Implement Terminology Delta Operations (#1536)

* Start refactoring terminology delta operations

* Work on delta operations

* Work on concept saving

* Split term services into smaller services

* Work on term delta operations

* Work on term svcs

* Work on term operations

* More work on delta uploader

* Add a test

* Wrk on term service

* Fix compile error

* Some refactoring

* Test fix

* Test fix

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Work on delta

* Work on tests#

* Test fixes

* Improve resequencing logic

* Build test

* More testing

* More build testing

* More work on tests

* CHange test logging

* Fix term service PID issue

* Update src/changes/changes.xml

Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Address review comment

* Some cleanup

* Test fix

* Fix some tests

* Test fixes

examples/src/main/java/example/ServerMetadataExamples.java

@@ -1,15 +1,13 @@
 package example;
 
+import ca.uhn.fhir.model.api.Tag;
+import ca.uhn.fhir.rest.annotation.Search;
+import org.hl7.fhir.r4.model.InstantType;
+import org.hl7.fhir.r4.model.Patient;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
-import ca.uhn.fhir.model.api.Tag;
-import ca.uhn.fhir.model.api.TagList;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.model.primitive.InstantDt;
-import ca.uhn.fhir.rest.annotation.Search;
-
 public class ServerMetadataExamples {
 
    // START SNIPPET: serverMethod
@@ -21,34 +19,21 @@ public class ServerMetadataExamples {
       Patient patient = new Patient();
       retVal.add(patient);
       patient.setId("Patient/123");
-      patient.addName().addFamily("Smith").addGiven("John");
-      
-      // Create a tag list and add it to the resource
-      TagList tags = new TagList();
-      tags.addTag(Tag.HL7_ORG_FHIR_TAG, "http://foo/tag1.html", "Some tag");
-      tags.addTag(Tag.HL7_ORG_FHIR_TAG, "http://foo/tag2.html", "Another tag");
-      ResourceMetadataKeyEnum.TAG_LIST.put(patient, tags);
-      
-      // Set some links (these can be provided as relative links or absolute)
-      // and the server will convert to absolute as appropriate
-      String linkAlternate = "Patient/7736";
-      ResourceMetadataKeyEnum.LINK_ALTERNATE.put(patient, linkAlternate);
-      String linkSearch = "Patient?name=smith&name=john";
-      ResourceMetadataKeyEnum.LINK_SEARCH.put(patient, linkSearch);
-      
-      // Set the published and updated dates
-      InstantDt pubDate = new InstantDt("2011-02-22");
-      ResourceMetadataKeyEnum.PUBLISHED.put(patient, pubDate);
-      InstantDt updatedDate = new InstantDt("2014-07-12T11:22:27Z");
-      ResourceMetadataKeyEnum.UPDATED.put(patient, updatedDate);
-      
-      // Set the resource title (note that if you are using HAPI's narrative
-      // generation capability, the narrative generator will often create
-      // useful titles automatically, and the server will create a default
-      // title if none is provided)
-      String title = "Patient John SMITH";
-      ResourceMetadataKeyEnum.TITLE.put(patient, title);
+      patient.addName().setFamily("Smith").addGiven("John");
       
+      // Add tags
+		patient.getMeta().addTag()
+			.setSystem(Tag.HL7_ORG_FHIR_TAG)
+			.setCode("some_tag")
+			.setDisplay("Some tag");
+		patient.getMeta().addTag()
+			.setSystem(Tag.HL7_ORG_FHIR_TAG)
+			.setCode("another_tag")
+			.setDisplay("Another tag");
+
+      // Set the last updated date
+		patient.getMeta().setLastUpdatedElement(new InstantType("2011-02-22T11:22:00.0122Z"));
+
       return retVal;
    }
    // END SNIPPET: serverMethod

hapi-fhir-base/pom.xml

@@ -120,6 +120,11 @@
 			<optional>true</optional>
 		</dependency>
 
+		<dependency>
+			<groupId>org.awaitility</groupId>
+			<artifactId>awaitility</artifactId>
+			<scope>test</scope>
+		</dependency>
 
 	</dependencies>
 

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

@@ -20,6 +20,7 @@ import ca.uhn.fhir.util.ReflectionUtil;
 import ca.uhn.fhir.util.VersionUtil;
 import ca.uhn.fhir.validation.FhirValidator;
 import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.jena.riot.Lang;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
@@ -896,6 +897,11 @@ public class FhirContext {
 		}
 	}
 
+	@Override
+	public String toString() {
+		return "FhirContext[" + myVersion.getVersion().name() + "]";
+	}
+
 	/**
 	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2 DSTU2}
 	 */

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnum.java

@@ -21,7 +21,6 @@ package ca.uhn.fhir.model.api;
  */
 
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
-import ca.uhn.fhir.model.primitive.DecimalDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
@@ -29,7 +28,6 @@ import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IAnyResource;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import java.io.Serializable;
@@ -92,29 +90,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.setUserData(DELETED_AT.name(), theObject);
 		}
 	};
-	/**
-	 * Denotes the search score which a given resource should match in a transaction. See the FHIR transaction definition for information about this. Corresponds to the value in
-	 * <code>Bundle.entry.score</code> in a Bundle resource.
-	 * <p>
-	 * Note that search URL is only used in FHIR DSTU2 and later.
-	 * </p>
-	 * <p>
-	 * Values for this key are of type <b>{@link DecimalDt}</b>
-	 * </p>
-	 */
-	public static final ResourceMetadataKeyEnum<DecimalDt> ENTRY_SCORE = new ResourceMetadataKeyEnum<DecimalDt>("ENTRY_SCORE") {
-		private static final long serialVersionUID = 1L;
 
-		@Override
-		public DecimalDt get(IResource theResource) {
-			return getDecimalFromMetadataOrNullIfNone(theResource.getResourceMetadata(), ENTRY_SCORE);
-		}
-
-		@Override
-		public void put(IResource theResource, DecimalDt theObject) {
-			theResource.getResourceMetadata().put(ENTRY_SCORE, theObject);
-		}
-	};
 	/**
 	 * If present and populated with a {@link BundleEntrySearchModeEnum}, contains the "bundle entry search mode", which is the value of the status field in the Bundle entry containing this resource.
 	 * The value for this key corresponds to field <code>Bundle.entry.search.mode</code>. This value can be set to provide a status value of "include" for included resources being returned by a
@@ -187,67 +163,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 		}
 
 	};
-	/**
-	 * If present and populated with a string, provides the "alternate link" (the link element in the bundle entry with <code>rel="alternate"</code>). Server implementations may populate this with a
-	 * complete URL, in which case the URL will be placed as-is in the bundle. They may alternately specify a resource relative URL (e.g. "Patient/1243") in which case the server will convert this to
-	 * an absolute URL at runtime.
-	 * <p>
-	 * Values for this key are of type <b>{@link String}</b>
-	 * </p>
-	 */
-	public static final ResourceMetadataKeyEnum<String> LINK_ALTERNATE = new ResourceMetadataKeyEnum<String>("LINK_ALTERNATE") {
-		private static final long serialVersionUID = 1L;
 
-		@Override
-		public String get(IResource theResource) {
-			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), LINK_ALTERNATE);
-		}
-
-		@Override
-		public void put(IResource theResource, String theObject) {
-			theResource.getResourceMetadata().put(LINK_ALTERNATE, theObject);
-		}
-	};
-	/**
-	 * If present and populated with a string, provides the "search link" (the link element in the bundle entry with <code>rel="search"</code>). Server implementations may populate this with a
-	 * complete URL, in which case the URL will be placed as-is in the bundle. They may alternately specify a resource relative URL (e.g. "Patient?name=tester") in which case the server will convert
-	 * this to an absolute URL at runtime.
-	 * <p>
-	 * Values for this key are of type <b>{@link String}</b>
-	 * </p>
-	 */
-	public static final ResourceMetadataKeyEnum<String> LINK_SEARCH = new ResourceMetadataKeyEnum<String>("LINK_SEARCH") {
-		private static final long serialVersionUID = 1L;
-
-		@Override
-		public String get(IResource theResource) {
-			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), LINK_SEARCH);
-		}
-
-		@Override
-		public void put(IResource theResource, String theObject) {
-			theResource.getResourceMetadata().put(LINK_SEARCH, theObject);
-		}
-	};
-	/**
-	 * The value for this key represents a previous ID used to identify this resource. This key is currently only used internally during transaction method processing.
-	 * <p>
-	 * Values for this key are of type <b>{@link IdDt}</b>
-	 * </p>
-	 */
-	public static final ResourceMetadataKeyEnum<IdDt> PREVIOUS_ID = new ResourceMetadataKeyEnum<IdDt>("PREVIOUS_ID") {
-		private static final long serialVersionUID = 1L;
-
-		@Override
-		public IdDt get(IResource theResource) {
-			return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata(), PREVIOUS_ID);
-		}
-
-		@Override
-		public void put(IResource theResource, IdDt theObject) {
-			theResource.getResourceMetadata().put(PREVIOUS_ID, theObject);
-		}
-	};
 	/**
 	 * The value for this key represents a {@link List} of profile IDs that this resource claims to conform to.
 	 * <p>
@@ -301,18 +217,8 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			if (obj == null) {
 				return null;
 			}
-			try {
-				@SuppressWarnings("unchecked")
-				List<BaseCodingDt> securityLabels = (List<BaseCodingDt>) obj;
-				if (securityLabels.isEmpty()) {
-					return null;
-				}
-				return securityLabels;
-			} catch (ClassCastException e) {
-				throw new InternalErrorException("Found an object of type '" + obj.getClass().getCanonicalName() + "' in resource metadata for key SECURITY_LABELS - Expected "
-					+ BaseCodingDt.class.getCanonicalName());
-			}
-
+			//noinspection unchecked
+			return (List<BaseCodingDt>) obj;
 		}
 
 		@Override
@@ -337,14 +243,9 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			Object retValObj = theResource.getResourceMetadata().get(TAG_LIST);
 			if (retValObj == null) {
 				return null;
-			} else if (retValObj instanceof TagList) {
-				if (((TagList) retValObj).isEmpty()) {
-					return null;
-				}
+			} else {
 				return (TagList) retValObj;
 			}
-			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + TAG_LIST.name() + " - Expected "
-				+ TagList.class.getCanonicalName());
 		}
 
 		@Override
@@ -352,25 +253,6 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			theResource.getResourceMetadata().put(TAG_LIST, theObject);
 		}
 	};
-	/**
-	 * If present and populated with a string (as an instance of {@link String}), this value contains the title for this resource, as supplied in any bundles containing the resource.
-	 * <p>
-	 * Values for this key are of type <b>{@link String}</b>
-	 * </p>
-	 */
-	public static final ResourceMetadataKeyEnum<String> TITLE = new ResourceMetadataKeyEnum<String>("TITLE") {
-		private static final long serialVersionUID = 1L;
-
-		@Override
-		public String get(IResource theResource) {
-			return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), TITLE);
-		}
-
-		@Override
-		public void put(IResource theResource, String theObject) {
-			theResource.getResourceMetadata().put(TITLE, theObject);
-		}
-	};
 	/**
 	 * The value for this key is the bundle entry <b>Updated</b> time. This is defined by FHIR as "Last Updated for resource". This value is also used for populating the "Last-Modified" header in the
 	 * case of methods that return a single resource (read, vread, etc.)
@@ -398,7 +280,10 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 	 * <p>
 	 * Values for this key are of type <b>{@link String}</b>
 	 * </p>
+	 *
+	 * @deprecated The {@link IResource#getId()} resource ID will now be populated with the version ID via the {@link IdDt#getVersionIdPart()} method
 	 */
+	@Deprecated
 	public static final ResourceMetadataKeyEnum<String> VERSION = new ResourceMetadataKeyEnum<String>("VERSION") {
 		private static final long serialVersionUID = 1L;
 
@@ -426,7 +311,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 
 		@Override
 		public IdDt get(IResource theResource) {
-			return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata(), VERSION_ID);
+			return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata());
 		}
 
 		@Override
@@ -474,32 +359,45 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 
 	public abstract void put(IResource theResource, T theObject);
 
-	@Override
-	public String toString() {
-		return myValue;
+	public static abstract class ResourceMetadataKeySupportingAnyResource<T, T2> extends ResourceMetadataKeyEnum<T> {
+
+		private static final long serialVersionUID = 1L;
+
+		public ResourceMetadataKeySupportingAnyResource(String theValue) {
+			super(theValue);
+		}
+
+		public abstract T2 get(IAnyResource theResource);
+
+		public abstract void put(IAnyResource theResource, T2 theObject);
+
 	}
 
-	private static DecimalDt getDecimalFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<DecimalDt> theKey) {
-		Object retValObj = theResourceMetadata.get(theKey);
-		if (retValObj == null) {
-			return null;
-		} else if (retValObj instanceof DecimalDt) {
-			if (((DecimalDt) retValObj).isEmpty()) {
-				return null;
-			}
-			return (DecimalDt) retValObj;
-		} else if (retValObj instanceof String) {
-			if (StringUtils.isBlank((String) retValObj)) {
-				return null;
-			}
-			return new DecimalDt((String) retValObj);
-		} else if (retValObj instanceof Double) {
-			return new DecimalDt((Double) retValObj);
+	public static final class ExtensionResourceMetadataKey extends ResourceMetadataKeyEnum<ExtensionDt> {
+		public ExtensionResourceMetadataKey(String theUrl) {
+			super(theUrl);
+		}
+
+		@Override
+		public ExtensionDt get(IResource theResource) {
+			Object retValObj = theResource.getResourceMetadata().get(this);
+			if (retValObj == null) {
+				return null;
+			} else if (retValObj instanceof ExtensionDt) {
+				return (ExtensionDt) retValObj;
+			}
+			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName()
+				+ "' in resource metadata for key " + this.name() + " - Expected "
+				+ ExtensionDt.class.getCanonicalName());
+		}
+
+		@Override
+		public void put(IResource theResource, ExtensionDt theObject) {
+			theResource.getResourceMetadata().put(this, theObject);
 		}
-		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
-			+ InstantDt.class.getCanonicalName());
 	}
 
+
 	@SuppressWarnings("unchecked")
 	private static <T extends Enum<?>> T getEnumFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<T> theKey, Class<T> theEnumType,
 																								IValueSetEnumBinder<T> theBinder) {
@@ -515,8 +413,8 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			+ InstantDt.class.getCanonicalName());
 	}
 
-	private static IdDt getIdFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<?> theKey) {
-		return toId(theKey, theResourceMetadata.get(theKey));
+	private static IdDt getIdFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata) {
+		return toId(ResourceMetadataKeyEnum.VERSION_ID, theResourceMetadata.get(ResourceMetadataKeyEnum.VERSION_ID));
 	}
 
 	private static List<IdDt> getIdListFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<?> theKey) {
@@ -586,49 +484,11 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
 			}
 			return (IdDt) retValObj;
 		} else if (retValObj instanceof Number) {
-			return new IdDt(((Number) retValObj).toString());
+			return new IdDt(retValObj.toString());
 		}
 		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
 			+ IdDt.class.getCanonicalName());
 	}
 
-	public static abstract class ResourceMetadataKeySupportingAnyResource<T, T2> extends ResourceMetadataKeyEnum<T> {
-
-		private static final long serialVersionUID = 1L;
-
-		public ResourceMetadataKeySupportingAnyResource(String theValue) {
-			super(theValue);
-		}
-
-		public abstract T2 get(IAnyResource theResource);
-
-		public abstract void put(IAnyResource theResource, T2 theObject);
-
-	}
-
-	public static final class ExtensionResourceMetadataKey extends ResourceMetadataKeyEnum<ExtensionDt> {
-		public ExtensionResourceMetadataKey(String url) {
-			super(url);
-		}
-
-		@Override
-		public ExtensionDt get(IResource theResource) {
-			Object retValObj = theResource.getResourceMetadata().get(this);
-			if (retValObj == null) {
-				return null;
-			} else if (retValObj instanceof ExtensionDt) {
-				return (ExtensionDt) retValObj;
-			}
-			throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName()
-				+ "' in resource metadata for key " + this.name() + " - Expected "
-				+ ExtensionDt.class.getCanonicalName());
-		}
-
-		@Override
-		public void put(IResource theResource, ExtensionDt theObject) {
-			theResource.getResourceMetadata().put(this, theObject);
-		}
-	}
-
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/Tag.java

@@ -168,18 +168,6 @@ public class Tag extends BaseElement implements IElement, IBaseCoding {
 		return this;
 	}
 
-	public String toHeaderValue() {
-		StringBuilder b = new StringBuilder();
-		b.append(this.getTerm());
-		if (isNotBlank(this.getLabel())) {
-			b.append("; label=\"").append(this.getLabel()).append('"');
-		}
-		if (isNotBlank(this.getScheme())) {
-			b.append("; scheme=\"").append(this.getScheme()).append('"');
-		}
-		return b.toString();
-	}
-
 	@Override
 	public String toString() {
 		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/api/IHttpResponse.java

@@ -33,12 +33,6 @@ import java.util.Map;
  */
 public interface IHttpResponse {
 
-	/**
-	 * @deprecated This method was deprecated in HAPI FHIR 2.2 because its name has a typo. Use {@link #bufferEntity()} instead.
-	 */
-	@Deprecated
-	void bufferEntitity() throws IOException;
-
 	/**
 	 * Buffer the message entity data.
 	 * <p>

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/TokenParam.java

@@ -248,26 +248,30 @@ public class TokenParam extends BaseParam /*implements IQueryParameterType*/ {
 
 	@Override
 	public boolean equals(Object theO) {
-		if (this == theO) return true;
+		if (this == theO) {
+			return true;
+		}
 
-		if (theO == null || getClass() != theO.getClass()) return false;
+		if (theO == null || getClass() != theO.getClass()) {
+			return false;
+		}
 
 		TokenParam that = (TokenParam) theO;
 
-		return new EqualsBuilder()
-			.append(myModifier, that.myModifier)
-			.append(mySystem, that.mySystem)
-			.append(myValue, that.myValue)
-			.isEquals();
+		EqualsBuilder b = new EqualsBuilder();
+		b.append(myModifier, that.myModifier);
+		b.append(mySystem, that.mySystem);
+		b.append(myValue, that.myValue);
+		return b.isEquals();
 	}
 
 	@Override
 	public int hashCode() {
-		return new HashCodeBuilder(17, 37)
-			.append(myModifier)
-			.append(mySystem)
-			.append(myValue)
-			.toHashCode();
+		HashCodeBuilder b = new HashCodeBuilder(17, 37);
+		b.append(myModifier);
+		b.append(mySystem);
+		b.append(myValue);
+		return b.toHashCode();
 	}
 
 	private static String toSystemValue(UriDt theSystem) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/AsyncUtil.java

@@ -0,0 +1,54 @@
+package ca.uhn.fhir.util;
+
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.TimeUnit;
+
+public class AsyncUtil {
+	private static final Logger ourLog = LoggerFactory.getLogger(AsyncUtil.class);
+
+	/**
+	 * Non instantiable
+	 */
+	private AsyncUtil() {
+	}
+
+	/**
+	 * Calls Thread.sleep and if an InterruptedException occurs, logs a warning but otherwise continues
+	 *
+	 * @param theMillis The number of millis to sleep
+	 * @return Did we sleep the whole amount
+	 */
+	public static boolean sleep(long theMillis) {
+		try {
+			Thread.sleep(theMillis);
+			return true;
+		} catch (InterruptedException theE) {
+			Thread.currentThread().interrupt();
+			ourLog.warn("Sleep for {}ms was interrupted", theMillis);
+			return false;
+		}
+	}
+
+	public static boolean awaitLatchAndThrowInternalErrorExceptionOnInterrupt(CountDownLatch theInitialCollectionLatch, long theTime, TimeUnit theTimeUnit) {
+		try {
+			return theInitialCollectionLatch.await(theTime, theTimeUnit);
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new InternalErrorException(e);
+		}
+	}
+
+	public static boolean awaitLatchAndIgnoreInterrupt(CountDownLatch theInitialCollectionLatch, long theTime, TimeUnit theTimeUnit) {
+		try {
+			return theInitialCollectionLatch.await(theTime, theTimeUnit);
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			ourLog.warn("Interrupted while waiting for latch");
+			return false;
+		}
+	}
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/AttachmentUtil.java

@@ -20,9 +20,8 @@ package ca.uhn.fhir.util;
  * #L%
  */
 
-import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
-import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
-import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.*;
+import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.ICompositeType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -35,12 +34,10 @@ public class AttachmentUtil {
 	 * Fetches the base64Binary value of Attachment.data, creating it if it does not
 	 * already exist.
 	 */
-	@SuppressWarnings("unchecked")
 	public static IPrimitiveType<byte[]> getOrCreateData(FhirContext theContext, ICompositeType theAttachment) {
 		return getOrCreateChild(theContext, theAttachment, "data", "base64Binary");
 	}
 
-	@SuppressWarnings("unchecked")
 	public static IPrimitiveType<String> getOrCreateContentType(FhirContext theContext, ICompositeType theAttachment) {
 		return getOrCreateChild(theContext, theAttachment, "contentType", "string");
 	}
@@ -64,6 +61,16 @@ public class AttachmentUtil {
 			});
 	}
 
+	public static void setUrl(FhirContext theContext, ICompositeType theAttachment, String theUrl) {
+		BaseRuntimeChildDefinition entryChild = getChild(theContext, theAttachment, "url");
+		assert entryChild != null : "Version " + theContext + " has no child " + "url";
+		String typeName = "uri";
+		if (theContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
+			typeName = "url";
+		}
+		entryChild.getMutator().setValue(theAttachment, newPrimitive(theContext, typeName, theUrl));
+	}
+
 	public static void setContentType(FhirContext theContext, ICompositeType theAttachment, String theContentType) {
 		BaseRuntimeChildDefinition entryChild = getChild(theContext, theAttachment, "contentType");
 		entryChild.getMutator().setValue(theAttachment, newPrimitive(theContext, "code", theContentType));
@@ -88,7 +95,9 @@ public class AttachmentUtil {
 	 */
 	@SuppressWarnings("unchecked")
 	static <T> IPrimitiveType<T> newPrimitive(FhirContext theContext, String theType, T theValue) {
-		IPrimitiveType<T> primitive = (IPrimitiveType<T>) theContext.getElementDefinition(theType).newInstance();
+		BaseRuntimeElementDefinition<?> elementDefinition = theContext.getElementDefinition(theType);
+		Validate.notNull(elementDefinition, "Unknown type %s for %s", theType, theContext);
+		IPrimitiveType<T> primitive = (IPrimitiveType<T>) elementDefinition.newInstance();
 		primitive.setValue(theValue);
 		return primitive;
 	}
@@ -100,4 +109,8 @@ public class AttachmentUtil {
 		BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(theElement.getClass());
 		return def.getChildByName(theName);
 	}
+
+	public static ICompositeType newInstance(FhirContext theFhirCtx) {
+		return (ICompositeType) theFhirCtx.getElementDefinition("Attachment").newInstance();
+	}
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java

@@ -72,6 +72,8 @@ public class ParametersUtil {
 	}
 
 	private static void addClientParameter(FhirContext theContext, Object theValue, IBaseResource theTargetResource, BaseRuntimeChildDefinition paramChild, BaseRuntimeElementCompositeDefinition<?> paramChildElem, String theName) {
+		Validate.notNull(theValue, "theValue must not be null");
+
 		if (theValue instanceof IBaseResource) {
 			IBase parameter = createParameterRepetition(theContext, theTargetResource, paramChild, paramChildElem, theName);
 			paramChildElem.getChildByName("resource").getMutator().addValue(parameter, (IBaseResource) theValue);
@@ -162,7 +164,6 @@ public class ParametersUtil {
 		IPrimitiveType<Boolean> value = (IPrimitiveType<Boolean>) theCtx.getElementDefinition("boolean").newInstance();
 		value.setValue(theValue);
 		addParameterToParameters(theCtx, theParameters, theName, value);
-
 	}
 
 	@SuppressWarnings("unchecked")

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.util;
 
 import com.google.common.annotations.VisibleForTesting;
+import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.time.DateUtils;
 
 import java.text.DecimalFormat;
@@ -9,8 +10,6 @@ import java.util.Date;
 import java.util.LinkedList;
 import java.util.concurrent.TimeUnit;
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -48,12 +47,14 @@ public class StopWatch {
 	private long myStarted = now();
 	private TaskTiming myCurrentTask;
 	private LinkedList<TaskTiming> myTasks;
+
 	/**
 	 * Constructor
 	 */
 	public StopWatch() {
 		super();
 	}
+
 	/**
 	 * Constructor
 	 *
@@ -63,7 +64,13 @@ public class StopWatch {
 		myStarted = theStart.getTime();
 	}
 
