Incremental work on large ValueSet expansion support; still need to fix asynchronous tests and actually use the terminology tables when expanding.

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

@@ -26,10 +26,15 @@ import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.query.Param;
 
+import java.util.Optional;
+
 public interface ITermValueSetConceptDao extends JpaRepository<TermValueSetConcept, Long> {
 
 	@Query("DELETE FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
 	@Modifying
-	void deleteTermValueSetConceptsByValueSetId(@Param("pid") Long theValueSetId);
+	void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
+
+	@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
+	Optional<TermValueSetConcept> findByValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
 
 }

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

@@ -30,6 +30,6 @@ public interface ITermValueSetConceptDesignationDao extends JpaRepository<TermVa
 
 	@Query("DELETE FROM TermValueSetConceptDesignation vscd WHERE vscd.myConcept.myValueSet.myId = :pid")
 	@Modifying
-	void deleteTermValueSetConceptDesignationsByValueSetId(@Param("pid") Long theValueSetId);
+	void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
 
 }

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

@@ -21,6 +21,9 @@ package ca.uhn.fhir.jpa.dao.data;
  */
 
 import ca.uhn.fhir.jpa.entity.TermValueSet;
+import ca.uhn.fhir.jpa.entity.TermValueSetExpansionStatusEnum;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
@@ -32,7 +35,7 @@ public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
 
 	@Query("DELETE FROM TermValueSet vs WHERE vs.myId = :pid")
 	@Modifying
-	void deleteTermValueSetById(@Param("pid") Long theId);
+	void deleteByTermValueSetId(@Param("pid") Long theId);
 
 	@Query("SELECT vs FROM TermValueSet vs WHERE vs.myResourcePid = :resource_pid")
 	Optional<TermValueSet> findByResourcePid(@Param("resource_pid") Long theResourcePid);
@@ -40,4 +43,7 @@ public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
 	@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url")
 	Optional<TermValueSet> findByUrl(@Param("url") String theUrl);
 
+	@Query("SELECT vs FROM TermValueSet vs WHERE vs.myExpansionStatus = :expansion_status")
+	Page<TermValueSet> findByExpansionStatus(Pageable pageable, @Param("expansion_status") TermValueSetExpansionStatusEnum theExpansionStatus);
+
 }

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

@@ -315,7 +315,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
 				try {
 					ValueSet valueSet = (ValueSet) theResource;
 					org.hl7.fhir.r4.model.ValueSet converted = VersionConvertor_30_40.convertValueSet(valueSet);
-					myHapiTerminologySvc.storeTermValueSetAndChildren(retVal, converted);
+					myHapiTerminologySvc.storeTermValueSet(retVal, converted);
 				} catch (FHIRException fe) {
 					throw new InternalErrorException(fe);
 				}

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

@@ -313,7 +313,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
 		if (myDaoConfig.isPreExpandValueSetsExperimental()) {
 			if (retVal.getDeleted() == null) {
 				ValueSet valueSet = (ValueSet) theResource;
-				myHapiTerminologySvc.storeTermValueSetAndChildren(retVal, valueSet);
+				myHapiTerminologySvc.storeTermValueSet(retVal, valueSet);
 			} else {
 				myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
 			}

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

@@ -101,6 +101,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 	private static boolean ourLastResultsFromTranslationCache; // For testing.
 	private static boolean ourLastResultsFromTranslationWithReverseCache; // For testing.
 	@Autowired
+	protected DaoRegistry myDaoRegistry;
+	@Autowired
 	protected ITermCodeSystemDao myCodeSystemDao;
 	@Autowired
 	protected ITermConceptDao myConceptDao;
@@ -151,8 +153,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 	private PlatformTransactionManager myTransactionManager;
 	@Autowired(required = false)
 	private IFulltextSearchSvc myFulltextSearchSvc;
+	@Autowired
+	private PlatformTransactionManager myTxManager;
 
-	private void addCodeIfNotAlreadyAdded(IValueSetCodeAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, TermConcept theConcept, boolean theAdd, AtomicInteger theCodeCounter) {
+	private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, TermConcept theConcept, boolean theAdd, AtomicInteger theCodeCounter) {
 		String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
 		String code = theConcept.getCode();
 		String display = theConcept.getDisplay();
@@ -160,28 +164,28 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, designations, theAdd, theCodeCounter, codeSystem, code, display);
 	}
 
-	private void addCodeIfNotAlreadyAdded(IValueSetCodeAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, Collection<TermConceptDesignation> theDesignations, boolean theAdd, AtomicInteger theCodeCounter, String theCodeSystem, String theCode, String theDisplay) {
+	private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, Collection<TermConceptDesignation> theDesignations, boolean theAdd, AtomicInteger theCodeCounter, String theCodeSystem, String theCode, String theDisplay) {
 		if (isNoneBlank(theCodeSystem, theCode)) {
 			if (theAdd && theAddedCodes.add(theCodeSystem + "|" + theCode)) {
-				theValueSetCodeAccumulator.includeCodeWithDesignations(theCodeSystem, theCode, theDisplay, theDesignations);
+				theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem, theCode, theDisplay, theDesignations);
 				theCodeCounter.incrementAndGet();
 			}
 
 			if (!theAdd && theAddedCodes.remove(theCodeSystem + "|" + theCode)) {
-				theValueSetCodeAccumulator.excludeCode(theCodeSystem, theCode);
+				theValueSetCodeAccumulator.excludeConcept(theCodeSystem, theCode);
 				theCodeCounter.decrementAndGet();
 			}
 		}
 	}
 
