Fix teerm sevice indexing

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java

@@ -101,6 +101,7 @@ public class BaseDstu3Config extends BaseConfig {
 	@Bean(name = "mySystemProviderDstu3")
 	public ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3 systemProviderDstu3() {
 		ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3 retVal = new ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3();
+		retVal.setContext(defaultFhirContext());
 		retVal.setDao(systemDaoDstu3());
 		return retVal;
 	}

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

@@ -1174,7 +1174,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				coordsParams = extractSearchParamCoords(theEntity, theResource);
 
 				// ourLog.info("Indexing resource: {}", entity.getId());
-				ourLog.info("Storing date indexes: {}", dateParams);
+				ourLog.trace("Storing date indexes: {}", dateParams);
 
 				tokenParams = new HashSet<ResourceIndexedSearchParamToken>();
 				for (BaseResourceIndexedSearchParam next : extractSearchParamTokens(theEntity, theResource)) {

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

@@ -37,8 +37,6 @@ import javax.persistence.criteria.Root;
 
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.domain.Page;
-import org.springframework.data.domain.PageRequest;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Propagation;
@@ -50,7 +48,6 @@ import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
 import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
 import ca.uhn.fhir.jpa.entity.ForcedId;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
-import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.util.ReindexFailureException;
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.model.api.TagList;
@@ -89,7 +86,6 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
 		txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
 		int retVal = doPerformReindexingPassForResources(theCount, txTemplate);
-		retVal += doPerformReindexingPassForConcepts(txTemplate);
 		return retVal;
 	}
 
@@ -152,37 +148,6 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 		});
 	}
 
-	private int doPerformReindexingPassForConcepts(TransactionTemplate txTemplate) {
-		return txTemplate.execute(new TransactionCallback<Integer>() {
-			@Override
-			public Integer doInTransaction(TransactionStatus theStatus) {
-				
-				int maxResult = 10000;
-				Page<TermConcept> resources = myTermConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
-				if (resources.hasContent() == false) {
-					return 0;
-				}
-
-				ourLog.info("Indexing {} / {} concepts", resources.getContent().size(), resources.getTotalElements());
-
-				int count = 0;
-				long start = System.currentTimeMillis();
-
-				for (TermConcept resourceTable : resources) {
-					resourceTable.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
-					myTermConceptDao.save(resourceTable);
-					count++;
-				}
-				
-				long delay = System.currentTimeMillis() - start;
-				long avg = (delay / resources.getContent().size());
-				ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, resources.getContent().size(), delay, avg });
-
-				return resources.getContent().size();
-			}
-		});
-	}
-
 	@Override
 	public TagList getAllTags(RequestDetails theRequestDetails) {
 		// Notify interceptors

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

@@ -78,7 +78,7 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
 	}
 	
 	@Override
-	public ValueSet expand(IIdType theId, String theFilter) {
+	public ValueSet expand(IIdType theId, String theFilter, RequestDetails theRequestDetails) {
 		ValueSet source = loadValueSetForExpansion(theId);
 		return expand(source, theFilter);
 
@@ -179,7 +179,7 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
 	}
 
 	@Override
-	public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CodingDt theCoding, CodeableConceptDt theCodeableConcept) {
+	public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CodingDt theCoding, CodeableConceptDt theCodeableConcept, RequestDetails theRequestDetails) {
 		List<IIdType> valueSetIds;
 
 		boolean haveCodeableConcept = theCodeableConcept != null && theCodeableConcept.getCoding().size() > 0;
@@ -212,7 +212,7 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
 		}
 
 		for (IIdType nextId : valueSetIds) {
-			ValueSet expansion = expand(nextId, null);
+			ValueSet expansion = expand(nextId, null, theRequestDetails);
 			List<ExpansionContains> contains = expansion.getExpansion().getContains();
 			ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
 			if (result != null) {
@@ -314,7 +314,7 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
 		
 		List<IIdType> valueSetIds = findCodeSystemIdsContainingSystemAndCode(code, system);
 		for (IIdType nextId : valueSetIds) {
-			ValueSet expansion = expand(nextId, null);
+			ValueSet expansion = expand(nextId, null, theRequestDetails);
 			List<ExpansionContains> contains = expansion.getExpansion().getContains();
 			LookupCodeResult result = lookup(contains, system, code);
 			if (result != null) {

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

@@ -24,9 +24,11 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
+import ca.uhn.fhir.rest.method.RequestDetails;
+
 public interface IFhirResourceDaoValueSet<T extends IBaseResource, CD, CC> extends IFhirResourceDao<T> {
 
-	T expand(IIdType theId, String theFilter);
+	T expand(IIdType theId, String theFilter, RequestDetails theRequestDetails);
 
 	T expand(T theSource, String theFilter);
 
@@ -34,7 +36,7 @@ public interface IFhirResourceDaoValueSet<T extends IBaseResource, CD, CC> exten
 
 	void purgeCaches();
 
-	ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept);
+	ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept, RequestDetails theRequestDetails);
 
 	public class ValidateCodeResult {
 		private String myDisplay;

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

@@ -26,6 +26,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import java.nio.file.FileVisitOption;
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
@@ -56,6 +57,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.util.LogicUtil;
+import ca.uhn.fhir.rest.method.RequestDetails;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.ElementUtil;
@@ -70,8 +72,8 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
 	private IFhirResourceDaoCodeSystem<CodeSystem, CodeableConcept, Coding> myCodeSystemDao;
 
 	@Override
-	public ValueSet expand(IIdType theId, String theFilter) {
+	public ValueSet expand(IIdType theId, String theFilter, RequestDetails theRequestDetails) {
-		ValueSet source = myValidationSupport.fetchResource(getContext(), ValueSet.class, theId.getValue());
+		ValueSet source = read(theId, theRequestDetails);
 		return expand(source, theFilter);
 	}
 
@@ -86,6 +88,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
 		ValueSetExpansionComponent expansion = outcome.getValueset().getExpansion();
 
 		ValueSet retVal = new ValueSet();
+		retVal.getMeta().setLastUpdated(new Date());
 		retVal.setExpansion(expansion);
 		return retVal;
 	}
@@ -166,7 +169,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
 
 	@Override
 	public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
-			IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding, CodeableConcept theCodeableConcept) {
+			IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
 
 		List<IIdType> valueSetIds = Collections.emptyList();
 		List<IIdType> codeSystemIds = Collections.emptyList();
@@ -205,7 +208,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
 		}
 
 		for (IIdType nextId : valueSetIds) {
-			ValueSet expansion = expand(nextId, null);
+			ValueSet expansion = expand(nextId, null, theRequestDetails);
 			List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
 			ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
 			if (result != null) {
@@ -219,7 +222,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
 		}
 
 		for (IIdType nextId : codeSystemIds) {
-			ValueSet expansion = expand(nextId, null);
+			ValueSet expansion = expand(nextId, null, theRequestDetails);
 			List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
 			ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
 			if (result != null) {

