem(persCs);
-			}
-		}
 	}
 
 	@Override

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

@@ -25,7 +25,9 @@ import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
@@ -61,6 +63,8 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 	@Autowired
 	private ITermCodeSystemDao myCsDao;
 	@Autowired
+	private ITermCodeSystemVersionDao myCsvDao;
+	@Autowired
 	private IValidationSupport myValidationSupport;
 	@Autowired
 	protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
@@ -84,6 +88,12 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 	@Nonnull
 	@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;
@@ -97,20 +107,25 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 
 		String code;
 		String system;
+		String codeSystemVersion = null;
 		if (haveCoding) {
 			code = theCoding.getCode();
 			system = theCoding.getSystem();
+			codeSystemVersion = theCoding.getVersion();
 		} else {
 			code = theCode.getValue();
 			system = theSystem.getValue();
+			if (theVersion != null) {
+				codeSystemVersion = theVersion.getValue();
+			}
 		}
 
-		ourLog.debug("Looking up {} / {}", system, code);
+		ourLog.debug("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 +137,13 @@ 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) {
+		String codingBVersion = theCodingB != null ? theCodingB.getVersion() : null;
+		String codingAVersion = theCodingA != null ? theCodingA.getVersion() : null;
+		return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, codingAVersion, codingBVersion);
+	}
+
 	@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);
@@ -131,13 +153,9 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 	protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
 		super.preDelete(theResourceToDelete, theEntityToDelete);
 
-		String codeSystemUrl = theResourceToDelete.getUrl();
+		HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
-		if (isNotBlank(codeSystemUrl)) {
+			theResourceToDelete.getVersion());
-			TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
+
-			if (persCs != null) {
-				myTermDeferredStorageSvc.deleteCodeSystem(persCs);
-			}
-		}
 	}
 
 	@Override

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

@@ -25,7 +25,9 @@ import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
@@ -65,6 +67,8 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 	@Autowired
 	private ITermCodeSystemDao myCsDao;
 	@Autowired
+	private ITermCodeSystemVersionDao myCsvDao;
+	@Autowired
 	private IValidationSupport myValidationSupport;
 	@Autowired
 	private FhirContext myFhirContext;
@@ -86,6 +90,12 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 	@Nonnull
 	@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;
@@ -99,20 +109,25 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 
 		String code;
 		String system;
+		String codeSystemVersion = null;
 		if (haveCoding) {
 			code = theCoding.getCode();
 			system = theCoding.getSystem();
+			codeSystemVersion = theCoding.getVersion();
 		} else {
 			code = theCode.getValue();
 			system = theSystem.getValue();
+			if (theVersion != null) {
+				codeSystemVersion = theVersion.getValue();
+			}
 		}
 
-		ourLog.info("Looking up {} / {}", system, code);
+		ourLog.debug("Looking up {} / {}, version {}", system, code, codeSystemVersion);
 
 		if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
 
-			ourLog.info("Code system {} is supported", 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;
 			}
@@ -124,6 +139,13 @@ 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) {
+		String codingBVersion = theCodingB != null ? theCodingB.getVersion() : null;
+		String codingAVersion = theCodingA != null ? theCodingA.getVersion() : null;
+		return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, codingAVersion, codingBVersion);
+	}
+
 	@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);
@@ -133,13 +155,9 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 	protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
 		super.preDelete(theResourceToDelete, theEntityToDelete);
 
-		String codeSystemUrl = theResourceToDelete.getUrl();
+		HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
-		if (isNotBlank(codeSystemUrl)) {
+			theResourceToDelete.getVersion());
-			TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
+
-			if (persCs != null) {
-				myTermDeferredStorageSvc.deleteCodeSystem(persCs);
-			}
-		}
 	}
 
 	@Override

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

@@ -58,7 +58,7 @@ public class TermCodeSystem implements Serializable {
 	@Column(name = "PID")
 	private Long myPid;
 	@OneToOne(fetch = FetchType.LAZY)
-	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_RES"))
+	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = true, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_RES"))
 	private ResourceTable myResource;
 	@Column(name = "RES_ID", insertable = false, updatable = false)
 	private Long myResourcePid;

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) {
@@ -84,13 +85,14 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
 		@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
 		@OperationParam(name = "codingA", min = 0, max = 1) Coding theCodingA,
 		@OperationParam(name = "codingB", min = 0, max = 1) Coding theCodingB,
+		@OperationParam(name="version", min=0, max=1) StringType theVersion,
 		RequestDetails theRequestDetails
 	) {
 
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
-			IFhirResourceDaoCodeSystem.SubsumesResult result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
+			IFhirResourceDaoCodeSystem.SubsumesResult result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, theRequestDetails);
 			return (Parameters) result.toParameters(theRequestDetails.getFhirContext());
 		} finally {
 			endRequest(theServletRequest);

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 {
@@ -84,13 +85,14 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
 		@OperationParam(name="system", min=0, max=1) UriType theSystem,
 		@OperationParam(name="codingA", min=0, max=1) Coding theCodingA,
 		@OperationParam(name="codingB", min=0, max=1) Coding theCodingB,
+		@OperationParam(name="version", min=0, max=1) StringType theVersion,
 		RequestDetails theRequestDetails
 	) {
 
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
-			IFhirResourceDaoCodeSystem.SubsumesResult result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
+			IFhirResourceDaoCodeSystem.SubsumesResult result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, theRequestDetails);
 			return (Parameters) result.toParameters(theRequestDetails.getFhirContext());
 		} finally {
 			endRequest(theServletRequest);

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 {
@@ -84,13 +85,14 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
 		@OperationParam(name="system", min=0, max=1) UriType theSystem,
 		@OperationParam(name="codingA", min=0, max=1) Coding theCodingA,
 		@OperationParam(name="codingB", min=0, max=1) Coding theCodingB,
+		@OperationParam(name="version", min=0, max=1) StringType theVersion,
 		RequestDetails theRequestDetails
 	) {
 
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
-			IFhirResourceDaoCodeSystem.SubsumesResult result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
+			IFhirResourceDaoCodeSystem.SubsumesResult result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, theRequestDetails);
 			return (Parameters) result.toParameters(theRequestDetails.getFhirContext());
 		} finally {
 			endRequest(theServletRequest);

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

@@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.term;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.ConceptValidationOptions;
-import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
@@ -126,7 +125,6 @@ import org.hl7.fhir.r4.model.IntegerType;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
-import org.hl7.fhir.utilities.validation.ValidationOptions;
 import org.quartz.JobExecutionContext;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
@@ -175,7 +173,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNoneBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import static org.apache.commons.lang3.StringUtils.isNotEmpty;
 
 public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	public static final int DEFAULT_FETCH_SIZE = 250;
@@ -238,14 +235,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	private ITermCodeSystemStorageSvc myConceptStorageSvc;
 	@Autowired
 	private ApplicationContext myApplicationContext;
-	@Autowired
-	private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
 	private volatile IValidationSupport myJpaValidationSupport;
 	private volatile IValidationSupport myValidationSupport;
 
 	@Override
 	public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
-		TermCodeSystemVersion cs = getCurrentCodeSystemVersion(theSystem);
+		TermCodeSystemVersion cs = getCurrentCodeSystemVersion(theSystem,null);
 		return cs != null;
 	}
 