-	private void addConceptsToList(IValueSetCodeAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, String theSystem, List<CodeSystem.ConceptDefinitionComponent> theConcept, boolean theAdd) {
+	private void addConceptsToList(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, String theSystem, List<CodeSystem.ConceptDefinitionComponent> theConcept, boolean theAdd) {
 		for (CodeSystem.ConceptDefinitionComponent next : theConcept) {
 			if (isNoneBlank(theSystem, next.getCode())) {
 				if (theAdd && theAddedCodes.add(theSystem + "|" + next.getCode())) {
-					theValueSetCodeAccumulator.includeCode(theSystem, next.getCode(), next.getDisplay());
+					theValueSetCodeAccumulator.includeConcept(theSystem, next.getCode(), next.getDisplay());
 				}
 				if (!theAdd && theAddedCodes.remove(theSystem + "|" + next.getCode())) {
-					theValueSetCodeAccumulator.excludeCode(theSystem, next.getCode());
+					theValueSetCodeAccumulator.excludeConcept(theSystem, next.getCode());
 				}
 			}
 			addConceptsToList(theValueSetCodeAccumulator, theAddedCodes, theSystem, next.getConcept(), theAdd);
@@ -389,9 +393,9 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 			TermValueSet existingTermValueSet = optionalExistingTermValueSetById.get();
 
 			ourLog.info("Deleting existing TermValueSet {} and its children...", existingTermValueSet.getId());
-			myValueSetConceptDesignationDao.deleteTermValueSetConceptDesignationsByValueSetId(existingTermValueSet.getId());
+			myValueSetConceptDesignationDao.deleteByTermValueSetId(existingTermValueSet.getId());
-			myValueSetConceptDao.deleteTermValueSetConceptsByValueSetId(existingTermValueSet.getId());
+			myValueSetConceptDao.deleteByTermValueSetId(existingTermValueSet.getId());
-			myValueSetDao.deleteTermValueSetById(existingTermValueSet.getId());
+			myValueSetDao.deleteByTermValueSetId(existingTermValueSet.getId());
 			ourLog.info("Done deleting existing TermValueSet {} and its children.", existingTermValueSet.getId());
 
 			ourLog.info("Flushing...");
@@ -457,7 +461,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 	@Transactional(propagation = Propagation.REQUIRED)
 	public ValueSet expandValueSet(ValueSet theValueSetToExpand) {
 
-		ValueSetExpansionComponentWithCodeAccumulator expansionComponent = new ValueSetExpansionComponentWithCodeAccumulator();
+		ValueSetExpansionComponentWithConceptAccumulator expansionComponent = new ValueSetExpansionComponentWithConceptAccumulator();
 		expansionComponent.setIdentifier(UUID.randomUUID().toString());
 		expansionComponent.setTimestamp(new Date());
 
@@ -476,11 +480,11 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 
 	@Override
 	@Transactional(propagation = Propagation.REQUIRED)
-	public void expandValueSet(ValueSet theValueSetToExpand, IValueSetCodeAccumulator theValueSetCodeAccumulator) {
+	public void expandValueSet(ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
 		expandValueSet(theValueSetToExpand, theValueSetCodeAccumulator, new AtomicInteger(0));
 	}
 
-	private void expandValueSet(ValueSet theValueSetToExpand, IValueSetCodeAccumulator theValueSetCodeAccumulator, AtomicInteger theCodeCounter) {
+	private void expandValueSet(ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator, AtomicInteger theCodeCounter) {
 		Set<String> addedCodes = new HashSet<>();
 
 		// Handle includes
@@ -509,7 +513,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		return retVal;
 	}
 
-	private void expandValueSetHandleIncludeOrExclude(IValueSetCodeAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, boolean theAdd, AtomicInteger theCodeCounter) {
+	private void expandValueSetHandleIncludeOrExclude(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, boolean theAdd, AtomicInteger theCodeCounter) {
 		String system = theInclude.getSystem();
 		boolean hasSystem = isNotBlank(system);
 		boolean hasValueSet = theInclude.getValueSet().size() > 0;
@@ -676,10 +680,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 							CodeSystem.ConceptDefinitionComponent code = findCode(codeSystemFromContext.getConcept(), nextCode);
 							if (code != null) {
 								if (theAdd && theAddedCodes.add(system + "|" + nextCode)) {
-									theValueSetCodeAccumulator.includeCode(system, nextCode, code.getDisplay());
+									theValueSetCodeAccumulator.includeConcept(system, nextCode, code.getDisplay());
 								}
 								if (!theAdd && theAddedCodes.remove(system + "|" + nextCode)) {
-									theValueSetCodeAccumulator.excludeCode(system, nextCode);
+									theValueSetCodeAccumulator.excludeConcept(system, nextCode);
 								}
 							}
 						}
@@ -706,7 +710,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 
 					}
 					if (isNoneBlank(nextConcept.getSystem(), nextConcept.getCode()) && !theAdd && theAddedCodes.remove(nextConcept.getSystem() + "|" + nextConcept.getCode())) {
-						theValueSetCodeAccumulator.excludeCode(nextConcept.getSystem(), nextConcept.getCode());
+						theValueSetCodeAccumulator.excludeConcept(nextConcept.getSystem(), nextConcept.getCode());
 					}
 				}
 