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

@@ -25,6 +25,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
@@ -39,6 +40,8 @@ import javax.persistence.Index;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.OneToMany;
+import javax.persistence.PrePersist;
+import javax.persistence.PreUpdate;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 import javax.persistence.Transient;
@@ -49,45 +52,54 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
+import org.apache.lucene.analysis.core.WhitespaceTokenizerFactory;
 import org.hibernate.search.annotations.Analyze;
 import org.hibernate.search.annotations.Analyzer;
+import org.hibernate.search.annotations.AnalyzerDef;
+import org.hibernate.search.annotations.AnalyzerDefs;
 import org.hibernate.search.annotations.Field;
 import org.hibernate.search.annotations.Fields;
 import org.hibernate.search.annotations.Indexed;
 import org.hibernate.search.annotations.Store;
+import org.hibernate.search.annotations.TokenizerDef;
 
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
 
 //@formatter:off
 @Entity
-@Indexed()	
+@Indexed(interceptor=DeferConceptIndexingInterceptor.class)	
 @Table(name="TRM_CONCEPT", uniqueConstraints= {
 	@UniqueConstraint(name="IDX_CONCEPT_CS_CODE", columnNames= {"CODESYSTEM_PID", "CODE"})
 }, indexes= {
 	@Index(name = "IDX_CONCEPT_INDEXSTATUS", columnList="INDEX_STATUS") 
 })
+@AnalyzerDefs({
+	@AnalyzerDef(name = "conceptParentPidsAnalyzer",
+		tokenizer = @TokenizerDef(factory = WhitespaceTokenizerFactory.class),
+		filters = {
+		})
+})
 //@formatter:on
 public class TermConcept implements Serializable {
 	private static final int MAX_DESC_LENGTH = 400;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
+
 	private static final long serialVersionUID = 1L;
 
-	@OneToMany(fetch=FetchType.LAZY, mappedBy="myParent")
+	@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade= {})
 	private Collection<TermConceptParentChildLink> myChildren;
 
-	@Column(name="CODE", length=100, nullable=false)
+	@Column(name = "CODE", length = 100, nullable = false)
-	@Fields({
+	@Fields({ @Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")), })
-		@Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")),
-	})
 	private String myCode;
 
 	@ManyToOne()
-	@JoinColumn(name="CODESYSTEM_PID", referencedColumnName="PID", foreignKey=@ForeignKey(name="FK_CONCEPT_PID_CS_PID"))
+	@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPT_PID_CS_PID"))
 	private TermCodeSystemVersion myCodeSystem;
 
-	@Column(name="CODESYSTEM_PID", insertable=false, updatable=false)
+	@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
-	@Fields({
+	@Fields({ @Field(name = "myCodeSystemVersionPid") })
-		@Field(name="myCodeSystemVersionPid")
-	})
 	private long myCodeSystemVersionPid;
 
 	//@formatter:off
@@ -102,21 +114,19 @@ public class TermConcept implements Serializable {
 	//@formatter:on
 
 	@Id()
-	@SequenceGenerator(name="SEQ_CONCEPT_PID", sequenceName="SEQ_CONCEPT_PID")
+	@SequenceGenerator(name = "SEQ_CONCEPT_PID", sequenceName = "SEQ_CONCEPT_PID")
-	@GeneratedValue(strategy=GenerationType.AUTO, generator="SEQ_CONCEPT_PID")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PID")
-	@Column(name="PID")
+	@Column(name = "PID")
 	private Long myId;
 
 	@Column(name = "INDEX_STATUS", nullable = true)
 	private Long myIndexStatus;
 
 	@Transient
-	@Fields({
+	@Field(name = "myParentPids", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "conceptParentPidsAnalyzer"))
-		@Field(name = "myParentPids", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
-	})
 	private String myParentPids;
 
-	@OneToMany(cascade= {}, fetch=FetchType.LAZY, mappedBy="myChild")
+	@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "myChild")
 	private Collection<TermConceptParentChildLink> myParents;
 
 	public TermConcept() {
@@ -155,7 +165,7 @@ public class TermConcept implements Serializable {
 			return true;
 		}
 
-		TermConcept obj = (TermConcept)theObj;
+		TermConcept obj = (TermConcept) theObj;
 
 		EqualsBuilder b = new EqualsBuilder();
 		b.append(myCodeSystem, obj.myCodeSystem);
@@ -190,6 +200,10 @@ public class TermConcept implements Serializable {
 		return myIndexStatus;
 	}
 
+	public String getParentPidsAsString() {
+		return myParentPids;
+	}
+
 	public Collection<TermConceptParentChildLink> getParents() {
 		if (myParents == null) {
 			myParents = new ArrayList<TermConceptParentChildLink>();
@@ -205,6 +219,28 @@ public class TermConcept implements Serializable {
 		return b.toHashCode();
 	}
 
+	private void parentPids(TermConcept theNextConcept, Set<Long> theParentPids) {
+		for (TermConceptParentChildLink nextParentLink : theNextConcept.getParents()) {
+			TermConcept parent = nextParentLink.getParent();
+			Long parentConceptId = parent.getId();
+			Validate.notNull(parentConceptId);
+			if (parent != null && theParentPids.add(parentConceptId)) {
+				parentPids(parent, theParentPids);
+			}
+		}
+	}
+
+	@PreUpdate
+	@PrePersist
+	public void prePersist() {
+		Set<Long> parentPids = new HashSet<Long>();
+		TermConcept entity = this;
+		parentPids(entity, parentPids);
+		entity.setParentPids(parentPids);
+
+		ourLog.trace("Code {}/{} has parents {}", entity.getId(), entity.getCode(), entity.getParentPidsAsString());
+	}
+
 	public void setCode(String theCode) {
 		myCode = theCode;
 	}
@@ -237,6 +273,10 @@ public class TermConcept implements Serializable {
 			b.append(next);
 		}
 
+		if (b.length() == 0) {
+			b.append("NONE");
+		}
+
 		myParentPids = b.toString();
 	}
 
@@ -244,5 +284,4 @@ public class TermConcept implements Serializable {
 	public String toString() {
 		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE).append("code", myCode).append("display", myDisplay).build();
 	}
-
 }

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

@@ -96,7 +96,55 @@ public class TermConceptParentChildLink implements Serializable {
 	}
 