@@ -932,19 +927,19 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 			case "parent":
 			case "child":
 				isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
-				handleFilterLoincParentChild(theQb, theBool, theFilter);
+				handleFilterLoincParentChild(theBool, theFilter);
 				break;
 			case "ancestor":
 				isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
-				handleFilterLoincAncestor(theSystem, theQb, theBool, theFilter);
+				handleFilterLoincAncestor(theSystem, theBool, theFilter);
 				break;
 			case "descendant":
 				isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
-				handleFilterLoincDescendant(theSystem, theQb, theBool, theFilter);
+				handleFilterLoincDescendant(theSystem, theBool, theFilter);
 				break;
 			case "copyright":
 				isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
-				handleFilterLoincCopyright(theQb, theBool, theFilter);
+				handleFilterLoincCopyright(theBool, theFilter);
 				break;
 			default:
 				handleFilterRegex(theBool, theFilter);
@@ -952,11 +947,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		}
 	}
 
-	private boolean isCodeSystemLoingOrThrowInvalidRequestException(String theSystem, String theProperty) {
+	private void isCodeSystemLoingOrThrowInvalidRequestException(String theSystem, String theProperty) {
 		if (!isCodeSystemLoinc(theSystem)) {
 			throw new InvalidRequestException("Invalid filter, property " + theProperty + " is LOINC-specific and cannot be used with system: " + theSystem);
 		}
-		return true;
 	}
 
 	private boolean isCodeSystemLoinc(String theSystem) {
@@ -1004,7 +998,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
-	private void handleFilterLoincParentChild(QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void handleFilterLoincParentChild(BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
 		switch (theFilter.getOp()) {
 			case EQUAL:
 				addLoincFilterParentChildEqual(theBool, theFilter.getProperty(), theFilter.getValue());
@@ -1037,29 +1031,29 @@ 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, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
 		switch (theFilter.getOp()) {
 			case EQUAL:
-				addLoincFilterAncestorEqual(theSystem, theQb, theBool, theFilter);
+				addLoincFilterAncestorEqual(theSystem, theBool, theFilter);
 				break;
 			case IN:
-				addLoincFilterAncestorIn(theSystem, theQb, theBool, theFilter);
+				addLoincFilterAncestorIn(theSystem, theBool, theFilter);
 				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, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
-		addLoincFilterAncestorEqual(theSystem, theQb, theBool, theFilter.getProperty(), theFilter.getValue());
+		addLoincFilterAncestorEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue());
 	}
 
-	private void addLoincFilterAncestorEqual(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, String theProperty, String theValue) {
+	private void addLoincFilterAncestorEqual(String theSystem, BooleanJunction<?> theBool, String theProperty, String theValue) {
 		List<Term> terms = getAncestorTerms(theSystem, theProperty, theValue);
 		theBool.must(new TermsQuery(terms));
 	}
 
-	private void addLoincFilterAncestorIn(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void addLoincFilterAncestorIn(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
 		String[] values = theFilter.getValue().split(",");
 		List<Term> terms = new ArrayList<>();
 		for (String value : values) {
@@ -1081,13 +1075,13 @@ 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, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
 		switch (theFilter.getOp()) {
 			case EQUAL:
 				addLoincFilterDescendantEqual(theSystem, theBool, theFilter);
 				break;
 			case IN:
-				addLoincFilterDescendantIn(theSystem, theQb, theBool, theFilter);
+				addLoincFilterDescendantIn(theSystem, theBool, theFilter);
 				break;
 			default:
 				throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
@@ -1103,7 +1097,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		theBool.must(new TermsQuery(terms));
 	}
 
-	private void addLoincFilterDescendantIn(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void addLoincFilterDescendantIn(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
 		String[] values = theFilter.getValue().split(",");
 		List<Term> terms = new ArrayList<>();
 		for (String value : values) {
@@ -1127,7 +1121,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		return retVal;
 	}
 
-	private void handleFilterLoincCopyright(QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
+	private void handleFilterLoincCopyright(BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
 		if (theFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
 
 			String copyrightFilterValue = defaultString(theFilter.getValue()).toLowerCase();
@@ -1364,6 +1358,11 @@ 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
@@ -1372,21 +1371,29 @@ 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 = getCurrentCodeSystemVersion(theCodeSystem, theVersion);
 			if (csv == null) {
-				return null;
+				return Optional.empty();
 			}
 			return myConceptDao.findByCodeSystemAndCode(csv, theCode);
 		});
 	}
 
 	@Nullable
-	private TermCodeSystemVersion getCurrentCodeSystemVersion(String theUri) {
+	private TermCodeSystemVersion getCurrentCodeSystemVersion(String theUri, String theVersion) {
-		TermCodeSystemVersion retVal = myCodeSystemCurrentVersionCache.get(theUri, uri -> myTxTemplate.execute(tx -> {
+		StringBuilder key = new StringBuilder(theUri);
+		if (theVersion != null) {
+			key.append("_").append(theVersion);
+		}
+		TermCodeSystemVersion retVal = myCodeSystemCurrentVersionCache.get(key.toString(), t -> myTxTemplate.execute(tx -> {
 			TermCodeSystemVersion csv = null;
-			TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(uri);
+			TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theUri);
-			if (cs != null && cs.getCurrentVersion() != null) {
+			if (cs != null) {
-				csv = cs.getCurrentVersion();
+				if (theVersion != null) {
+					csv = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(cs.getPid(), theVersion);
+				} else if (cs.getCurrentVersion() != null) {
+					csv = cs.getCurrentVersion();
+				}
 			}
 			if (csv != null) {
 				return csv;
@@ -1820,20 +1827,30 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		ourLog.info("Done storing TermValueSet[{}] for {}", termValueSet.getId(), theValueSet.getIdElement().toVersionless().getValueAsString());
 	}
 
+	@Override
+	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, null, null);
+	}
+
 	@Override
 	@Transactional
-	public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {
+	public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB, IPrimitiveType<String> theSystemVersion, String theCodingAVersion, String theCodingBVersion) {
-		VersionIndependentConcept conceptA = toConcept(theCodeA, theSystem, theCodingA);
+		VersionIndependentConceptWithSystemVersion conceptA = toConcept(theCodeA, theSystem, theCodingA, theSystemVersion, theCodingAVersion);
-		VersionIndependentConcept conceptB = toConcept(theCodeB, theSystem, theCodingB);
+		VersionIndependentConceptWithSystemVersion conceptB = toConcept(theCodeB, theSystem, theCodingB, theSystemVersion, theCodingBVersion);
 
 		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())
+		if (!StringUtils.equals(conceptA.getCodeSystemVersion(), conceptB.getCodeSystemVersion())) {
+			throw new InvalidRequestException("Unable to test subsumption across different code system versions");
+		}
+
+		TermConcept codeA = findCode(conceptA.getSystem(), conceptA.getCode(), conceptA.getCodeSystemVersion())
 			.orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptA));
 
-		TermConcept codeB = findCode(conceptB.getSystem(), conceptB.getCode())
+		TermConcept codeB = findCode(conceptB.getSystem(), conceptB.getCode(), conceptB.getCodeSystemVersion())
 			.orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptB));
 
 		FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
@@ -1852,10 +1869,10 @@ 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();
 
@@ -2116,6 +2133,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 					while (scrollableResultsIterator.hasNext()) {
 						TermConceptMapGroupElement nextElement = scrollableResultsIterator.next();
+						// TODO: The invocation of the size() below does not seem to be necessary but for some reason, removing it causes tests in TerminologySvcImplR4Test to fail.
 						nextElement.getConceptMapGroupElementTargets().size();
 						myEntityManager.detach(nextElement);
 