@@ -716,10 +720,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		}
 	}
 
-	private void expandWithoutHibernateSearch(IValueSetCodeAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
+	private void expandWithoutHibernateSearch(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
 		ourLog.trace("Hibernate search is not enabled");
-		if (theValueSetCodeAccumulator instanceof ValueSetExpansionComponentWithCodeAccumulator) {
+		if (theValueSetCodeAccumulator instanceof ValueSetExpansionComponentWithConceptAccumulator) {
-			Validate.isTrue(((ValueSetExpansionComponentWithCodeAccumulator) theValueSetCodeAccumulator).getParameter().isEmpty(), "Can not expand ValueSet with parameters - Hibernate Search is not enabled on this server.");
+			Validate.isTrue(((ValueSetExpansionComponentWithConceptAccumulator) theValueSetCodeAccumulator).getParameter().isEmpty(), "Can not expand ValueSet with parameters - Hibernate Search is not enabled on this server.");
 		}
 		Validate.isTrue(theInclude.getFilter().isEmpty(), "Can not expand ValueSet with filters - Hibernate Search is not enabled on this server.");
 		Validate.isTrue(isNotBlank(theSystem), "Can not expand ValueSet without explicit system - Hibernate Search is not enabled on this server.");
@@ -1491,9 +1495,46 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		ourLog.info("Done storing TermConceptMap.");
 	}
 
+	@Scheduled(fixedDelay = 1000)
+	@Transactional
+	@Override
+	public synchronized void preExpandValueSetToTerminologyTables() {
+		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
+				Optional<TermValueSet> optionalTermValueSet = getNextTermValueSetNotExpanded();
+				if (optionalTermValueSet.isPresent()) {
+					TermValueSet termValueSet = optionalTermValueSet.get();
+					termValueSet.setExpansionStatus(TermValueSetExpansionStatusEnum.EXPANSION_IN_PROGRESS);
+					myValueSetDao.saveAndFlush(termValueSet);
+
+					ValueSet valueSet = getValueSetFromResourceTable(termValueSet.getResource());
+
+					expandValueSet(valueSet, new ValueSetConceptAccumulator(termValueSet, myValueSetConceptDao, myValueSetConceptDesignationDao));
+
+					termValueSet.setExpansionStatus(TermValueSetExpansionStatusEnum.EXPANDED);
+					myValueSetDao.saveAndFlush(termValueSet);
+				}
+			}
+		});
+	}
+
+	protected abstract ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable);
+
+	private Optional<TermValueSet> getNextTermValueSetNotExpanded() {
+		Optional<TermValueSet> retVal = Optional.empty();
+		Page<TermValueSet> page = myValueSetDao.findByExpansionStatus(PageRequest.of(0, 1), TermValueSetExpansionStatusEnum.NOT_EXPANDED);
+
+		if (!page.getContent().isEmpty()) {
+			retVal = Optional.of(page.getContent().get(0));
+		}
+
+		return retVal;
+	}
+
 	@Override
 	@Transactional
-	public void storeTermValueSetAndChildren(ResourceTable theResourceTable, ValueSet theValueSet) {
+	public void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet) {
 		ourLog.info("Storing TermValueSet {}", theValueSet.getIdElement().getValue());
 