 
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((myChild == null) ? 0 : myChild.hashCode());
+		result = prime * result + ((myCodeSystem == null) ? 0 : myCodeSystem.hashCode());
+		result = prime * result + ((myParent == null) ? 0 : myParent.hashCode());
+		result = prime * result + ((myRelationshipType == null) ? 0 : myRelationshipType.hashCode());
+		return result;
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if (getClass() != obj.getClass())
+			return false;
+		TermConceptParentChildLink other = (TermConceptParentChildLink) obj;
+		if (myChild == null) {
+			if (other.myChild != null)
+				return false;
+		} else if (!myChild.equals(other.myChild))
+			return false;
+		if (myCodeSystem == null) {
+			if (other.myCodeSystem != null)
+				return false;
+		} else if (!myCodeSystem.equals(other.myCodeSystem))
+			return false;
+		if (myParent == null) {
+			if (other.myParent != null)
+				return false;
+		} else if (!myParent.equals(other.myParent))
+			return false;
+		if (myRelationshipType != other.myRelationshipType)
+			return false;
+		return true;
+	}
+
+
 	public enum RelationshipTypeEnum{
+		// ********************************************
+		// IF YOU ADD HERE MAKE SURE ORDER IS PRESERVED
 		ISA
 	}
+
+
+	public Long getId() {
+		return myPid;
+	}
 }

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

@@ -53,7 +53,8 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
 			@IdParam(optional=true) IdDt theId,
 			@OperationParam(name="valueSet", min=0, max=1) ValueSet theValueSet,
 			@OperationParam(name="identifier", min=0, max=1) UriDt theIdentifier,
-			@OperationParam(name = "filter", min=0, max=1) StringDt theFilter) {
+			@OperationParam(name = "filter", min=0, max=1) StringDt theFilter,
+			RequestDetails theRequestDetails) {
 		//@formatter:on
 		
 		boolean haveId = theId != null && theId.hasIdPart();
@@ -72,7 +73,7 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
 		try {
 			IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> dao = (IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt>) getDao();
 			if (haveId) {
-				return dao.expand(theId, toFilterString(theFilter));
+				return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
 			} else if (haveIdentifier) {
 				return dao.expandByIdentifier(theIdentifier.getValue(), toFilterString(theFilter));
 			} else {
@@ -155,14 +156,15 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
 			@OperationParam(name="system", min=0, max=1) UriDt theSystem,
 			@OperationParam(name="display", min=0, max=1) StringDt theDisplay,
 			@OperationParam(name="coding", min=0, max=1) CodingDt theCoding,
-			@OperationParam(name="codeableConcept", min=0, max=1) CodeableConceptDt theCodeableConcept
+			@OperationParam(name="codeableConcept", min=0, max=1) CodeableConceptDt theCodeableConcept, 
+			RequestDetails theRequestDetails
 			) {
 		//@formatter:on
 		
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> dao = (IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt>) getDao();
-			ValidateCodeResult result = dao.validateCode(theValueSetIdentifier, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept);
+			ValidateCodeResult result = dao.validateCode(theValueSetIdentifier, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
 			Parameters retVal = new Parameters();
 			retVal.addParameter().setName("result").setValue(new BooleanDt(result.isResult()));
 			if (isNotBlank(result.getMessage())) {

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

@@ -39,6 +39,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.method.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
 public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDstu3<ValueSet> {
@@ -50,7 +51,8 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
 			@IdParam(optional=true) IdType theId,
 			@OperationParam(name="valueSet", min=0, max=1) ValueSet theValueSet,
 			@OperationParam(name="identifier", min=0, max=1) UriType theIdentifier,
-			@OperationParam(name = "filter", min=0, max=1) StringType theFilter) {
+			@OperationParam(name = "filter", min=0, max=1) StringType theFilter, 
+			RequestDetails theRequestDetails) {
 		//@formatter:on
 		
 		boolean haveId = theId != null && theId.hasIdPart();
@@ -69,7 +71,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
 		try {
 			IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
 			if (haveId) {
-				return dao.expand(theId, toFilterString(theFilter));
+				return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
 			} else if (haveIdentifier) {
 				return dao.expandByIdentifier(theIdentifier.getValue(), toFilterString(theFilter));
 			} else {
@@ -118,14 +120,15 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
 			@OperationParam(name="system", min=0, max=1) UriType theSystem,
 			@OperationParam(name="display", min=0, max=1) StringType theDisplay,
 			@OperationParam(name="coding", min=0, max=1) Coding theCoding,
-			@OperationParam(name="codeableConcept", min=0, max=1) CodeableConcept theCodeableConcept
+			@OperationParam(name="codeableConcept", min=0, max=1) CodeableConcept theCodeableConcept, 
+			RequestDetails theRequestDetails
 			) {
 		//@formatter:on
 		
 		startRequest(theServletRequest);
 		try {
 			IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
-			ValidateCodeResult result = dao.validateCode(theValueSetIdentifier, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept);
+			ValidateCodeResult result = dao.validateCode(theValueSetIdentifier, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
 			Parameters retVal = new Parameters();
 			retVal.addParameter().setName("result").setValue(new BooleanType(result.isResult()));
 			if (isNotBlank(result.getMessage())) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/DeferConceptIndexingInterceptor.java

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.jpa.search;
+
+import org.hibernate.search.indexes.interceptor.EntityIndexingInterceptor;
+import org.hibernate.search.indexes.interceptor.IndexingOverride;
+
+import ca.uhn.fhir.jpa.entity.TermConcept;
+
+public class DeferConceptIndexingInterceptor  implements EntityIndexingInterceptor<TermConcept> {
+
+	@Override
+	public IndexingOverride onAdd(TermConcept theEntity) {
+		if (theEntity.getIndexStatus() == null) {
+			return IndexingOverride.SKIP;
+		}
+				
+		return IndexingOverride.APPLY_DEFAULT;
+	}
+	
+	@Override
+	public IndexingOverride onCollectionUpdate(TermConcept theEntity) {
+		return IndexingOverride.APPLY_DEFAULT;
+	}
+
+
+	@Override
+	public IndexingOverride onDelete(TermConcept theEntity) {
+		return IndexingOverride.APPLY_DEFAULT;
+	}
+
+	@Override
+	public IndexingOverride onUpdate(TermConcept theEntity) {
+		return onAdd(theEntity);
+	}
+
+}

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.term;
  */
 
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.IdentityHashMap;
@@ -32,10 +33,17 @@ import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.persistence.PersistenceContextType;
 
+import org.apache.commons.lang3.time.DateUtils;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
 import org.springframework.scheduling.annotation.Scheduled;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionTemplate;
 
 import com.google.common.base.Stopwatch;
 
@@ -50,6 +58,8 @@ 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.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.ObjectUtil;
@@ -85,6 +95,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 	protected EntityManager myEntityManager;
 	
 	private boolean myProcessDeferred = true;
+	private long myNextReindexPass;
 
 	private boolean addToSet(Set<TermConcept> theSetToPopulate, TermConcept theConcept) {
 		boolean retVal = theSetToPopulate.add(theConcept);
@@ -209,15 +220,6 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		return cs;
 	}
 	