@@ -2180,7 +2198,6 @@ 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) {
@@ -2223,7 +2240,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 			}
 		}
 
-		CodeValidationResult retVal = null;
+		CodeValidationResult retVal;
 		if (valueSet != null) {
 			retVal = new InMemoryTerminologyServerValidationSupport(myContext).validateCodeInValueSet(theValidationSupportContext, theValidationOptions, theCodeSystem, theCode, theDisplay, valueSet);
 		} else {
@@ -2456,14 +2473,31 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	@NotNull
-	private static VersionIndependentConcept toConcept(IPrimitiveType<String> theCodeType, IPrimitiveType<String> theSystemType, IBaseCoding theCodingType) {
+	private VersionIndependentConceptWithSystemVersion toConcept(IPrimitiveType<String> theCodeType, IPrimitiveType<String> theSystemType, IBaseCoding theCodingType, IPrimitiveType<String> theSystemVersionType, String theCodingVersionType) {
 		String code = theCodeType != null ? theCodeType.getValueAsString() : null;
 		String system = theSystemType != null ? theSystemType.getValueAsString() : null;
+		String systemVersion = theSystemVersionType != null ? theSystemVersionType.getValueAsString() : null;
 		if (theCodingType != null) {
 			code = theCodingType.getCode();
 			system = theCodingType.getSystem();
+			systemVersion = theCodingVersionType;
 		}
-		return new VersionIndependentConcept(system, code);
+		return new VersionIndependentConceptWithSystemVersion(system, code, systemVersion);
+	}
+
+	private static class VersionIndependentConceptWithSystemVersion extends VersionIndependentConcept {
+
+		String myCodeSystemVersion;
+
+		public VersionIndependentConceptWithSystemVersion(String theSystem, String theCode, String theSystemVersion) {
+			super(theSystem, theCode);
+			myCodeSystemVersion = theSystemVersion;
+		}
+
+		public String getCodeSystemVersion() {
+			return myCodeSystemVersion;
+		}
+
 	}
 
 	/**

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

@@ -231,6 +231,26 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		});
 	}
 
+	@Override
+	@Transactional(propagation = Propagation.NEVER)
+	public void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
+		// Delete TermCodeSystemVersion
+		ourLog.info(" * Deleting code system version {}", theCodeSystemVersion.getCodeSystemVersionId());
+		deleteCodeSystemVersion(theCodeSystemVersion.getPid());
+
+		// Check if the version deleted is the current version. If so, delete TermCodeSystem as well.
+		TermCodeSystem termCodeSystem = theCodeSystemVersion.getCodeSystem();
+		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
+		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
+		txTemplate.executeWithoutResult(t -> {
+			if (myCodeSystemVersionDao.findByCodeSystemPid(termCodeSystem.getPid()).size() == 0) {
+				ourLog.info(" * Deleting code system {}", termCodeSystem.getPid());
+				deleteCodeSystem(termCodeSystem);
+			}
+		});
+
+	}
+
 	/**
 	 * Returns the number of saved concepts
 	 */
@@ -284,16 +304,19 @@ 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) {
-						getOrCreateTermCodeSystem(codeSystemResourcePid, theCodeSystem.getUrl(), theCodeSystem.getUrl(), theResourceEntity);
+						TermCodeSystemVersion codeSystemVersion = getExistingTermCodeSystemVersion(termCodeSystem.getPid(), theCodeSystem.getVersion());
-						return;
+						if (codeSystemVersion != null) {
+							TermCodeSystem myCodeSystemEntity = getOrCreateDistinctTermCodeSystem(codeSystemResourcePid, theCodeSystem.getUrl(), theCodeSystem.getUrl(), theCodeSystem.getVersion(), theResourceEntity);
+							return;
+						}
 					}
 				}
 
@@ -338,29 +361,33 @@ 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();
+		 * Get CodeSystem and validate CodeSystemVersion
-		ourLog.debug("Done flushing");
+		 */
+		TermCodeSystem codeSystem = getOrCreateDistinctTermCodeSystem(theCodeSystemResourcePid, theSystemUri, theSystemName, theSystemVersionId, theCodeSystemResourceTable);
+
+		/*
+		 * Delete version being replaced.
+		 */
+
+		if(existing != null) {
+			ourLog.info("Deleting old code system version {}", existing.getPid());
+			Long codeSystemVersionPid = existing.getPid();
+			deleteCodeSystemVersion(codeSystemVersionPid);
+
+		}
 
 		/*
 		 * Do the upload
 		 */
 
-		TermCodeSystem codeSystem = getOrCreateTermCodeSystem(theCodeSystemResourcePid, theSystemUri, theSystemName, theCodeSystemResourceTable);
-
 		theCodeSystemVersion.setCodeSystem(codeSystem);
 
 		theCodeSystemVersion.setCodeSystemDisplayName(theSystemName);
@@ -408,6 +435,17 @@ 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);
 
@@ -455,10 +493,12 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 				ourLog.info(" * Removing code system version {} as current version of code system {}", theCodeSystemVersionPid, codeSystem.getPid());
 				codeSystem.setCurrentVersion(null);
 				myCodeSystemDao.save(codeSystem);
+				myCodeSystemDao.flush();
 			}
 
 			ourLog.info(" * Deleting code system version");
-			myCodeSystemVersionDao.deleteById(theCodeSystemVersionPid);
+			myCodeSystemVersionDao.delete(theCodeSystemVersionPid);
+			myCodeSystemVersionDao.flush();
 		});
 
 	}
@@ -651,28 +691,48 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 	}
 
 	@Nonnull
-	private TermCodeSystem getOrCreateTermCodeSystem(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, ResourceTable theCodeSystemResourceTable) {
+	private TermCodeSystem getOrCreateDistinctTermCodeSystem(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, ResourceTable theCodeSystemResourceTable) {
 		TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theSystemUri);
 		if (codeSystem == null) {
 			codeSystem = myCodeSystemDao.findByResourcePid(theCodeSystemResourcePid.getIdAsLong());
 			if (codeSystem == null) {
 				codeSystem = new TermCodeSystem();
 			}
-			codeSystem.setResource(theCodeSystemResourceTable);
-		} else {
-			if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemResourceTable.getId())) {
-				String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
-					codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
-				throw new UnprocessableEntityException(msg);
-			}
 		}
 
+		codeSystem.setResource(theCodeSystemResourceTable);
 		codeSystem.setCodeSystemUri(theSystemUri);
 		codeSystem.setName(theSystemName);
 		codeSystem = myCodeSystemDao.save(codeSystem);
+		checkForCodeSystemVersionDuplicate(codeSystem,theSystemUri, theSystemVersionId, theCodeSystemResourceTable);
 		return codeSystem;
 	}
 