 		ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
@@ -1513,58 +1554,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		String url = termValueSet.getUrl();
 		Optional<TermValueSet> optionalExistingTermValueSetByUrl = myValueSetDao.findByUrl(url);
 		if (!optionalExistingTermValueSetByUrl.isPresent()) {
+
 			myValueSetDao.save(termValueSet);
-			int conceptsSaved = 0;
-			int designationsSaved = 0;
-
-			// FIXME: DM 2019-07-15 - Here we should call expandValueSet(ValueSet theValueSetToExpand, IValueSetCodeAccumulator theValueSetCodeAccumulator).
-			// FIXME: DM 2019-07-15 - We need an implementation IValueSetCodeAccumulator that saves ValueSetConcept records and their children.
-			ValueSet expandedValueSet = expandValueSet(theValueSet);
-			if (expandedValueSet.hasExpansion()) {
-				if (expandedValueSet.getExpansion().hasTotal() && expandedValueSet.getExpansion().getTotal() > 0) {
-					TermValueSetConcept concept;
-					for (ValueSet.ValueSetExpansionContainsComponent contains : expandedValueSet.getExpansion().getContains()) {
-						ValidateUtil.isNotBlankOrThrowInvalidRequest(contains.getSystem(), "ValueSet contains a concept with no system value");
-						ValidateUtil.isNotBlankOrThrowInvalidRequest(contains.getCode(), "ValueSet contains a concept with no code value");
-
-						concept = new TermValueSetConcept();
-						concept.setValueSet(termValueSet);
-						concept.setSystem(contains.getSystem());
-						concept.setCode(contains.getCode());
-						concept.setDisplay(contains.hasDisplay() ? contains.getDisplay() : null);
-						myValueSetConceptDao.save(concept);
-
-						TermValueSetConceptDesignation designation;
-						for (ValueSet.ConceptReferenceDesignationComponent containedDesignation : contains.getDesignation()) {
-							ValidateUtil.isNotBlankOrThrowInvalidRequest(containedDesignation.getValue(), "ValueSet contains a concept designation with no value");
-
-							designation = new TermValueSetConceptDesignation();
-							designation.setConcept(concept);
-							designation.setLanguage(containedDesignation.hasLanguage() ? containedDesignation.getLanguage() : null);
-							if (containedDesignation.hasUse()) {
-								designation.setUseSystem(containedDesignation.getUse().hasSystem() ? containedDesignation.getUse().getSystem() : null);
-								designation.setUseCode(containedDesignation.getUse().hasCode() ? containedDesignation.getUse().getCode() : null);
-								designation.setUseDisplay(containedDesignation.getUse().hasDisplay() ? containedDesignation.getUse().getDisplay() : null);
-							}
-							designation.setValue(containedDesignation.getValue());
-							myValueSetConceptDesignationDao.save(designation);
-
-							if (designationsSaved++ % 250 == 0) {
-								ourLog.info("Have pre-expanded {} designations in ValueSet", designationsSaved);
-								myValueSetConceptDesignationDao.flush();
-							}
-						}
-
-						// TODO: DM 2019-07-16 - We need TermValueSetConceptProperty, similar to TermConceptProperty.
-						// TODO: DM 2019-07-16 - We should also populate TermValueSetConceptProperty entities here.
-
-						if (conceptsSaved++ % 250 == 0) {
-							ourLog.info("Have pre-expanded {} concepts in ValueSet", conceptsSaved);
-							myValueSetConceptDao.flush();
-						}
-					}
-				}
-			}
 
 		} else {
 			TermValueSet existingTermValueSet = optionalExistingTermValueSetByUrl.get();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.term;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
@@ -81,13 +82,18 @@ public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
 		return null;
 	}
 
+	@Override
+	protected ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
+		throw new UnsupportedOperationException();
+	}
+
 	@Override
 	public IBaseResource expandValueSet(IBaseResource theValueSetToExpand) {
 		throw new UnsupportedOperationException();
 	}
 
 	@Override
-	public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetCodeAccumulator theValueSetCodeAccumulator) {
+	public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
 		throw new UnsupportedOperationException();
 	}
 

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

@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.UrlUtil;
@@ -177,7 +178,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
 	}
 
 	@Override
-	public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetCodeAccumulator theValueSetCodeAccumulator) {
+	public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
 		ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
 
 		try {
@@ -292,6 +293,20 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
 		}
 	}
 
+	@Override
+	protected org.hl7.fhir.r4.model.ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
+		ValueSet valueSet = myValueSetResourceDao.toResource(ValueSet.class, theResourceTable, null, false);
+
+		org.hl7.fhir.r4.model.ValueSet valueSetR4;
+		try {
+			valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
+		} catch (FHIRException e) {
+			throw new InternalErrorException(e);
+		}
+
+		return valueSetR4;
+	}
+
 	@Override
 	public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
 		return myTerminologySvc.supportsSystem(theSystem);

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

@@ -3,9 +3,9 @@ package ca.uhn.fhir.jpa.term;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.UrlUtil;
-import ca.uhn.fhir.util.ValidateUtil;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
@@ -138,7 +138,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
 	}
 
 	@Override
-	public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetCodeAccumulator theValueSetCodeAccumulator) {
+	public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
 		ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
 		super.expandValueSet(valueSetToExpand, theValueSetCodeAccumulator);
 	}
@@ -231,6 +231,11 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
 		return myValidationSupport.fetchCodeSystem(myContext, theSystem);
 	}
 
+	@Override
+	protected ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
+		return myValueSetResourceDao.toResource(ValueSet.class, theResourceTable, null, false);
+	}
+
 	@Override
 	public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
 		return supportsSystem(theSystem);

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

@@ -44,14 +44,14 @@ public interface IHapiTerminologySvc {
 
 	ValueSet expandValueSet(ValueSet theValueSetToExpand);
 
-	void expandValueSet(ValueSet theValueSetToExpand, IValueSetCodeAccumulator theValueSetCodeAccumulator);
+	void expandValueSet(ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator);
 
 	/**
 	 * Version independent
 	 */
 	IBaseResource expandValueSet(IBaseResource theValueSetToExpand);
 
-	void expandValueSet(IBaseResource theValueSetToExpand, IValueSetCodeAccumulator theValueSetCodeAccumulator);
+	void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator);
 
 	List<VersionIndependentConcept> expandValueSet(String theValueSet);
 
@@ -94,7 +94,7 @@ public interface IHapiTerminologySvc {
 
 	void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap);
 
-	void storeTermValueSetAndChildren(ResourceTable theResourceTable, ValueSet theValueSet);
+	void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet);
 
 	boolean supportsSystem(String theCodeSystem);
 
@@ -107,4 +107,6 @@ public interface IHapiTerminologySvc {
 	AtomicInteger applyDeltaCodesystemsAdd(String theSystem, @Nullable String theParent, CodeSystem theValue);
 