-	private void parentPids(TermConcept theNextConcept, Set<Long> theParentPids) {
-		for (TermConceptParentChildLink nextParentLink : theNextConcept.getParents()){
-			TermConcept parent = nextParentLink.getParent();
-			if (parent != null && theParentPids.add(parent.getId())) {
-				parentPids(parent, theParentPids);
-			}
-		}
-	}
-
 	private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, int theTotalConcepts) {
 		if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
 			return;
@@ -231,12 +233,8 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		theConcept.setCodeSystem(theCodeSystem);
 		theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
 
-		Set<Long> parentPids = new HashSet<Long>();
-		parentPids(theConcept, parentPids);
-		theConcept.setParentPids(parentPids);
-
 		if (theConceptsStack.size() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
-			myConceptDao.save(theConcept);
+			saveConcept(theConcept);
 		} else {
 			myConceptsToSaveLater.add(theConcept);
 		}
@@ -247,7 +245,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 
 		for (TermConceptParentChildLink next : theConcept.getChildren()) {
 			if (theConceptsStack.size() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
-				myConceptParentChildLinkDao.save(next);
+				saveConceptLink(next);
 			} else {
 				myConceptLinksToSaveLater.add(next);
 			}
@@ -255,6 +253,44 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		
 	}
 
+	private void saveConceptLink(TermConceptParentChildLink next) {
+		if (next.getId() == null) {
+			myConceptParentChildLinkDao.save(next);
+		}
+	}
+
+	private int saveConcept(TermConcept theConcept) {
+		int retVal = 0;
+		retVal += ensureParentsSaved(theConcept.getParents());
+		if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
+			retVal++;
+			theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
+			myConceptDao.saveAndFlush(theConcept);
+		}
+		
+		ourLog.trace("Saved {} and got PID {}", theConcept.getCode(), theConcept.getId());
+		return retVal;
+	}
+
+	private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
+		ourLog.trace("Checking {} parents", theParents.size());
+		int retVal = 0;
+		
+		for (TermConceptParentChildLink nextLink : theParents) {
+			if (nextLink.getRelationshipType() == RelationshipTypeEnum.ISA) {
+				TermConcept nextParent = nextLink.getParent();
+				retVal += ensureParentsSaved(nextParent.getParents());
+				if (nextParent.getId() == null) {
+					myConceptDao.saveAndFlush(nextParent);
+					retVal++;
+					ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
+				}
+			}
+		}
+		
+		return retVal;
+	}
+
 	private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
 		if (theNext.getCodeSystem() != null) {
 			return;
@@ -270,17 +306,21 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 	@Override
 	public synchronized void saveDeferred() {
 		if (!myProcessDeferred || ((myConceptsToSaveLater.isEmpty() && myConceptLinksToSaveLater.isEmpty()))) {
-			return;
+			processReindexing();
 		}
 		
 		int codeCount = 0, relCount = 0;
+		StopWatch stopwatch = new StopWatch();
 		
 		int count = Math.min(myDaoConfig.getDeferIndexingForCodesystemsOfSize(), myConceptsToSaveLater.size());
 		ourLog.info("Saving {} deferred concepts...", count);
 		while (codeCount < count && myConceptsToSaveLater.size() > 0) {
 			TermConcept next = myConceptsToSaveLater.remove(0);
-			myConceptDao.save(next);
+			codeCount += saveConcept(next);
-			codeCount++;
+		}
+
+		if (codeCount > 0) {
+			ourLog.info("Saved {} deferred concepts ({} codes remain and {} relationships remain) in {}ms ({}ms / code)", new Object[] {codeCount, myConceptsToSaveLater.size(), myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount)});
 		}
 		
 		if (codeCount == 0) {
@@ -288,12 +328,54 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 			ourLog.info("Saving {} deferred concept relationships...", count);
 			while (relCount < count && myConceptLinksToSaveLater.size() > 0) {
 				TermConceptParentChildLink next = myConceptLinksToSaveLater.remove(0);
-				myConceptParentChildLinkDao.save(next);
+				saveConceptLink(next);
 				relCount++;
 			}
 		}
 		
-		ourLog.info("Saved {} deferred concepts ({} remain) and {} deferred relationships ({} remain)", new Object[] {codeCount, myConceptsToSaveLater.size(), relCount, myConceptLinksToSaveLater.size()});
+		if (relCount > 0) {
+			ourLog.info("Saved {} deferred relationships ({} remain) in {}ms ({}ms / code)", new Object[] {relCount, myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount)});
+		}
+		
+		if ((myConceptsToSaveLater.size() + myConceptLinksToSaveLater.size()) == 0) {
+			ourLog.info("All deferred concepts and relationships have now been synchronized to the database");
+		}
+	}
+
+	@Autowired
+	private PlatformTransactionManager myTransactionMgr;
+	
+	private void processReindexing() {
+		if (System.currentTimeMillis() < myNextReindexPass) {
+			return;
+		}
+		
+		TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
+		tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
+		tt.execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				int maxResult = 1000;
+				Page<TermConcept> resources = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
+				if (resources.hasContent() == false) {
+					myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
+					return;
+				}
+
+				ourLog.info("Indexing {} / {} concepts", resources.getContent().size(), resources.getTotalElements());
+
+				int count = 0;
+				StopWatch stopwatch = new StopWatch();
+
+				for (TermConcept resourceTable : resources) {
+					saveConcept(resourceTable);
+					count++;
+				}
+				
+				ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, resources.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
+			}
+		});
+
 	}
 
 	@Override

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

@@ -29,6 +29,7 @@ import java.util.List;
 import java.util.Set;
 
 import org.apache.lucene.search.Query;
+import org.apache.lucene.search.QueryWrapperFilter;
 import org.hibernate.search.jpa.FullTextEntityManager;
 import org.hibernate.search.jpa.FullTextQuery;
 import org.hibernate.search.query.dsl.BooleanJunction;
@@ -78,56 +79,38 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 	@Autowired
 	private ValueSetExpander myValueSetExpander;
 
-	@Override
+	private void addCodeIfNotAlreadyAdded(String system, ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
-	public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
+		if (addedCodes.add(nextConcept.getCode())) {
-		ValueSet source = new ValueSet();
+			ValueSetExpansionContainsComponent contains = retVal.addContains();
-		source.getCompose().addImport(theValueSet);
+			contains.setCode(nextConcept.getCode());
-		try {
+			contains.setSystem(system);
-			ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
+			contains.setDisplay(nextConcept.getDisplay());
-
-			ValueSetExpansionOutcome outcome = myValueSetExpander.expand(source);
-			for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
-				retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
-			}
-
-			return retVal;
-
-		} catch (Exception e) {
-			throw new InternalErrorException(e);
 		}
-
 	}
 