-	public StopWatch(long theL) {
+	/**
+	 * Constructor
+	 *
+	 * @param theStart The time that the stopwatch was started
+	 */
+	public StopWatch(long theStart) {
+		myStarted = theStart;
 	}
 
 	private void addNewlineIfContentExists(StringBuilder theB) {
@@ -120,6 +127,8 @@ public class StopWatch {
 				b.append(": ");
 				b.append(formatMillis(delta));
 			}
+		} else {
+			b.append("No tasks");
 		}
 
 		TaskTiming last = null;
@@ -257,12 +266,11 @@ public class StopWatch {
 	 */
 	public void startTask(String theTaskName) {
 		endCurrentTask();
-		if (isNotBlank(theTaskName)) {
-			myCurrentTask = new TaskTiming()
-				.setTaskName(theTaskName)
-				.setStart(now());
-			myTasks.add(myCurrentTask);
-		}
+		Validate.notBlank(theTaskName, "Task name must not be blank");
+		myCurrentTask = new TaskTiming()
+			.setTaskName(theTaskName)
+			.setStart(now());
+		myTasks.add(myCurrentTask);
 	}
 
 	/**
@@ -331,18 +339,18 @@ public class StopWatch {
 	/**
 	 * Append a right-aligned and zero-padded numeric value to a `StringBuilder`.
 	 */
-	static private void append(StringBuilder tgt, String pfx, int dgt, long val) {
-		tgt.append(pfx);
-		if (dgt > 1) {
-			int pad = (dgt - 1);
-			for (long xa = val; xa > 9 && pad > 0; xa /= 10) {
+	static void appendRightAlignedNumber(StringBuilder theStringBuilder, String thePrefix, int theNumberOfDigits, long theValueToAppend) {
+		theStringBuilder.append(thePrefix);
+		if (theNumberOfDigits > 1) {
+			int pad = (theNumberOfDigits - 1);
+			for (long xa = theValueToAppend; xa > 9 && pad > 0; xa /= 10) {
 				pad--;
 			}
 			for (int xa = 0; xa < pad; xa++) {
-				tgt.append('0');
+				theStringBuilder.append('0');
 			}
 		}
-		tgt.append(val);
+		theStringBuilder.append(theValueToAppend);
 	}
 
 	/**
@@ -399,11 +407,11 @@ public class StopWatch {
 			}
 		} else {
 			long millisAsLong = (long) theMillis;
-			append(buf, "", 2, ((millisAsLong % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
-			append(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_HOUR) / DateUtils.MILLIS_PER_MINUTE));
-			append(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_SECOND));
+			appendRightAlignedNumber(buf, "", 2, ((millisAsLong % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
+			appendRightAlignedNumber(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_HOUR) / DateUtils.MILLIS_PER_MINUTE));
+			appendRightAlignedNumber(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_SECOND));
 			if (theMillis <= DateUtils.MILLIS_PER_MINUTE) {
-				append(buf, ".", 3, (millisAsLong % DateUtils.MILLIS_PER_SECOND));
+				appendRightAlignedNumber(buf, ".", 3, (millisAsLong % DateUtils.MILLIS_PER_SECOND));
 			}
 		}
 		return buf.toString();

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/SchemaBaseValidator.java

@@ -19,26 +19,32 @@ package ca.uhn.fhir.validation;
  * limitations under the License.
  * #L%
  */
-import java.io.*;
-import java.nio.charset.Charset;
-import java.util.*;
-
-import javax.xml.XMLConstants;
-import javax.xml.transform.Source;
-import javax.xml.transform.stream.StreamSource;
-import javax.xml.validation.*;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.io.input.BOMInputStream;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.w3c.dom.ls.LSInput;
-import org.w3c.dom.ls.LSResourceResolver;
-import org.xml.sax.*;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.input.BOMInputStream;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.w3c.dom.ls.LSInput;
+import org.w3c.dom.ls.LSResourceResolver;
+import org.xml.sax.SAXException;
+import org.xml.sax.SAXNotRecognizedException;
+import org.xml.sax.SAXParseException;
+
+import javax.xml.XMLConstants;
+import javax.xml.transform.Source;
+import javax.xml.transform.stream.StreamSource;
+import javax.xml.validation.Schema;
+import javax.xml.validation.SchemaFactory;
+import javax.xml.validation.Validator;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.StringReader;
+import java.nio.charset.StandardCharsets;
+import java.util.*;
 
 public class SchemaBaseValidator implements IValidatorModule {
 	public static final String RESOURCES_JAR_NOTE = "Note that as of HAPI FHIR 1.2, DSTU2 validation files are kept in a separate JAR (hapi-fhir-validation-resources-XXX.jar) which must be added to your classpath. See the HAPI FHIR download page for more information.";
@@ -47,7 +53,7 @@ public class SchemaBaseValidator implements IValidatorModule {
 	private static final Set<String> SCHEMA_NAMES;
 
 	static {
-		HashSet<String> sn = new HashSet<String>();
+		HashSet<String> sn = new HashSet<>();
 		sn.add("xml.xsd");
 		sn.add("xhtml1-strict.xsd");
 		sn.add("fhir-single.xsd");
@@ -59,15 +65,15 @@ public class SchemaBaseValidator implements IValidatorModule {
 		SCHEMA_NAMES = Collections.unmodifiableSet(sn);
 	}
 
-	private Map<String, Schema> myKeyToSchema = new HashMap<String, Schema>();
+	private final Map<String, Schema> myKeyToSchema = new HashMap<>();
 	private FhirContext myCtx;
 
 	public SchemaBaseValidator(FhirContext theContext) {
 		myCtx = theContext;
 	}
 
-	private void doValidate(IValidationContext<?> theContext, String schemaName) {
-		Schema schema = loadSchema("dstu", schemaName);
+	private void doValidate(IValidationContext<?> theContext) {
+		Schema schema = loadSchema();
 
 		try {
 			Validator validator = schema.newValidator();
@@ -81,14 +87,14 @@ public class SchemaBaseValidator implements IValidatorModule {
 			}
 
 			try {
-			/*
-			 * See https://github.com/jamesagnew/hapi-fhir/issues/339
-			 * https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
-			 */
+				/*
+				 * See https://github.com/jamesagnew/hapi-fhir/issues/339
+				 * https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
+				 */
 				validator.setProperty(XMLConstants.ACCESS_EXTERNAL_DTD, "");
 				validator.setProperty(XMLConstants.ACCESS_EXTERNAL_SCHEMA, "");
-			}catch (SAXNotRecognizedException ex){
-				ourLog.warn("Jaxp 1.5 Support not found.",ex);
+			} catch (SAXNotRecognizedException ex) {
+				ourLog.warn("Jaxp 1.5 Support not found.", ex);
 			}
 
 			validator.validate(new StreamSource(new StringReader(encodedResource)));
@@ -99,17 +105,14 @@ public class SchemaBaseValidator implements IValidatorModule {
 			message.setMessage(e.getLocalizedMessage());
 			message.setSeverity(ResultSeverityEnum.FATAL);
 			theContext.addValidationMessage(message);
-		} catch (SAXException e) {
-			// Catch all
-			throw new ConfigurationException("Could not load/parse schema file", e);
-		} catch (IOException e) {
+		} catch (SAXException | IOException e) {
 			// Catch all
 			throw new ConfigurationException("Could not load/parse schema file", e);
 		}
 	}
 
-	private Schema loadSchema(String theVersion, String theSchemaName) {
-		String key = theVersion + "-" + theSchemaName;
+	private Schema loadSchema() {
+		String key = "fhir-single.xsd";
 
 		synchronized (myKeyToSchema) {
 			Schema schema = myKeyToSchema.get(key);
@@ -117,81 +120,52 @@ public class SchemaBaseValidator implements IValidatorModule {
 				return schema;
 			}
 
-			Source baseSource = loadXml(null, theSchemaName);
+			Source baseSource = loadXml("fhir-single.xsd");
 
 			SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
 			schemaFactory.setResourceResolver(new MyResourceResolver());
 
 			try {
 				try {
-				/*
-				 * See https://github.com/jamesagnew/hapi-fhir/issues/339
-				 * https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
-				 */
+					/*
+					 * See https://github.com/jamesagnew/hapi-fhir/issues/339
+					 * https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
+					 */
 					schemaFactory.setProperty(XMLConstants.ACCESS_EXTERNAL_DTD, "");
-				}catch (SAXNotRecognizedException snex){
-					ourLog.warn("Jaxp 1.5 Support not found.",snex);
+				} catch (SAXNotRecognizedException e) {
+					ourLog.warn("Jaxp 1.5 Support not found.", e);
 				}
-				schema = schemaFactory.newSchema(new Source[] { baseSource });
+				schema = schemaFactory.newSchema(new Source[]{baseSource});
 			} catch (SAXException e) {
-				throw new ConfigurationException("Could not load/parse schema file: " + theSchemaName, e);
+				throw new ConfigurationException("Could not load/parse schema file: " + "fhir-single.xsd", e);
 			}
 			myKeyToSchema.put(key, schema);
 			return schema;
 		}
 	}
 
-	private Source loadXml(String theSystemId, String theSchemaName) {
+	Source loadXml(String theSchemaName) {
 		String pathToBase = myCtx.getVersion().getPathToSchemaDefinitions() + '/' + theSchemaName;
 		ourLog.debug("Going to load resource: {}", pathToBase);
-		InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
-		if (baseIs == null) {
-			throw new InternalErrorException("Schema not found. " + RESOURCES_JAR_NOTE);
+		try (InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase)) {
+			if (baseIs == null) {
+				throw new InternalErrorException("Schema not found. " + RESOURCES_JAR_NOTE);
+			}
+			try (BOMInputStream bomInputStream = new BOMInputStream(baseIs, false)) {
+				try (InputStreamReader baseReader = new InputStreamReader(bomInputStream, StandardCharsets.UTF_8)) {
+					// Buffer so that we can close the input stream
+					String contents = IOUtils.toString(baseReader);
+					return new StreamSource(new StringReader(contents), null);
+				}
+			}
+		} catch (IOException e) {
+			throw new InternalErrorException(e);
 		}
-		baseIs = new BOMInputStream(baseIs, false);
-		InputStreamReader baseReader = new InputStreamReader(baseIs, Charset.forName("UTF-8"));
-		Source baseSource = new StreamSource(baseReader, theSystemId);
-		//FIXME resource leak
-		return baseSource;
 	}
 
 	@Override
 	public void validateResource(IValidationContext<IBaseResource> theContext) {
-		doValidate(theContext, "fhir-single.xsd");
-	}
-
-	private static class MyErrorHandler implements org.xml.sax.ErrorHandler {
-
-		private IValidationContext<?> myContext;
-
-		public MyErrorHandler(IValidationContext<?> theContext) {
-			myContext = theContext;
-		}
-
-		private void addIssue(SAXParseException theException, ResultSeverityEnum theSeverity) {
-			SingleValidationMessage message = new SingleValidationMessage();
-			message.setLocationLine(theException.getLineNumber());
-			message.setLocationCol(theException.getColumnNumber());
-			message.setMessage(theException.getLocalizedMessage());
-			message.setSeverity(theSeverity);
-			myContext.addValidationMessage(message);
-		}
-
-		@Override
-		public void error(SAXParseException theException) {
-			addIssue(theException, ResultSeverityEnum.ERROR);
-		}
-
-		@Override
-		public void fatalError(SAXParseException theException) {
-			addIssue(theException, ResultSeverityEnum.FATAL);
-		}
-
-		@Override
-		public void warning(SAXParseException theException) {
-			addIssue(theException, ResultSeverityEnum.WARNING);
-		}
-
+		doValidate(theContext);
 	}
 
 	private final class MyResourceResolver implements LSResourceResolver {
@@ -225,4 +199,38 @@ public class SchemaBaseValidator implements IValidatorModule {
 		}
 	}
 
+	private static class MyErrorHandler implements org.xml.sax.ErrorHandler {
+
+		private IValidationContext<?> myContext;
+
+		MyErrorHandler(IValidationContext<?> theContext) {
+			myContext = theContext;
+		}
+
+		private void addIssue(SAXParseException theException, ResultSeverityEnum theSeverity) {
+			SingleValidationMessage message = new SingleValidationMessage();
+			message.setLocationLine(theException.getLineNumber());
+			message.setLocationCol(theException.getColumnNumber());
+			message.setMessage(theException.getLocalizedMessage());
+			message.setSeverity(theSeverity);
+			myContext.addValidationMessage(message);
+		}
+
+		@Override
+		public void error(SAXParseException theException) {
+			addIssue(theException, ResultSeverityEnum.ERROR);
+		}
+
+		@Override
+		public void fatalError(SAXParseException theException) {
+			addIssue(theException, ResultSeverityEnum.FATAL);
+		}
+
+		@Override
+		public void warning(SAXParseException theException) {
+			addIssue(theException, ResultSeverityEnum.WARNING);
+		}
+
+	}
+
 }

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

@@ -125,9 +125,9 @@ ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownPath=Unable to find content
 ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownType=Content in resource of type {0} at path {1} is not appropriate for binary storage: {2}
 
 
-ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
-ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
-ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
-ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
 
 ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}

hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnumTest.java

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.model.api;
+
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class ResourceMetadataKeyEnumTest {
+
+	@Test
+	public void testHashCode() {
+		assertEquals(-60968467, ResourceMetadataKeyEnum.PUBLISHED.hashCode());
+	}
+
+	@Test
+	public void testEquals() {
+		assertNotEquals(ResourceMetadataKeyEnum.PROFILES, null);
+		assertNotEquals(ResourceMetadataKeyEnum.PROFILES, "");
+		assertNotEquals(ResourceMetadataKeyEnum.PROFILES, ResourceMetadataKeyEnum.PUBLISHED);
+		assertEquals(ResourceMetadataKeyEnum.PROFILES, ResourceMetadataKeyEnum.PROFILES);
+	}
+
+
+	@Test
+	public void testExtensionResourceEquals() {
+		assertNotEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://bar"));
+		assertNotEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), null);
+		assertNotEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), "");
+		assertEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"));
+
+		ResourceMetadataKeyEnum.ExtensionResourceMetadataKey foo = new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo");
+		assertEquals(foo, foo);
+	}
+
+
+}

hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/TagTest.java

@@ -0,0 +1,46 @@
+package ca.uhn.fhir.model.api;
+
+import org.junit.Test;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+
+import static org.junit.Assert.*;
+
+public class TagTest {
+
+	@Test
+	public void testEquals() {
+		Tag tag1 = new Tag().setScheme("scheme").setTerm("term").setLabel("label");
+		Tag tag2 = new Tag().setScheme("scheme").setTerm("term").setLabel("label");
+		Tag tag3 = new Tag().setScheme("scheme2").setTerm("term").setLabel("label");
+		Tag tag4 = new Tag().setScheme("scheme").setTerm("term2").setLabel("label");
+
+		assertEquals(tag1, tag1);
+		assertEquals(tag1, tag2);
+		assertNotEquals(tag1, tag3);
+		assertNotEquals(tag1, tag4);
+		assertNotEquals(tag1, null);
+		assertNotEquals(tag1, "");
+	}
+
+	@Test
+	public void testHashCode() {
+		Tag tag1 = new Tag().setScheme("scheme").setTerm("term").setLabel("label");
+		assertEquals(1920714536, tag1.hashCode());
+	}
+
+	@Test
+	public void testConstructors() throws URISyntaxException {
+		assertTrue(new Tag().isEmpty());
+		assertFalse(new Tag("http://foo").isEmpty());
+		assertFalse(new Tag("http://foo", "http://bar").isEmpty());
+		assertFalse(new Tag(new URI("http://foo"), new URI("http://bar"), "Label").isEmpty());
+		assertTrue(new Tag((URI)null, null, "Label").isEmpty());
+
+		assertEquals("http://foo", new Tag(new URI("http://foo"), new URI("http://bar"), "Label").getSystem());
+		assertEquals("http://bar", new Tag(new URI("http://foo"), new URI("http://bar"), "Label").getCode());
+		assertEquals("Label", new Tag(new URI("http://foo"), new URI("http://bar"), "Label").getDisplay());
+	}
+
+}

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/TokenParamTest.java

@@ -2,13 +2,34 @@ package ca.uhn.fhir.rest.param;
 
 import org.junit.Test;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
 
 public class TokenParamTest {
 	@Test
 	public void testEquals() {
 		TokenParam tokenParam1 = new TokenParam("foo", "bar");
 		TokenParam tokenParam2 = new TokenParam("foo", "bar");
+		TokenParam tokenParam3 = new TokenParam("foo", "baz");
+		assertEquals(tokenParam1, tokenParam1);
 		assertEquals(tokenParam1, tokenParam2);
+		assertNotEquals(tokenParam1, tokenParam3);
+		assertNotEquals(tokenParam1, null);
+		assertNotEquals(tokenParam1, "");
 	}
+
+	@Test
+	public void testHashCode() {
+		TokenParam tokenParam1 = new TokenParam("foo", "bar");
+		assertEquals(4716638, tokenParam1.hashCode());
+	}
+
+
+	@Test
+	public void testIsEmpty() {
+		assertFalse(new TokenParam("foo", "bar").isEmpty());
+		assertTrue(new TokenParam("", "").isEmpty());
+		assertTrue(new TokenParam().isEmpty());
+		assertEquals("", new TokenParam().getValueNotNull());
+	}
+
 }

hapi-fhir-base/src/test/java/ca/uhn/fhir/util/AsyncUtilTest.java

@@ -0,0 +1,62 @@
+package ca.uhn.fhir.util;
+
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.junit.Test;
+
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import static org.awaitility.Awaitility.await;
+
+public class AsyncUtilTest {
+
+	@Test
+	public void testSleep() {
+		AsyncUtil.sleep(10);
+	}
+
+	@Test
+	public void testSleepWithInterrupt() {
+		AtomicBoolean outcomeHolder = new AtomicBoolean(true);
+		Thread thread = new Thread(() -> {
+			boolean outcome = AsyncUtil.sleep(10000);
+			outcomeHolder.set(outcome);
+		});
+		thread.start();
+		thread.interrupt();
+		await().until(()-> outcomeHolder.get() == false);
+	}
+
+	@Test
+	public void testAwaitLatchAndThrowInternalErrorException() {
+		AtomicBoolean outcomeHolder = new AtomicBoolean(false);
+
+		CountDownLatch latch = new CountDownLatch(1);
+		Thread thread = new Thread(() -> {
+			try {
+				AsyncUtil.awaitLatchAndThrowInternalErrorExceptionOnInterrupt(latch, 10, TimeUnit.SECONDS);
+			} catch (InternalErrorException e) {
+				outcomeHolder.set(true);
+			}
+		});
+		thread.start();
+		thread.interrupt();
+		await().until(()-> outcomeHolder.get());
+	}
+
+	@Test
+	public void testAwaitLatchIgnoreInterruption() {
+		AtomicBoolean outcomeHolder = new AtomicBoolean(true);
+
+		CountDownLatch latch = new CountDownLatch(1);
+		Thread thread = new Thread(() -> {
+			boolean outcome = AsyncUtil.awaitLatchAndIgnoreInterrupt(latch, 10, TimeUnit.SECONDS);
+			outcomeHolder.set(outcome);
+		});
+		thread.start();
+		thread.interrupt();
+		await().until(()-> outcomeHolder.get() == false);
+	}
+
+}

hapi-fhir-base/src/test/java/ca/uhn/fhir/util/StopWatchTest.java

@@ -128,6 +128,56 @@ public class StopWatchTest {
 		assertEquals("TASK1: 500ms\nTASK2: 100ms", taskDurations);
 	}
 
+	@Test
+	public void testFormatTaskDurationsDelayBetweenTasks() {
+		StopWatch sw = new StopWatch();
+
+		StopWatch.setNowForUnitTestForUnitTest(1000L);
+		sw.startTask("TASK1");
+
+		StopWatch.setNowForUnitTestForUnitTest(1500L);
+		sw.endCurrentTask();
+
+		StopWatch.setNowForUnitTestForUnitTest(2000L);
+		sw.startTask("TASK2");
+
+		StopWatch.setNowForUnitTestForUnitTest(2100L);
+		sw.endCurrentTask();
+
+		StopWatch.setNowForUnitTestForUnitTest(2200L);
+		String taskDurations = sw.formatTaskDurations();
+		ourLog.info(taskDurations);
+		assertEquals("TASK1: 500ms\n" +
+			"Between: 500ms\n" +
+			"TASK2: 100ms\n" +
+			"After last task: 100ms", taskDurations);
+	}
+
+	@Test
+	public void testFormatTaskDurationsLongDelayBeforeStart() {
+		StopWatch sw = new StopWatch(0);
+
+		StopWatch.setNowForUnitTestForUnitTest(1000L);
+		sw.startTask("TASK1");
+
+		StopWatch.setNowForUnitTestForUnitTest(1500L);
+		sw.startTask("TASK2");
+
+		StopWatch.setNowForUnitTestForUnitTest(1600L);
+		String taskDurations = sw.formatTaskDurations();
+		ourLog.info(taskDurations);
+		assertEquals("Before first task: 1000ms\nTASK1: 500ms\nTASK2: 100ms", taskDurations);
+	}
+
+	@Test
+	public void testFormatTaskDurationsNoTasks() {
+		StopWatch sw = new StopWatch(0);
+
+		String taskDurations = sw.formatTaskDurations();
+		ourLog.info(taskDurations);
+		assertEquals("No tasks", taskDurations);
+	}
+
 	@Test
 	public void testFormatThroughput60Ops4Min() {
 		StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -4));
@@ -210,4 +260,34 @@ public class StopWatchTest {
 		assertThat(string, matchesPattern("^[0-9]{3,4}ms$"));
 	}
 
+
+	@Test
+	public void testAppendRightAlignedNumber() {
+		StringBuilder b= new StringBuilder();
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 0, 100);
+		assertEquals("PFX100", b.toString());
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 1, 100);
+		assertEquals("PFX100", b.toString());
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 2, 100);
+		assertEquals("PFX100", b.toString());
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 3, 100);
+		assertEquals("PFX100", b.toString());
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 4, 100);
+		assertEquals("PFX0100", b.toString());
+
+		b.setLength(0);
+		StopWatch.appendRightAlignedNumber(b, "PFX", 10, 100);
+		assertEquals("PFX0000000100", b.toString());
+	}
+
 }

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ToggleSearchParametersCommand.java

@@ -20,7 +20,7 @@ package ca.uhn.fhir.cli;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
@@ -44,7 +44,7 @@ public class ToggleSearchParametersCommand extends BaseCommand {
 		Options options = new Options();
 		addFhirVersionOption(options);
 		addBaseUrlOption(options);
-		addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
+		addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + ITermLoaderSvc.SCT_URI + ")");
 		addBasicAuthOption(options);
 		return options;
 	}

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java

@@ -20,35 +20,32 @@ package ca.uhn.fhir.cli;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
-import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
-import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
+import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
+import ca.uhn.fhir.util.AttachmentUtil;
 import ca.uhn.fhir.util.ParametersUtil;
+import com.google.common.base.Charsets;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
-import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.instance.model.api.ICompositeType;
 
-import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.stream.Collectors;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
 public class UploadTerminologyCommand extends BaseCommand {
-	public static final String UPLOAD_TERMINOLOGY = "upload-terminology";
+	static final String UPLOAD_TERMINOLOGY = "upload-terminology";
 	// TODO: Don't use qualified names for loggers in HAPI CLI.
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UploadTerminologyCommand.class);
 
@@ -68,9 +65,8 @@ public class UploadTerminologyCommand extends BaseCommand {
 
 		addFhirVersionOption(options);
 		addBaseUrlOption(options);
-		addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
+		addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + ITermLoaderSvc.SCT_URI + ")");
 		addOptionalOption(options, "d", "data", true, "Local file to use to upload (can be a raw file or a ZIP containing the raw file)");
-		addOptionalOption(options, null, "custom", false, "Indicates that this upload uses the HAPI FHIR custom external terminology format");
 		addOptionalOption(options, "m", "mode", true, "The upload mode: SNAPSHOT (default), ADD, REMOVE");
 		addBasicAuthOption(options);
 		addVerboseLoggingOption(options);
@@ -109,104 +105,86 @@ public class UploadTerminologyCommand extends BaseCommand {
 
 		switch (mode) {
 			case SNAPSHOT:
-				uploadSnapshot(inputParameters, termUrl, datafile, theCommandLine, client);
+				invokeOperation(theCommandLine, termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM);
 				break;
 			case ADD:
-				uploadDelta(theCommandLine, termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD, false);
+				invokeOperation(theCommandLine, termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD);
 				break;
 			case REMOVE:
-				uploadDelta(theCommandLine, termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE, true);
+				invokeOperation(theCommandLine, termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE);
 				break;
 		}
 