+	private void checkForCodeSystemVersionDuplicate(TermCodeSystem theCodeSystem, String theSystemUri, String theSystemVersionId, ResourceTable theCodeSystemResourceTable) {
+		// Check if CodeSystemVersion entity already exists.
+		TermCodeSystemVersion codeSystemVersionEntity;
+		String msg = null;
+		if (theSystemVersionId == null) {
+			codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(theCodeSystem.getPid());
+			if (codeSystemVersionEntity != null) {
+				msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
+					codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
+			}
+		} else {
+			codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(theCodeSystem.getPid(), theSystemVersionId);
+			if (codeSystemVersionEntity != null) {
+				msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrlAndVersion", theSystemUri,
+					theSystemVersionId, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
+			}
+		}
+		// Throw exception if the CodeSystemVersion is being duplicated.
+		if (codeSystemVersionEntity != null) {
+			if (!ObjectUtil.equals(codeSystemVersionEntity.getResource().getId(), theCodeSystemResourceTable.getId())) {
+				throw new UnprocessableEntityException(msg);
+			}
+		}
+	}
+
 	private void populateCodeSystemVersionProperties(TermCodeSystemVersion theCodeSystemVersion, CodeSystem theCodeSystemResource, ResourceTable theResourceTable) {
 		theCodeSystemVersion.setResource(theResourceTable);
 		theCodeSystemVersion.setCodeSystemDisplayName(theCodeSystemResource.getName());

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
 import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
 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.TermConceptParentChildLink;
 import ca.uhn.fhir.jpa.model.sched.HapiJob;
@@ -68,6 +69,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 	protected PlatformTransactionManager myTransactionMgr;
 	private boolean myProcessDeferred = true;
 	private List<TermCodeSystem> myDefferedCodeSystemsDeletions = Collections.synchronizedList(new ArrayList<>());
+	private List<TermCodeSystemVersion> myDefferedCodeSystemVersionsDeletions = Collections.synchronizedList(new ArrayList<>());
 	private List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
 	private List<ValueSet> myDeferredValueSets = Collections.synchronizedList(new ArrayList<>());
 	private List<ConceptMap> myDeferredConceptMaps = Collections.synchronizedList(new ArrayList<>());
@@ -115,6 +117,12 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 		myDefferedCodeSystemsDeletions.add(theCodeSystem);
 	}
 
+	@Override
+	@Transactional
+	public void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
+		myDefferedCodeSystemVersionsDeletions.add(theCodeSystemVersion);
+	}
+
 	@Override
 	public void saveAllDeferred() {
 		while (!isStorageQueueEmpty()) {
@@ -266,6 +274,12 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 	}
 
 	private void processDeferredCodeSystemDeletions() {
+
+		for (TermCodeSystemVersion next : myDefferedCodeSystemVersionsDeletions) {
+			myCodeSystemStorageSvc.deleteCodeSystemVersion(next);
+		}
+
+		myDefferedCodeSystemVersionsDeletions.clear();
 		for (TermCodeSystem next : myDefferedCodeSystemsDeletions) {
 			myCodeSystemStorageSvc.deleteCodeSystem(next);
 		}
@@ -300,7 +314,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 	}
 
 	private boolean isDeferredCodeSystemDeletions() {
-		return !myDefferedCodeSystemsDeletions.isEmpty();
+		return !myDefferedCodeSystemsDeletions.isEmpty() || !myDefferedCodeSystemVersionsDeletions.isEmpty();
 	}
 
 	private boolean isDeferredConcepts() {

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/ITermCodeSystemStorageSvc.java

@@ -41,6 +41,8 @@ public interface ITermCodeSystemStorageSvc {
 
 	void deleteCodeSystem(TermCodeSystem theCodeSystem);
 
+	void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion);
+
 	void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable);
 
 	/**

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.term.api;
  */
 
 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.TermConceptParentChildLink;
 import org.hl7.fhir.r4.model.ConceptMap;
@@ -54,6 +55,8 @@ public interface ITermDeferredStorageSvc {
 
 	void deleteCodeSystem(TermCodeSystem theCodeSystem);
 
+	void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion);
+
 	/**
 	 * This is mostly here for unit tests - Saves any and all deferred concepts and links
 	 */

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, String theCodingAVersion, String theCodingBVersion);
+
 	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/FhirResourceDaoR4CodeSystemTest.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -8,11 +9,14 @@ import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Test;
 
 import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
 
@@ -35,15 +39,7 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
 	@Test
 	public void testDeleteLargeCompleteCodeSystem() {
 
-		CodeSystem cs = new CodeSystem();
+		IIdType id = createLargeCodeSystem(null);
-		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
-		cs.setUrl("http://foo");
-		for (int i = 0; i < 222; i++) {
-			cs.addConcept().setCode("CODE" + i);
-		}
-		IIdType id = myCodeSystemDao.create(cs).getId().toUnqualifiedVersionless();
-		myTerminologyDeferredStorageSvc.saveDeferred();
-		myTerminologyDeferredStorageSvc.saveDeferred();
 
 		runInTransaction(() -> {
 			assertEquals(1, myTermCodeSystemDao.count());
@@ -72,6 +68,122 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testDeleteCodeSystemVersion() {
+
+		// Create code system with two versions.
+		IIdType id_first = createLargeCodeSystem("1");
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertNotNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+			List<ResourceTable> resourceList = myResourceTableDao.findAll();
+			assertEquals(222, myTermConceptDao.count());
+			assertEquals(1, resourceList.size());
+			assertNull(resourceList.get(0).getDeleted());
+		});
+
+		IIdType id_second = createLargeCodeSystem("2");
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertNotNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
+			assertEquals(2, myTermCodeSystemVersionDao.count());
+			assertEquals(444, myTermConceptDao.count());
+			List<ResourceTable> resourceList = myResourceTableDao.findAll();
+			assertEquals(2, resourceList.size());
+			long active = resourceList
+				.stream()
+				.filter(t -> t.getDeleted() == null).count();
+			assertEquals(2, active);
+		});
+
+		// Attempt to delete first version
+		myCodeSystemDao.delete(id_first, mySrd);
+
+		// Only the resource will be deleted initially
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertNotNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
+			assertEquals(2, myTermCodeSystemVersionDao.count());
+			assertEquals(444, myTermConceptDao.count());
+			List<ResourceTable> resourceList = myResourceTableDao.findAll();
+			assertEquals(2, resourceList.size());
+			long active = resourceList
+				.stream()
+				.filter(t -> t.getDeleted() == null).count();
+			assertEquals(1, active);
+		});
+
+		// Now the background scheduler will do its thing
+		myTerminologyDeferredStorageSvc.saveDeferred();
+
+		// Entities for first resource should be gone now.
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertNotNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+			assertEquals(222, myTermConceptDao.count());
+			List<ResourceTable> resourceList = myResourceTableDao.findAll();
+			assertEquals(2, resourceList.size());
+			long active = resourceList
+				.stream()
+				.filter(t -> t.getDeleted() == null).count();
+			assertEquals(1, active);
+		});
+
+		// Attempt to delete second version
+		myCodeSystemDao.delete(id_second, mySrd);
+
+		// Only the resource will be deleted initially
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertNotNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+			assertEquals(222,  myTermConceptDao.count());
+			List<ResourceTable> resourceList = myResourceTableDao.findAll();
+			assertEquals(2, resourceList.size());
+			long active = resourceList
+				.stream()
+				.filter(t -> t.getDeleted() == null).count();
+			assertEquals(0, active);
+		});
+
+		// Now the background scheduler will do its thing
+		myTerminologyDeferredStorageSvc.saveDeferred();
+
+		// The remaining versions and Code System entities should be gone now.
+		runInTransaction(() -> {
+			assertEquals(0, myTermCodeSystemDao.count());
+			assertNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
+			assertEquals(0, myTermCodeSystemVersionDao.count());
+			List<ResourceTable> resourceList = myResourceTableDao.findAll();
+			assertEquals(2, resourceList.size());
+			long active = resourceList
+				.stream()
+				.filter(t -> t.getDeleted() == null).count();
+			assertEquals(0, active);
+		});
+
+	}
+
+	private IIdType createLargeCodeSystem(String theVersion) {
+		CodeSystem cs = new CodeSystem();
+		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		cs.setUrl("http://foo");
+		if (theVersion != null) {
+			cs.setVersion(theVersion);
+		}
+		for (int i = 0; i < 222; i++) {
+			cs.addConcept().setCode("CODE" + i);
+		}
+		IIdType id = myCodeSystemDao.create(cs).getId().toUnqualifiedVersionless();
+		myTerminologyDeferredStorageSvc.saveDeferred();
+		myTerminologyDeferredStorageSvc.saveDeferred();
+		return id;
+	}
+
 	@AfterAll
 	public static void afterClassClearContext() {
 		TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);