-	@Override
+	private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
-	@Transactional(propagation=Propagation.REQUIRED)
+		bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
-	public void storeNewCodeSystemVersion(String theSystem, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails) {
+	}
-		CodeSystem cs = new org.hl7.fhir.dstu3.model.CodeSystem();
-		cs.setUrl(theSystem);
-		cs.setContent(CodeSystemContentMode.NOTPRESENT);
-		
-		DaoMethodOutcome createOutcome = myCodeSystemResourceDao.create(cs, "CodeSystem?url=" + UrlUtil.escape(theSystem), theRequestDetails);
-		IIdType csId = createOutcome.getId().toUnqualifiedVersionless();
-		if (createOutcome.getCreated() != Boolean.TRUE) {
-			CodeSystem existing = myCodeSystemResourceDao.read(csId, theRequestDetails);
-			csId = myCodeSystemResourceDao.update(existing, theRequestDetails).getId();
-			
-			ourLog.info("Created new version of CodeSystem, got ID: {}", csId.toUnqualified().getValue());
-		}
-		
-		ResourceTable resource = (ResourceTable) myCodeSystemResourceDao.readEntity(csId);
-		Long codeSystemResourcePid = resource.getId();
-
-		ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
-
-		theCodeSystemVersion.setResource(resource);
-		theCodeSystemVersion.setResourceVersionId(resource.getVersion());
-		super.storeNewCodeSystemVersion(codeSystemResourcePid, theSystem, theCodeSystemVersion);
 
+	private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
+		//@formatter:off
+		Query textQuery = qb
+				.phrase()
+				.withSlop(2)
+				.onField("myDisplay").boostedTo(4.0f)
+				.andField("myDisplayEdgeNGram").boostedTo(2.0f)
+				//.andField("myDisplayNGram").boostedTo(1.0f)
+				//.andField("myDisplayPhonetic").boostedTo(0.5f)
+				.sentence(nextFilter.getValue().toLowerCase()).createQuery();
+		bool.must(textQuery);
+		//@formatter:on
 	}
 
 	@Override
 	public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
 		String system = theInclude.getSystem();
+		ourLog.info("Starting expansion around code system: {}", system);
+
 		TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
 		TermCodeSystemVersion csv = cs.getCurrentVersion();
 
@@ -167,27 +150,40 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 			bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
 
 			for (ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
-				if (nextFilter.getProperty().equals("display") && nextFilter.getOp() == FilterOperator.EQUAL) {
+				if (isNotBlank(nextFilter.getValue())) {
-					if (isNotBlank(nextFilter.getValue())) {
+					if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == FilterOperator.EQUAL) {
-						bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
+						addDisplayFilterExact(qb, bool, nextFilter);
-					}
+					} else if (nextFilter.getProperty().equals("display") && nextFilter.getOp() == FilterOperator.EQUAL) {
-				} else if (nextFilter.getOp() == FilterOperator.ISA) {
+						if (nextFilter.getValue().trim().contains(" ")) {
-					if (isNotBlank(nextFilter.getValue())) {
+							addDisplayFilterExact(qb, bool, nextFilter);
+						} else {
+							addDisplayFilterInexact(qb, bool, nextFilter);
+						}
+					} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == FilterOperator.ISA) {
 						TermConcept code = super.findCode(system, nextFilter.getValue());
+						if (code == null) {
+							throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
+						}
+
+						ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
 						bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
+					} else {
+						throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
 					}
-				} else {
-					throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
 				}
 			}
 
 			Query luceneQuery = bool.createQuery();
 			FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
+			jpaQuery.setMaxResults(1000);
+
 			@SuppressWarnings("unchecked")
 			List<TermConcept> result = jpaQuery.getResultList();
 			for (TermConcept nextConcept : result) {
 				addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
 			}
+			
+			retVal.setTotal(jpaQuery.getResultSize());
 		}
 
 		if (!haveIncludeCriteria) {
@@ -197,18 +193,28 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 			}
 		}
 
-		retVal.setTotal(retVal.getContains().size());
 
 		return retVal;
 	}
 
-	private void addCodeIfNotAlreadyAdded(String system, ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
+	@Override
-		if (addedCodes.add(nextConcept.getCode())) {
+	public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
-			ValueSetExpansionContainsComponent contains = retVal.addContains();
+		ValueSet source = new ValueSet();
-			contains.setCode(nextConcept.getCode());
+		source.getCompose().addImport(theValueSet);
-			contains.setSystem(system);
+		try {
-			contains.setDisplay(nextConcept.getDisplay());
+			ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
+
+			ValueSetExpansionOutcome outcome = myValueSetExpander.expand(source);
+			for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
+				retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
+			}
+
+			return retVal;
+
+		} catch (Exception e) {
+			throw new InternalErrorException(e);
 		}
+
 	}
 
 	@Override
@@ -238,6 +244,33 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 		return super.supportsSystem(theSystem);
 	}
 
+	@Override
+	@Transactional(propagation = Propagation.REQUIRED)
+	public void storeNewCodeSystemVersion(String theSystem, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails) {
+		CodeSystem cs = new org.hl7.fhir.dstu3.model.CodeSystem();
+		cs.setUrl(theSystem);
+		cs.setContent(CodeSystemContentMode.NOTPRESENT);
+
+		DaoMethodOutcome createOutcome = myCodeSystemResourceDao.create(cs, "CodeSystem?url=" + UrlUtil.escape(theSystem), theRequestDetails);
+		IIdType csId = createOutcome.getId().toUnqualifiedVersionless();
+		if (createOutcome.getCreated() != Boolean.TRUE) {
+			CodeSystem existing = myCodeSystemResourceDao.read(csId, theRequestDetails);
+			csId = myCodeSystemResourceDao.update(existing, theRequestDetails).getId();
+
+			ourLog.info("Created new version of CodeSystem, got ID: {}", csId.toUnqualified().getValue());
+		}
+
+		ResourceTable resource = (ResourceTable) myCodeSystemResourceDao.readEntity(csId);
+		Long codeSystemResourcePid = resource.getId();
+
+		ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
+
+		theCodeSystemVersion.setResource(resource);
+		theCodeSystemVersion.setResourceVersionId(resource.getVersion());
+		super.storeNewCodeSystemVersion(codeSystemResourcePid, theSystem, theCodeSystemVersion);
+
+	}
+
 	@CoverageIgnore
 	@Override
 	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {

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

@@ -24,15 +24,12 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.io.BufferedInputStream;
 import java.io.ByteArrayInputStream;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
-import java.io.OutputStream;
 import java.io.Reader;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -47,7 +44,6 @@ import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVParser;
 import org.apache.commons.csv.CSVRecord;
 import org.apache.commons.csv.QuoteMode;
-import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
@@ -102,6 +98,8 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
 				}
 				ourLog.info(b.toString(), theConcept.getCode());
 				childIter.remove();
+				nextChild.getParents().remove(next);
+				
 			} else {
 				dropCircularRefs(nextChild, theChain, theCode2concept, theCircularCounter);
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/StopWatch.java