 	}
 
-	private void uploadDelta(CommandLine theCommandLine, String theTermUrl, String[] theDatafile, IGenericClient theClient, IBaseParameters theInputParameters, String theOperationName, boolean theFlatten) {
-		ParametersUtil.addParameterToParametersUri(myFhirCtx, theInputParameters, "url", theTermUrl);
+	private void invokeOperation(CommandLine theCommandLine, String theTermUrl, String[] theDatafile, IGenericClient theClient, IBaseParameters theInputParameters, String theOperationName) throws ParseException {
+		ParametersUtil.addParameterToParametersUri(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_SYSTEM, theTermUrl);
 
-		List<IHapiTerminologyLoaderSvc.FileDescriptor> fileDescriptors = new ArrayList<>();
+		ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+		ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream, Charsets.UTF_8);
+		boolean haveCompressedContents = false;
+		try {
+			for (String nextDataFile : theDatafile) {
+
+				try (FileInputStream fileInputStream = new FileInputStream(nextDataFile)) {
+					if (!nextDataFile.endsWith(".zip")) {
+
+						ourLog.info("Compressing and adding file: {}", nextDataFile);
+						ZipEntry nextEntry = new ZipEntry(stripPath(nextDataFile));
+						zipOutputStream.putNextEntry(nextEntry);
+
+						IOUtils.copy(fileInputStream, zipOutputStream);
+						haveCompressedContents = true;
+
+						zipOutputStream.flush();
+						ourLog.info("Finished compressing {} into {}", nextEntry.getSize(), nextEntry.getCompressedSize());
+
+					} else {
+
+						ourLog.info("Adding file: {}", nextDataFile);
+						ICompositeType attachment = AttachmentUtil.newInstance(myFhirCtx);
+						AttachmentUtil.setUrl(myFhirCtx, attachment, "file:" + nextDataFile);
+						AttachmentUtil.setData(myFhirCtx, attachment, IOUtils.toByteArray(fileInputStream));
+						ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_FILE, attachment);
 
-		for (String next : theDatafile) {
-			try (FileInputStream inputStream = new FileInputStream(next)) {
-				byte[] bytes = IOUtils.toByteArray(inputStream);
-				fileDescriptors.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
-					@Override
-					public String getFilename() {
-						return next;
 					}
+				}
 
-					@Override
-					public InputStream getInputStream() {
-						return new ByteArrayInputStream(bytes);
-					}
-				});
-			} catch (IOException e) {
-				throw new CommandFailureException("Failed to read from file \"" + next + "\": " + e.getMessage());
 			}
+			zipOutputStream.flush();
+			zipOutputStream.close();
+		} catch (IOException e) {
+			throw new ParseException(e.toString());
 		}
 
-		TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
-		TerminologyLoaderSvcImpl.LoadedFileDescriptors descriptors = new TerminologyLoaderSvcImpl.LoadedFileDescriptors(fileDescriptors);
-		TerminologyLoaderSvcImpl.processCustomTerminologyFiles(descriptors, codeSystemVersion);
-
-		CodeSystem codeSystem = new CodeSystem();
-		codeSystem.setUrl(theTermUrl);
-		addCodesToCodeSystem(codeSystemVersion.getConcepts(), codeSystem.getConcept(), theFlatten);
-
-		ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, "value", codeSystem);
-
-		if (theCommandLine.hasOption("custom")) {
-			ParametersUtil.addParameterToParametersCode(myFhirCtx, theInputParameters, "contentMode", "custom");
+		if (haveCompressedContents) {
+			ICompositeType attachment = AttachmentUtil.newInstance(myFhirCtx);
+			AttachmentUtil.setUrl(myFhirCtx, attachment, "file:/files.zip");
+			AttachmentUtil.setData(myFhirCtx, attachment, byteArrayOutputStream.toByteArray());
+			ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_FILE, attachment);
 		}
 
 		ourLog.info("Beginning upload - This may take a while...");
 
-		IBaseParameters response = theClient
-			.operation()
-			.onType(myFhirCtx.getResourceDefinition("CodeSystem").getImplementingClass())
-			.named(theOperationName)
-			.withParameters(theInputParameters)
-			.execute();
+		if (ourLog.isDebugEnabled() || "true".equals(System.getProperty("test"))) {
+		ourLog.info("Submitting parameters: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(theInputParameters));
+		}
 
-		ourLog.info("Upload complete!");
-		ourLog.info("Response:\n{}", myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
-	}
-
-	private void addCodesToCodeSystem(Collection<TermConcept> theSourceConcepts, List<CodeSystem.ConceptDefinitionComponent> theTargetConcept, boolean theFlatten) {
-		for (TermConcept nextSourceConcept : theSourceConcepts) {
-
-			CodeSystem.ConceptDefinitionComponent nextTarget = new CodeSystem.ConceptDefinitionComponent();
-			nextTarget.setCode(nextSourceConcept.getCode());
-			nextTarget.setDisplay(nextSourceConcept.getDisplay());
-			theTargetConcept.add(nextTarget);
-
-			List<TermConcept> children = nextSourceConcept.getChildren().stream().map(t -> t.getChild()).collect(Collectors.toList());
-			if (theFlatten) {
-				addCodesToCodeSystem(children, theTargetConcept, theFlatten);
-			} else {
-				addCodesToCodeSystem(children, nextTarget.getConcept(), theFlatten);
+		IBaseParameters response;
+		try {
+			response = theClient
+				.operation()
+				.onType(myFhirCtx.getResourceDefinition("CodeSystem").getImplementingClass())
+				.named(theOperationName)
+				.withParameters(theInputParameters)
+				.execute();
+		} catch (BaseServerResponseException e) {
+			if (e.getOperationOutcome() != null) {
+				ourLog.error("Received the following response:\n{}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
 			}
-
-		}
-	}
-
-	private void uploadSnapshot(IBaseParameters theInputparameters, String theTermUrl, String[] theDatafile, CommandLine theCommandLine, IGenericClient theClient) {
-		ParametersUtil.addParameterToParametersUri(myFhirCtx, theInputparameters, "url", theTermUrl);
-		for (String next : theDatafile) {
-			ParametersUtil.addParameterToParametersString(myFhirCtx, theInputparameters, "localfile", next);
-		}
-		if (theCommandLine.hasOption("custom")) {
-			ParametersUtil.addParameterToParametersCode(myFhirCtx, theInputparameters, "contentMode", "custom");
+			throw e;
 		}
 
-		ourLog.info("Beginning upload - This may take a while...");
-
-		IBaseParameters response = theClient
-			.operation()
-			.onType(myFhirCtx.getResourceDefinition("CodeSystem").getImplementingClass())
-			.named(JpaConstants.OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM)
-			.withParameters(theInputparameters)
-			.execute();
 
 		ourLog.info("Upload complete!");
 		ourLog.info("Response:\n{}", myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
@@ -216,4 +194,12 @@ public class UploadTerminologyCommand extends BaseCommand {
 		SNAPSHOT, ADD, REMOVE
 	}
 
+	public static String stripPath(String thePath) {
+		String retVal = thePath;
+		if (retVal.contains("/")) {
+			retVal = retVal.substring(retVal.lastIndexOf("/"));
+		}
+		return retVal;
+	}
+
 }

hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on.xml

@@ -34,7 +34,7 @@
 	<!--
 	It's useful to have this log when uploading big terminologies
 	-->
-	<logger name="ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl" additivity="false" level="info">
+	<logger name="ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl" additivity="false" level="info">
 		<appender-ref ref="STDOUT" />
 	</logger>
 

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java

@@ -1,18 +1,20 @@
 package ca.uhn.fhir.cli;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.BaseTest;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.UploadStatistics;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.test.utilities.JettyUtil;
+import com.google.common.base.Charsets;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.hamcrest.Matchers;
-import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.IdType;
 import org.junit.After;
 import org.junit.Before;
@@ -25,15 +27,19 @@ import org.mockito.junit.MockitoJUnitRunner;
 
 import java.io.*;
 import java.util.List;
-import java.util.concurrent.atomic.AtomicInteger;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
 
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.greaterThan;
+import static org.hamcrest.Matchers.matchesPattern;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.*;
 
 @RunWith(MockitoJUnitRunner.class)
-public class UploadTerminologyCommandTest {
+public class UploadTerminologyCommandTest extends BaseTest {
 
 	static {
 		System.setProperty("test", "true");
@@ -42,26 +48,24 @@ public class UploadTerminologyCommandTest {
 	private Server myServer;
 	private FhirContext myCtx = FhirContext.forR4();
 	@Mock
-	private IHapiTerminologyLoaderSvc myTerminologyLoaderSvc;
-	@Mock
-	private IHapiTerminologySvc myTerminologySvc;
+	private ITermLoaderSvc myTermLoaderSvc;
 	@Captor
-	private ArgumentCaptor<List<IHapiTerminologyLoaderSvc.FileDescriptor>> myDescriptorList;
-	@Captor
-	private ArgumentCaptor<CodeSystem> myCodeSystemCaptor;
+	private ArgumentCaptor<List<ITermLoaderSvc.FileDescriptor>> myDescriptorListCaptor;
 
 	private int myPort;
 	private String myConceptsFileName = "target/concepts.csv";
 	private String myHierarchyFileName = "target/hierarchy.csv";
 	private File myConceptsFile = new File(myConceptsFileName);
 	private File myHierarchyFile = new File(myHierarchyFileName);
+	private File myArchiveFile;
+	private String myArchiveFileName;
 
 	@Test
-	public void testTerminologyUpload_AddDelta() throws IOException {
+	public void testAddDelta() throws IOException {
 
 		writeConceptAndHierarchyFiles();
 
-		when(myTerminologySvc.applyDeltaCodesystemsAdd(eq("http://foo"), any(), any())).thenReturn(new AtomicInteger(100));
+		when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
 
 		App.main(new String[]{
 			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
@@ -73,25 +77,69 @@ public class UploadTerminologyCommandTest {
 			"-d", myHierarchyFileName
 		});
 
-		verify(myTerminologySvc, times(1)).applyDeltaCodesystemsAdd(any(), isNull(), myCodeSystemCaptor.capture());
+		verify(myTermLoaderSvc, times(1)).loadDeltaAdd(eq("http://foo"), myDescriptorListCaptor.capture(), any());
 
-		CodeSystem codeSystem = myCodeSystemCaptor.getValue();
-		assertEquals(1, codeSystem.getConcept().size());
-		assertEquals("http://foo", codeSystem.getUrl());
-		assertEquals("ANIMALS", codeSystem.getConcept().get(0).getCode());
-		assertEquals("Animals", codeSystem.getConcept().get(0).getDisplay());
-		assertEquals(2, codeSystem.getConcept().get(0).getConcept().size());
-		assertEquals("CATS", codeSystem.getConcept().get(0).getConcept().get(0).getCode());
-		assertEquals("Cats", codeSystem.getConcept().get(0).getConcept().get(0).getDisplay());
-		assertEquals("DOGS", codeSystem.getConcept().get(0).getConcept().get(1).getCode());
-		assertEquals("Dogs", codeSystem.getConcept().get(0).getConcept().get(1).getDisplay());
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
+		assertEquals(1, listOfDescriptors.size());
+		assertEquals("file:/files.zip", listOfDescriptors.get(0).getFilename());
+		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
 	}
 
 	@Test
-	public void testTerminologyUpload_RemoveDelta() throws IOException {
+	public void testAddDeltaUsingCompressedFile() throws IOException {
+
+		writeConceptAndHierarchyFiles();
+		writeArchiveFile(myConceptsFile, myHierarchyFile);
+
+		when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+
+		App.main(new String[]{
+			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+			"-v", "r4",
+			"-m", "ADD",
+			"-t", "http://localhost:" + myPort,
+			"-u", "http://foo",
+			"-d", myArchiveFileName
+		});
+
+		verify(myTermLoaderSvc, times(1)).loadDeltaAdd(eq("http://foo"), myDescriptorListCaptor.capture(), any());
+
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
+		assertEquals(1, listOfDescriptors.size());
+		assertThat(listOfDescriptors.get(0).getFilename(), matchesPattern("^file:.*temp.*\\.zip$"));
+		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
+	}
+
+	private void writeArchiveFile(File... theFiles) throws IOException {
+		ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+		ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream, Charsets.UTF_8);
+
+		for (File next : theFiles) {
+			ZipEntry nextEntry = new ZipEntry(UploadTerminologyCommand.stripPath(next.getAbsolutePath()));
+			zipOutputStream.putNextEntry(nextEntry);
+
+			try (FileInputStream fileInputStream = new FileInputStream(next)) {
+				IOUtils.copy(fileInputStream, zipOutputStream);
+			}
+
+		}
+
+		zipOutputStream.flush();
+		zipOutputStream.close();
+
+		myArchiveFile = File.createTempFile("temp", ".zip");
+		myArchiveFile.deleteOnExit();
+		myArchiveFileName = myArchiveFile.getAbsolutePath();
+		try (FileOutputStream fos = new FileOutputStream(myArchiveFile, false)) {
+			fos.write(byteArrayOutputStream.toByteArray());
+		}
+	}
+
+	@Test
+	public void testRemoveDelta() throws IOException {
 		writeConceptAndHierarchyFiles();
 
-		when(myTerminologySvc.applyDeltaCodesystemsRemove(eq("http://foo"), any())).thenReturn(new AtomicInteger(100));
+		when(myTermLoaderSvc.loadDeltaRemove(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
 
 		App.main(new String[]{
 			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
@@ -103,46 +151,38 @@ public class UploadTerminologyCommandTest {
 			"-d", myHierarchyFileName
 		});
 
-		verify(myTerminologySvc, times(1)).applyDeltaCodesystemsRemove(any(), myCodeSystemCaptor.capture());
+		verify(myTermLoaderSvc, times(1)).loadDeltaRemove(eq("http://foo"), myDescriptorListCaptor.capture(), any());
+
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
+		assertEquals(1, listOfDescriptors.size());
+		assertEquals("file:/files.zip", listOfDescriptors.get(0).getFilename());
+		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
 
-		CodeSystem codeSystem = myCodeSystemCaptor.getValue();
-		assertEquals(3, codeSystem.getConcept().size());
-		assertEquals("http://foo", codeSystem.getUrl());
-		assertEquals("ANIMALS", codeSystem.getConcept().get(0).getCode());
-		assertEquals("Animals", codeSystem.getConcept().get(0).getDisplay());
-		assertEquals("CATS", codeSystem.getConcept().get(1).getCode());
-		assertEquals("Cats", codeSystem.getConcept().get(1).getDisplay());
-		assertEquals("DOGS", codeSystem.getConcept().get(2).getCode());
-		assertEquals("Dogs", codeSystem.getConcept().get(2).getDisplay());
 	}
 
 	@Test
-	public void testTerminologyUpload_Snapshot() throws IOException {
+	public void testSnapshot() throws IOException {
 
 		writeConceptAndHierarchyFiles();
 
-		when(myTerminologyLoaderSvc.loadCustom(eq("http://foo"), any(), any())).thenReturn(new IHapiTerminologyLoaderSvc.UploadStatistics(100, new IdType("CodeSystem/123")));
+		when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
 
 		App.main(new String[]{
 			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
 			"-v", "r4",
 			"-m", "SNAPSHOT",
-			"--custom",
 			"-t", "http://localhost:" + myPort,
 			"-u", "http://foo",
 			"-d", myConceptsFileName,
 			"-d", myHierarchyFileName
 		});
 
-		verify(myTerminologyLoaderSvc, times(1)).loadCustom(any(), myDescriptorList.capture(), any());
+		verify(myTermLoaderSvc, times(1)).loadCustom(any(), myDescriptorListCaptor.capture(), any());
 
-		List<IHapiTerminologyLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorList.getValue();
-		assertEquals(2, listOfDescriptors.size());
-
-		assertThat(listOfDescriptors.get(0).getFilename(), Matchers.endsWith("concepts.csv"));
-		assertInputStreamEqualsFile(myConceptsFile, listOfDescriptors.get(0).getInputStream());
-		assertThat(listOfDescriptors.get(1).getFilename(), Matchers.endsWith("hierarchy.csv"));
-		assertInputStreamEqualsFile(myHierarchyFile, listOfDescriptors.get(1).getInputStream());
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
+		assertEquals(1, listOfDescriptors.size());
+		assertEquals("file:/files.zip", listOfDescriptors.get(0).getFilename());
+		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
 	}
 
 
@@ -161,27 +201,41 @@ public class UploadTerminologyCommandTest {
 		}
 	}
 
-	private void assertInputStreamEqualsFile(File theExpectedFile, InputStream theActualInputStream) throws IOException {
-		try (FileInputStream fis = new FileInputStream(theExpectedFile)) {
-			byte[] expectedBytes = IOUtils.toByteArray(fis);
-			byte[] actualBytes = IOUtils.toByteArray(theActualInputStream);
-			assertArrayEquals(expectedBytes, actualBytes);
+	@Test
+	public void testAddInvalidFileName() throws IOException {
+
+		writeConceptAndHierarchyFiles();
+
+		try {
+			App.main(new String[]{
+				UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+				"-v", "r4",
+				"-m", "ADD",
+				"-t", "http://localhost:" + myPort,
+				"-u", "http://foo",
+				"-d", myConceptsFileName + "/foo.csv",
+				"-d", myHierarchyFileName
+			});
+		} catch (Error e) {
+			assertThat(e.toString(), Matchers.containsString("FileNotFoundException: target/concepts.csv/foo.csv"));
 		}
 	}
 
+
 	@After
 	public void after() throws Exception {
 		JettyUtil.closeServer(myServer);
 
 		FileUtils.deleteQuietly(myConceptsFile);
 		FileUtils.deleteQuietly(myHierarchyFile);
+		FileUtils.deleteQuietly(myArchiveFile);
 	}
 
 	@Before
-	public void start() throws Exception {
+	public void before() throws Exception {
 		myServer = new Server(0);
 
-		TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTerminologyLoaderSvc, myTerminologySvc);
+		TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTermLoaderSvc);
 
 		ServletHandler proxyHandler = new ServletHandler();
 		RestfulServer servlet = new RestfulServer(myCtx);

hapi-fhir-client-okhttp/src/main/java/ca/uhn/fhir/okhttp/client/OkHttpRestfulResponse.java

@@ -51,23 +51,19 @@ public class OkHttpRestfulResponse extends BaseHttpResponse implements IHttpResp
 		this.myResponse = theResponse;
 	}
 
-	@Override
-	public void bufferEntitity() throws IOException {
-		bufferEntity();
-	}
-
 	@Override
 	public void bufferEntity() throws IOException {
 		if (myEntityBuffered) {
 			return;
 		}
-		InputStream responseEntity = readEntity();
-		if (responseEntity != null) {
-			myEntityBuffered = true;
-			try {
-				myEntityBytes = IOUtils.toByteArray(responseEntity);
-			} catch (IllegalStateException e) {
-				throw new InternalErrorException(e);
+		try (InputStream responseEntity = readEntity()) {
+			if (responseEntity != null) {
+				myEntityBuffered = true;
+				try {
+					myEntityBytes = IOUtils.toByteArray(responseEntity);
+				} catch (IllegalStateException e) {
+					throw new InternalErrorException(e);
+				}
 			}
 		}
 	}

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/apache/ApacheHttpResponse.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.rest.client.apache;
  */
 import java.io.*;
 import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.util.*;
 
 import ca.uhn.fhir.rest.client.impl.BaseHttpResponse;
@@ -53,25 +54,19 @@ public class ApacheHttpResponse extends BaseHttpResponse implements IHttpRespons
 		this.myResponse = theResponse;
 	}
 
-	@Deprecated // override deprecated method
-	@Override
-	public void bufferEntitity() throws IOException {
-		bufferEntity();
-	}
-
 	@Override
 	public void bufferEntity() throws IOException {
 		if (myEntityBuffered) {
 			return;
 		}
-		InputStream respEntity = readEntity();
-		if (respEntity != null) {
-			this.myEntityBuffered = true;
-			try {
-				this.myEntityBytes = IOUtils.toByteArray(respEntity);
-			} catch (IllegalStateException e) {
-				// FIXME resouce leak
-				throw new InternalErrorException(e);
+		try (InputStream respEntity = readEntity()) {
+			if (respEntity != null) {
+				this.myEntityBuffered = true;
+				try {
+					this.myEntityBytes = IOUtils.toByteArray(respEntity);
+				} catch (IllegalStateException e) {
+					throw new InternalErrorException(e);
+				}
 			}
 		}
 	}
@@ -103,7 +98,7 @@ public class ApacheHttpResponse extends BaseHttpResponse implements IHttpRespons
 			if (Constants.STATUS_HTTP_204_NO_CONTENT != myResponse.getStatusLine().getStatusCode()) {
 				ourLog.debug("Response did not specify a charset, defaulting to utf-8");
 			}
-			charset = Charset.forName("UTF-8");
+			charset = StandardCharsets.UTF_8;
 		}
 
 		return new InputStreamReader(readEntity(), charset);
@@ -115,11 +110,7 @@ public class ApacheHttpResponse extends BaseHttpResponse implements IHttpRespons
 		if (myResponse.getAllHeaders() != null) {
 			for (Header next : myResponse.getAllHeaders()) {
 				String name = next.getName().toLowerCase();
-				List<String> list = headers.get(name);
-				if (list == null) {
-					list = new ArrayList<>();
-					headers.put(name, list);
-				}
+				List<String> list = headers.computeIfAbsent(name, k -> new ArrayList<>());
 				list.add(next.getValue());
 			}
 

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/interceptor/LoggingInterceptor.java

@@ -22,6 +22,7 @@ package ca.uhn.fhir.rest.client.interceptor;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -94,9 +95,7 @@ public class LoggingInterceptor implements IClientInterceptor {
 				if (content != null) {
 					myLog.info("Client request body:\n{}", content);
 				}
-			} catch (IllegalStateException e) {
-				myLog.warn("Failed to replay request contents (during logging attempt, actual FHIR call did not fail)", e);
-			} catch (IOException e) {
+			} catch (IllegalStateException | IOException e) {
 				myLog.warn("Failed to replay request contents (during logging attempt, actual FHIR call did not fail)", e);
 			}
 		}
@@ -147,11 +146,8 @@ public class LoggingInterceptor implements IClientInterceptor {
 		}
 
 		if (myLogResponseBody) {
-			//TODO: Use of a deprecated method should be resolved.
-			theResponse.bufferEntitity();
-			InputStream respEntity = null;
-			try  {
-				respEntity = theResponse.readEntity();
+			theResponse.bufferEntity();
+			try (InputStream respEntity = theResponse.readEntity()) {
 				if (respEntity != null) {
 					final byte[] bytes;
 					try {
@@ -159,12 +155,10 @@ public class LoggingInterceptor implements IClientInterceptor {
 					} catch (IllegalStateException e) {
 						throw new InternalErrorException(e);
 					}
-					myLog.info("Client response body:\n{}", new String(bytes, "UTF-8"));
+					myLog.info("Client response body:\n{}", new String(bytes, StandardCharsets.UTF_8));
 				} else {
 					myLog.info("Client response body: (none)");
 				}
-			} finally {
-				IOUtils.closeQuietly(respEntity);
 			}
 		}
 	}
@@ -178,7 +172,9 @@ public class LoggingInterceptor implements IClientInterceptor {
 				Iterator<String> values = theHeaders.get(key).iterator();
 				while(values.hasNext()) {
 					String value = values.next();
-						b.append(key + ": " + value);
+						b.append(key);
+						b.append(": ");
+						b.append(value);
 						if (nameEntries.hasNext() || values.hasNext()) {
 							b.append('\n');
 						}

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/client/JaxRsHttpResponse.java

@@ -51,11 +51,6 @@ public class JaxRsHttpResponse extends BaseHttpResponse implements IHttpResponse
 		this.myResponse = theResponse;
 	}
 
-	@Override
-	public void bufferEntitity() throws IOException {
-		bufferEntity();
-	}
-
 	@Override
 	public void bufferEntity() throws IOException {
 		if(!myBufferedEntity && myResponse.hasEntity()) {

hapi-fhir-jpaserver-base/pom.xml

@@ -46,7 +46,6 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-csv</artifactId>
-			<version>1.3</version>
 		</dependency>
 
 		<dependency>

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

@@ -0,0 +1,19 @@
+package ca.uhn.fhir.jpa;
+
+import com.google.common.base.Charsets;
+import org.apache.commons.io.IOUtils;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+public class BaseTest {
+
+	protected String loadResource(String theClasspath) throws IOException {
+		InputStream stream = BaseTest.class.getResourceAsStream(theClasspath);
+		if (stream==null) {
+			throw new IllegalArgumentException("Unable to find resource: " + theClasspath);
+		}
+		return IOUtils.toString(stream, Charsets.UTF_8);
+	}
+
+}