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/ResourceProviderR4CodeSystemTest.java

@@ -325,6 +325,7 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 				.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("FOO"))
 				.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentB"))
 				.execute();
+			fail();
 		} catch (InvalidRequestException e) {
 			assertEquals("HTTP 400 Bad Request: Unknown code: [http://parentchild|FOO]", e.getMessage());
 		}
@@ -340,6 +341,7 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 				.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentB"))
 				.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("FOO"))
 				.execute();
+			fail();
 		} catch (InvalidRequestException e) {
 			assertEquals("HTTP 400 Bad Request: Unknown code: [http://parentchild|FOO]", e.getMessage());
 		}
@@ -355,6 +357,7 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
 				.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD + "A").setCode("ChildAA"))
 				.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD + "B").setCode("ParentA"))
 				.execute();
+			fail();
 		} catch (InvalidRequestException e) {
 			assertEquals("HTTP 400 Bad Request: Unable to test subsumption across different code systems", e.getMessage());
 		}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CodeSystemVersionedTest.java

@@ -0,0 +1,769 @@
+package ca.uhn.fhir.jpa.provider.r4;
+
+import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.CodeType;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Enumerations;
+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 org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.io.IOException;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.fail;
+
+public class ResourceProviderR4CodeSystemVersionedTest extends BaseResourceProviderR4Test {
+
+	private static final String SYSTEM_PARENTCHILD = "http://parentchild";
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4CodeSystemVersionedTest.class);
+
+	@BeforeEach
+	@Transactional
+	public void before02() throws IOException {
+		CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs-v1.xml");
+		myCodeSystemDao.create(cs, mySrd);
+
+		cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs-v2.xml");
+		myCodeSystemDao.create(cs, mySrd);
+
+		ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
+		myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
+
+		CodeSystem parentChildCs = new CodeSystem();
+		parentChildCs.setUrl(SYSTEM_PARENTCHILD);
+		parentChildCs.setVersion("1");
+		parentChildCs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		parentChildCs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		parentChildCs.setHierarchyMeaning(CodeSystem.CodeSystemHierarchyMeaning.ISA);
+
+		CodeSystem.ConceptDefinitionComponent parentA = parentChildCs.addConcept().setCode("ParentA").setDisplay("Parent A");
+		parentA.addConcept().setCode("ChildAA").setDisplay("Child AA");
+		parentA.addConcept().setCode("ParentC").setDisplay("Parent C");
+		parentChildCs.addConcept().setCode("ParentB").setDisplay("Parent B");
+
+		myCodeSystemDao.create(parentChildCs);
+
+		parentChildCs = new CodeSystem();
+		parentChildCs.setVersion("2");
+		parentChildCs.setUrl(SYSTEM_PARENTCHILD);
+		parentChildCs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		parentChildCs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		parentChildCs.setHierarchyMeaning(CodeSystem.CodeSystemHierarchyMeaning.ISA);
+
+		parentA = parentChildCs.addConcept().setCode("ParentA").setDisplay("Parent A v2");
+		parentA.addConcept().setCode("ChildAA").setDisplay("Child AA v2");
+		parentA.addConcept().setCode("ParentB").setDisplay("Parent B v2");
+		parentChildCs.addConcept().setCode("ParentC").setDisplay("Parent C v2");
+
+		myCodeSystemDao.create(parentChildCs);
+
+	}
+
+	@Test
+	public void testLookupOnExternalCodeMultiVersion() {
+		ResourceProviderR4ValueSetTest.createExternalCs(myCodeSystemDao, myResourceTableDao, myTermCodeSystemStorageSvc, mySrd, "1");
+		ResourceProviderR4ValueSetTest.createExternalCs(myCodeSystemDao, myResourceTableDao, myTermCodeSystemStorageSvc, mySrd, "2");
+
+		// First test with no version specified (should return from last version created)
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("ParentA"))
+			.andParameter("system", new UriType(FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals("SYSTEM NAME", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("2", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals("Parent A2", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+		// With HTTP GET
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("ParentA"))
+			.andParameter("system", new UriType(FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM))
+			.useHttpGet()
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("SYSTEM NAME"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals(("2"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals("Parent A2", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+		// Test with version 1 specified.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("ParentA"))
+			.andParameter("system", new UriType(FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM))
+			.andParameter("version", new StringType("1"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals("SYSTEM NAME", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("1", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals("Parent A1", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+		// With HTTP GET
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("ParentA"))
+			.andParameter("system", new UriType(FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM))
+			.andParameter("version", new StringType("1"))
+			.useHttpGet()
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("SYSTEM NAME"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals(("1"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals("Parent A1", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+		// Test with version 2 specified.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("ParentA"))
+			.andParameter("system", new UriType(FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM))
+			.andParameter("version", new StringType("2"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals("SYSTEM NAME", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("2", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals("Parent A2", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+		// With HTTP GET
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("ParentA"))
+			.andParameter("system", new UriType(FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM))
+			.andParameter("version", new StringType("2"))
+			.useHttpGet()
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("SYSTEM NAME"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals(("2"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals("Parent A2", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+	}
+
+	@Test
+	public void testLookupOperationByCodeAndSystemBuiltInCode() {
+		// First test with no version specified (should return the one and only version defined).
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("ACSN"))
+			.andParameter("system", new UriType("http://terminology.hl7.org/CodeSystem/v2-0203"))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals("v2.0203", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("2.9", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals("Accession ID", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+		// Repeat with version specified.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("ACSN"))
+			.andParameter("system", new UriType("http://terminology.hl7.org/CodeSystem/v2-0203"))
+			.andParameter("version", new StringType("2.9"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals("v2.0203", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("2.9", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals("Accession ID", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+	}
+
+	@Test
+	public void testLookupOperationByCodeAndSystemBuiltInNonexistentVersion() {
+		try {
+			myClient
+				.operation()
+				.onType(CodeSystem.class)
+				.named("lookup")
+				.withParameter(Parameters.class, "code", new CodeType("ACSN"))
+				.andParameter("system", new UriType("http://hl7.org/fhir/v2/0203"))
+				.andParameter("version", new StringType("2.8"))
+				.execute();
+			fail();
+		} catch (ResourceNotFoundException e) {
+			ourLog.info("Lookup failed as expected");
+		}
+	}
+
+	@Test
+	public void testLookupOperationByCodeAndSystemUserDefinedCode() {
+		// First test with no version specified (should return from last version created)
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("8450-9"))
+			.andParameter("system", new UriType("http://acme.org"))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("ACME Codes"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("2", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals(("Systolic blood pressure--expiration v2"), ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+		// Test with version 1 specified.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("8450-9"))
+			.andParameter("system", new UriType("http://acme.org"))
+			.andParameter("version", new StringType("1"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("ACME Codes"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("1", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals(("Systolic blood pressure--expiration"), ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+		// Test with version 2 specified
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("8450-9"))
+			.andParameter("system", new UriType("http://acme.org"))