 	AtomicInteger applyDeltaCodesystemsRemove(String theSystem, CodeSystem theDelta);
+
+	void preExpandValueSetToTerminologyTables();
 }

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

@@ -24,12 +24,12 @@ import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
 
 import java.util.Collection;
 
-public interface IValueSetCodeAccumulator {
+public interface IValueSetConceptAccumulator {
 
-	void includeCode(String theSystem, String theCode, String theDisplay);
+	void includeConcept(String theSystem, String theCode, String theDisplay);
 
-	void includeCodeWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations);
+	void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations);
 
-	void excludeCode(String theSystem, String theCode);
+	void excludeConcept(String theSystem, String theCode);
 
 }

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

@@ -0,0 +1,141 @@
+package ca.uhn.fhir.jpa.term;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
+import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
+import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
+import ca.uhn.fhir.jpa.entity.TermValueSet;
+import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
+import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
+import ca.uhn.fhir.util.ValidateUtil;
+
+import javax.annotation.Nonnull;
+import java.util.Collection;
+import java.util.Optional;
+
+import static org.apache.commons.lang3.StringUtils.*;
+
+public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValueSetConceptAccumulator.class);
+
+	private TermValueSet myTermValueSet;
+	private ITermValueSetConceptDao myValueSetConceptDao;
+	private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
+	private int myConceptsSaved;
+	private int myDesignationsSaved;
+
+	public ValueSetConceptAccumulator(@Nonnull TermValueSet theTermValueSet, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
+		myTermValueSet = theTermValueSet;
+		myValueSetConceptDao = theValueSetConceptDao;
+		myValueSetConceptDesignationDao = theValueSetConceptDesignationDao;
+		myConceptsSaved = 0;
+		myDesignationsSaved = 0;
+	}
+
+	@Override
+	public void includeConcept(String theSystem, String theCode, String theDisplay) {
+		saveConcept(theSystem, theCode, theDisplay);
+	}
+
+	@Override
+	public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
+		TermValueSetConcept concept = saveConcept(theSystem, theCode, theDisplay);
+		for (TermConceptDesignation designation : theDesignations) {
+			saveConceptDesignation(concept, designation);
+		}
+	}
+
+	@Override
+	public void excludeConcept(String theSystem, String theCode) {
+		if (isAnyBlank(theSystem, theCode)) {
+			return;
+		}
+
+		// Get existing entity so it can be deleted.
+		Optional<TermValueSetConcept> optionalConcept = myValueSetConceptDao.findByValueSetIdSystemAndCode(myTermValueSet.getId(), theSystem, theCode);
+
+		if (optionalConcept.isPresent()) {
+			TermValueSetConcept concept = optionalConcept.get();
+
+			ourLog.info("Excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
+			for (TermValueSetConceptDesignation designation : concept.getDesignations()) {
+				myValueSetConceptDesignationDao.deleteById(designation.getId());
+			}
+			myValueSetConceptDao.deleteById(concept.getId());
+			ourLog.info("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
+
+			ourLog.info("Flushing...");
+			myValueSetConceptDesignationDao.flush();
+			myValueSetConceptDao.flush();
+			ourLog.info("Done flushing.");
+		}
+	}
+
+	private TermValueSetConcept saveConcept(String theSystem, String theCode, String theDisplay) {
+		ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystem, "ValueSet contains a concept with no system value");
+		ValidateUtil.isNotBlankOrThrowInvalidRequest(theCode, "ValueSet contains a concept with no code value");
+
+		TermValueSetConcept concept = new TermValueSetConcept();
+		concept.setValueSet(myTermValueSet);
+		concept.setSystem(theSystem);
+		concept.setCode(theCode);
+		if (isNotBlank(theDisplay)) {
+			concept.setDisplay(theDisplay);
+		}
+		myValueSetConceptDao.save(concept);
+
+		if (myConceptsSaved++ % 250 == 0) {
+			ourLog.info("Have pre-expanded {} concepts in ValueSet[{}]", myConceptsSaved, myTermValueSet.getUrl());
+			myValueSetConceptDao.flush();
+		}
+
+		return concept;
+	}
+
+	private TermValueSetConceptDesignation saveConceptDesignation(TermValueSetConcept theConcept, TermConceptDesignation theDesignation) {
+		ValidateUtil.isNotBlankOrThrowInvalidRequest(theDesignation.getValue(), "ValueSet contains a concept designation with no value");
+
+		TermValueSetConceptDesignation designation = new TermValueSetConceptDesignation();
+		designation.setConcept(theConcept);
+		designation.setLanguage(theDesignation.getLanguage());
+		if (isNoneBlank(theDesignation.getUseSystem(), theDesignation.getUseCode())) {
+			designation.setUseSystem(theDesignation.getUseSystem());
+			designation.setUseCode(theDesignation.getUseCode());
+			if (isNotBlank(theDesignation.getUseDisplay())) {
+				designation.setUseDisplay(theDesignation.getUseDisplay());
+			}
+		}
+		designation.setValue(theDesignation.getValue());
+		myValueSetConceptDesignationDao.save(designation);
+
+		if (myDesignationsSaved++ % 250 == 0) {
+			ourLog.info("Have pre-expanded {} designations in ValueSet[{}]", myDesignationsSaved, myTermValueSet.getUrl());
+			myValueSetConceptDesignationDao.flush();
+		}
+
+		return designation;
+	}
+
+	// TODO: DM 2019-07-16 - We need TermValueSetConceptProperty, similar to TermConceptProperty.
+	// TODO: DM 2019-07-16 - We should also populate TermValueSetConceptProperty entities here.
+	// TODO: DM 2019-07-30 - Expansions don't include the properties themselves; they are needed to facilitate filters and parameterized expansions.
+}