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

@@ -32,6 +32,13 @@ import ca.uhn.fhir.jpa.subscription.module.cache.LinkedBlockingQueueSubscribable
 import ca.uhn.fhir.jpa.subscription.module.channel.ISubscribableChannelFactory;
 import ca.uhn.fhir.jpa.subscription.module.matcher.ISubscriptionMatcher;
 import ca.uhn.fhir.jpa.subscription.module.matcher.InMemorySubscriptionMatcher;
+import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
+import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
 import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
@@ -256,7 +263,6 @@ public abstract class BaseConfig {
 	}
 
 
-
 	public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) {
 		theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer()));
 		theFactory.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfigDstu3Plus.java

@@ -0,0 +1,34 @@
+package ca.uhn.fhir.jpa.config;
+
+import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
+import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
+import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public abstract class BaseConfigDstu3Plus extends BaseConfig {
+
+	@Bean
+	public ITermCodeSystemStorageSvc termCodeSystemStorageSvc() {
+		return new TermCodeSystemStorageSvcImpl();
+	}
+
+	@Bean
+	public ITermDeferredStorageSvc termDeferredStorageSvc() {
+		return new TermDeferredStorageSvcImpl();
+	}
+
+	@Bean
+	public ITermReindexingSvc termReindexingSvc() {
+		return new TermReindexingSvcImpl();
+	}
+
+	@Bean
+	public abstract ITermVersionAdapterSvc terminologyVersionAdapterSvc();
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java

@@ -7,8 +7,10 @@ import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu2;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryDstu2;
-import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu2;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.TermReadSvcDstu2;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcDstu2;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 import ca.uhn.fhir.validation.IValidatorModule;
@@ -134,8 +136,8 @@ public class BaseDstu2Config extends BaseConfig {
 	}
 
 	@Bean(autowire = Autowire.BY_TYPE)
-	public IHapiTerminologySvc terminologyService() {
-		return new HapiTerminologySvcDstu2();
+	public ITermReadSvc terminologyService() {
+		return new TermReadSvcDstu2();
 	}
 
 }

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

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.config.dstu3;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.ParserOptions;
 import ca.uhn.fhir.jpa.config.BaseConfig;
+import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@@ -12,10 +13,12 @@ import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu3;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryDstu3;
-import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu3;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvcDstu3;
-import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
+import ca.uhn.fhir.jpa.term.TermReadSvcDstu3;
+import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
+import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcDstu3;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
 import ca.uhn.fhir.validation.IValidatorModule;
@@ -26,7 +29,6 @@ import org.hl7.fhir.dstu3.hapi.validation.CachingValidationSupport;
 import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.r5.utils.IResourceValidator;
-import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Lazy;
@@ -55,13 +57,19 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 @Configuration
 @EnableTransactionManagement
-public class BaseDstu3Config extends BaseConfig {
+public class BaseDstu3Config extends BaseConfigDstu3Plus {
 
 	@Override
 	public FhirContext fhirContext() {
 		return fhirContextDstu3();
 	}
 
+	@Bean
+	@Override
+	public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
+		return new TermVersionAdapterSvcDstu3();
+	}
+
 	@Bean
 	@Primary
 	public FhirContext fhirContextDstu3() {
@@ -109,10 +117,9 @@ public class BaseDstu3Config extends BaseConfig {
 		return new JpaValidationSupportChainDstu3();
 	}
 
-	@Bean(name = "myJpaValidationSupportDstu3", autowire = Autowire.BY_NAME)
+	@Bean(name = "myJpaValidationSupportDstu3")
 	public ca.uhn.fhir.jpa.dao.dstu3.IJpaValidationSupportDstu3 jpaValidationSupportDstu3() {
-		ca.uhn.fhir.jpa.dao.dstu3.JpaValidationSupportDstu3 retVal = new ca.uhn.fhir.jpa.dao.dstu3.JpaValidationSupportDstu3();
-		return retVal;
+		return new ca.uhn.fhir.jpa.dao.dstu3.JpaValidationSupportDstu3();
 	}
 
 	@Bean(name = "myResourceCountsCache")
@@ -122,13 +129,12 @@ public class BaseDstu3Config extends BaseConfig {
 		return retVal;
 	}
 
-	@Bean(autowire = Autowire.BY_TYPE)
+	@Bean
 	public IFulltextSearchSvc searchDaoDstu3() {
-		FulltextSearchSvcImpl searchDao = new FulltextSearchSvcImpl();
-		return searchDao;
+		return new FulltextSearchSvcImpl();
 	}
 
-	@Bean(autowire = Autowire.BY_TYPE)
+	@Bean
 	public SearchParamExtractorDstu3 searchParamExtractor() {
 		return new SearchParamExtractorDstu3();
 	}
@@ -138,10 +144,9 @@ public class BaseDstu3Config extends BaseConfig {
 		return new SearchParamRegistryDstu3();
 	}
 
-	@Bean(name = "mySystemDaoDstu3", autowire = Autowire.BY_NAME)
+	@Bean(name = "mySystemDaoDstu3")
 	public IFhirSystemDao<org.hl7.fhir.dstu3.model.Bundle, org.hl7.fhir.dstu3.model.Meta> systemDaoDstu3() {
-		ca.uhn.fhir.jpa.dao.dstu3.FhirSystemDaoDstu3 retVal = new ca.uhn.fhir.jpa.dao.dstu3.FhirSystemDaoDstu3();
-		return retVal;
+		return new ca.uhn.fhir.jpa.dao.dstu3.FhirSystemDaoDstu3();
 	}
 
 	@Bean(name = "mySystemProviderDstu3")
@@ -152,18 +157,18 @@ public class BaseDstu3Config extends BaseConfig {
 		return retVal;
 	}
 
-	@Bean(autowire = Autowire.BY_TYPE)
-	public IHapiTerminologyLoaderSvc terminologyLoaderService() {
-		return new TerminologyLoaderSvcImpl();
+	@Bean
+	public ITermLoaderSvc termLoaderService() {
+		return new TermLoaderSvcImpl();
 	}
 
-	@Bean(autowire = Autowire.BY_TYPE)
-	public IHapiTerminologySvcDstu3 terminologyService() {
-		return new HapiTerminologySvcDstu3();
+	@Bean
+	public ITermReadSvcDstu3 terminologyService() {
+		return new TermReadSvcDstu3();
 	}
 
 	@Primary
-	@Bean(autowire = Autowire.BY_NAME, name = "myJpaValidationSupportChainDstu3")
+	@Bean(name = "myJpaValidationSupportChainDstu3")
 	public IValidationSupport validationSupportChainDstu3() {
 		return new CachingValidationSupport(jpaValidationSupportChain());
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.config.r4;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.ParserOptions;
 import ca.uhn.fhir.jpa.config.BaseConfig;
+import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@@ -12,10 +13,10 @@ import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR4;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR4;
-import ca.uhn.fhir.jpa.term.HapiTerminologySvcR4;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
-import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
+import ca.uhn.fhir.jpa.term.*;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR4;
 import ca.uhn.fhir.validation.IValidatorModule;
@@ -55,13 +56,19 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 @Configuration
 @EnableTransactionManagement
-public class BaseR4Config extends BaseConfig {
+public class BaseR4Config extends BaseConfigDstu3Plus {
 
 	@Override
 	public FhirContext fhirContext() {
 		return fhirContextR4();
 	}
 
+	@Bean
+	@Override
+	public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
+		return new TermVersionAdapterSvcR4();
+	}
+
 	@Bean
 	@Primary
 	public FhirContext fhirContextR4() {
@@ -154,13 +161,13 @@ public class BaseR4Config extends BaseConfig {
 	}
 
 	@Bean(autowire = Autowire.BY_TYPE)
-	public IHapiTerminologyLoaderSvc terminologyLoaderService() {
-		return new TerminologyLoaderSvcImpl();
+	public ITermLoaderSvc termLoaderService() {
+		return new TermLoaderSvcImpl();
 	}
 
 	@Bean(autowire = Autowire.BY_TYPE)
-	public IHapiTerminologySvcR4 terminologyService() {
-		return new HapiTerminologySvcR4();
+	public ITermReadSvcR4 terminologyService() {
+		return new TermReadSvcR4();
 	}
 
 	@Primary

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.config.r5;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.ParserOptions;
 import ca.uhn.fhir.jpa.config.BaseConfig;
+import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@@ -12,10 +13,10 @@ import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR5;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR5;
-import ca.uhn.fhir.jpa.term.HapiTerminologySvcR5;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR5;
-import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
+import ca.uhn.fhir.jpa.term.*;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR5;
 import ca.uhn.fhir.validation.IValidatorModule;
@@ -55,13 +56,19 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 @Configuration
 @EnableTransactionManagement
-public class BaseR5Config extends BaseConfig {
+public class BaseR5Config extends BaseConfigDstu3Plus {
 
 	@Override
 	public FhirContext fhirContext() {
 		return fhirContextR5();
 	}
 
+	@Bean
+	@Override
+	public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
+		return new TermVersionAdapterSvcR5();
+	}
+
 	@Bean
 	@Primary
 	public FhirContext fhirContextR5() {
@@ -154,13 +161,13 @@ public class BaseR5Config extends BaseConfig {
 	}
 
 	@Bean(autowire = Autowire.BY_TYPE)
-	public IHapiTerminologyLoaderSvc terminologyLoaderService() {
-		return new TerminologyLoaderSvcImpl();
+	public ITermLoaderSvc terminologyLoaderService() {
+		return new TermLoaderSvcImpl();
 	}
 
 	@Bean(autowire = Autowire.BY_TYPE)
-	public IHapiTerminologySvcR5 terminologyService() {
-		return new HapiTerminologySvcR5();
+	public ITermReadSvcR5 terminologyService() {
+		return new TermReadSvcR5();
 	}
 
 	@Primary

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

@@ -20,13 +20,13 @@ import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
-import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
 import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
 import ca.uhn.fhir.jpa.searchparam.extractor.LogicalReferenceHelper;
 import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.util.AddRemoveCount;
 import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
 import ca.uhn.fhir.model.api.IResource;
@@ -53,7 +53,6 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetai
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.MetaUtil;
-import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.XmlUtil;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Charsets;
@@ -62,8 +61,6 @@ import com.google.common.hash.HashFunction;
 import com.google.common.hash.Hashing;
 import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.Validate;
-import org.hibernate.Session;
-import org.hibernate.internal.SessionImpl;
 import org.hl7.fhir.instance.model.api.*;
 import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.slf4j.Logger;
@@ -81,7 +78,6 @@ import javax.annotation.PostConstruct;
 import javax.persistence.*;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
-import javax.persistence.criteria.Predicate;
 import javax.persistence.criteria.Root;
 import javax.xml.stream.events.Characters;
 import javax.xml.stream.events.XMLEvent;
@@ -139,7 +135,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	@Autowired
 	protected ISearchParamRegistry mySerarchParamRegistry;
 	@Autowired
-	protected IHapiTerminologySvc myTerminologySvc;
+	protected ITermReadSvc myTerminologySvc;
 	@Autowired
 	protected IResourceHistoryTableDao myResourceHistoryTableDao;
 	@Autowired
@@ -161,8 +157,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	@Autowired
 	private ISearchCacheSvc mySearchCacheSvc;
 	@Autowired
-	private ISearchResultCacheSvc mySearchResultCacheSvc;
-	@Autowired
 	private ISearchParamPresenceSvc mySearchParamPresenceSvc;
 	@Autowired
 	private DaoRegistry myDaoRegistry;
@@ -192,20 +186,18 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	 * none was created, returns null.
 	 */
 	protected ForcedId createForcedIdIfNeeded(ResourceTable theEntity, IIdType theId, boolean theCreateForPureNumericIds) {
+		ForcedId retVal = null;
 		if (theId.isEmpty() == false && theId.hasIdPart() && theEntity.getForcedId() == null) {
-			if (!theCreateForPureNumericIds && IdHelperService.isValidPid(theId)) {
-				return null;
+			if (theCreateForPureNumericIds || !IdHelperService.isValidPid(theId)) {
+				retVal = new ForcedId();
+				retVal.setResourceType(theEntity.getResourceType());
+				retVal.setForcedId(theId.getIdPart());
+				retVal.setResource(theEntity);
+				theEntity.setForcedId(retVal);
 			}
-
-			ForcedId fid = new ForcedId();
-			fid.setResourceType(theEntity.getResourceType());
-			fid.setForcedId(theId.getIdPart());
-			fid.setResource(theEntity);
-			theEntity.setForcedId(fid);
-			return fid;
 		}
 
-		return null;
+		return retVal;
 	}
 
 	private void extractTagsHapi(IResource theResource, ResourceTable theEntity, Set<ResourceTag> allDefs) {
@@ -285,39 +277,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 
 	}
 
-	private void findMatchingTagIds(RequestDetails theRequest, String theResourceName, IIdType theResourceId, Set<Long> tagIds, Class<? extends BaseTag> entityClass) {
-		{
-			CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
-			CriteriaQuery<Tuple> cq = builder.createTupleQuery();
-			Root<? extends BaseTag> from = cq.from(entityClass);
-			cq.multiselect(from.get("myTagId").as(Long.class)).distinct(true);
-
-			if (theResourceName != null) {
-				Predicate typePredicate = builder.equal(from.get("myResourceType"), theResourceName);
-				if (theResourceId != null) {
-					cq.where(typePredicate, builder.equal(from.get("myResourceId"), myIdHelperService.translateForcedIdToPid(theResourceName, theResourceId.getIdPart(), theRequest)));
-				} else {
-					cq.where(typePredicate);
-				}
-			}
-
-			TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
-			for (Tuple next : query.getResultList()) {
-				tagIds.add(next.get(0, Long.class));
-			}
-		}
-	}
-
-	protected void flushJpaSession() {
-		SessionImpl session = (SessionImpl) myEntityManager.unwrap(Session.class);
-		int insertionCount = session.getActionQueue().numberOfInsertions();
-		int updateCount = session.getActionQueue().numberOfUpdates();
-
-		StopWatch sw = new StopWatch();
-		myEntityManager.flush();
-		ourLog.debug("Session flush took {}ms for {} inserts and {} updates", sw.getMillis(), insertionCount, updateCount);
-	}
-
 	private Set<ResourceTag> getAllTagDefinitions(ResourceTable theEntity) {
 		HashSet<ResourceTag> retVal = Sets.newHashSet();
 		if (theEntity.isHasTags()) {
@@ -358,7 +317,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		}
 	}
 
-	@SuppressWarnings("unchecked")
 	public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
 		return myDaoRegistry.getResourceDaoOrNull(theType);
 	}
@@ -446,6 +404,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 			newVersion = Long.toString(newVersionLong);
 		}
 
+		assert theResourceId != null;
 		IIdType newId = theResourceId.withVersion(newVersion);
 		theResource.getIdElement().setValue(newId.getValue());
 		theSavedEntity.setVersion(newVersionLong);

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

@@ -39,7 +39,7 @@ import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
 import ca.uhn.fhir.jpa.util.*;
 import ca.uhn.fhir.model.api.*;
@@ -64,7 +64,6 @@ import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
 import com.google.common.collect.Sets;
-import org.apache.commons.lang3.ObjectUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
@@ -135,7 +134,7 @@ public class SearchBuilder implements ISearchBuilder {
 	@Autowired
 	private ISearchParamRegistry mySearchParamRegistry;
 	@Autowired
-	private IHapiTerminologySvc myTerminologySvc;
+	private ITermReadSvc myTerminologySvc;
 	@Autowired
 	private MatchUrlService myMatchUrlService;
 	private List<Long> myAlsoIncludePids;

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.TokenParam;
@@ -41,6 +42,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import javax.annotation.Nonnull;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
@@ -54,21 +56,22 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 
 	@Autowired
 	private ITermCodeSystemDao myCsDao;
-
 	@Autowired
 	private ValidationSupportChain myValidationSupport;
+	@Autowired
+	protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
 
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
-		List<IIdType> valueSetIds;
 		Set<Long> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest );
-		valueSetIds = new ArrayList<>();
+		List<IIdType> valueSetIds = new ArrayList<>();
 		for (Long next : ids) {
 			valueSetIds.add(new IdType("CodeSystem", next));
 		}
 		return valueSetIds;
 	}
 
+	@Nonnull
 	@Override
 	public IContextValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
 		boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
@@ -119,7 +122,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 		if (isNotBlank(codeSystemUrl)) {
 			TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
 			if (persCs != null) {
-				myTerminologySvc.deleteCodeSystem(persCs);
+				myTerminologyCodeSystemStorageSvc.deleteCodeSystem(persCs);
 			}
 		}
 	}
@@ -134,7 +137,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 		org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
 		addPidToResource(theEntity, cs);
 
-		myTerminologySvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
+		myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
 
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java

@@ -27,7 +27,7 @@ import ca.uhn.fhir.jpa.term.TranslationResult;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.hl7.fhir.convertors.VersionConvertor_30_40;
@@ -42,11 +42,9 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
 public class FhirResourceDaoConceptMapDstu3 extends FhirResourceDaoDstu3<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
 	@Autowired
-	private IHapiTerminologySvc myHapiTerminologySvc;
+	private ITermReadSvc myHapiTerminologySvc;
 
 	@Override
 	public TranslationResult translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {

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

@@ -24,7 +24,7 @@ import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -62,7 +62,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
 	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
 
 	@Autowired
-	private IHapiTerminologySvc myHapiTerminologySvc;
+	private ITermReadSvc myHapiTerminologySvc;
 
 	@Autowired
 	private DefaultProfileValidationSupport myDefaultProfileValidationSupport;

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.TokenParam;
@@ -56,6 +57,8 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
 	private ITermCodeSystemDao myCsDao;
 	@Autowired
 	private ValidationSupportChain myValidationSupport;
+	@Autowired
+	protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
 
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
@@ -122,7 +125,7 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
 		if (isNotBlank(codeSystemUrl)) {
 			TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
 			if (persCs != null) {
-				myTerminologySvc.deleteCodeSystem(persCs);
+				myTerminologyCodeSystemStorageSvc.deleteCodeSystem(persCs);
 			}
 		}
 	}
@@ -135,7 +138,7 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
 		CodeSystem cs = (CodeSystem) theResource;
 		addPidToResource(theEntity, theResource);
 
-		myTerminologySvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
+		myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
 
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java

@@ -24,7 +24,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.term.TranslationMatch;
 import ca.uhn.fhir.jpa.term.TranslationRequest;
 import ca.uhn.fhir.jpa.term.TranslationResult;
@@ -38,11 +38,9 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
 public class FhirResourceDaoConceptMapR4 extends FhirResourceDaoR4<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
 	@Autowired
-	private IHapiTerminologySvc myHapiTerminologySvc;
+	private ITermReadSvc myHapiTerminologySvc;
 
 	@Override
 	public TranslationResult translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {

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

@@ -24,7 +24,7 @@ import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -56,7 +56,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
 
 	@Autowired
-	private IHapiTerminologySvc myHapiTerminologySvc;
+	private ITermReadSvc myHapiTerminologySvc;
 
 	@Autowired
 	private DefaultProfileValidationSupport myDefaultProfileValidationSupport;

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.TokenParam;
@@ -56,6 +57,8 @@ public class FhirResourceDaoCodeSystemR5 extends FhirResourceDaoR5<CodeSystem> i
 	private ITermCodeSystemDao myCsDao;
 	@Autowired
 	private ValidationSupportChain myValidationSupport;
+	@Autowired
+	protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
 
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
@@ -122,7 +125,7 @@ public class FhirResourceDaoCodeSystemR5 extends FhirResourceDaoR5<CodeSystem> i
 		if (isNotBlank(codeSystemUrl)) {
 			TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
 			if (persCs != null) {
-				myTerminologySvc.deleteCodeSystem(persCs);
+				myTerminologyCodeSystemStorageSvc.deleteCodeSystem(persCs);
 			}
 		}
 	}
@@ -135,7 +138,7 @@ public class FhirResourceDaoCodeSystemR5 extends FhirResourceDaoR5<CodeSystem> i
 		CodeSystem cs = (CodeSystem) theResource;
 		addPidToResource(theEntity, theResource);
 
-		myTerminologySvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), theEntity);
+		myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), theEntity);
 
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java

@@ -24,7 +24,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.term.TranslationMatch;
 import ca.uhn.fhir.jpa.term.TranslationRequest;
 import ca.uhn.fhir.jpa.term.TranslationResult;
@@ -41,7 +41,7 @@ import java.util.Set;
 
 public class FhirResourceDaoConceptMapR5 extends FhirResourceDaoR5<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
 	@Autowired
-	private IHapiTerminologySvc myHapiTerminologySvc;
+	private ITermReadSvc myHapiTerminologySvc;
 
 	@Override
 	public TranslationResult translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {

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

@@ -24,7 +24,7 @@ import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -56,7 +56,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
 
 	@Autowired
-	private IHapiTerminologySvc myHapiTerminologySvc;
+	private ITermReadSvc myHapiTerminologySvc;
 
 	@Autowired
 	private DefaultProfileValidationSupport myDefaultProfileValidationSupport;

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

@@ -22,6 +22,8 @@ package ca.uhn.fhir.jpa.entity;
 
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.util.ValidateUtil;
+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;
 
@@ -39,17 +41,17 @@ import static org.apache.commons.lang3.StringUtils.length;
 @Entity()
 //@formatter:on
 public class TermCodeSystem implements Serializable {
-	private static final long serialVersionUID = 1L;
-
-	private static final int MAX_NAME_LENGTH = 200;
 	public static final int MAX_URL_LENGTH = 200;
-
+	private static final long serialVersionUID = 1L;
+	private static final int MAX_NAME_LENGTH = 200;
 	@Column(name = "CODE_SYSTEM_URI", nullable = false, length = MAX_URL_LENGTH)
 	private String myCodeSystemUri;
 
 	@OneToOne()
 	@JoinColumn(name = "CURRENT_VERSION_PID", referencedColumnName = "PID", nullable = true, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_CURVER"))
 	private TermCodeSystemVersion myCurrentVersion;
+	@Column(name = "CURRENT_VERSION_PID", nullable = true, insertable = false, updatable = false)
+	private Long myCurrentVersionPid;
 	@Id()
 	@SequenceGenerator(name = "SEQ_CODESYSTEM_PID", sequenceName = "SEQ_CODESYSTEM_PID")
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CODESYSTEM_PID")
@@ -70,12 +72,32 @@ public class TermCodeSystem implements Serializable {
 		super();
 	}
 
-	public String getCodeSystemUri() {
-		return myCodeSystemUri;
+	@Override
+	public boolean equals(Object theO) {
+		if (this == theO) {
+			return true;
+		}
+
+		if (theO == null || getClass() != theO.getClass()) {
+			return false;
+		}
+
+		TermCodeSystem that = (TermCodeSystem) theO;
+
+		EqualsBuilder b = new EqualsBuilder();
+		b.append(myCodeSystemUri, that.myCodeSystemUri);
+		return b.isEquals();
 	}
 
-	public String getName() {
-		return myName;
+	@Override
+	public int hashCode() {
+		HashCodeBuilder b = new HashCodeBuilder(17, 37);
+		b.append(myCodeSystemUri);
+		return b.toHashCode();
+	}
+
+	public String getCodeSystemUri() {
+		return myCodeSystemUri;
 	}
 
 	public TermCodeSystem setCodeSystemUri(@Nonnull String theCodeSystemUri) {
@@ -86,6 +108,15 @@ public class TermCodeSystem implements Serializable {
 		return this;
 	}
 
+	public String getName() {
+		return myName;
+	}
+
+	public TermCodeSystem setName(String theName) {
+		myName = left(theName, MAX_NAME_LENGTH);
+		return this;
+	}
+
 	public TermCodeSystemVersion getCurrentVersion() {
 		return myCurrentVersion;
 	}
@@ -103,11 +134,6 @@ public class TermCodeSystem implements Serializable {
 		return myResource;
 	}
 
-	public TermCodeSystem setName(String theName) {
-		myName = left(theName, MAX_NAME_LENGTH);
-		return this;
-	}
-
 	public TermCodeSystem setResource(ResourceTable theResource) {
 		myResource = theResource;
 		return this;
@@ -115,12 +141,13 @@ public class TermCodeSystem implements Serializable {
 
 	@Override
 	public String toString() {
-		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
-			.append("codeSystemUri", myCodeSystemUri)
-			.append("currentVersion", myCurrentVersion)
-			.append("pid", myPid)
-			.append("resourcePid", myResourcePid)
-			.append("name", myName)
+		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+		b.append("pid", myPid);
+		b.append("codeSystemUri", myCodeSystemUri);
+		b.append("currentVersionPid", myCurrentVersionPid);
+		b.append("resourcePid", myResourcePid);
+		b.append("name", myName);
+		return b
 			.toString();
 	}
 }