+			.andParameter("version", new StringType("2"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("ACME Codes"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("2", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals(("Systolic blood pressure--expiration v2"), ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+	}
+
+	@Test
+	public void testLookupOperationByCodeAndSystemUserDefinedNonExistentVersion() {
+		try {
+			myClient
+				.operation()
+				.onType(CodeSystem.class)
+				.named("lookup")
+				.withParameter(Parameters.class, "code", new CodeType("8450-9"))
+				.andParameter("system", new UriType("http://acme.org"))
+				.andParameter("version", new StringType("3"))
+				.execute();
+			fail();
+		} catch (ResourceNotFoundException e) {
+			ourLog.info("Lookup failed as expected");
+		}
+	}
+
+	@Test
+	public void testLookupOperationByCoding() {
+		// First test with no version specified (should return from last version created)
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "coding", new Coding().setSystem("http://acme.org").setCode("8450-9"))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("ACME Codes"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("2",  ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals(("Systolic blood pressure--expiration v2"), ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+		// Test with version set to 1
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "coding", new Coding().setSystem("http://acme.org").setCode("8450-9").setVersion("1"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("ACME Codes"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("1",  ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals(("Systolic blood pressure--expiration"), ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+		// Test with version set to 2
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "coding", new Coding().setSystem("http://acme.org").setCode("8450-9").setVersion("2"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("ACME Codes"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("version", respParam.getParameter().get(1).getName());
+		assertEquals("2",  ((StringType) respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(2).getName());
+		assertEquals(("Systolic blood pressure--expiration v2"), ((StringType) respParam.getParameter().get(2).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(3).getName());
+		assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
+
+	}
+
+	@Test
+	public void testSubsumesOnCodes_Subsumes() {
+		// First test with no version specified (should return result for last version created).
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codeA", new CodeType("ParentB"))
+			.andParameter("codeB", new CodeType("ParentA"))
+			.andParameter("system", new UriType(SYSTEM_PARENTCHILD))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMES.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 1.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codeA", new CodeType("ParentC"))
+			.andParameter("codeB", new CodeType("ParentA"))
+			.andParameter("system", new UriType(SYSTEM_PARENTCHILD))
+			.andParameter("version", new StringType("1"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMES.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 2.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codeA", new CodeType("ParentB"))
+			.andParameter("codeB", new CodeType("ParentA"))
+			.andParameter("system", new UriType(SYSTEM_PARENTCHILD))
+			.andParameter("version", new StringType("2"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMES.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+	}
+
+	@Test
+	public void testSubsumesOnCodes_Subsumedby() {
+		// First test with no version specified (should return result for last version created).
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codeA", new CodeType("ParentA"))
+			.andParameter("codeB", new CodeType("ParentB"))
+			.andParameter("system", new UriType(SYSTEM_PARENTCHILD))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMEDBY.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 1.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codeA", new CodeType("ParentA"))
+			.andParameter("codeB", new CodeType("ParentC"))
+			.andParameter("system", new UriType(SYSTEM_PARENTCHILD))
+			.andParameter("version", new StringType("1"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMEDBY.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 2.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codeA", new CodeType("ParentA"))
+			.andParameter("codeB", new CodeType("ParentB"))
+			.andParameter("system", new UriType(SYSTEM_PARENTCHILD))
+			.andParameter("version", new StringType("2"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMEDBY.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+	}
+
+	@Test
+	public void testSubsumesOnCodes_Disjoint() {
+		// First test with no version specified (should return result for last version created).
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codeA", new CodeType("ParentA"))
+			.andParameter("codeB", new CodeType("ParentC"))
+			.andParameter("system", new UriType(SYSTEM_PARENTCHILD))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.NOTSUBSUMED.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 1
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codeA", new CodeType("ParentA"))
+			.andParameter("codeB", new CodeType("ParentB"))
+			.andParameter("system", new UriType(SYSTEM_PARENTCHILD))
+			.andParameter("version", new StringType("1"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.NOTSUBSUMED.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 2
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codeA", new CodeType("ParentA"))
+			.andParameter("codeB", new CodeType("ParentC"))
+			.andParameter("system", new UriType(SYSTEM_PARENTCHILD))
+			.andParameter("version", new StringType("2"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.NOTSUBSUMED.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+	}
+
+	@Test
+	public void testSubsumesOnCodings_MismatchedCsVersions() {
+		try {
+			myClient
+				.operation()
+				.onType(CodeSystem.class)
+				.named(JpaConstants.OPERATION_SUBSUMES)
+				.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ChildAA").setVersion("1"))
+				.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentA").setVersion("2"))
+				.execute();
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("HTTP 400 Bad Request: Unable to test subsumption across different code system versions", e.getMessage());
+		}
+	}
+
+
+	@Test
+	public void testSubsumesOnCodings_Subsumes() {
+		// First test with no version specified (should return result for last version created).
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentB"))
+			.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentA"))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMES.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 1.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentC").setVersion("1"))
+			.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentA").setVersion("1"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMES.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 2.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentB").setVersion("2"))
+			.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentA").setVersion("2"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMES.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+	}
+
+
+	@Test
+	public void testSubsumesOnCodings_Subsumedby() {
+		// First test with no version specified (should return result for last version created).
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentA"))
+			.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentB"))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMEDBY.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 1.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentA").setVersion("1"))
+			.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentC").setVersion("1"))
+			.execute();
+
+		 resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMEDBY.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 2.
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentA").setVersion("2"))
+			.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentB").setVersion("2"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.SUBSUMEDBY.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+	}
+
+	@Test
+	public void testSubsumesOnCodings_Disjoint() {
+		// First test with no version specified (should return result for last version created).
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentA"))
+			.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentC"))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.NOTSUBSUMED.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 1
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentA").setVersion("1"))
+			.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentB").setVersion("1"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.NOTSUBSUMED.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+		// Test with version set to 2
+		respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_SUBSUMES)
+			.withParameter(Parameters.class, "codingA", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentA").setVersion("2"))
+			.andParameter("codingB", new Coding().setSystem(SYSTEM_PARENTCHILD).setCode("ParentC").setVersion("2"))
+			.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertEquals(1, respParam.getParameter().size());
+		assertEquals("outcome", respParam.getParameter().get(0).getName());
+		assertEquals(ConceptSubsumptionOutcome.NOTSUBSUMED.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
+
+	}
+
+
+}

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;
@@ -1089,4 +1090,38 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
 		return codeSystem;
 	}
 