@@ -32,4 +32,14 @@ public class StopWatch {
 		return retVal;
 	}
 	
+	public long getMillis() {
+		long now = System.currentTimeMillis();
+		long retVal = now - myStarted;
+		return retVal;
+	}
+	
+	public double getMillisPerOperation(int theNumOperations) {
+		return ((double)getMillis()) / Math.max(1.0, theNumOperations);
+	}
+	
 }

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

@@ -16,7 +16,6 @@ import org.junit.Before;
 import org.junit.Test;
 import org.springframework.transaction.annotation.Transactional;
 
-import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
@@ -25,7 +24,6 @@ import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.model.primitive.UriDt;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 
 public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
@@ -58,7 +56,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		StringDt display = null;
 		CodingDt coding = null;
 		CodeableConceptDt codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertFalse(result.isResult());
 	}
 
@@ -71,7 +69,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		StringDt display = null;
 		CodingDt coding = null;
 		CodeableConceptDt codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertTrue(result.isResult());
 		assertEquals("Systolic blood pressure--expiration", result.getDisplay());
 	}
@@ -85,7 +83,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		StringDt display = null;
 		CodingDt coding = null;
 		CodeableConceptDt codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertTrue(result.isResult());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
@@ -99,7 +97,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		StringDt display = new StringDt("Systolic blood pressure at First encounterXXXX");
 		CodingDt coding = null;
 		CodeableConceptDt codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertFalse(result.isResult());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
@@ -113,7 +111,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		StringDt display = new StringDt("Systolic blood pressure at First encounter");
 		CodingDt coding = null;
 		CodeableConceptDt codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertTrue(result.isResult());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
@@ -127,7 +125,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		StringDt display = null;
 		CodingDt coding = null;
 		CodeableConceptDt codeableConcept = new CodeableConceptDt("http://loinc.org", "11378-7");
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertTrue(result.isResult());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
@@ -141,7 +139,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		StringDt display = null;
 		CodingDt coding = null;
 		CodeableConceptDt codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertTrue(result.isResult());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
@@ -150,7 +148,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 	public void testExpandById() throws IOException {
 		String resp;
 
-		ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null);
+		ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null, mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		// @formatter:off
@@ -175,7 +173,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		 * Filter with display name
 		 */
 
-		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"));
+		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off
@@ -188,7 +186,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
 		 * Filter with code
 		 */
 
-		expanded = myValueSetDao.expand(myExtensionalVsId, ("11378"));
+		expanded = myValueSetDao.expand(myExtensionalVsId, ("11378"), mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off

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

@@ -26,7 +26,6 @@ import org.junit.Test;
 import org.springframework.transaction.annotation.Transactional;
 
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 
 public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
@@ -62,7 +61,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 		StringType display = null;
 		Coding coding = null;
 		CodeableConcept codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertFalse(result.isResult());
 	}
 
@@ -75,7 +74,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 		StringType display = null;
 		Coding coding = null;
 		CodeableConcept codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertTrue(result.isResult());
 		assertEquals("Systolic blood pressure--expiration", result.getDisplay());
 	}
@@ -89,7 +88,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 		StringType display = null;
 		Coding coding = null;
 		CodeableConcept codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertTrue(result.isResult());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
@@ -103,7 +102,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 		StringType display = new StringType("Systolic blood pressure at First encounterXXXX");
 		Coding coding = null;
 		CodeableConcept codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertFalse(result.isResult());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
@@ -117,7 +116,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 		StringType display = new StringType("Systolic blood pressure at First encounter");
 		Coding coding = null;
 		CodeableConcept codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertTrue(result.isResult());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
@@ -132,7 +131,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 		Coding coding = null;
 		CodeableConcept codeableConcept = new CodeableConcept();
 		codeableConcept.addCoding().setSystem("http://acme.org").setCode("11378-7");
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertTrue(result.isResult());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
@@ -146,7 +145,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 		StringType display = null;
 		Coding coding = null;
 		CodeableConcept codeableConcept = null;
-		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
+		ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
 		assertTrue(result.isResult());
 		assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
 	}
@@ -155,7 +154,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 	public void testExpandById() throws IOException {
 		String resp;
 
-		ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null);
+		ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null, mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">")); 
@@ -176,7 +175,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
 		 * Filter with display name
 		 */
 
-		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"));
+		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off

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

@@ -24,7 +24,6 @@ import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.model.primitive.UriDt;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 
 public class ResourceProviderDstu2ValueSetTest extends BaseResourceProviderDstu2Test {
@@ -251,7 +250,7 @@ public class ResourceProviderDstu2ValueSetTest extends BaseResourceProviderDstu2
 		expanded = (ValueSet) respParam.getParameter().get(0).getResource();
 		//@formatter:on
 
-		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"));
+		expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
 		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
 		ourLog.info(resp);
 		//@formatter:off

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

@@ -1,9 +1,12 @@
 package ca.uhn.fhir.jpa.provider.dstu3;
 
+import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest.*;
 import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.containsStringIgnoringCase;
 import static org.hamcrest.Matchers.not;
 import static org.hamcrest.Matchers.stringContainsInOrder;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.fail;
 
@@ -12,25 +15,33 @@ import java.io.IOException;
 import org.hl7.fhir.dstu3.model.BooleanType;
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.CodeType;
-import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.Parameters;
 import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.dstu3.model.UriType;
 import org.hl7.fhir.dstu3.model.ValueSet;
+import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
+import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
+import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
 import org.springframework.transaction.annotation.Transactional;
 
+import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.TestUtil;
 
 public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu3ValueSetTest.class);
 	private IIdType myExtensionalVsId;
+	private IIdType myLocalValueSetId;
+	private ValueSet myLocalVs;
 
 	@AfterClass
 	public static void afterClassClearContext() {
@@ -78,6 +89,140 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 
 	}
 