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

@@ -21,8 +21,11 @@ package ca.uhn.fhir.jpa.entity;
  */
 
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.ValidateUtil;
+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 javax.persistence.*;
 import java.io.Serializable;
@@ -36,10 +39,8 @@ import static org.apache.commons.lang3.StringUtils.length;
 )
 @Entity()
 public class TermCodeSystemVersion implements Serializable {
-	private static final long serialVersionUID = 1L;
-
 	public static final int MAX_VERSION_LENGTH = 200;
-
+	private static final long serialVersionUID = 1L;
 	@OneToMany(fetch = FetchType.LAZY, mappedBy = "myCodeSystem")
 	private Collection<TermConcept> myConcepts;
 
@@ -84,34 +85,6 @@ public class TermCodeSystemVersion implements Serializable {
 		super();
 	}
 
-	@CoverageIgnore
-	@Override
-	public boolean equals(Object obj) {
-		if (this == obj) {
-			return true;
-		}
-		if (obj == null) {
-			return false;
-		}
-		if (!(obj instanceof TermCodeSystemVersion)) {
-			return false;
-		}
-		TermCodeSystemVersion other = (TermCodeSystemVersion) obj;
-		if ((myResource.getId() == null) != (other.myResource.getId() == null)) {
-			return false;
-		} else if (!myResource.getId().equals(other.myResource.getId())) {
-			return false;
-		}
-
-		if (myCodeSystemVersionId == null) {
-			if (other.myCodeSystemVersionId != null) {
-				return false;
-			}
-		} else if (!myCodeSystemVersionId.equals(other.myCodeSystemVersionId)) {
-			return false;
-		}
-		return true;
-	}
 
 	public TermCodeSystem getCodeSystem() {
 		return myCodeSystem;
@@ -154,13 +127,30 @@ public class TermCodeSystemVersion implements Serializable {
 		return this;
 	}
 
+	@Override
+	public boolean equals(Object theO) {
+		if (this == theO) {
+			return true;
+		}
+
+		if (theO == null || getClass() != theO.getClass()) {
+			return false;
+		}
+
+		TermCodeSystemVersion that = (TermCodeSystemVersion) theO;
+
+		return new EqualsBuilder()
+			.append(myCodeSystemVersionId, that.myCodeSystemVersionId)
+			.append(myCodeSystemPid, that.myCodeSystemPid)
+			.isEquals();
+	}
+
 	@Override
 	public int hashCode() {
-		final int prime = 31;
-		int result = 1;
-		result = prime * result + ((myResource.getId() == null) ? 0 : myResource.getId().hashCode());
-		result = prime * result + ((myCodeSystemVersionId == null) ? 0 : myCodeSystemVersionId.hashCode());
-		return result;
+		HashCodeBuilder b = new HashCodeBuilder(17, 37);
+		b.append(myCodeSystemVersionId);
+		b.append(myCodeSystemPid);
+		return b.toHashCode();
 	}
 
 	public String getCodeSystemDisplayName() {
@@ -180,4 +170,19 @@ public class TermCodeSystemVersion implements Serializable {
 		getConcepts().add(concept);
 		return concept;
 	}
+
+	@Override
+	public String toString() {
+		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+		b.append("pid", myId);
+		b.append("codeSystemResourcePid", myResourcePid);
+		b.append("codeSystemPid", myCodeSystemPid);
+		b.append("codeSystemVersionId", myCodeSystemVersionId);
+		return b.toString();
+	}
+
+	TermCodeSystemVersion setCodeSystemPidForUnitTest(long theCodeSystemPid) {
+		myCodeSystemPid = theCodeSystemPid;
+		return this;
+	}
 }

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

@@ -37,6 +37,7 @@ import javax.persistence.Index;
 import javax.persistence.*;
 import java.io.Serializable;
 import java.util.*;
+import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.left;
 import static org.apache.commons.lang3.StringUtils.length;
@@ -108,6 +109,13 @@ public class TermConcept implements Serializable {
 		setCode(theCode);
 	}
 
+	public TermConcept addChild(RelationshipTypeEnum theRelationshipType) {
+		TermConcept child = new TermConcept();
+		child.setCodeSystemVersion(myCodeSystem);
+		addChild(child, theRelationshipType);
+		return child;
+	}
+
 	public TermConceptParentChildLink addChild(TermConcept theChild, RelationshipTypeEnum theRelationshipType) {
 		Validate.notNull(theRelationshipType, "theRelationshipType must not be null");
 		TermConceptParentChildLink link = new TermConceptParentChildLink();
@@ -200,7 +208,7 @@ public class TermConcept implements Serializable {
 
 	public TermConcept setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
 		myCodeSystem = theCodeSystemVersion;
-		if (theCodeSystemVersion.getPid() != null) {
+		if (theCodeSystemVersion != null && theCodeSystemVersion.getPid() != null) {
 			myCodeSystemVersionPid = theCodeSystemVersion.getPid();
 		}
 		return this;
@@ -365,10 +373,13 @@ public class TermConcept implements Serializable {
 
 	@Override
 	public String toString() {
-		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
-			.append("code", myCode)
-			.append("display", myDisplay)
-			.build();
+		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+		b.append("code", myCode);
+		b.append("display", myDisplay);
+		if (mySequence != null) {
+			b.append("sequence", mySequence);
+		}
+		return b.build();
 	}
 
 	public List<IContextValidationSupport.BaseConceptProperty> toValidationProperties() {
@@ -387,4 +398,13 @@ public class TermConcept implements Serializable {
 		}
 		return retVal;
 	}
+
+	/**
+	 * Returns a view of {@link #getChildren()} but containing the actual child codes
+	 */
+	public List<TermConcept> getChildCodes() {
+		return getChildren().stream().map(t -> t.getChild()).collect(Collectors.toList());
+	}
+
+
 }

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

@@ -20,11 +20,16 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
+import org.hibernate.search.annotations.Field;
+import org.hibernate.search.annotations.Fields;
+
 import javax.persistence.*;
 import java.io.Serializable;
 
 @Entity
-@Table(name = "TRM_CONCEPT_PC_LINK")
+@Table(name = "TRM_CONCEPT_PC_LINK", indexes = {
+	@Index(name = "IDX_TRMCONCPCLNK_CSV", columnList = "CODESYSTEM_PID")
+})
 public class TermConceptParentChildLink implements Serializable {
 	private static final long serialVersionUID = 1L;
 
@@ -39,6 +44,10 @@ public class TermConceptParentChildLink implements Serializable {
 	@JoinColumn(name = "CODESYSTEM_PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CS"))
 	private TermCodeSystemVersion myCodeSystem;
 
+	@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false, nullable = false)
+	@Fields({@Field(name = "myCodeSystemVersionPid")})
+	private long myCodeSystemVersionPid;
+
 	@ManyToOne(cascade = {})
 	@JoinColumn(name = "PARENT_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_PARENT"))
 	private TermConcept myParent;

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

@@ -22,9 +22,8 @@ package ca.uhn.fhir.jpa.provider;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc.UploadStatistics;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.UploadStatistics;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -34,140 +33,46 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.AttachmentUtil;
 import ca.uhn.fhir.util.ParametersUtil;
 import ca.uhn.fhir.util.ValidateUtil;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.ICompositeType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.hl7.fhir.r4.model.CodeSystem;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import javax.annotation.Nonnull;
 import javax.servlet.http.HttpServletRequest;
 import java.io.*;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.concurrent.atomic.AtomicInteger;
 
 import static org.apache.commons.lang3.StringUtils.*;
 
 public class TerminologyUploaderProvider extends BaseJpaProvider {
 
-	public static final String CONCEPT_COUNT = "conceptCount";
-	public static final String TARGET = "target";
-	public static final String PARENT_CODE = "parentCode";
-	public static final String VALUE = "value";
+	public static final String PARAM_FILE = "file";
+	public static final String PARAM_SYSTEM = "system";
+	private static final String RESP_PARAM_CONCEPT_COUNT = "conceptCount";
+	private static final String RESP_PARAM_TARGET = "target";
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyUploaderProvider.class);
-	private static final String PACKAGE = "package";
+	private static final String RESP_PARAM_SUCCESS = "success";
 
 	@Autowired
 	private FhirContext myCtx;
 	@Autowired
-	private IHapiTerminologyLoaderSvc myTerminologyLoaderSvc;
-	@Autowired
-	private IHapiTerminologySvc myTerminologySvc;
+	private ITermLoaderSvc myTerminologyLoaderSvc;
 
 	/**
 	 * Constructor
 	 */
 	public TerminologyUploaderProvider() {
-		this(null, null, null);
+		this(null, null);
 	}
 
 	/**
 	 * Constructor
 	 */
-	public TerminologyUploaderProvider(FhirContext theContext, IHapiTerminologyLoaderSvc theTerminologyLoaderSvc, IHapiTerminologySvc theTerminologySvc) {
+	public TerminologyUploaderProvider(FhirContext theContext, ITermLoaderSvc theTerminologyLoaderSvc) {
 		myCtx = theContext;
 		myTerminologyLoaderSvc = theTerminologyLoaderSvc;
-		myTerminologySvc = theTerminologySvc;
-	}
-
-
-	/**
-	 * <code>
-	 * $apply-codesystem-delta-add
-	 * </code>
-	 */
-	@Operation(typeName = "CodeSystem", name = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD, idempotent = false, returnParameters = {
-	})
-	public IBaseParameters applyCodeSystemDeltaAdd(
-		HttpServletRequest theServletRequest,
-		@OperationParam(name = PARENT_CODE, min = 0, max = 1) IPrimitiveType<String> theParentCode,
-		@OperationParam(name = VALUE, min = 0, max = 1) IBaseResource theValue,
-		RequestDetails theRequestDetails
-	) {
-
-		startRequest(theServletRequest);
-		try {
-
-			CodeSystem value;
-			if (theValue instanceof CodeSystem) {
-				value = (CodeSystem) theValue;
-			} else if (theValue instanceof org.hl7.fhir.dstu3.model.CodeSystem) {
-				value = VersionConvertor_30_40.convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theValue);
-			} else if (theValue instanceof org.hl7.fhir.r5.model.CodeSystem) {
-				value = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theValue);
-			} else {
-				throw new InvalidRequestException("Value must be present and be a CodeSystem");
-			}
-
-			String system = value.getUrl();
-			String parentCode = theParentCode != null ? theParentCode.getValue() : null;
-
-			AtomicInteger counter = myTerminologySvc.applyDeltaCodesystemsAdd(system, parentCode, value);
-
-			IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
-			ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, "success", true);
-			ParametersUtil.addParameterToParametersInteger(myCtx, retVal, "addedConcepts", counter.get());
-			return retVal;
-
-		} finally {
-			endRequest(theServletRequest);
-		}
-
-	}
-
-
-	/**
-	 * <code>
-	 * $apply-codesystem-delta-remove
-	 * </code>
-	 */
-	@Operation(typeName = "CodeSystem", name = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE, idempotent = false, returnParameters = {
-	})
-	public IBaseParameters applyCodeSystemDeltaRemove(
-		HttpServletRequest theServletRequest,
-		@OperationParam(name = VALUE, min = 1, max = 1) IBaseResource theValue,
-		RequestDetails theRequestDetails
-	) {
-
-		startRequest(theServletRequest);
-		try {
-
-			CodeSystem value;
-			if (theValue instanceof CodeSystem) {
-				value = (CodeSystem) theValue;
-			} else if (theValue instanceof org.hl7.fhir.dstu3.model.CodeSystem) {
-				value = VersionConvertor_30_40.convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theValue);
-			} else if (theValue instanceof org.hl7.fhir.r5.model.CodeSystem) {
-				value = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theValue);
-			} else {
-				throw new InvalidRequestException("Value must be present and be a CodeSystem");
-			}
-
-			String system = value.getUrl();
-
-			AtomicInteger counter = myTerminologySvc.applyDeltaCodesystemsRemove(system, value);
-
-			IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
-			ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, "success", true);
-			ParametersUtil.addParameterToParametersInteger(myCtx, retVal, "removedConcepts", counter.get());
-			return retVal;
-
-		} finally {
-			endRequest(theServletRequest);
-		}
-
 	}
 
 	/**
@@ -178,28 +83,31 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 	@Operation(typeName = "CodeSystem", name = JpaConstants.OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM, idempotent = false, returnParameters = {
 //		@OperationParam(name = "conceptCount", type = IntegerType.class, min = 1)
 	})
-	public IBaseParameters uploadExternalCodeSystem(
+	public IBaseParameters uploadSnapshot(
 		HttpServletRequest theServletRequest,
-		@OperationParam(name = "url", min = 1, typeName = "uri") IPrimitiveType<String> theCodeSystemUrl,
-		@OperationParam(name = "contentMode", min = 0, typeName = "code") IPrimitiveType<String> theContentMode,
+		@OperationParam(name = PARAM_SYSTEM, min = 1, typeName = "uri") IPrimitiveType<String> theCodeSystemUrl,
 		@OperationParam(name = "localfile", min = 1, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> theLocalFile,
-		@OperationParam(name = PACKAGE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> thePackage,
+		@OperationParam(name = PARAM_FILE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> theFiles,
 		RequestDetails theRequestDetails
 	) {
 
 		startRequest(theServletRequest);
 
+		if (theCodeSystemUrl == null || isBlank(theCodeSystemUrl.getValueAsString())) {
+			throw new InvalidRequestException("Missing mandatory parameter: " + PARAM_SYSTEM);
+		}
+
 		if (theLocalFile == null || theLocalFile.size() == 0) {
-			if (thePackage == null || thePackage.size() == 0) {
+			if (theFiles == null || theFiles.size() == 0) {
 				throw new InvalidRequestException("No 'localfile' or 'package' parameter, or package had no data");
 			}
-			for (ICompositeType next : thePackage) {
+			for (ICompositeType next : theFiles) {
 				ValidateUtil.isTrueOrThrowInvalidRequest(myCtx.getElementDefinition(next.getClass()).getName().equals("Attachment"), "Package must be of type Attachment");
 			}
 		}
 
 		try {
-			List<IHapiTerminologyLoaderSvc.FileDescriptor> localFiles = new ArrayList<>();
+			List<ITermLoaderSvc.FileDescriptor> localFiles = new ArrayList<>();
 			if (theLocalFile != null && theLocalFile.size() > 0) {
 				for (IPrimitiveType<String> nextLocalFile : theLocalFile) {
 					if (isNotBlank(nextLocalFile.getValue())) {
@@ -208,7 +116,7 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 						if (!nextFile.exists() || !nextFile.isFile()) {
 							throw new InvalidRequestException("Unknown file: " + nextFile.getName());
 						}
-						localFiles.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
+						localFiles.add(new ITermLoaderSvc.FileDescriptor() {
 							@Override
 							public String getFilename() {
 								return nextFile.getAbsolutePath();
@@ -227,15 +135,15 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 				}
 			}
 
-			if (thePackage != null) {
-				for (ICompositeType nextPackage : thePackage) {
+			if (theFiles != null) {
+				for (ICompositeType nextPackage : theFiles) {
 					final String url = AttachmentUtil.getOrCreateUrl(myCtx, nextPackage).getValueAsString();
 
 					if (isBlank(url)) {
 						throw new UnprocessableEntityException("Package is missing mandatory url element");
 					}
 
-					localFiles.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
+					localFiles.add(new ITermLoaderSvc.FileDescriptor() {
 						@Override
 						public String getFilename() {
 							return url;
@@ -250,33 +158,29 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 				}
 			}
 
-			String codeSystemUrl = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
-			codeSystemUrl = defaultString(codeSystemUrl);
+			String codeSystemUrl = theCodeSystemUrl.getValue();
+			codeSystemUrl = trim(codeSystemUrl);
 
-			String contentMode = theContentMode != null ? theContentMode.getValue() : null;
 			UploadStatistics stats;
-			if ("custom".equals(contentMode)) {
-				stats = myTerminologyLoaderSvc.loadCustom(codeSystemUrl, localFiles, theRequestDetails);
-			} else {
-				switch (codeSystemUrl) {
-					case IHapiTerminologyLoaderSvc.SCT_URI:
-						stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
-						break;
-					case IHapiTerminologyLoaderSvc.LOINC_URI:
-						stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
-						break;
-					case IHapiTerminologyLoaderSvc.IMGTHLA_URI:
-						stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
-						break;
-					default:
-						throw new InvalidRequestException("Unknown URL: " + codeSystemUrl);
-				}
+			switch (codeSystemUrl) {
+				case ITermLoaderSvc.SCT_URI:
+					stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
+					break;
+				case ITermLoaderSvc.LOINC_URI:
+					stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
+					break;
+				case ITermLoaderSvc.IMGTHLA_URI:
+					stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
+					break;
+				default:
+					stats = myTerminologyLoaderSvc.loadCustom(codeSystemUrl, localFiles, theRequestDetails);
+					break;
 			}
 
 			IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
-			ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, "success", true);
-			ParametersUtil.addParameterToParametersInteger(myCtx, retVal, CONCEPT_COUNT, stats.getConceptCount());
-			ParametersUtil.addParameterToParametersReference(myCtx, retVal, TARGET, stats.getTarget().getValue());
+			ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, RESP_PARAM_SUCCESS, true);
+			ParametersUtil.addParameterToParametersInteger(myCtx, retVal, RESP_PARAM_CONCEPT_COUNT, stats.getUpdatedConceptCount());
+			ParametersUtil.addParameterToParametersReference(myCtx, retVal, RESP_PARAM_TARGET, stats.getTarget().getValue());
 
 			return retVal;
 		} finally {
@@ -284,5 +188,100 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 		}
 	}
 
+	/**
+	 * <code>
+	 * $apply-codesystem-delta-add
+	 * </code>
+	 */
+	@Operation(typeName = "CodeSystem", name = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD, idempotent = false, returnParameters = {
+	})
+	public IBaseParameters uploadDeltaAdd(
+		HttpServletRequest theServletRequest,
+		@OperationParam(name = PARAM_SYSTEM, min = 1, max = 1, typeName = "uri") IPrimitiveType<String> theSystem,
+		@OperationParam(name = PARAM_FILE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> theFiles,
+		RequestDetails theRequestDetails
+	) {
+
+		startRequest(theServletRequest);
+		try {
+			validateHaveSystem(theSystem);
+			validateHaveFiles(theFiles);
+
+			List<ITermLoaderSvc.FileDescriptor> files = convertAttachmentsToFileDescriptors(theFiles);
+			UploadStatistics outcome = myTerminologyLoaderSvc.loadDeltaAdd(theSystem.getValue(), files, theRequestDetails);
+			return toDeltaResponse(outcome);
+		} finally {
+			endRequest(theServletRequest);
+		}
+
+	}
+
+
+	/**
+	 * <code>
+	 * $apply-codesystem-delta-remove
+	 * </code>
+	 */
+	@Operation(typeName = "CodeSystem", name = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE, idempotent = false, returnParameters = {
+	})
+	public IBaseParameters uploadDeltaRemove(
+		HttpServletRequest theServletRequest,
+		@OperationParam(name = PARAM_SYSTEM, min = 1, max = 1, typeName = "uri") IPrimitiveType<String> theSystem,
+		@OperationParam(name = PARAM_FILE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> theFiles,
+		RequestDetails theRequestDetails
+	) {
+
+		startRequest(theServletRequest);
+		try {
+			validateHaveSystem(theSystem);
+			validateHaveFiles(theFiles);
+
+			List<ITermLoaderSvc.FileDescriptor> files = convertAttachmentsToFileDescriptors(theFiles);
+			UploadStatistics outcome = myTerminologyLoaderSvc.loadDeltaRemove(theSystem.getValue(), files, theRequestDetails);
+			return toDeltaResponse(outcome);
+		} finally {
+			endRequest(theServletRequest);
+		}
+
+	}
+
+	private void validateHaveSystem(IPrimitiveType<String> theSystem) {
+		if (theSystem == null || isBlank(theSystem.getValueAsString())) {
+			throw new InvalidRequestException("Missing mandatory parameter: " + PARAM_SYSTEM);
+		}
+	}
+
+	private void validateHaveFiles(List<ICompositeType> theFiles) {
+		if (theFiles != null) {
+			for (ICompositeType nextFile : theFiles) {
+				if (!nextFile.isEmpty()) {
+					return;
+				}
+			}
+		}
+		throw new InvalidRequestException("Missing mandatory parameter: " + PARAM_FILE);
+	}
+
+	@Nonnull
+	private List<ITermLoaderSvc.FileDescriptor> convertAttachmentsToFileDescriptors(@OperationParam(name = PARAM_FILE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> theFiles) {
+		List<ITermLoaderSvc.FileDescriptor> files = new ArrayList<>();
+		for (ICompositeType next : theFiles) {
+			byte[] nextData = AttachmentUtil.getOrCreateData(myCtx, next).getValue();
+			String nextUrl = AttachmentUtil.getOrCreateUrl(myCtx, next).getValue();
+			ValidateUtil.isTrueOrThrowInvalidRequest(nextData != null && nextData.length > 0, "Missing Attachment.data value");
+			ValidateUtil.isNotBlankOrThrowUnprocessableEntity(nextUrl, "Missing Attachment.url value");
+
+			files.add(new ITermLoaderSvc.ByteArrayFileDescriptor(nextUrl, nextData));
+		}
+		return files;
+	}
+
+	private IBaseParameters toDeltaResponse(UploadStatistics theOutcome) {
+		IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
+		ParametersUtil.addParameterToParametersInteger(myCtx, retVal, RESP_PARAM_CONCEPT_COUNT, theOutcome.getUpdatedConceptCount());
+		ParametersUtil.addParameterToParametersReference(myCtx, retVal, RESP_PARAM_TARGET, theOutcome.getTarget().getValue());
+		return retVal;
+	}
+
 
 }

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

@@ -53,6 +53,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.method.PageMethodBinding;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.rest.server.util.ICachedSearchDetails;
+import ca.uhn.fhir.util.AsyncUtil;
 import ca.uhn.fhir.util.StopWatch;
 import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.Validate;
@@ -76,6 +77,7 @@ import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import javax.annotation.PostConstruct;
 import javax.persistence.EntityManager;
@@ -154,14 +156,16 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 	public void cancelAllActiveSearches() {
 		for (SearchTask next : myIdToSearchTask.values()) {
 			next.requestImmediateAbort();
-			try {
-				next.getCompletionLatch().await(30, TimeUnit.SECONDS);
-			} catch (InterruptedException e) {
-				ourLog.warn("Failed to wait for completion", e);
-			}
+			AsyncUtil.awaitLatchAndIgnoreInterrupt(next.getCompletionLatch(), 30, TimeUnit.SECONDS);
 		}
 	}
 
+	@SuppressWarnings("SameParameterValue")
+	@VisibleForTesting
+	void setMaxMillisToWaitForRemoteResultsForUnitTest(long theMaxMillisToWaitForRemoteResults) {
+		myMaxMillisToWaitForRemoteResults = theMaxMillisToWaitForRemoteResults;
+	}
+
 	/**
 	 * This method is called by the HTTP client processing thread in order to
 	 * fetch resources.
@@ -189,18 +193,16 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				if (searchTask != null) {
 					ourLog.trace("Local search found");
 					List<Long> resourcePids = searchTask.getResourcePids(theFrom, theTo);
-					if (resourcePids != null) {
-						ourLog.trace("Local search returned {} pids, wanted {}-{} - Search: {}", resourcePids.size(), theFrom, theTo, searchTask.getSearch());
+					ourLog.trace("Local search returned {} pids, wanted {}-{} - Search: {}", resourcePids.size(), theFrom, theTo, searchTask.getSearch());
 
-						/*
-						 * Generally, if a search task is open, the fastest possible thing is to just return its results. This
-						 * will work most of the time, but can fail if the task hit a search threshold and the client is requesting
-						 * results beyond that threashold. In that case, we'll keep going below, since that will trigger another
-						 * task.
-						 */
-						if ((searchTask.getSearch().getNumFound() - searchTask.getSearch().getNumBlocked()) >= theTo || resourcePids.size() == (theTo - theFrom)) {
-							return resourcePids;
-						}
+					/*
+					 * Generally, if a search task is open, the fastest possible thing is to just return its results. This
+					 * will work most of the time, but can fail if the task hit a search threshold and the client is requesting
+					 * results beyond that threashold. In that case, we'll keep going below, since that will trigger another
+					 * task.
+					 */
+					if ((searchTask.getSearch().getNumFound() - searchTask.getSearch().getNumBlocked()) >= theTo || resourcePids.size() == (theTo - theFrom)) {
+						return resourcePids;
 					}
 				}
 			}
@@ -244,11 +246,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				}
 			}
 