+	public static CodeSystem createExternalCs(IFhirResourceDao<CodeSystem> theCodeSystemDao, IResourceTableDao theResourceTableDao, ITermCodeSystemStorageSvc theTermCodeSystemStorageSvc, ServletRequestDetails theRequestDetails, String theCodeSystemVersion) {
+		CodeSystem codeSystem = new CodeSystem();
+		codeSystem.setUrl(URL_MY_CODE_SYSTEM);
+		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
+		codeSystem.setVersion(theCodeSystemVersion);
+		IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();
+
+		ResourceTable table = theResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
+
+		TermCodeSystemVersion cs = new TermCodeSystemVersion();
+		cs.setResource(table);
+
+		TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A" + theCodeSystemVersion);
+		cs.getConcepts().add(parentA);
+
+		TermConcept childAA = new TermConcept(cs, "childAA").setDisplay("Child AA" + theCodeSystemVersion);
+		parentA.addChild(childAA, RelationshipTypeEnum.ISA);
+
+		TermConcept childAAA = new TermConcept(cs, "childAAA").setDisplay("Child AAA" + theCodeSystemVersion);
+		childAA.addChild(childAAA, RelationshipTypeEnum.ISA);
+
+		TermConcept childAAB = new TermConcept(cs, "childAAB").setDisplay("Child AAB" + theCodeSystemVersion);
+		childAA.addChild(childAAB, RelationshipTypeEnum.ISA);
+
+		TermConcept childAB = new TermConcept(cs, "childAB").setDisplay("Child AB" + theCodeSystemVersion);
+		parentA.addChild(childAB, RelationshipTypeEnum.ISA);
+
+		TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B" + theCodeSystemVersion);
+		cs.getConcepts().add(parentB);
+
+		theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", theCodeSystemVersion, cs, table);
+		return codeSystem;
+	}
+
 }

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

@@ -1,11 +1,17 @@
 package ca.uhn.fhir.jpa.term;
 
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.CodeType;
 import org.junit.jupiter.api.Test;
 
+import java.util.ArrayList;
+
+import static org.junit.jupiter.api.Assertions.fail;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
@@ -13,39 +19,115 @@ 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();
+		CodeSystem firstUpload = createCodeSystemWithMoreThan100Concepts();
+		CodeSystem duplicateUpload = createCodeSystemWithMoreThan100Concepts();
 
-		// Create CodeSystem resource
+		testCreatingAndUpdatingCodeSystemEntity(firstUpload, duplicateUpload, 125, "Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/");
-		ResourceTable codeSystemResourceEntity = (ResourceTable) myCodeSystemDao.create(upload, mySrd).getEntity();
 
-		// Update the CodeSystem resource
+		runInTransaction(() -> {
-		runInTransaction(() -> myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(upload, codeSystemResourceEntity));
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+			TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri(URL_MY_CODE_SYSTEM);
 
-		/*
+			TermCodeSystemVersion myTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull( myTermCodeSystem.getPid());
-			Because there are more than 100 concepts in the code system, the first 100 will be persisted immediately and
+			assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion.getPid());
-			the remaining 25 concepts will be queued up for "deferred save".
+			assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion.getResource().getId());
+		});
+	}
+
+
+	@Test
+	public void testStoreNewCodeSystemVersionForExistingCodeSystemVersionId() {
+		CodeSystem firstUpload = createCodeSystemWithMoreThan100Concepts();
+		firstUpload.setVersion("1");
+
+		CodeSystem duplicateUpload = createCodeSystemWithMoreThan100Concepts();
+		duplicateUpload.setVersion("1");
+
+		testCreatingAndUpdatingCodeSystemEntity(firstUpload, duplicateUpload, 125,"Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\" and CodeSystem.version \"1\", already have one with resource ID: CodeSystem/");
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+			TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri(URL_MY_CODE_SYSTEM);
+
+			TermCodeSystemVersion myTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion( myTermCodeSystem.getPid(), "1");
+			assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion.getPid());
+			assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion.getResource().getId());
+		});
+
+		// Now add a second version
+		firstUpload = createCodeSystemWithMoreThan100Concepts();
+		firstUpload.setVersion("2");
+
+		duplicateUpload = createCodeSystemWithMoreThan100Concepts();
+		duplicateUpload.setVersion("2");
+
+		testCreatingAndUpdatingCodeSystemEntity(firstUpload, duplicateUpload, 251,"Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\" and CodeSystem.version \"2\", already have one with resource ID: CodeSystem/");
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(2, myTermCodeSystemVersionDao.count());
+			TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri(URL_MY_CODE_SYSTEM);
+
+			TermCodeSystemVersion mySecondTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2");
+			assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), mySecondTermCodeSystemVersion.getPid());
+			assertEquals(myTermCodeSystem.getResource().getId(), mySecondTermCodeSystemVersion.getResource().getId());
+		});
 
-			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;
 
 	}
 
+	private void testCreatingAndUpdatingCodeSystemEntity(CodeSystem theUpload, CodeSystem theDuplicate, int expectedCnt, String theDuplicateErrorBaseMsg) {
+
+		// Create CodeSystem resource
+		ResourceTable codeSystemResourceEntity = (ResourceTable) myCodeSystemDao.create(theUpload, mySrd).getEntity();
+
+		// Create the CodeSystem and CodeSystemVersion entities
+		validateCodeSystemUpdates(expectedCnt);
+
+		// Update the CodeSystem
+		theUpload.addConcept(new CodeSystem.ConceptDefinitionComponent(new CodeType("codeB")));
+		// Update the CodeSystem and CodeSystemVersion entities
+		runInTransaction(() -> myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(theUpload, codeSystemResourceEntity));
+		validateCodeSystemUpdates(expectedCnt+1);
+
+		// Try duplicating the CodeSystem
+		Long originalResId = codeSystemResourceEntity.getId();
+		try {
+			myCodeSystemDao.create(theDuplicate, mySrd);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals(theDuplicateErrorBaseMsg + originalResId, e.getMessage());
+		}
+
+		// Try updating code system when content mode is NOT PRESENT
+		theUpload.setConcept(new ArrayList<>());
+		theUpload.setContent((CodeSystem.CodeSystemContentMode.NOTPRESENT));
+		runInTransaction(() -> myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(theUpload, codeSystemResourceEntity));
+		validateCodeSystemUpdates(expectedCnt+1);
+
+	}
+
+	private void validateCodeSystemUpdates(int theExpectedConceptCount) {
+		myTerminologyDeferredStorageSvc.setProcessDeferred(true);
+		myTerminologyDeferredStorageSvc.saveDeferred();
+		myTerminologyDeferredStorageSvc.setProcessDeferred(false);
+		assertEquals(theExpectedConceptCount, myTermConceptDao.count());
+
+	}
 
 }

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

@@ -343,6 +343,37 @@ 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());
+
+		// Update LOINC marked as version 2.67
+		myFiles = new ZipCollectionBuilder();
+		addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v267_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("2.67", 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(3)).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 {
@@ -383,7 +414,11 @@ 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

@@ -4,6 +4,9 @@ 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;
@@ -21,7 +24,6 @@ import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
 import org.hl7.fhir.r4.model.UriType;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.model.codesystems.HttpVerb;
-import org.hl7.fhir.utilities.validation.ValidationOptions;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -32,9 +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;
@@ -1802,10 +1809,10 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
 		createCodeSystem();
 
 		IValidationSupport.CodeValidationResult validation = myTermSvc.validateCode(new ValidationSupportContext(myValidationSupport), new ConceptValidationOptions(), CS_URL, "ParentWithNoChildrenA", null, null);
-		assertEquals(true, validation.isOk());
+		assertTrue(validation.isOk());
 
 		validation = myTermSvc.validateCode(new ValidationSupportContext(myValidationSupport), new ConceptValidationOptions(), CS_URL, "ZZZZZZZ", null, null);
-		assertEquals(false, validation.isOk());
+		assertFalse(validation.isOk());
 	}
 