+	@Test
+	public void testExpandLocalVsAgainstExternalCs() throws IOException {
+		createExternalCsAndLocalVs();
+		assertNotNull(myLocalValueSetId);
+		
+		//@formatter:off
+		Parameters respParam = ourClient
+			.operation()
+			.onInstance(myLocalValueSetId)
+			.named("expand")
+			.withNoParameters(Parameters.class)
+			.execute();
+		ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
+		//@formatter:on
+		
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
+		ourLog.info(resp);
+		
+		assertThat(resp, containsStringIgnoringCase("<code value=\"childAAA\"/>"));
+		assertThat(resp, containsStringIgnoringCase("<code value=\"childAAB\"/>"));
+		assertThat(resp, not(containsStringIgnoringCase("<code value=\"ParentA\"/>")));
+		
+	}
+
+	@Test
+	public void testExpandLocalVsWithUnknownCode() throws IOException {
+		createExternalCsAndLocalVsWithUnknownCode();
+		assertNotNull(myLocalValueSetId);
+		
+		//@formatter:off
+		try {
+			ourClient
+				.operation()
+				.onInstance(myLocalValueSetId)
+				.named("expand")
+				.withNoParameters(Parameters.class)
+				.execute();
+		} catch (InvalidRequestException e) {
+			assertEquals("HTTP 400 Bad Request: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
+		}
+		//@formatter:on
+	}
+
+	@Test
+	public void testExpandInlineVsAgainstBuiltInCs() throws IOException {
+		createLocalVsPointingAtBuiltInCodeSystem();
+		assertNotNull(myLocalValueSetId);
+		
+		//@formatter:off
+		Parameters respParam = ourClient
+			.operation()
+			.onType(ValueSet.class)
+			.named("expand")
+			.withParameter(Parameters.class, "valueSet", myLocalVs)
+			.execute();
+		ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
+		//@formatter:on
+		
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
+		ourLog.info(resp);
+		
+		assertThat(resp, containsStringIgnoringCase("<code value=\"M\"/>"));
+	}
+
+	@Test
+	public void testExpandLocalVsAgainstBuiltInCs() throws IOException {
+		createLocalVsPointingAtBuiltInCodeSystem();
+		assertNotNull(myLocalValueSetId);
+		
+		//@formatter:off
+		Parameters respParam = ourClient
+			.operation()
+			.onInstance(myLocalValueSetId)
+			.named("expand")
+			.withNoParameters(Parameters.class)
+			.execute();
+		ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
+		//@formatter:on
+		
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
+		ourLog.info(resp);
+		
+		assertThat(resp, containsStringIgnoringCase("<code value=\"M\"/>"));
+	}
+
+	@Test
+	public void testExpandLocalVsCanonicalAgainstExternalCs() throws IOException {
+		createExternalCsAndLocalVs();
+		assertNotNull(myLocalValueSetId);
+		
+		//@formatter:off
+		Parameters respParam = ourClient
+			.operation()
+			.onType(ValueSet.class)
+			.named("expand")
+			.withParameter(Parameters.class, "identifier", new UriType(URL_MY_VALUE_SET))
+			.execute();
+		ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
+		//@formatter:on
+		
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
+		ourLog.info(resp);
+		
+		assertThat(resp, containsStringIgnoringCase("<code value=\"childAAA\"/>"));
+		assertThat(resp, containsStringIgnoringCase("<code value=\"childAAB\"/>"));
+		assertThat(resp, not(containsStringIgnoringCase("<code value=\"ParentA\"/>")));
+		
+	}
+
+	@Test
+	public void testExpandInlineVsAgainstExternalCs() throws IOException {
+		createExternalCsAndLocalVs();
+		assertNotNull(myLocalVs);
+		myLocalVs.setId("");
+		
+		//@formatter:off
+		Parameters respParam = ourClient
+			.operation()
+			.onType(ValueSet.class)
+			.named("expand")
+			.withParameter(Parameters.class, "valueSet", myLocalVs)
+			.execute();
+		ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
+		//@formatter:on
+		
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
+		ourLog.info(resp);
+		
+		assertThat(resp, containsStringIgnoringCase("<code value=\"childAAA\"/>"));
+		assertThat(resp, containsStringIgnoringCase("<code value=\"childAAB\"/>"));
+		assertThat(resp, not(containsStringIgnoringCase("<code value=\"ParentA\"/>")));
+		
+	}
+
 	@Test
 	public void testExpandByIdWithFilter() throws IOException {
 
@@ -231,4 +376,102 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 		assertEquals(true, ((BooleanType)respParam.getParameter().get(0).getValue()).booleanValue());
 	}
 	
+	
+	
+	
+	
+	private CodeSystem createExternalCs() {
+		CodeSystem codeSystem = new CodeSystem();
+		codeSystem.setUrl(URL_MY_CODE_SYSTEM);
+		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
+		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
+
+		ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
+
+		TermCodeSystemVersion cs = new TermCodeSystemVersion();
+		cs.setResource(table);
+		cs.setResourceVersionId(table.getVersion());
+
+		TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
+		cs.getConcepts().add(parentA);
+
+		TermConcept childAA = new TermConcept(cs, "childAA").setDisplay("Child AA");
+		parentA.addChild(childAA, RelationshipTypeEnum.ISA);
+
+		TermConcept childAAA = new TermConcept(cs, "childAAA").setDisplay("Child AAA");
+		childAA.addChild(childAAA, RelationshipTypeEnum.ISA);
+
+		TermConcept childAAB = new TermConcept(cs, "childAAB").setDisplay("Child AAB");
+		childAA.addChild(childAAB, RelationshipTypeEnum.ISA);
+
+		TermConcept childAB = new TermConcept(cs, "childAB").setDisplay("Child AB");
+		parentA.addChild(childAB, RelationshipTypeEnum.ISA);
+
+		TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
+		cs.getConcepts().add(parentB);
+
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, cs);
+		return codeSystem;
+	}
+
+	private void createExternalCsAndLocalVs() {
+		CodeSystem codeSystem = createExternalCs();
+
+		createLocalVs(codeSystem);
+	}
+
+	private void createExternalCsAndLocalVsWithUnknownCode() {
+		CodeSystem codeSystem = createExternalCs();
+
+		createLocalVsWithUnknownCode(codeSystem);
+	}
+
+	private void createLocalCsAndVs() {
+		//@formatter:off
+		CodeSystem codeSystem = new CodeSystem();
+		codeSystem.setUrl(URL_MY_CODE_SYSTEM);
+		codeSystem.setContent(CodeSystemContentMode.COMPLETE);		
+		codeSystem
+			.addConcept().setCode("A").setDisplay("Code A")
+				.addConcept(new ConceptDefinitionComponent().setCode("AA").setDisplay("Code AA")
+					.addConcept(new ConceptDefinitionComponent().setCode("AAA").setDisplay("Code AAA"))
+				)
+				.addConcept(new ConceptDefinitionComponent().setCode("AB").setDisplay("Code AB"));
+		codeSystem
+			.addConcept().setCode("B").setDisplay("Code B")
+				.addConcept(new ConceptDefinitionComponent().setCode("BA").setDisplay("Code BA"))
+				.addConcept(new ConceptDefinitionComponent().setCode("BB").setDisplay("Code BB"));
+		//@formatter:on
+		myCodeSystemDao.create(codeSystem, mySrd);
+
+		createLocalVs(codeSystem);
+	}
+
+
+	private void createLocalVs(CodeSystem codeSystem) {
+		myLocalVs = new ValueSet();
+		myLocalVs.setUrl(URL_MY_VALUE_SET);
+		ConceptSetComponent include = myLocalVs.getCompose().addInclude();
+		include.setSystem(codeSystem.getUrl());
+		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("childAA");
+		myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
+	}
+
+	private void createLocalVsWithUnknownCode(CodeSystem codeSystem) {
+		myLocalVs = new ValueSet();
+		myLocalVs.setUrl(URL_MY_VALUE_SET);
+		ConceptSetComponent include = myLocalVs.getCompose().addInclude();
+		include.setSystem(codeSystem.getUrl());
+		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("childFOOOOOOO");
+		myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
+	}
+
+	private void createLocalVsPointingAtBuiltInCodeSystem() {
+		myLocalVs = new ValueSet();
+		myLocalVs.setUrl(URL_MY_VALUE_SET);
+		ConceptSetComponent include = myLocalVs.getCompose().addInclude();
+		include.setSystem("http://hl7.org/fhir/v3/MaritalStatus");
+		myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
+	}
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderDstu3Test.java