-			try {
-				Thread.sleep(500);
-			} catch (InterruptedException e) {
-				// ignore
-			}
+			AsyncUtil.sleep(500);
 		}
 
 		ourLog.trace("Finished looping");
@@ -627,14 +625,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		Integer awaitInitialSync() {
 			ourLog.trace("Awaiting initial sync");
 			do {
-				try {
-					if (getInitialCollectionLatch().await(250, TimeUnit.MILLISECONDS)) {
-						break;
-					}
-				} catch (InterruptedException e) {
-					// Shouldn't happen
-					Thread.currentThread().interrupt();
-					throw new InternalErrorException(e);
+				if (AsyncUtil.awaitLatchAndThrowInternalErrorExceptionOnInterrupt(getInitialCollectionLatch(), 250L, TimeUnit.MILLISECONDS)) {
+					break;
 				}
 			} while (getSearch().getStatus() == SearchStatusEnum.LOADING);
 			ourLog.trace("Initial sync completed");
@@ -663,7 +655,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			return sb;
 		}
 
-		public List<Long> getResourcePids(int theFromIndex, int theToIndex) {
+		@Nonnull
+		List<Long> getResourcePids(int theFromIndex, int theToIndex) {
 			ourLog.debug("Requesting search PIDs from {}-{}", theFromIndex, theToIndex);
 
 			boolean keepWaiting;
@@ -698,11 +691,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 				if (keepWaiting) {
 					ourLog.info("Waiting as we only have {} results - Search status: {}", mySyncedPids.size(), mySearch.getStatus());
-					try {
-						Thread.sleep(500);
-					} catch (InterruptedException theE) {
-						// ignore
-					}
+					AsyncUtil.sleep(500L);
 				}
 			} while (keepWaiting);
 
@@ -1081,11 +1070,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 					}
 
 					if (myLoadingThrottleForUnitTests != null) {
-						try {
-							Thread.sleep(myLoadingThrottleForUnitTests);
-						} catch (InterruptedException e) {
-							// ignore
-						}
+						AsyncUtil.sleep(myLoadingThrottleForUnitTests);
 					}
 
 				}

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

@@ -48,17 +48,15 @@ import java.util.List;
 import java.util.Optional;
 
 public class DatabaseSearchCacheSvcImpl extends BaseSearchCacheSvcImpl {
-	private static final Logger ourLog = LoggerFactory.getLogger(DatabaseSearchCacheSvcImpl.class);
-
 	/*
 	 * Be careful increasing this number! We use the number of params here in a
-	 * DELETE FROM foo WHERE params IN (aaaa)
+	 * DELETE FROM foo WHERE params IN (term,term,term...)
 	 * type query and this can fail if we have 1000s of params
 	 */
 	public static final int DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_STMT = 500;
 	public static final int DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_PAS = 20000;
 	public static final long DEFAULT_CUTOFF_SLACK = 10 * DateUtils.MILLIS_PER_SECOND;
-
+	private static final Logger ourLog = LoggerFactory.getLogger(DatabaseSearchCacheSvcImpl.class);
 	private static int ourMaximumResultsToDeleteInOneStatement = DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_STMT;
 	private static int ourMaximumResultsToDeleteInOnePass = DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_PAS;
 	private static Long ourNowForUnitTests;
@@ -108,6 +106,14 @@ public class DatabaseSearchCacheSvcImpl extends BaseSearchCacheSvcImpl {
 	}
 
 
+	void setSearchDaoForUnitTest(ISearchDao theSearchDao) {
+		mySearchDao = theSearchDao;
+	}
+
+	void setTxManagerForUnitTest(PlatformTransactionManager theTxManager) {
+		myTxManager = theTxManager;
+	}
+
 	@Override
 	@Transactional(Transactional.TxType.NEVER)
 	public Optional<Search> tryToMarkSearchAsInProgress(Search theSearch) {
@@ -185,7 +191,7 @@ public class DatabaseSearchCacheSvcImpl extends BaseSearchCacheSvcImpl {
 
 		int count = toDelete.getContent().size();
 		if (count > 0) {
-			if (ourLog.isDebugEnabled()) {
+			if (ourLog.isDebugEnabled() || "true".equalsIgnoreCase(System.getProperty("test"))) {
 				Long total = tt.execute(t -> mySearchDao.count());
 				ourLog.debug("Deleted {} searches, {} remaining", count, total);
 			}

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

@@ -0,0 +1,14 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.util.ValidateUtil;
+import org.hl7.fhir.r4.model.CodeSystem;
+
+public abstract class BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
+
+
+	protected void validateCodeSystemForStorage(CodeSystem theCodeSystemResource) {
+		ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theCodeSystemResource.getUrl(), "Can not store a CodeSystem without a valid URL");
+	}
+
+}

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

@@ -0,0 +1,123 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.input.BOMInputStream;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+public class LoadedFileDescriptors implements Closeable {
+	private static final Logger ourLog = LoggerFactory.getLogger(LoadedFileDescriptors.class);
+	private List<File> myTemporaryFiles = new ArrayList<>();
+	private List<ITermLoaderSvc.FileDescriptor> myUncompressedFileDescriptors = new ArrayList<>();
+
+	LoadedFileDescriptors(List<ITermLoaderSvc.FileDescriptor> theFileDescriptors) {
+		try {
+			for (ITermLoaderSvc.FileDescriptor next : theFileDescriptors) {
+				if (next.getFilename().toLowerCase().endsWith(".zip")) {
+					ourLog.info("Uncompressing {} into temporary files", next.getFilename());
+					try (InputStream inputStream = next.getInputStream()) {
+						try (BufferedInputStream bufferedInputStream = new BufferedInputStream(inputStream)) {
+							try (ZipInputStream zis = new ZipInputStream(bufferedInputStream)) {
+								for (ZipEntry nextEntry; (nextEntry = zis.getNextEntry()) != null; ) {
+									BOMInputStream fis = new BOMInputStream(zis);
+									File nextTemporaryFile = File.createTempFile("hapifhir", ".tmp");
+									ourLog.info("Creating temporary file: {}", nextTemporaryFile.getAbsolutePath());
+									nextTemporaryFile.deleteOnExit();
+									try (FileOutputStream fos = new FileOutputStream(nextTemporaryFile, false)) {
+										IOUtils.copy(fis, fos);
+										String nextEntryFileName = nextEntry.getName();
+										myUncompressedFileDescriptors.add(new ITermLoaderSvc.FileDescriptor() {
+											@Override
+											public String getFilename() {
+												return nextEntryFileName;
+											}
+
+											@Override
+											public InputStream getInputStream() {
+												try {
+													return new FileInputStream(nextTemporaryFile);
+												} catch (FileNotFoundException e) {
+													throw new InternalErrorException(e);
+												}
+											}
+										});
+										myTemporaryFiles.add(nextTemporaryFile);
+									}
+								}
+							}
+						}
+					}
+				} else {
+					myUncompressedFileDescriptors.add(next);
+				}
+
+			}
+		} catch (IOException e) {
+			throw new InternalErrorException(e);
+		}
+
+	}
+
+	public boolean hasFile(String theFilename) {
+		return myUncompressedFileDescriptors
+			.stream()
+			.map(t -> t.getFilename().replaceAll(".*[\\\\/]", "")) // Strip the path from the filename
+			.anyMatch(t -> t.equals(theFilename));
+	}
+
+	@Override
+	public void close() {
+		for (File next : myTemporaryFiles) {
+			ourLog.info("Deleting temporary file: {}", next.getAbsolutePath());
+			FileUtils.deleteQuietly(next);
+		}
+	}
+
+	List<ITermLoaderSvc.FileDescriptor> getUncompressedFileDescriptors() {
+		return myUncompressedFileDescriptors;
+	}
+
+	private List<String> notFound(List<String> theExpectedFilenameFragments) {
+		Set<String> foundFragments = new HashSet<>();
+		for (String nextExpected : theExpectedFilenameFragments) {
+			for (ITermLoaderSvc.FileDescriptor next : myUncompressedFileDescriptors) {
+				if (next.getFilename().contains(nextExpected)) {
+					foundFragments.add(nextExpected);
+					break;
+				}
+			}
+		}
+
+		ArrayList<String> notFoundFileNameFragments = new ArrayList<>(theExpectedFilenameFragments);
+		notFoundFileNameFragments.removeAll(foundFragments);
+		return notFoundFileNameFragments;
+	}
+
+	void verifyMandatoryFilesExist(List<String> theExpectedFilenameFragments) {
+		List<String> notFound = notFound(theExpectedFilenameFragments);
+		if (!notFound.isEmpty()) {
+			throw new UnprocessableEntityException("Could not find the following mandatory files in input: " + notFound);
+		}
+	}
+
+	void verifyOptionalFilesExist(List<String> theExpectedFilenameFragments) {
+		List<String> notFound = notFound(theExpectedFilenameFragments);
+		if (!notFound.isEmpty()) {
+			ourLog.warn("Could not find the following optional files: " + notFound);
+		}
+	}
+
+
+}

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

@@ -0,0 +1,757 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.data.*;
+import ca.uhn.fhir.jpa.dao.index.IdHelperService;
+import ca.uhn.fhir.jpa.entity.*;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
+import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.ObjectUtil;
+import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.util.ValidateUtil;
+import com.google.common.collect.ArrayListMultimap;
+import com.google.common.collect.ListMultimap;
+import org.apache.commons.lang3.Validate;
+import org.hibernate.ScrollMode;
+import org.hibernate.ScrollableResults;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Slice;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionDefinition;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import javax.annotation.Nonnull;
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
+import javax.persistence.PersistenceContextType;
+import javax.persistence.TypedQuery;
+import javax.persistence.criteria.CriteriaBuilder;
+import javax.persistence.criteria.CriteriaQuery;
+import javax.persistence.criteria.Predicate;
+import javax.persistence.criteria.Root;
+import java.util.*;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.function.Supplier;
+import java.util.stream.Collectors;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
+	private static final Logger ourLog = LoggerFactory.getLogger(TermCodeSystemStorageSvcImpl.class);
+	private static final Object PLACEHOLDER_OBJECT = new Object();
+	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
+	protected EntityManager myEntityManager;
+	@Autowired
+	protected ITermCodeSystemDao myCodeSystemDao;
+	@Autowired
+	protected ITermCodeSystemVersionDao myCodeSystemVersionDao;
+	@Autowired
+	protected ITermConceptDao myConceptDao;
+	@Autowired
+	protected ITermConceptPropertyDao myConceptPropertyDao;
+	@Autowired
+	protected ITermConceptDesignationDao myConceptDesignationDao;
+	@Autowired
+	protected IdHelperService myIdHelperService;
+	@Autowired
+	private PlatformTransactionManager myTransactionManager;
+	@Autowired
+	private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
+	@Autowired
+	private ITermVersionAdapterSvc myTerminologyVersionAdapterSvc;
+	@Autowired
+	private ITermDeferredStorageSvc myDeferredStorageSvc;
+	@Autowired
+	private FhirContext myContext;
+	@Autowired
+	private ITermReadSvc myTerminologySvc;
+	@Autowired
+	private DaoConfig myDaoConfig;
+	@Autowired
+	private IResourceTableDao myResourceTableDao;
+
+	@Override
+	public Long getValueSetResourcePid(IIdType theIdType) {
+		return getValueSetResourcePid(theIdType, null);
+	}
+
+	private Long getValueSetResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
+		return myIdHelperService.translateForcedIdToPid(theIdType, theRequestDetails);
+	}
+
+	@Transactional
+	@Override
+	public UploadStatistics applyDeltaCodeSystemsAdd(String theSystem, CustomTerminologySet theAdditions) {
+		ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystem, "No system provided");
+		validateDstu3OrNewer();
+		theAdditions.validateNoCycleOrThrowInvalidRequest();
+
+		TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
+		if (cs == null) {
+			CodeSystem codeSystemResource = new CodeSystem();
+			codeSystemResource.setUrl(theSystem);
+			codeSystemResource.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+			myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(codeSystemResource);
+
+			cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
+		}
+
+		TermCodeSystemVersion csv = cs.getCurrentVersion();
+		Validate.notNull(csv);
+
+		CodeSystem codeSystem = myTerminologySvc.getCodeSystemFromContext(theSystem);
+		if (codeSystem.getContent() != CodeSystem.CodeSystemContentMode.NOTPRESENT) {
+			throw new InvalidRequestException("CodeSystem with url[" + theSystem + "] can not apply a delta - wrong content mode: " + codeSystem.getContent());
+		}
+
+		Validate.notNull(cs);
+		Validate.notNull(cs.getPid());
+
+		IIdType codeSystemId = cs.getResource().getIdDt();
+
+		// Load all concepts for the code system
+		Map<String, Long> codeToConceptPid = new HashMap<>();
+		{
+			ourLog.info("Loading all concepts in CodeSystem versionPid[{}] and url[{}]", cs.getPid(), theSystem);
+			StopWatch sw = new StopWatch();
+			CriteriaBuilder criteriaBuilder = myEntityManager.getCriteriaBuilder();
+			CriteriaQuery<TermConcept> query = criteriaBuilder.createQuery(TermConcept.class);
+			Root<TermConcept> root = query.from(TermConcept.class);
+			Predicate predicate = criteriaBuilder.equal(root.get("myCodeSystemVersionPid").as(Long.class), csv.getPid());
+			query.where(predicate);
+			TypedQuery<TermConcept> typedQuery = myEntityManager.createQuery(query.select(root));
+			org.hibernate.query.Query<TermConcept> hibernateQuery = (org.hibernate.query.Query<TermConcept>) typedQuery;
+			ScrollableResults scrollableResults = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
+			try (ScrollableResultsIterator<TermConcept> scrollableResultsIterator = new ScrollableResultsIterator<>(scrollableResults)) {
+				while (scrollableResultsIterator.hasNext()) {
+					TermConcept next = scrollableResultsIterator.next();
+					codeToConceptPid.put(next.getCode(), next.getId());
+				}
+			}
+			ourLog.info("Loaded {} concepts in {}", codeToConceptPid.size(), sw.toString());
+		}
+
+		// Load all parent/child links
+		ListMultimap<String, String> parentCodeToChildCodes = ArrayListMultimap.create();
+		ListMultimap<String, String> childCodeToParentCodes = ArrayListMultimap.create();
+		{
+			ourLog.info("Loading all parent/child relationships in CodeSystem url[" + theSystem + "]");
+			int count = 0;
+			StopWatch sw = new StopWatch();
+			CriteriaBuilder criteriaBuilder = myEntityManager.getCriteriaBuilder();
+			CriteriaQuery<TermConceptParentChildLink> query = criteriaBuilder.createQuery(TermConceptParentChildLink.class);
+			Root<TermConceptParentChildLink> root = query.from(TermConceptParentChildLink.class);
+			Predicate predicate = criteriaBuilder.equal(root.get("myCodeSystemVersionPid").as(Long.class), csv.getPid());
+			root.fetch("myChild");
+			root.fetch("myParent");
+			query.where(predicate);
+			TypedQuery<TermConceptParentChildLink> typedQuery = myEntityManager.createQuery(query.select(root));
+			org.hibernate.query.Query<TermConceptParentChildLink> hibernateQuery = (org.hibernate.query.Query<TermConceptParentChildLink>) typedQuery;
+			ScrollableResults scrollableResults = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
+			try (ScrollableResultsIterator<TermConceptParentChildLink> scrollableResultsIterator = new ScrollableResultsIterator<>(scrollableResults)) {
+				while (scrollableResultsIterator.hasNext()) {
+					TermConceptParentChildLink next = scrollableResultsIterator.next();
+					String parentCode = next.getParent().getCode();
+					String childCode = next.getChild().getCode();
+					parentCodeToChildCodes.put(parentCode, childCode);
+					childCodeToParentCodes.put(childCode, parentCode);
+					count++;
+				}
+			}
+			ourLog.info("Loaded {} parent/child relationships in {}", count, sw.toString());
+		}
+
+		// Account for root codes in the parent->child map
+		for (String nextCode : codeToConceptPid.keySet()) {
+			if (childCodeToParentCodes.get(nextCode).isEmpty()) {
+				parentCodeToChildCodes.put("", nextCode);
+			}
+		}
+
+		UploadStatistics retVal = new UploadStatistics(codeSystemId);
+
+		// Add root concepts
+		for (TermConcept nextRootConcept : theAdditions.getRootConcepts()) {
+			List<String> parentCodes = Collections.emptyList();
+			addConcept(csv, codeToConceptPid, parentCodes, nextRootConcept, parentCodeToChildCodes, retVal, true);
+		}
+
+		// Add unanchored child concepts
+		for (TermConcept nextUnanchoredChild : theAdditions.getUnanchoredChildConceptsToParentCodes().keySet()) {
+			List<String> nextParentCodes = theAdditions.getUnanchoredChildConceptsToParentCodes().get(nextUnanchoredChild);
+			addConcept(csv, codeToConceptPid, nextParentCodes, nextUnanchoredChild, parentCodeToChildCodes, retVal, true);
+		}
+
+		return retVal;
+	}
+
+	@Transactional
+	@Override
+	public UploadStatistics applyDeltaCodeSystemsRemove(String theSystem, CustomTerminologySet theValue) {
+		ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystem, "No system provided");
+		validateDstu3OrNewer();
+
+		TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
+		if (cs == null) {
+			throw new InvalidRequestException("Unknown code system: " + theSystem);
+		}
+
+		AtomicInteger removeCounter = new AtomicInteger(0);
+
+		for (TermConcept nextSuppliedConcept : theValue.getRootConcepts()) {
+			Optional<TermConcept> conceptOpt = myTerminologySvc.findCode(theSystem, nextSuppliedConcept.getCode());
+			if (conceptOpt.isPresent()) {
+				TermConcept concept = conceptOpt.get();
+				deleteConceptChildrenAndConcept(concept, removeCounter);
+			}
+		}
+
+		IIdType target = cs.getResource().getIdDt();
+		return new UploadStatistics(removeCounter.get(), target);
+	}
+
+	@Override
+	public void deleteCodeSystem(TermCodeSystem theCodeSystem) {
+		ourLog.info(" * Deleting code system {}", theCodeSystem.getPid());
+
+		myEntityManager.flush();
+		TermCodeSystem cs = myCodeSystemDao.findById(theCodeSystem.getPid()).orElseThrow(IllegalStateException::new);
+		cs.setCurrentVersion(null);
+		myCodeSystemDao.save(cs);
+		myCodeSystemDao.flush();
+
+		List<TermCodeSystemVersion> codeSystemVersions = myCodeSystemVersionDao.findByCodeSystemPid(theCodeSystem.getPid());
+		for (TermCodeSystemVersion next : codeSystemVersions) {
+			deleteCodeSystemVersion(next.getPid());
+		}
+		myCodeSystemVersionDao.deleteForCodeSystem(theCodeSystem);
+		myCodeSystemDao.delete(theCodeSystem);
+
+		myEntityManager.flush();
+	}
+
+	/**
+	 * Returns the number of saved concepts
+	 */
+	@Override
+	public int saveConcept(TermConcept theConcept) {
+		int retVal = 0;
+
+		/*
+		 * If the concept has an ID, we're reindexing, so there's no need to
+		 * save parent concepts first (it's way too slow to do that)
+		 */
+		if (theConcept.getId() == null) {
+			retVal += ensureParentsSaved(theConcept.getParents());
+		}
+
+		if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
+			retVal++;
+			theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
+			theConcept.setUpdated(new Date());
+			myConceptDao.save(theConcept);
+
+			for (TermConceptProperty next : theConcept.getProperties()) {
+				myConceptPropertyDao.save(next);
+			}
+
+			for (TermConceptDesignation next : theConcept.getDesignations()) {
+				myConceptDesignationDao.save(next);
+			}
+		}
+
+		ourLog.trace("Saved {} and got PID {}", theConcept.getCode(), theConcept.getId());
+		return retVal;
+	}
+
+	@Override
+	@Transactional(propagation = Propagation.MANDATORY)
+	public void storeNewCodeSystemVersionIfNeeded(CodeSystem theCodeSystem, ResourceTable theResourceEntity) {
+		if (theCodeSystem != null && isNotBlank(theCodeSystem.getUrl())) {
+			String codeSystemUrl = theCodeSystem.getUrl();
+			if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.COMPLETE || theCodeSystem.getContent() == null || theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
+				ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", theResourceEntity.getIdDt().getValue(), theCodeSystem.getContentElement().getValueAsString());
+
+				Long codeSystemResourcePid = getCodeSystemResourcePid(theCodeSystem.getIdElement());
+
+				/*
+				 * If this is a not-present codesystem, we don't want to store a new version if one
+				 * already exists, since that will wipe out the existing concepts. We do create or update
+				 * the TermCodeSystem table though, since that allows the DB to reject changes
+				 * that would result in duplicate CodeSysten.url values.
+				 */
+				if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
+					TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theCodeSystem.getUrl());
+					if (codeSystem != null) {
+						getOrCreateTermCodeSystem(codeSystemResourcePid, theCodeSystem.getUrl(), theCodeSystem.getUrl(), theResourceEntity);
+						return;
+					}
+				}
+
+				TermCodeSystemVersion persCs = new TermCodeSystemVersion();
+
+				populateCodeSystemVersionProperties(persCs, theCodeSystem, theResourceEntity);
+
+				persCs.getConcepts().addAll(BaseTermReadSvcImpl.toPersistedConcepts(theCodeSystem.getConcept(), persCs));
+				ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
+				storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, theCodeSystem.getName(), theCodeSystem.getVersion(), persCs, theResourceEntity);
+			}
+
+		}
+	}
+
+	@Override
+	@Transactional(propagation = Propagation.REQUIRED)
+	public IIdType storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequest, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
+		Validate.notBlank(theCodeSystemResource.getUrl(), "theCodeSystemResource must have a URL");
+
+		IIdType csId = myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(theCodeSystemResource);
+		Long codeSystemResourcePid = myIdHelperService.translateForcedIdToPid(csId, theRequest);
+		ResourceTable resource = myResourceTableDao.getOne(codeSystemResourcePid);
+
+		ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
+
+		populateCodeSystemVersionProperties(theCodeSystemVersion, theCodeSystemResource, resource);
+
+		storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemResource.getName(), theCodeSystemResource.getVersion(), theCodeSystemVersion, resource);
+
+		myDeferredStorageSvc.addConceptMapsToStorageQueue(theConceptMaps);
+		myDeferredStorageSvc.addValueSetsToStorageQueue(theValueSets);
+
+		return csId;
+	}
+
+	@Override
+	@Transactional(propagation = Propagation.REQUIRED)
+	public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
+		ourLog.info("Storing code system");
+
+		ValidateUtil.isTrueOrThrowInvalidRequest(theCodeSystemVersion.getResource() != null, "No resource supplied");
+		ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
+
+		// Grab the existing versions so we can delete them later
+		List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourcePid);
+
+		/*
+		 * For now we always delete old versions. At some point it would be nice to allow configuration to keep old versions.
+		 */
+
+		ourLog.info("Deleting old code system versions");
+		for (TermCodeSystemVersion next : existing) {
+			Long codeSystemVersionPid = next.getPid();
+			deleteCodeSystemVersion(codeSystemVersionPid);
+		}
+
+		ourLog.info("Flushing...");
+		myConceptDao.flush();
+		ourLog.info("Done flushing");
+
+		/*
+		 * Do the upload
+		 */
+
+		TermCodeSystem codeSystem = getOrCreateTermCodeSystem(theCodeSystemResourcePid, theSystemUri, theSystemName, theCodeSystemResourceTable);
+
+		theCodeSystemVersion.setCodeSystem(codeSystem);
+
+		theCodeSystemVersion.setCodeSystemDisplayName(theSystemName);
+		theCodeSystemVersion.setCodeSystemVersionId(theSystemVersionId);
+
+		ourLog.info("Validating all codes in CodeSystem for storage (this can take some time for large sets)");
+
+		// Validate the code system
+		ArrayList<String> conceptsStack = new ArrayList<>();
+		IdentityHashMap<TermConcept, Object> allConcepts = new IdentityHashMap<>();
+		int totalCodeCount = 0;
+		for (TermConcept next : theCodeSystemVersion.getConcepts()) {
+			totalCodeCount += validateConceptForStorage(next, theCodeSystemVersion, conceptsStack, allConcepts);
+		}
+
+		ourLog.info("Saving version containing {} concepts", totalCodeCount);
+
+		TermCodeSystemVersion codeSystemVersion = myCodeSystemVersionDao.saveAndFlush(theCodeSystemVersion);
+
+		ourLog.info("Saving code system");
+
+		codeSystem.setCurrentVersion(theCodeSystemVersion);
+		codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
+
+		ourLog.info("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
+
+		for (TermConcept next : theCodeSystemVersion.getConcepts()) {
+			populateVersion(next, codeSystemVersion);
+		}
+
+		ourLog.info("Saving {} concepts...", totalCodeCount);
+
+		IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
+		for (TermConcept next : theCodeSystemVersion.getConcepts()) {
+			persistChildren(next, codeSystemVersion, conceptsStack2, totalCodeCount);
+		}
+
+		ourLog.info("Done saving concepts, flushing to database");
+
+		myConceptDao.flush();
+		myConceptParentChildLinkDao.flush();
+
+		ourLog.info("Done deleting old code system versions");
+
+		if (myDeferredStorageSvc.isStorageQueueEmpty() == false) {
+			ourLog.info("Note that some concept saving has been deferred");
+		}
+	}
+
+	private void deleteCodeSystemVersion(final Long theCodeSystemVersionPid) {
+		ourLog.info(" * Deleting code system version {}", theCodeSystemVersionPid);
+
+		PageRequest page1000 = PageRequest.of(0, 1000);
+
+		// Parent/Child links
+		{
+			String descriptor = "parent/child links";
+			Supplier<Slice<TermConceptParentChildLink>> loader = () -> myConceptParentChildLinkDao.findByCodeSystemVersion(page1000, theCodeSystemVersionPid);
+			Supplier<Integer> counter = () -> myConceptParentChildLinkDao.countByCodeSystemVersion(theCodeSystemVersionPid);
+			doDelete(descriptor, loader, counter, myConceptParentChildLinkDao);
+		}
+
+		// Properties
+		{
+			String descriptor = "concept properties";
+			Supplier<Slice<TermConceptProperty>> loader = () -> myConceptPropertyDao.findByCodeSystemVersion(page1000, theCodeSystemVersionPid);
+			Supplier<Integer> counter = () -> myConceptPropertyDao.countByCodeSystemVersion(theCodeSystemVersionPid);
+			doDelete(descriptor, loader, counter, myConceptPropertyDao);
+		}
+
+		// Designations
+		{
+			String descriptor = "concept designations";
+			Supplier<Slice<TermConceptDesignation>> loader = () -> myConceptDesignationDao.findByCodeSystemVersion(page1000, theCodeSystemVersionPid);
+			Supplier<Integer> counter = () -> myConceptDesignationDao.countByCodeSystemVersion(theCodeSystemVersionPid);
+			doDelete(descriptor, loader, counter, myConceptDesignationDao);
+		}
+
+		// Concepts
+		{
+			String descriptor = "concepts";
+			// For some reason, concepts are much slower to delete, so use a smaller batch size
+			PageRequest page100 = PageRequest.of(0, 100);
+			Supplier<Slice<TermConcept>> loader = () -> myConceptDao.findByCodeSystemVersion(page100, theCodeSystemVersionPid);
+			Supplier<Integer> counter = () -> myConceptDao.countByCodeSystemVersion(theCodeSystemVersionPid);
+			doDelete(descriptor, loader, counter, myConceptDao);
+		}
+
+		Optional<TermCodeSystem> codeSystemOpt = myCodeSystemDao.findWithCodeSystemVersionAsCurrentVersion(theCodeSystemVersionPid);
+		if (codeSystemOpt.isPresent()) {
+			TermCodeSystem codeSystem = codeSystemOpt.get();
+			ourLog.info(" * Removing code system version {} as current version of code system {}", theCodeSystemVersionPid, codeSystem.getPid());
+			codeSystem.setCurrentVersion(null);
+			myCodeSystemDao.save(codeSystem);
+		}
+
+		ourLog.info(" * Deleting code system version");
+		myCodeSystemVersionDao.deleteById(theCodeSystemVersionPid);
+
+	}
+
+	private void validateDstu3OrNewer() {
+		Validate.isTrue(myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3), "Terminology operations only supported in DSTU3+ mode");
+	}
+
+	private void addConcept(TermCodeSystemVersion theCsv, Map<String, Long> theCodeToConceptPid, Collection<String> theParentCodes, TermConcept theConceptToAdd, ListMultimap<String, String> theParentCodeToChildCodes, UploadStatistics theStatisticsTracker, boolean theForceResequence) {
+		TermConcept nextConceptToAdd = theConceptToAdd;
+
+		String nextCodeToAdd = nextConceptToAdd.getCode();
+		String parentDescription = "(root concept)";
+		Set<TermConcept> parentConcepts = new HashSet<>();
+		if (!theParentCodes.isEmpty()) {
+			parentDescription = "[" + String.join(", ", theParentCodes) + "]";
+			for (String nextParentCode : theParentCodes) {
+				Long nextParentCodePid = theCodeToConceptPid.get(nextParentCode);
+				if (nextParentCodePid == null) {
+					throw new InvalidRequestException("Unable to add code \"" + nextCodeToAdd + "\" to unknown parent: " + nextParentCode);
+				}
+				parentConcepts.add(myConceptDao.getOne(nextParentCodePid));
+			}
+		}
+
+		ourLog.info("Saving concept {} with parent {}", theStatisticsTracker.getUpdatedConceptCount(), parentDescription);
+
+		if (theCodeToConceptPid.containsKey(nextCodeToAdd)) {
+
+			TermConcept existingCode = myConceptDao.getOne(theCodeToConceptPid.get(nextCodeToAdd));
+			existingCode.setIndexStatus(null);
+			existingCode.setDisplay(nextConceptToAdd.getDisplay());
+			nextConceptToAdd = existingCode;
+
+		}
+
+		if (theConceptToAdd.getSequence() == null || theForceResequence) {
+			// If this is a new code, give it a sequence number based on how many concepts the
+			// parent already has (or the highest number, if the code has multiple parents)
+			int sequence = 0;
+			for (String nextParentCode : theParentCodes) {
+				theParentCodeToChildCodes.put(nextParentCode, nextCodeToAdd);
+				sequence = Math.max(sequence, theParentCodeToChildCodes.get(nextParentCode).size());
+			}
+			if (theParentCodes.isEmpty()) {
+				theParentCodeToChildCodes.put("", nextCodeToAdd);
+				sequence = Math.max(sequence, theParentCodeToChildCodes.get("").size());
+			}
+			nextConceptToAdd.setSequence(sequence);
+		}
+
+
+		// Drop any old parent-child links if they aren't explicitly specified in the
+		// hierarchy being added
+		for (Iterator<TermConceptParentChildLink> iter = nextConceptToAdd.getParents().iterator(); iter.hasNext(); ) {
+			TermConceptParentChildLink nextLink = iter.next();
+			String parentCode = nextLink.getParent().getCode();
+			boolean shouldRemove = !theParentCodes.contains(parentCode);
+			if (shouldRemove) {
+				ourLog.info("Dropping existing parent/child link from {} -> {}", parentCode, nextCodeToAdd);
+				myConceptParentChildLinkDao.delete(nextLink);
+				iter.remove();
+
+				List<TermConceptParentChildLink> parentChildrenList = nextLink.getParent().getChildren();
+				parentChildrenList.remove(nextLink);
+			}
+		}
+
+		nextConceptToAdd.setParentPids(null);
+		nextConceptToAdd.setCodeSystemVersion(theCsv);
+		nextConceptToAdd = myConceptDao.save(nextConceptToAdd);
+
+		Long nextConceptPid = nextConceptToAdd.getId();
+		Validate.notNull(nextConceptPid);
+		theCodeToConceptPid.put(nextCodeToAdd, nextConceptPid);
+		theStatisticsTracker.incrementUpdatedConceptCount();
+
+		// Add link to new child to the parent if this link doesn't already exist (this will be the
+		// case for concepts being added to an existing child concept, but won't be the case when
+		// we're recursively adding children)
+		for (TermConcept nextParentConcept : parentConcepts) {
+			if (nextParentConcept.getChildren().stream().noneMatch(t->t.getChild().getCode().equals(nextCodeToAdd))) {
+				TermConceptParentChildLink parentLink = new TermConceptParentChildLink();
+				parentLink.setParent(nextParentConcept);
+				parentLink.setChild(nextConceptToAdd);
+				parentLink.setCodeSystem(theCsv);
+				parentLink.setRelationshipType(TermConceptParentChildLink.RelationshipTypeEnum.ISA);
+				nextParentConcept.getChildren().add(parentLink);
+				nextConceptToAdd.getParents().add(parentLink);
+				myConceptParentChildLinkDao.save(parentLink);
+			}
+		}
+
+		// Save children recursively
+		for (TermConceptParentChildLink nextChildConceptLink : nextConceptToAdd.getChildren()) {
+
+			TermConcept nextChild = nextChildConceptLink.getChild();
+			Collection<String> parentCodes = nextChild.getParents().stream().map(t -> t.getParent().getCode()).collect(Collectors.toList());
+			addConcept(theCsv, theCodeToConceptPid, parentCodes, nextChild, theParentCodeToChildCodes, theStatisticsTracker, false);
+
+			if (nextChildConceptLink.getId() == null) {
+				nextChildConceptLink.setCodeSystem(theCsv);
+				myConceptParentChildLinkDao.save(nextChildConceptLink);
+			}
+		}
+
+	}
+
+	private Long getCodeSystemResourcePid(IIdType theIdType) {
+		return getCodeSystemResourcePid(theIdType, null);
+	}
+
+	private Long getCodeSystemResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
+		return myIdHelperService.translateForcedIdToPid(theIdType, theRequestDetails);
+	}
+
+	private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, int theTotalConcepts) {
+		if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
+			return;
+		}
+
+		if (theConceptsStack.size() == 1 || theConceptsStack.size() % 10000 == 0) {
+			float pct = (float) theConceptsStack.size() / (float) theTotalConcepts;
+			ourLog.info("Have processed {}/{} concepts ({}%)", theConceptsStack.size(), theTotalConcepts, (int) (pct * 100.0f));
+		}
+
+		theConcept.setCodeSystemVersion(theCodeSystem);
+		theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
+
+		if (theConceptsStack.size() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
+			saveConcept(theConcept);
+		} else {
+			myDeferredStorageSvc.addConceptToStorageQueue(theConcept);
+		}
+
+		for (TermConceptParentChildLink next : theConcept.getChildren()) {
+			persistChildren(next.getChild(), theCodeSystem, theConceptsStack, theTotalConcepts);
+		}
+
+		for (TermConceptParentChildLink next : theConcept.getChildren()) {
+			if (theConceptsStack.size() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
+				saveConceptLink(next);
+			} else {
+				myDeferredStorageSvc.addConceptLinkToStorageQueue(next);
+			}
+		}
+
+	}
+
+	private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
+		if (theNext.getCodeSystemVersion() != null) {
+			return;
+		}
+		theNext.setCodeSystemVersion(theCodeSystemVersion);
+		for (TermConceptParentChildLink next : theNext.getChildren()) {
+			populateVersion(next.getChild(), theCodeSystemVersion);
+		}
+	}
+
+	private void saveConceptLink(TermConceptParentChildLink next) {
+		if (next.getId() == null) {
+			myConceptParentChildLinkDao.save(next);
+		}
+	}
+
+	private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
+		ourLog.trace("Checking {} parents", theParents.size());
+		int retVal = 0;
+
+		for (TermConceptParentChildLink nextLink : theParents) {
+			if (nextLink.getRelationshipType() == TermConceptParentChildLink.RelationshipTypeEnum.ISA) {
+				TermConcept nextParent = nextLink.getParent();
+				retVal += ensureParentsSaved(nextParent.getParents());
+				if (nextParent.getId() == null) {
+					nextParent.setUpdated(new Date());
+					myConceptDao.saveAndFlush(nextParent);
+					retVal++;
+					ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
+				}
+			}
+		}
+
+		return retVal;
+	}
+
+	@Nonnull
+	private TermCodeSystem getOrCreateTermCodeSystem(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, ResourceTable theCodeSystemResourceTable) {
+		TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theSystemUri);
+		if (codeSystem == null) {
+			codeSystem = myCodeSystemDao.findByResourcePid(theCodeSystemResourcePid);
+			if (codeSystem == null) {
+				codeSystem = new TermCodeSystem();
+			}
+			codeSystem.setResource(theCodeSystemResourceTable);
+		} else {
+			if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemResourceTable.getId())) {
+				String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
+					codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
+				throw new UnprocessableEntityException(msg);
+			}
+		}
+
+		codeSystem.setCodeSystemUri(theSystemUri);
+		codeSystem.setName(theSystemName);
+		codeSystem = myCodeSystemDao.save(codeSystem);
+		return codeSystem;
+	}
+
+	private void populateCodeSystemVersionProperties(TermCodeSystemVersion theCodeSystemVersion, CodeSystem theCodeSystemResource, ResourceTable theResourceTable) {
+		theCodeSystemVersion.setResource(theResourceTable);
+		theCodeSystemVersion.setCodeSystemDisplayName(theCodeSystemResource.getName());
+		theCodeSystemVersion.setCodeSystemVersionId(theCodeSystemResource.getVersion());
+	}
+
+	private void deleteConceptChildrenAndConcept(TermConcept theConcept, AtomicInteger theRemoveCounter) {
+		for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
+			deleteConceptChildrenAndConcept(nextChildLink.getChild(), theRemoveCounter);
+			myConceptParentChildLinkDao.delete(nextChildLink);
+		}
+
+		myConceptDesignationDao.deleteAll(theConcept.getDesignations());
+		myConceptPropertyDao.deleteAll(theConcept.getProperties());
+		myConceptDao.delete(theConcept);
+		theRemoveCounter.incrementAndGet();
+	}
+
+
+	private <T> void doDelete(String theDescriptor, Supplier<Slice<T>> theLoader, Supplier<Integer> theCounter, JpaRepository<T, ?> theDao) {
+		int count;
+		ourLog.info(" * Deleting {}", theDescriptor);
+		int totalCount = theCounter.get();
+		StopWatch sw = new StopWatch();
+		count = 0;
+		while (true) {
+			Slice<T> link = theLoader.get();
+			if (!link.hasContent()) {
+				break;
+			}
+
+			TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
+			txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
+			txTemplate.execute(t -> {
+				theDao.deleteAll(link);
+				return null;
+			});
+
+			count += link.getNumberOfElements();
+			ourLog.info(" * {} {} deleted - {}/sec - ETA: {}", count, theDescriptor, sw.formatThroughput(count, TimeUnit.SECONDS), sw.getEstimatedTimeRemaining(count, totalCount));
+		}
+		theDao.flush();
+	}
+
+
+	private int validateConceptForStorage(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, ArrayList<String> theConceptsStack,
+													  IdentityHashMap<TermConcept, Object> theAllConcepts) {
+		ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() != null, "CodeSystemVersion is null");
+		ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() == theCodeSystem, "CodeSystems are not equal");
+		ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "CodeSystem contains a code with no code value");
+
+		if (theConceptsStack.contains(theConcept.getCode())) {
+			throw new InvalidRequestException("CodeSystem contains circular reference around code " + theConcept.getCode());
+		}
+		theConceptsStack.add(theConcept.getCode());
+
+		int retVal = 0;
+		if (theAllConcepts.put(theConcept, theAllConcepts) == null) {
+			if (theAllConcepts.size() % 1000 == 0) {
+				ourLog.info("Have validated {} concepts", theAllConcepts.size());
+			}
+			retVal = 1;
+		}
+
+		for (TermConceptParentChildLink next : theConcept.getChildren()) {
+			next.setCodeSystem(theCodeSystem);
+			retVal += validateConceptForStorage(next.getChild(), theCodeSystem, theConceptsStack, theAllConcepts);
+		}
+
+		theConceptsStack.remove(theConceptsStack.size() - 1);
+
+		return retVal;
+	}
+
+
+}