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

@@ -27,10 +27,10 @@ import org.hl7.fhir.r4.model.ValueSet;
 import java.util.Collection;
 
 @Block()
-public class ValueSetExpansionComponentWithCodeAccumulator extends ValueSet.ValueSetExpansionComponent implements IValueSetCodeAccumulator {
+public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.ValueSetExpansionComponent implements IValueSetConceptAccumulator {
 
 	@Override
-	public void includeCode(String theSystem, String theCode, String theDisplay) {
+	public void includeConcept(String theSystem, String theCode, String theDisplay) {
 		ValueSet.ValueSetExpansionContainsComponent contains = this.addContains();
 		contains.setSystem(theSystem);
 		contains.setCode(theCode);
@@ -38,7 +38,7 @@ public class ValueSetExpansionComponentWithCodeAccumulator extends ValueSet.Valu
 	}
 
 	@Override
-	public void includeCodeWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
+	public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
 		ValueSet.ValueSetExpansionContainsComponent contains = this.addContains();
 		contains.setSystem(theSystem);
 		contains.setCode(theCode);
@@ -58,7 +58,7 @@ public class ValueSetExpansionComponentWithCodeAccumulator extends ValueSet.Valu
 	}
 
 	@Override
-	public void excludeCode(String theSystem, String theCode) {
+	public void excludeConcept(String theSystem, String theCode) {
 		this
 			.getContains()
 			.removeIf(t ->

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

@@ -11,6 +11,7 @@ import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
+import com.google.common.collect.Lists;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.r4.model.*;
@@ -42,7 +43,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 	@Rule
 	public final ExpectedException expectedException = ExpectedException.none();
 	@Mock
-	IValueSetCodeAccumulator myValueSetCodeAccumulator;
+	IValueSetConceptAccumulator myValueSetCodeAccumulator;
 	private IIdType myConceptMapId;
 	private IIdType myExtensionalCsId;
 	private IIdType myExtensionalVsId;
@@ -135,6 +136,11 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		loadAndPersistValueSet();
 	}
 
+	private void loadAndPersistCodeSystemAndValueSetWithDesignationsAndExclude() throws IOException {
+		loadAndPersistCodeSystemWithDesignations();
+		loadAndPersistValueSetWithExclude();
+	}
+
 	private void loadAndPersistCodeSystem() throws IOException {
 		CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
 		persistCodeSystem(codeSystem);
@@ -159,6 +165,11 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		persistValueSet(valueSet);
 	}
 
+	private void loadAndPersistValueSetWithExclude() throws IOException {
+		ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs-with-exclude.xml");
+		persistValueSet(valueSet);
+	}
+
 	private void persistValueSet(ValueSet theValueSet) {
 		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
 			@Override
@@ -589,7 +600,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		include.setSystem(CS_URL);
 
 		myTermSvc.expandValueSet(vs, myValueSetCodeAccumulator);
-		verify(myValueSetCodeAccumulator, times(9)).includeCodeWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
+		verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
 	}
 
 	@Test
@@ -625,15 +636,24 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 				TermConcept concept = concepts.get(0);
 				assertEquals("8450-9", concept.getCode());
 				assertEquals("Systolic blood pressure--expiration", concept.getDisplay());
-				assertEquals(1, concept.getDesignations().size());
+				assertEquals(2, concept.getDesignations().size());
 
-				TermConceptDesignation designation = concept.getDesignations().iterator().next();
+				List<TermConceptDesignation> designations = Lists.newArrayList(concept.getDesignations().iterator());
+
+				TermConceptDesignation designation = designations.get(0);
 				assertEquals("nl", designation.getLanguage());
 				assertEquals("http://snomed.info/sct", designation.getUseSystem());
 				assertEquals("900000000000013009", designation.getUseCode());
 				assertEquals("Synonym", designation.getUseDisplay());
 				assertEquals("Systolische bloeddruk - expiratie", designation.getValue());
 
+				designation = designations.get(1);
+				assertEquals("sv", designation.getLanguage());
+				assertEquals("http://snomed.info/sct", designation.getUseSystem());
+				assertEquals("900000000000013009", designation.getUseCode());
+				assertEquals("Synonym", designation.getUseDisplay());
+				assertEquals("Systoliskt blodtryck - utgång", designation.getValue());
+
 				concept = concepts.get(1);
 				assertEquals("11378-7", concept.getCode());
 				assertEquals("Systolic blood pressure at First encounter", concept.getDisplay());
@@ -948,29 +968,50 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
 		ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
 
-		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
+		runInTransaction(()->{
-			@Override
-			protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
 			Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsId.getIdPartAsLong());
 			assertTrue(optionalValueSetByResourcePid.isPresent());
 