 	@Test
@@ -1904,4 +1911,109 @@ 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");
+
+		IIdType id_v2 = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
+		codes = myTermSvc.findCodesBelow(id_v2.getIdPartAsLong(), id_v2.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_v2.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/extensional-case-3-cs-v1.xml

@@ -0,0 +1,101 @@
+<CodeSystem xmlns="http://hl7.org/fhir">
+	<url value="http://acme.org" />
+	<version value="1"/>
+	<name value="ACME Codes" />
+	<concept>
+		<code value="8450-9" />
+		<display value="Systolic blood pressure--expiration" />
+	</concept>
+	<concept>
+		<code value="11378-7" />
+		<display value="Systolic blood pressure at First encounter" />
+	</concept>
+	<concept>
+		<code value="8493-9" />
+		<display value="Systolic blood pressure 10 hour minimum" />
+	</concept>
+	<concept>
+		<code value="8494-7" />
+		<display value="Systolic blood pressure 12 hour minimum" />
+	</concept>
+	<concept>
+		<code value="8495-4" />
+		<display value="Systolic blood pressure 24 hour minimum" />
+	</concept>
+	<concept>
+		<code value="8451-7" />
+		<display value="Systolic blood pressure--inspiration" />
+	</concept>
+	<concept>
+		<code value="8452-5" />
+		<display value="Systolic blood pressure.inspiration - expiration" />
+	</concept>
+	<concept>
+		<code value="8459-0" />
+		<display value="Systolic blood pressure--sitting" />
+	</concept>
+	<concept>
+		<code value="8460-8" />
+		<display value="Systolic blood pressure--standing" />
+	</concept>
+	<concept>
+		<code value="8461-6" />
+		<display value="Systolic blood pressure--supine" />
+	</concept>
+	<concept>
+		<code value="8479-8" />
+		<display value="Systolic blood pressure by palpation" />
+	</concept>
+	<concept>
+		<code value="8480-6" />
+		<display value="Systolic blood pressure" />
+	</concept>
+	<concept>
+		<code value="8481-4" />
+		<display value="Systolic blood pressure 1 hour maximum" />
+	</concept>
+	<concept>
+		<code value="8482-2" />
+		<display value="Systolic blood pressure 8 hour maximum" />
+	</concept>
+	<concept>
+		<code value="8483-0" />
+		<display value="Systolic blood pressure 10 hour maximum" />
+	</concept>
+	<concept>
+		<code value="8484-8" />
+		<display value="Systolic blood pressure 12 hour maximum" />
+	</concept>
+	<concept>
+		<code value="8485-5" />
+		<display value="Systolic blood pressure 24 hour maximum" />
+	</concept>
+	<concept>
+		<code value="8486-3" />
+		<display value="Systolic blood pressure 1 hour mean" />
+	</concept>
+	<concept>
+		<code value="8487-1" />
+		<display value="Systolic blood pressure 8 hour mean" />
+	</concept>
+	<concept>
+		<code value="8488-9" />
+		<display value="Systolic blood pressure 10 hour mean" />
+	</concept>
+	<concept>
+		<code value="8489-7" />
+		<display value="Systolic blood pressure 12 hour mean" />
+	</concept>
+	<concept>
+		<code value="8490-5" />
+		<display value="Systolic blood pressure 24 hour mean" />
+	</concept>
+	<concept>
+		<code value="8491-3" />
+		<display value="Systolic blood pressure 1 hour minimum" />
+	</concept>
+	<concept>
+		<code value="8492-1" />
+		<display value="Systolic blood pressure 8 hour minimum" />
+	</concept>
+</CodeSystem>

hapi-fhir-jpaserver-base/src/test/resources/extensional-case-3-cs-v2.xml

@@ -0,0 +1,101 @@
+<CodeSystem xmlns="http://hl7.org/fhir">
+	<url value="http://acme.org" />
+	<version value="2"/>
+	<name value="ACME Codes" />
+	<concept>
+		<code value="8450-9" />
+		<display value="Systolic blood pressure--expiration v2" />
+	</concept>
+	<concept>
+		<code value="11378-7" />
+		<display value="Systolic blood pressure at First encounter v2" />
+	</concept>
+	<concept>
+		<code value="8493-9" />
+		<display value="Systolic blood pressure 10 hour minimum v2" />
+	</concept>
+	<concept>
+		<code value="8494-7" />
+		<display value="Systolic blood pressure 12 hour minimum v2" />
+	</concept>
+	<concept>
+		<code value="8495-4" />
+		<display value="Systolic blood pressure 24 hour minimum v2" />
+	</concept>
+	<concept>
+		<code value="8451-7" />
+		<display value="Systolic blood pressure--inspiration v2" />
+	</concept>
+	<concept>
+		<code value="8452-5" />
+		<display value="Systolic blood pressure.inspiration - expiration v2" />
+	</concept>
+	<concept>
+		<code value="8459-0" />
+		<display value="Systolic blood pressure--sitting v2" />
+	</concept>
+	<concept>
+		<code value="8460-8" />
+		<display value="Systolic blood pressure--standing v2" />
+	</concept>
+	<concept>
+		<code value="8461-6" />
+		<display value="Systolic blood pressure--supine v2" />
+	</concept>
+	<concept>
+		<code value="8479-8" />
+		<display value="Systolic blood pressure by palpation v2" />
+	</concept>
+	<concept>
+		<code value="8480-6" />
+		<display value="Systolic blood pressure v2" />
+	</concept>
+	<concept>
+		<code value="8481-4" />
+		<display value="Systolic blood pressure 1 hour maximum v2" />
+	</concept>
+	<concept>
+		<code value="8482-2" />
+		<display value="Systolic blood pressure 8 hour maximum v2" />
+	</concept>
+	<concept>
+		<code value="8483-0" />
+		<display value="Systolic blood pressure 10 hour maximum v2" />
+	</concept>
+	<concept>
+		<code value="8484-8" />
+		<display value="Systolic blood pressure 12 hour maximum v2" />
+	</concept>
+	<concept>
+		<code value="8485-5" />
+		<display value="Systolic blood pressure 24 hour maximum v2" />
+	</concept>
+	<concept>
+		<code value="8486-3" />
+		<display value="Systolic blood pressure 1 hour mean v2" />
+	</concept>
+	<concept>
+		<code value="8487-1" />
+		<display value="Systolic blood pressure 8 hour mean v2" />
+	</concept>
+	<concept>
+		<code value="8488-9" />
+		<display value="Systolic blood pressure 10 hour mean v2" />
+	</concept>
+	<concept>
+		<code value="8489-7" />
+		<display value="Systolic blood pressure 12 hour mean v2" />
+	</concept>
+	<concept>
+		<code value="8490-5" />
+		<display value="Systolic blood pressure 24 hour mean v2" />
+	</concept>
+	<concept>
+		<code value="8491-3" />
+		<display value="Systolic blood pressure 1 hour minimum v2" />
+	</concept>
+	<concept>
+		<code value="8492-1" />
+		<display value="Systolic blood pressure 8 hour minimum v2" />
+	</concept>
+</CodeSystem>

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) {

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

@@ -254,7 +254,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
 				return retVal;
 			}
 		});
-		when(mockSupport.lookupCode(any(), any(), any())).thenAnswer(t -> {
+		when(mockSupport.lookupCode(any(), any(), any(), any())).thenAnswer(t -> {
 			String system = t.getArgument(1, String.class);
 			String code = t.getArgument(2, String.class);
 			if (myValidConcepts.contains(system + "___" + code)) {