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

@@ -0,0 +1,260 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
+import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
+import ca.uhn.fhir.jpa.model.sched.FireAtIntervalJob;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.util.StopWatch;
+import com.google.common.annotations.VisibleForTesting;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.quartz.JobExecutionContext;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionDefinition;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import javax.annotation.PostConstruct;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
+
+	private static final int SCHEDULE_INTERVAL_MILLIS = 5000;
+	private static final Logger ourLog = LoggerFactory.getLogger(TermDeferredStorageSvcImpl.class);
+	@Autowired
+	protected ITermConceptDao myConceptDao;
+	@Autowired
+	protected PlatformTransactionManager myTransactionMgr;
+	private boolean myProcessDeferred = true;
+	private List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
+	private List<ValueSet> myDeferredValueSets = Collections.synchronizedList(new ArrayList<>());
+	private List<ConceptMap> myDeferredConceptMaps = Collections.synchronizedList(new ArrayList<>());
+	private List<TermConceptParentChildLink> myConceptLinksToSaveLater = Collections.synchronizedList(new ArrayList<>());
+	@Autowired
+	private DaoConfig myDaoConfig;
+	@Autowired
+	private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
+	@Autowired
+	private ISchedulerService mySchedulerService;
+	@Autowired
+	private ITermVersionAdapterSvc myTerminologyVersionAdapterSvc;
+	@Autowired
+	private ITermCodeSystemStorageSvc myConceptStorageSvc;
+
+	@Override
+	public void addConceptToStorageQueue(TermConcept theConcept) {
+		Validate.notNull(theConcept);
+		myDeferredConcepts.add(theConcept);
+	}
+
+	@Override
+	public void addConceptLinkToStorageQueue(TermConceptParentChildLink theConceptLink) {
+		Validate.notNull(theConceptLink);
+		myConceptLinksToSaveLater.add(theConceptLink);
+	}
+
+	@Override
+	public void addConceptMapsToStorageQueue(List<ConceptMap> theConceptMaps) {
+		Validate.notNull(theConceptMaps);
+		myDeferredConceptMaps.addAll(theConceptMaps);
+	}
+
+	@Override
+	public void addValueSetsToStorageQueue(List<ValueSet> theValueSets) {
+		Validate.notNull(theValueSets);
+		myDeferredValueSets.addAll(theValueSets);
+	}
+
+	@Override
+	public void setProcessDeferred(boolean theProcessDeferred) {
+		myProcessDeferred = theProcessDeferred;
+	}
+
+	private void processDeferredConceptMaps() {
+		int count = Math.min(myDeferredConceptMaps.size(), 20);
+		for (ConceptMap nextConceptMap : new ArrayList<>(myDeferredConceptMaps.subList(0, count))) {
+			ourLog.info("Creating ConceptMap: {}", nextConceptMap.getId());
+			myTerminologyVersionAdapterSvc.createOrUpdateConceptMap(nextConceptMap);
+			myDeferredConceptMaps.remove(nextConceptMap);
+		}
+		ourLog.info("Saved {} deferred ConceptMap resources, have {} remaining", count, myDeferredConceptMaps.size());
+	}
+
+	private void processDeferredConcepts() {
+		int codeCount = 0, relCount = 0;
+		StopWatch stopwatch = new StopWatch();
+
+		int count = Math.min(myDaoConfig.getDeferIndexingForCodesystemsOfSize(), myDeferredConcepts.size());
+		ourLog.info("Saving {} deferred concepts...", count);
+		while (codeCount < count && myDeferredConcepts.size() > 0) {
+			TermConcept next = myDeferredConcepts.remove(0);
+			codeCount += myConceptStorageSvc.saveConcept(next);
+		}
+
+		if (codeCount > 0) {
+			ourLog.info("Saved {} deferred concepts ({} codes remain and {} relationships remain) in {}ms ({}ms / code)",
+				codeCount, myDeferredConcepts.size(), myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount));
+		}
+
+		if (codeCount == 0) {
+			count = Math.min(myDaoConfig.getDeferIndexingForCodesystemsOfSize(), myConceptLinksToSaveLater.size());
+			ourLog.info("Saving {} deferred concept relationships...", count);
+			while (relCount < count && myConceptLinksToSaveLater.size() > 0) {
+				TermConceptParentChildLink next = myConceptLinksToSaveLater.remove(0);
+
+				if (!myConceptDao.findById(next.getChild().getId()).isPresent() || !myConceptDao.findById(next.getParent().getId()).isPresent()) {
+					ourLog.warn("Not inserting link from child {} to parent {} because it appears to have been deleted", next.getParent().getCode(), next.getChild().getCode());
+					continue;
+				}
+
+				saveConceptLink(next);
+				relCount++;
+			}
+		}
+
+		if (relCount > 0) {
+			ourLog.info("Saved {} deferred relationships ({} remain) in {}ms ({}ms / entry)",
+				relCount, myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(relCount));
+		}
+
+		if ((myDeferredConcepts.size() + myConceptLinksToSaveLater.size()) == 0) {
+			ourLog.info("All deferred concepts and relationships have now been synchronized to the database");
+		}
+	}
+
+	private void processDeferredValueSets() {
+		int count = Math.min(myDeferredValueSets.size(), 20);
+		for (ValueSet nextValueSet : new ArrayList<>(myDeferredValueSets.subList(0, count))) {
+			ourLog.info("Creating ValueSet: {}", nextValueSet.getId());
+			myTerminologyVersionAdapterSvc.createOrUpdateValueSet(nextValueSet);
+			myDeferredValueSets.remove(nextValueSet);
+		}
+		ourLog.info("Saved {} deferred ValueSet resources, have {} remaining", count, myDeferredValueSets.size());
+	}
+
+	/**
+	 * This method is present only for unit tests, do not call from client code
+	 */
+	@VisibleForTesting
+	public synchronized void clearDeferred() {
+		myDeferredValueSets.clear();
+		myDeferredConceptMaps.clear();
+		myDeferredConcepts.clear();
+	}
+
+	@Transactional(propagation = Propagation.NEVER)
+	@Override
+	public synchronized void saveDeferred() {
+		if (isProcessDeferredPaused()) {
+			return;
+		}
+
+		TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
+		tt.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
+		if (isDeferredConceptsOrConceptLinksToSaveLater()) {
+			tt.execute(t -> {
+				processDeferredConcepts();
+				return null;
+			});
+		}
+
+		if (isDeferredValueSets()) {
+			tt.execute(t -> {
+				processDeferredValueSets();
+				return null;
+			});
+		}
+		if (isDeferredConceptMaps()) {
+			tt.execute(t -> {
+				processDeferredConceptMaps();
+				return null;
+			});
+		}
+
+	}
+
+	@Override
+	public boolean isStorageQueueEmpty() {
+		boolean retVal = true;
+		retVal &= !isProcessDeferredPaused();
+		retVal &= !isDeferredConcepts();
+		retVal &= !isConceptLinksToSaveLater();
+		retVal &= !isDeferredValueSets();
+		retVal &= !isDeferredConceptMaps();
+		return retVal;
+	}
+
+
+	private void saveConceptLink(TermConceptParentChildLink next) {
+		if (next.getId() == null) {
+			myConceptParentChildLinkDao.save(next);
+		}
+	}
+
+	private boolean isProcessDeferredPaused() {
+		return !myProcessDeferred;
+	}
+
+	private boolean isDeferredConceptsOrConceptLinksToSaveLater() {
+		return isDeferredConcepts() || isConceptLinksToSaveLater();
+	}
+
+	private boolean isDeferredConcepts() {
+		return !myDeferredConcepts.isEmpty();
+	}
+
+	private boolean isConceptLinksToSaveLater() {
+		return !myConceptLinksToSaveLater.isEmpty();
+	}
+
+	private boolean isDeferredValueSets() {
+		return !myDeferredValueSets.isEmpty();
+	}
+
+	private boolean isDeferredConceptMaps() {
+		return !myDeferredConceptMaps.isEmpty();
+	}
+
+	@PostConstruct
+	public void registerScheduledJob() {
+		// Register scheduled job to save deferred concepts
+		// In the future it would be great to make this a cluster-aware task somehow
+		ScheduledJobDefinition jobDefinition = new ScheduledJobDefinition();
+		jobDefinition.setId(BaseTermReadSvcImpl.class.getName() + "_saveDeferred");
+		jobDefinition.setJobClass(SaveDeferredJob.class);
+		mySchedulerService.scheduleFixedDelay(SCHEDULE_INTERVAL_MILLIS, false, jobDefinition);
+	}
+
+	public static class SaveDeferredJob extends FireAtIntervalJob {
+
+		@Autowired
+		private ITermDeferredStorageSvc myTerminologySvc;
+
+		/**
+		 * Constructor
+		 */
+		public SaveDeferredJob() {
+			super(SCHEDULE_INTERVAL_MILLIS);
+		}
+
+		@Override
+		protected void doExecute(JobExecutionContext theContext) {
+			myTerminologySvc.saveDeferred();
+		}
+	}
+
+}