 			Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
 			assertTrue(optionalValueSetByUrl.isPresent());
 
-				TermValueSet valueSet = optionalValueSetByUrl.get();
+			TermValueSet termValueSet = optionalValueSetByUrl.get();
-				assertSame(optionalValueSetByResourcePid.get(), valueSet);
+			assertSame(optionalValueSetByResourcePid.get(), termValueSet);
-				ourLog.info("ValueSet:\n" + valueSet.toString());
+			ourLog.info("ValueSet:\n" + termValueSet.toString());
-				assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", valueSet.getUrl());
+			assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
-				assertEquals("Terminology Services Connectation #1 Extensional case #2", valueSet.getName());
+			assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
-				assertEquals(codeSystem.getConcept().size(), valueSet.getConcepts().size());
+			assertEquals(0, termValueSet.getConcepts().size()); // DM 2019-07-30: Concepts are persisted in the background.
-				assertEquals(TermValueSetExpansionStatusEnum.NOT_EXPANDED, valueSet.getExpansionStatus());
+			assertEquals(TermValueSetExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
+		});
 
-				TermValueSetConcept concept = valueSet.getConcepts().get(0);
+		// FIXME: DM 2019-07-31 - Wait for ValueSet expansion status to be EXPANDED.
+		try {
+			Thread.sleep(10000);
+		} catch (InterruptedException theE) {
+			theE.printStackTrace();
+		}
+
+		runInTransaction(()->{
+			Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsId.getIdPartAsLong());
+			assertTrue(optionalValueSetByResourcePid.isPresent());
+
+			Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
+			assertTrue(optionalValueSetByUrl.isPresent());
+
+			TermValueSet termValueSet = optionalValueSetByUrl.get();
+			assertSame(optionalValueSetByResourcePid.get(), termValueSet);
+			ourLog.info("ValueSet:\n" + termValueSet.toString());
+			assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
+			assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
+			assertEquals(codeSystem.getConcept().size(), termValueSet.getConcepts().size());
+			assertEquals(TermValueSetExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
+
+			TermValueSetConcept concept = termValueSet.getConcepts().get(0);
 			ourLog.info("Code:\n" + concept.toString());
 			assertEquals("http://acme.org", concept.getSystem());
 			assertEquals("8450-9", concept.getCode());
 			assertEquals("Systolic blood pressure--expiration", concept.getDisplay());
-				assertEquals(1, concept.getDesignations().size());
+			assertEquals(2, concept.getDesignations().size());
 
 			TermValueSetConceptDesignation designation = concept.getDesignations().get(0);
 			assertEquals("nl", designation.getLanguage());
@@ -979,7 +1020,14 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 			assertEquals("Synonym", designation.getUseDisplay());
 			assertEquals("Systolische bloeddruk - expiratie", designation.getValue());
 
-				concept = valueSet.getConcepts().get(1);
+			designation = concept.getDesignations().get(1);
+			assertEquals("sv", designation.getLanguage());
+			assertEquals("http://snomed.info/sct", designation.getUseSystem());
+			assertEquals("900000000000013009", designation.getUseCode());
+			assertEquals("Synonym", designation.getUseDisplay());
+			assertEquals("Systoliskt blodtryck - utgång", designation.getValue());
+
+			concept = termValueSet.getConcepts().get(1);
 			ourLog.info("Code:\n" + concept.toString());
 			assertEquals("http://acme.org", concept.getSystem());
 			assertEquals("11378-7", concept.getCode());
@@ -988,7 +1036,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 
 			// ...
 
-				concept = valueSet.getConcepts().get(22);
+			concept = termValueSet.getConcepts().get(22);
 			ourLog.info("Code:\n" + concept.toString());
 			assertEquals("http://acme.org", concept.getSystem());
 			assertEquals("8491-3", concept.getCode());
@@ -1002,13 +1050,115 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 			assertEquals("Synonym", designation.getUseDisplay());
 			assertEquals("Systolische bloeddruk minimaal 1 uur", designation.getValue());
 