@@ -367,6 +367,19 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
+	@Test
+	public void testMarkResourcesForReindexing() throws Exception {
+		HttpGet get = new HttpGet(ourServerBase + "/$mark-all-resources-for-reindexing");
+		CloseableHttpResponse http = ourHttpClient.execute(get);
+		try {
+			String output = IOUtils.toString(http.getEntity().getContent());
+			ourLog.info(output);
+			assertEquals(200, http.getStatusLine().getStatusCode());
+		} finally {
+			IOUtils.closeQuietly(http);;
+		}
+	}
+	
 	@Transactional(propagation = Propagation.NEVER)
 	@Test
 	public void testSuggestKeywords() throws Exception {

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

@@ -30,10 +30,6 @@ public class TerminologyLoaderSvcIntegrationTest extends BaseJpaDstu3Test {
 	@Test
 	@Ignore
 	public void testLoadAndStoreSnomedCt() {
-		Map<String, File> files = new HashMap<String, File>();
-		files.put(TerminologyLoaderSvc.SCT_FILE_CONCEPT, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Concept_Full_INT_20160131.txt"));
-		files.put(TerminologyLoaderSvc.SCT_FILE_DESCRIPTION, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Description_Full-en_INT_20160131.txt"));
-		files.put(TerminologyLoaderSvc.SCT_FILE_RELATIONSHIP, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Relationship_Full_INT_20160131.txt"));
 //		myLoader.processSnomedCtFiles(files, mySrd);
 	}
 

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

@@ -1,17 +1,17 @@
 package ca.uhn.fhir.jpa.term;
 
-import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInRelativeOrder;
 import static org.hamcrest.Matchers.hasItem;
 import static org.hamcrest.Matchers.not;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.fail;
-import static org.mockito.Mockito.any;
+import static org.mockito.Matchers.any;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.verify;
 
 import java.io.ByteArrayOutputStream;
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -25,6 +25,7 @@ import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.Validate;
 import org.junit.AfterClass;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.mockito.ArgumentCaptor;
@@ -79,6 +80,21 @@ public class TerminologyLoaderSvcTest {
 		mySvc.loadLoinc(list(bos1.toByteArray(), bos2.toByteArray()), details);
 	}
 
+	
+	/**
+	 * This is just for trying stuff, it won't run without
+	 * local files external to the git repo
+	 */
+	@Ignore
+	@Test
+	public void testLoadSnomedCtAgainstRealFile() throws Exception {
+		byte[] bytes = IOUtils.toByteArray(new FileInputStream("/Users/james/Downloads/SnomedCT_Release_INT_20160131_Full.zip"));
+		
+		RequestDetails details = mock(RequestDetails.class);
+		mySvc.loadSnomedCt(list(bytes), details);
+	}
+	
+	
 	@Test
 	public void testLoadSnomedCt() throws Exception {
 		ByteArrayOutputStream bos = new ByteArrayOutputStream();

hapi-fhir-jpaserver-base/src/test/resources/sct/sct2_Concept_Full_INT_20160131.txt

@@ -17,3 +17,4 @@ id	effectiveTime	active	moduleId	definitionStatusId
 207527008	20020131	1	900000000000207008	900000000000074008
 207527008	20040731	1	900000000000207008	900000000000073002
 207527008	20090731	0	900000000000207008	900000000000074008
+404684003	20040131	1	900000000000207008	900000000000074008

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

@@ -67,6 +67,8 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
 		ValueSetExpansionOutcome vso;
 		try {
 			vso = getExpander().expand(theSource);
+		} catch (InvalidRequestException e) {
+			throw e;
 		} catch (Exception e) {
 			throw new InternalErrorException(e);
 		}
@@ -125,7 +127,9 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
 
 	@Override
 	public ValueSetExpander getExpander() {
-		return new ValueSetExpanderSimple(this, this);
+		ValueSetExpanderSimple retVal = new ValueSetExpanderSimple(this, this);
+		retVal.setMaxExpansionSize(Integer.MAX_VALUE);
+		return retVal;
 	}
 
 	@Override

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/terminologies/ValueSetExpanderSimple.java

@@ -70,8 +70,10 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
 	private Set<String> excludeKeys = new HashSet<String>();
 	private ValueSetExpanderFactory factory;
 	private ValueSet focus;
+	private int maxExpansionSize = 500;
 
 	private Map<String, ValueSetExpansionContainsComponent> map = new HashMap<String, ValueSet.ValueSetExpansionContainsComponent>();
+	private int total;
 
 	public ValueSetExpanderSimple(IWorkerContext context, ValueSetExpanderFactory factory) {
 		super();
@@ -79,6 +81,10 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
 		this.factory = factory;
 	}
 
+	public void setMaxExpansionSize(int theMaxExpansionSize) {
+		maxExpansionSize = theMaxExpansionSize;
+	}
+
 	private void addCode(String system, String code, String display) {
 		ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
 		n.setSystem(system);
@@ -101,7 +107,7 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
 	}
 
 	private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params) throws ETooCostly {
-		if (expand.getContains().size() > 500)
+		if (expand.getContains().size() > maxExpansionSize)
 			throw new ETooCostly("Too many codes to display (>" + Integer.toString(expand.getContains().size()) + ")");
 		for (ValueSetExpansionParameterComponent p : expand.getParameter()) {
 			if (!existsInParams(params, p.getName(), p.getValue()))
@@ -111,6 +117,8 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
 		for (ValueSetExpansionContainsComponent c : expand.getContains()) {
 			addCode(c.getSystem(), c.getCode(), c.getDisplay());
 		}
+		
+		total = expand.getTotal();
 	}
 
 	private void excludeCode(String theSystem, String theCode) {
@@ -171,6 +179,11 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
 					focus.getExpansion().getContains().add(c);
 				}
 			}
+			
+			if (total > 0) {
+				focus.getExpansion().setTotal(total);
+			}
+			
 			return new ValueSetExpansionOutcome(focus, null);
 		} catch (RuntimeException e) {
 			// TODO: we should put something more specific instead of just Exception below, since