-				concept = valueSet.getConcepts().get(23);
+			concept = termValueSet.getConcepts().get(23);
 			ourLog.info("Code:\n" + concept.toString());
 			assertEquals("http://acme.org", concept.getSystem());
 			assertEquals("8492-1", concept.getCode());
 			assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
 			assertEquals(0, concept.getDesignations().size());
+		});
 	}
+
+	@Test
+	public void testStoreTermValueSetAndChildrenWithExclude() throws Exception {
+		myDaoConfig.setPreExpandValueSetsExperimental(true);
+
+		loadAndPersistCodeSystemAndValueSetWithDesignationsAndExclude();
+
+		CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
+		ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
+
+		ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
+		ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
+
+		runInTransaction(()->{
+			Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsId.getIdPartAsLong());
+			assertTrue(optionalValueSetByResourcePid.isPresent());
+
+			Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
+			assertTrue(optionalValueSetByUrl.isPresent());
+
+			TermValueSet termValueSet = optionalValueSetByUrl.get();
+			assertSame(optionalValueSetByResourcePid.get(), termValueSet);
+			ourLog.info("ValueSet:\n" + termValueSet.toString());
+			assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
+			assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
+			assertEquals(0, termValueSet.getConcepts().size()); // DM 2019-07-30: Concepts are persisted in the background.
+			assertEquals(TermValueSetExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
+		});
+
+		// FIXME: DM 2019-07-31 - Wait for ValueSet expansion status to be EXPANDED.
+		try {
+			Thread.sleep(10000);
+		} catch (InterruptedException theE) {
+			theE.printStackTrace();
+		}
+
+		runInTransaction(()->{
+			Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsId.getIdPartAsLong());
+			assertTrue(optionalValueSetByResourcePid.isPresent());
+
+			Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
+			assertTrue(optionalValueSetByUrl.isPresent());
+
+			TermValueSet termValueSet = optionalValueSetByUrl.get();
+			assertSame(optionalValueSetByResourcePid.get(), termValueSet);
+			ourLog.info("ValueSet:\n" + termValueSet.toString());
+			assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
+			assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
+			assertEquals(codeSystem.getConcept().size() - 2, termValueSet.getConcepts().size());
+			assertEquals(TermValueSetExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
+
+			TermValueSetConcept concept = termValueSet.getConcepts().get(0);
+			ourLog.info("Code:\n" + concept.toString());
+			assertEquals("http://acme.org", concept.getSystem());
+			assertEquals("8450-9", concept.getCode());
+			assertEquals("Systolic blood pressure--expiration", concept.getDisplay());
+			assertEquals(2, concept.getDesignations().size());
+
+			TermValueSetConceptDesignation designation = concept.getDesignations().get(0);
+			assertEquals("nl", designation.getLanguage());
+			assertEquals("http://snomed.info/sct", designation.getUseSystem());
+			assertEquals("900000000000013009", designation.getUseCode());
+			assertEquals("Synonym", designation.getUseDisplay());
+			assertEquals("Systolische bloeddruk - expiratie", designation.getValue());
+
+			designation = concept.getDesignations().get(1);
+			assertEquals("sv", designation.getLanguage());
+			assertEquals("http://snomed.info/sct", designation.getUseSystem());
+			assertEquals("900000000000013009", designation.getUseCode());
+			assertEquals("Synonym", designation.getUseDisplay());
+			assertEquals("Systoliskt blodtryck - utgång", designation.getValue());
+
+			concept = termValueSet.getConcepts().get(1);
+			ourLog.info("Code:\n" + concept.toString());
+			assertEquals("http://acme.org", concept.getSystem());
+			assertEquals("11378-7", concept.getCode());
+			assertEquals("Systolic blood pressure at First encounter", concept.getDisplay());
+			assertEquals(0, concept.getDesignations().size());
+
+			// ...
+
+			concept = termValueSet.getConcepts().get(22 - 2);
+			ourLog.info("Code:\n" + concept.toString());
+			assertEquals("http://acme.org", concept.getSystem());
+			assertEquals("8491-3", concept.getCode());
+			assertEquals("Systolic blood pressure 1 hour minimum", concept.getDisplay());
+			assertEquals(1, concept.getDesignations().size());
+
+			designation = concept.getDesignations().get(0);
+			assertEquals("nl", designation.getLanguage());
+			assertEquals("http://snomed.info/sct", designation.getUseSystem());
+			assertEquals("900000000000013009", designation.getUseCode());
+			assertEquals("Synonym", designation.getUseDisplay());
+			assertEquals("Systolische bloeddruk minimaal 1 uur", designation.getValue());
+
+			concept = termValueSet.getConcepts().get(23 - 2);
+			ourLog.info("Code:\n" + concept.toString());
+			assertEquals("http://acme.org", concept.getSystem());
+			assertEquals("8492-1", concept.getCode());
+			assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
+			assertEquals(0, concept.getDesignations().size());
 		});
 	}
 

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

@@ -12,6 +12,15 @@
 			</use>
 			<value value="Systolische bloeddruk - expiratie"/>
 		</designation>
+		<designation>
+			<language value="sv"/>
+			<use>
+				<system value="http://snomed.info/sct"/>
+				<code value="900000000000013009"/>
+				<display value="Synonym"/>
+			</use>
+			<value value="Systoliskt blodtryck - utgång"/>
+		</designation>
 	</concept>
 	<concept>
 		<code value="11378-7" />

hapi-fhir-jpaserver-base/src/test/resources/extensional-case-3-vs-with-exclude.xml

@@ -0,0 +1,31 @@
+<ValueSet xmlns="http://hl7.org/fhir">
+	<url value="http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2" />
+	<identifier>
+		<value value="http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2" />
+	</identifier>
+	<name value="Terminology Services Connectation #1 Extensional case #2" />
+	<publisher value="Grahame Grieve" />
+	<contact>
+		<telecom>
+			<system value="email" />
+			<value value="grahame@healthintersections.com.au" />
+		</telecom>
+	</contact>
+	<description value="an enumeration of codes defined by LOINC" />
+	<status value="draft" />
+	<experimental value="true" />
+	<compose>
+		<include>
+			<system value="http://acme.org"/>
+		</include>
+		<exclude>
+			<system value="http://acme.org"/>
+			<concept>
+				<code value="8489-7" />
+			</concept>
+			<concept>
+				<code value="8490-5" />
+			</concept>
+		</exclude>
+	</compose>
+</ValueSet>