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

@@ -4,8 +4,10 @@ import ca.uhn.fhir.context.FhirContext;
 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.term.custom.ConceptHandler;
-import ca.uhn.fhir.jpa.term.custom.HierarchyHandler;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
 import ca.uhn.fhir.jpa.term.loinc.*;
 import ca.uhn.fhir.jpa.term.snomedct.SctHandlerConcept;
 import ca.uhn.fhir.jpa.term.snomedct.SctHandlerDescription;
@@ -15,7 +17,6 @@ import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.ValidateUtil;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Charsets;
@@ -23,9 +24,7 @@ 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.io.input.BOMInputStream;
 import org.apache.commons.lang3.ObjectUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
@@ -41,8 +40,7 @@ import javax.validation.constraints.NotNull;
 import java.io.*;
 import java.util.*;
 import java.util.Map.Entry;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
+import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -67,64 +65,29 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * #L%
  */
 
-public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
-	public static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_";
-	public static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en";
-	public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
-
-	public static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt";
-	public static final String IMGTHLA_HLA_XML = "hla.xml";
-
+public class TermLoaderSvcImpl implements ITermLoaderSvc {
 	public static final String CUSTOM_CONCEPTS_FILE = "concepts.csv";
 	public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.csv";
-	public static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
-	public static final String CUSTOM_CODESYSTEM_XML = "codesystem.xml";
+	static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt";
+	static final String IMGTHLA_HLA_XML = "hla.xml";
+	static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
+	private static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_";
+	private static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en";
+	private static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
+	private static final String CUSTOM_CODESYSTEM_XML = "codesystem.xml";
 
 	private static final int LOG_INCREMENT = 1000;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImpl.class);
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermLoaderSvcImpl.class);
 	// FYI: Hardcoded to R4 because that's what the term svc uses internally
 	private final FhirContext myCtx = FhirContext.forR4();
 	@Autowired
-	private IHapiTerminologySvc myTermSvc;
-
-	private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain, Map<String, TermConcept> theCode2concept, Counter theCircularCounter) {
-
-		theChain.add(theConcept.getCode());
-		for (Iterator<TermConceptParentChildLink> childIter = theConcept.getChildren().iterator(); childIter.hasNext(); ) {
-			TermConceptParentChildLink next = childIter.next();
-			TermConcept nextChild = next.getChild();
-			if (theChain.contains(nextChild.getCode())) {
-
-				StringBuilder b = new StringBuilder();
-				b.append("Removing circular reference code ");
-				b.append(nextChild.getCode());
-				b.append(" from parent ");
-				b.append(next.getParent().getCode());
-				b.append(". Chain was: ");
-				for (String nextInChain : theChain) {
-					TermConcept nextCode = theCode2concept.get(nextInChain);
-					b.append(nextCode.getCode());
-					b.append('[');
-					b.append(StringUtils.substring(nextCode.getDisplay(), 0, 20).replace("[", "").replace("]", "").trim());
-					b.append("] ");
-				}
-				ourLog.info(b.toString(), theConcept.getCode());
-				childIter.remove();
-				nextChild.getParents().remove(next);
-
-			} else {
-				dropCircularRefs(nextChild, theChain, theCode2concept, theCircularCounter);
-			}
-		}
-		theChain.remove(theChain.size() - 1);
-
-	}
+	private ITermDeferredStorageSvc myDeferredStorageSvc;
+	@Autowired
+	private ITermCodeSystemStorageSvc myCodeSystemStorageSvc;
 
 	@Override
 	public UploadStatistics loadImgthla(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
-		LoadedFileDescriptors descriptors = null;
-		try {
-			descriptors = new LoadedFileDescriptors(theFiles);
+		try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
 			List<String> mandatoryFilenameFragments = Arrays.asList(
 				IMGTHLA_HLA_NOM_TXT,
 				IMGTHLA_HLA_XML
@@ -134,15 +97,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 			ourLog.info("Beginning IMGTHLA processing");
 
 			return processImgthlaFiles(descriptors, theRequestDetails);
-		} finally {
-			IOUtils.closeQuietly(descriptors);
 		}
 	}
 
 	@Override
 	public UploadStatistics loadLoinc(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
 		try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
-			List<String> loincUploadPropertiesFragment = Arrays.asList(
+			List<String> loincUploadPropertiesFragment = Collections.singletonList(
 				LOINC_UPLOAD_PROPERTIES_FILE.getCode()
 			);
 			descriptors.verifyMandatoryFilesExist(loincUploadPropertiesFragment);
@@ -180,23 +141,6 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		}
 	}
 
-	@NotNull
-	private Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
-		Properties retVal = new Properties();
-		for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
-			if (next.getFilename().endsWith(thePropertiesFile)) {
-				try {
-					try (InputStream inputStream = next.getInputStream()) {
-						retVal.load(inputStream);
-					}
-				} catch (IOException e) {
-					throw new InternalErrorException("Failed to read " + thePropertiesFile, e);
-				}
-			}
-		}
-		return retVal;
-	}
-
 	@Override
 	public UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
 		try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
@@ -216,8 +160,6 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 	@Override
 	public UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
 		try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
-			IRecordHandler handler;
-
 			Optional<String> codeSystemContent = loadFile(descriptors, CUSTOM_CODESYSTEM_JSON, CUSTOM_CODESYSTEM_XML);
 			CodeSystem codeSystem;
 			if (codeSystemContent.isPresent()) {
@@ -233,14 +175,83 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 				codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
 			}
 
-			TermCodeSystemVersion csv = new TermCodeSystemVersion();
-			final Map<String, TermConcept> code2concept = processCustomTerminologyFiles(descriptors, csv);
+			CustomTerminologySet terminologySet = CustomTerminologySet.load(descriptors, false);
+			TermCodeSystemVersion csv = terminologySet.toCodeSystemVersion();
 
 			IIdType target = storeCodeSystem(theRequestDetails, csv, codeSystem, null, null);
-			return new UploadStatistics(code2concept.size(), target);
+			return new UploadStatistics(terminologySet.getSize(), target);
 		}
 	}
 
+
+	@Override
+	public UploadStatistics loadDeltaAdd(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
+		ourLog.info("Processing terminology delta ADD for system[{}] with files: {}", theSystem, theFiles.stream().map(t -> t.getFilename()).collect(Collectors.toList()));
+		try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
+			CustomTerminologySet terminologySet = CustomTerminologySet.load(descriptors, false);
+			return myCodeSystemStorageSvc.applyDeltaCodeSystemsAdd(theSystem, terminologySet);
+		}
+	}
+
+	@Override
+	public UploadStatistics loadDeltaRemove(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
+		ourLog.info("Processing terminology delta REMOVE for system[{}] with files: {}", theSystem, theFiles.stream().map(t -> t.getFilename()).collect(Collectors.toList()));
+		try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
+			CustomTerminologySet terminologySet = CustomTerminologySet.load(descriptors, true);
+			return myCodeSystemStorageSvc.applyDeltaCodeSystemsRemove(theSystem, terminologySet);
+		}
+	}
+
+	private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain, Map<String, TermConcept> theCode2concept) {
+
+		theChain.add(theConcept.getCode());
+		for (Iterator<TermConceptParentChildLink> childIter = theConcept.getChildren().iterator(); childIter.hasNext(); ) {
+			TermConceptParentChildLink next = childIter.next();
+			TermConcept nextChild = next.getChild();
+			if (theChain.contains(nextChild.getCode())) {
+
+				StringBuilder b = new StringBuilder();
+				b.append("Removing circular reference code ");
+				b.append(nextChild.getCode());
+				b.append(" from parent ");
+				b.append(next.getParent().getCode());
+				b.append(". Chain was: ");
+				for (String nextInChain : theChain) {
+					TermConcept nextCode = theCode2concept.get(nextInChain);
+					b.append(nextCode.getCode());
+					b.append('[');
+					b.append(StringUtils.substring(nextCode.getDisplay(), 0, 20).replace("[", "").replace("]", "").trim());
+					b.append("] ");
+				}
+				ourLog.info(b.toString(), theConcept.getCode());
+				childIter.remove();
+				nextChild.getParents().remove(next);
+
+			} else {
+				dropCircularRefs(nextChild, theChain, theCode2concept);
+			}
+		}
+		theChain.remove(theChain.size() - 1);
+
+	}
+
+	@NotNull
+	private Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
+		Properties retVal = new Properties();
+		for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
+			if (next.getFilename().endsWith(thePropertiesFile)) {
+				try {
+					try (InputStream inputStream = next.getInputStream()) {
+						retVal.load(inputStream);
+					}
+				} catch (IOException e) {
+					throw new InternalErrorException("Failed to read " + thePropertiesFile, e);
+				}
+			}
+		}
+		return retVal;
+	}
+
 	private Optional<String> loadFile(LoadedFileDescriptors theDescriptors, String... theFilenames) {
 		for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
 			for (String nextFilename : theFilenames) {
@@ -257,15 +268,14 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		return Optional.empty();
 	}
 
-	UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
+	private UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
 		final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
-		final Map<String, TermConcept> code2concept = new HashMap<>();
 		final List<ValueSet> valueSets = new ArrayList<>();
 		final List<ConceptMap> conceptMaps = new ArrayList<>();
 
 		CodeSystem imgthlaCs;
 		try {
-			String imgthlaCsString = IOUtils.toString(BaseHapiTerminologySvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/imgthla/imgthla.xml"), Charsets.UTF_8);
+			String imgthlaCsString = IOUtils.toString(BaseTermReadSvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/imgthla/imgthla.xml"), Charsets.UTF_8);
 			imgthlaCs = FhirContext.forR4().newXmlParser().parseResource(CodeSystem.class, imgthlaCsString);
 		} catch (IOException e) {
 			throw new InternalErrorException("Failed to load imgthla.xml", e);
@@ -353,7 +363,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 
 		int valueSetCount = valueSets.size();
 		int rootConceptCount = codeSystemVersion.getConcepts().size();
-		int conceptCount = code2concept.size();
+		int conceptCount = rootConceptCount;
 		ourLog.info("Have {} total concepts, {} root concepts, {} ValueSets", conceptCount, rootConceptCount, valueSetCount);
 
 		// remove this when fully implemented ...
@@ -372,7 +382,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 
 		CodeSystem loincCs;
 		try {
-			String loincCsString = IOUtils.toString(BaseHapiTerminologySvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/loinc/loinc.xml"), Charsets.UTF_8);
+			String loincCsString = IOUtils.toString(BaseTermReadSvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/loinc/loinc.xml"), Charsets.UTF_8);
 			loincCs = FhirContext.forR4().newXmlParser().parseResource(CodeSystem.class, loincCsString);
 		} catch (IOException e) {
 			throw new InternalErrorException("Failed to load loinc.xml", e);
@@ -501,7 +511,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		retVal.setPublisher("Regenstrief Institute, Inc.");
 		retVal.setDescription("A value set that includes all LOINC codes");
 		retVal.setCopyright("This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/");
-		retVal.getCompose().addInclude().setSystem(IHapiTerminologyLoaderSvc.LOINC_URI);
+		retVal.getCompose().addInclude().setSystem(ITermLoaderSvc.LOINC_URI);
 
 		return retVal;
 	}
@@ -540,7 +550,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 			long count = circularCounter.getThenAdd();
 			float pct = ((float) count / rootConcepts.size()) * 100.0f;
 			ourLog.info(" * Scanning for circular refs - have scanned {} / {} codes ({}%)", count, rootConcepts.size(), pct);
-			dropCircularRefs(next, new ArrayList<>(), code2concept, circularCounter);
+			dropCircularRefs(next, new ArrayList<>(), code2concept);
 		}
 
 		codeSystemVersion.getConcepts().addAll(rootConcepts.values());
@@ -555,8 +565,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 	}
 
 	@VisibleForTesting
-	void setTermSvcForUnitTests(IHapiTerminologySvc theTermSvc) {
-		myTermSvc = theTermSvc;
+	void setTermDeferredStorageSvc(ITermDeferredStorageSvc theDeferredStorageSvc) {
+		myDeferredStorageSvc = theDeferredStorageSvc;
+	}
+
+	@VisibleForTesting
+	void setTermCodeSystemStorageSvcForUnitTests(ITermCodeSystemStorageSvc theTermCodeSystemStorageSvc) {
+		myCodeSystemStorageSvc = theTermCodeSystemStorageSvc;
 	}
 
 	private IIdType storeCodeSystem(RequestDetails theRequestDetails, final TermCodeSystemVersion theCodeSystemVersion, CodeSystem theCodeSystem, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
@@ -566,135 +581,14 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		List<ConceptMap> conceptMaps = ObjectUtils.defaultIfNull(theConceptMaps, Collections.emptyList());
 
 		IIdType retVal;
-		myTermSvc.setProcessDeferred(false);
-		retVal = myTermSvc.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
-		myTermSvc.setProcessDeferred(true);
+		myDeferredStorageSvc.setProcessDeferred(false);
+		retVal = myCodeSystemStorageSvc.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
+		myDeferredStorageSvc.setProcessDeferred(true);
 
 		return retVal;
 	}
 
-	public static class LoadedFileDescriptors implements Closeable {
-
-		private List<File> myTemporaryFiles = new ArrayList<>();
-		private List<IHapiTerminologyLoaderSvc.FileDescriptor> myUncompressedFileDescriptors = new ArrayList<>();
-
-		public LoadedFileDescriptors(List<IHapiTerminologyLoaderSvc.FileDescriptor> theFileDescriptors) {
-			try {
-				for (FileDescriptor next : theFileDescriptors) {
-					if (next.getFilename().toLowerCase().endsWith(".zip")) {
-						ourLog.info("Uncompressing {} into temporary files", next.getFilename());
-						try (InputStream inputStream = next.getInputStream()) {
-							ZipInputStream zis = new ZipInputStream(new BufferedInputStream(inputStream));
-							for (ZipEntry nextEntry; (nextEntry = zis.getNextEntry()) != null; ) {
-								BOMInputStream fis = new BOMInputStream(zis);
-								File nextTemporaryFile = File.createTempFile("hapifhir", ".tmp");
-								nextTemporaryFile.deleteOnExit();
-								FileOutputStream fos = new FileOutputStream(nextTemporaryFile, false);
-								IOUtils.copy(fis, fos);
-								String nextEntryFileName = nextEntry.getName();
-								myUncompressedFileDescriptors.add(new FileDescriptor() {
-									@Override
-									public String getFilename() {
-										return nextEntryFileName;
-									}
-
-									@Override
-									public InputStream getInputStream() {
-										try {
-											return new FileInputStream(nextTemporaryFile);
-										} catch (FileNotFoundException e) {
-											throw new InternalErrorException(e);
-										}
-									}
-								});
-								myTemporaryFiles.add(nextTemporaryFile);
-							}
-						}
-					} else {
-						myUncompressedFileDescriptors.add(next);
-					}
-
-				}
-			} catch (Exception e) {
-				close();
-				throw new InternalErrorException(e);
-			}
-		}
-
-		boolean hasFile(String theFilename) {
-			return myUncompressedFileDescriptors
-				.stream()
-				.map(t -> t.getFilename().replaceAll(".*[\\\\/]", "")) // Strip the path from the filename
-				.anyMatch(t -> t.equals(theFilename));
-		}
-
-		@Override
-		public void close() {
-			for (File next : myTemporaryFiles) {
-				FileUtils.deleteQuietly(next);
-			}
-		}
-
-		List<IHapiTerminologyLoaderSvc.FileDescriptor> getUncompressedFileDescriptors() {
-			return myUncompressedFileDescriptors;
-		}
-
-		private List<String> notFound(List<String> theExpectedFilenameFragments) {
-			Set<String> foundFragments = new HashSet<>();
-			for (String nextExpected : theExpectedFilenameFragments) {
-				for (FileDescriptor next : myUncompressedFileDescriptors) {
-					if (next.getFilename().contains(nextExpected)) {
-						foundFragments.add(nextExpected);
-						break;
-					}
-				}
-			}
-
-			ArrayList<String> notFoundFileNameFragments = new ArrayList<>(theExpectedFilenameFragments);
-			notFoundFileNameFragments.removeAll(foundFragments);
-			return notFoundFileNameFragments;
-		}
-
-		private void verifyMandatoryFilesExist(List<String> theExpectedFilenameFragments) {
-			List<String> notFound = notFound(theExpectedFilenameFragments);
-			if (!notFound.isEmpty()) {
-				throw new UnprocessableEntityException("Could not find the following mandatory files in input: " + notFound);
-			}
-		}
-
-		private void verifyOptionalFilesExist(List<String> theExpectedFilenameFragments) {
-			List<String> notFound = notFound(theExpectedFilenameFragments);
-			if (!notFound.isEmpty()) {
-				ourLog.warn("Could not find the following optional files: " + notFound);
-			}
-		}
-
-
-	}
-
-	@Nonnull
-	public static Map<String, TermConcept> processCustomTerminologyFiles(LoadedFileDescriptors theDescriptors, TermCodeSystemVersion theCsv) {
-		IRecordHandler handler;// Concept File
-		final Map<String, TermConcept> code2concept = new HashMap<>();
-		handler = new ConceptHandler(code2concept, theCsv);
-		iterateOverZipFile(theDescriptors, CUSTOM_CONCEPTS_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
-
-		// Hierarchy
-		if (theDescriptors.hasFile(CUSTOM_HIERARCHY_FILE)) {
-			handler = new HierarchyHandler(code2concept);
-			iterateOverZipFile(theDescriptors, CUSTOM_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
-		}
-
-		// Add root concepts to CodeSystemVersion
-		for (TermConcept nextConcept : code2concept.values()) {
-			if (nextConcept.getParents().isEmpty()) {
-				theCsv.getConcepts().add(nextConcept);
-			}
-		}
-		return code2concept;
-	}
-
-	private static void iterateOverZipFile(LoadedFileDescriptors theDescriptors, String theFileNamePart, IRecordHandler theHandler, char theDelimiter, QuoteMode theQuoteMode, boolean theIsPartialFilename) {
+	public static void iterateOverZipFile(LoadedFileDescriptors theDescriptors, String theFileNamePart, IRecordHandler theHandler, char theDelimiter, QuoteMode theQuoteMode, boolean theIsPartialFilename) {
 
 		boolean foundMatch = false;
 		for (FileDescriptor nextZipBytes : theDescriptors.getUncompressedFileDescriptors()) {
@@ -748,9 +642,12 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 	}
 
 	@Nonnull
-	public static CSVParser newCsvRecords(char theDelimiter, QuoteMode theQuoteMode, Reader theReader) throws IOException {
+	private static CSVParser newCsvRecords(char theDelimiter, QuoteMode theQuoteMode, Reader theReader) throws IOException {
 		CSVParser parsed;
-		CSVFormat format = CSVFormat.newFormat(theDelimiter).withFirstRecordAsHeader();
+		CSVFormat format = CSVFormat
+			.newFormat(theDelimiter)
+			.withFirstRecordAsHeader()
+			.withTrim();
 		if (theQuoteMode != null) {
 			format = format.withQuote('"').withQuoteMode(theQuoteMode);
 		}
@@ -769,12 +666,11 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		return retVal;
 	}
 
-	public static TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
+	public static TermConcept getOrCreateConcept(Map<String, TermConcept> id2concept, String id) {
 		TermConcept concept = id2concept.get(id);
 		if (concept == null) {
 			concept = new TermConcept();
 			id2concept.put(id, concept);
-			concept.setCodeSystemVersion(codeSystemVersion);
 		}
 		return concept;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu2.java

@@ -25,9 +25,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.CodeSystem;
-import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.springframework.beans.factory.annotation.Autowired;
 
@@ -36,7 +34,7 @@ import java.util.List;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
-public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
+public class TermReadSvcDstu2 extends BaseTermReadSvcImpl {
 
 	@Autowired
 	private IValidationSupport myValidationSupport;
@@ -65,22 +63,7 @@ public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
 	}
 
 	@Override
-	protected IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource) {
-		throw new UnsupportedOperationException();
-	}
-
-	@Override
-	protected void createOrUpdateConceptMap(ConceptMap theNextConceptMap) {
-		throw new UnsupportedOperationException();
-	}
-
-	@Override
-	protected void createOrUpdateValueSet(ValueSet theValueSet) {
-		throw new UnsupportedOperationException();
-	}
-
-	@Override
-	protected CodeSystem getCodeSystemFromContext(String theSystem) {
+	public CodeSystem getCodeSystemFromContext(String theSystem) {
 		return null;
 	}
 

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

@@ -2,13 +2,13 @@ package ca.uhn.fhir.jpa.term;
 
 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.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.CoverageIgnore;
-import ca.uhn.fhir.util.UrlUtil;
 import ca.uhn.fhir.util.ValidateUtil;
 import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
@@ -19,7 +19,6 @@ import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
@@ -32,7 +31,6 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /*
@@ -55,27 +53,22 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * #L%
  */
 
-public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implements IValidationSupport, IHapiTerminologySvcDstu3 {
+public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidationSupport, ITermReadSvcDstu3 {
 
 	@Autowired
 	@Qualifier("myValueSetDaoDstu3")
 	private IFhirResourceDao<ValueSet> myValueSetResourceDao;
 	@Autowired
-	@Qualifier("myConceptMapDaoDstu3")
-	private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
-	@Autowired
-	private IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemResourceDao;
-	@Autowired
 	private IValidationSupport myValidationSupport;
 	@Autowired
-	private IHapiTerminologySvc myTerminologySvc;
+	private ITermReadSvc myTerminologySvc;
 	@Autowired
 	private PlatformTransactionManager myTransactionManager;
 
 	/**
 	 * Constructor
 	 */
-	public HapiTerminologySvcDstu3() {
+	public TermReadSvcDstu3() {
 		super();
 	}
 
@@ -102,55 +95,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
 		return false;
 	}
 
-	@Override
-	protected IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
-		CodeSystem resourceToStore;
-		try {
-			resourceToStore = VersionConvertor_30_40.convertCodeSystem(theCodeSystemResource);
-		} catch (FHIRException e) {
-			throw new InternalErrorException(e);
-		}
-		validateCodeSystemForStorage(theCodeSystemResource);
-		if (isBlank(resourceToStore.getIdElement().getIdPart())) {
-			String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
-			return myCodeSystemResourceDao.update(resourceToStore, matchUrl).getId();
-		} else {
-			return myCodeSystemResourceDao.update(resourceToStore).getId();
-		}
-	}
-
-	@Override
-	protected void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
-		ConceptMap resourceToStore;
-		try {
-			resourceToStore = VersionConvertor_30_40.convertConceptMap(theConceptMap);
-		} catch (FHIRException e) {
-			throw new InternalErrorException(e);
-		}
-		if (isBlank(resourceToStore.getIdElement().getIdPart())) {
-			String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
-			myConceptMapResourceDao.update(resourceToStore, matchUrl);
-		} else {
-			myConceptMapResourceDao.update(resourceToStore);
-		}
-	}
-
-	@Override
-	protected void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
-		ValueSet valueSetDstu3;
-		try {
-			valueSetDstu3 = VersionConvertor_30_40.convertValueSet(theValueSet);
-		} catch (FHIRException e) {
-			throw new InternalErrorException(e);
-		}
-
-		if (isBlank(valueSetDstu3.getIdElement().getIdPart())) {
-			String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
-			myValueSetResourceDao.update(valueSetDstu3, matchUrl);
-		} else {
-			myValueSetResourceDao.update(valueSetDstu3);
-		}
-	}
 
 	@Override
 	public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
@@ -303,7 +247,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
 	}
 
 	@Override
-	protected org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
+	public org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
 		CodeSystem codeSystem = myValidationSupport.fetchCodeSystem(myContext, theSystem);
 		try {
 			return VersionConvertor_30_40.convertCodeSystem(codeSystem);

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

@@ -5,11 +5,10 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
 import ca.uhn.fhir.util.CoverageIgnore;
-import ca.uhn.fhir.util.UrlUtil;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
@@ -27,7 +26,6 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /*
@@ -50,14 +48,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * #L%
  */
 
-public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements IHapiTerminologySvcR4 {
+public class TermReadSvcR4 extends BaseTermReadSvcImpl implements ITermReadSvcR4 {
 
-	@Autowired
-	@Qualifier("myConceptMapDaoR4")
-	private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
-	@Autowired
-	@Qualifier("myCodeSystemDaoR4")
-	private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
 	@Autowired
 	@Qualifier("myValueSetDaoR4")
 	private IFhirResourceDao<ValueSet> myValueSetResourceDao;
@@ -89,36 +81,6 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
 		return false;
 	}
 
-	@Override
-	protected IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
-		validateCodeSystemForStorage(theCodeSystemResource);
-		if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
-			String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
-			return myCodeSystemResourceDao.update(theCodeSystemResource, matchUrl).getId();
-		} else {
-			return myCodeSystemResourceDao.update(theCodeSystemResource).getId();
-		}
-	}
-
-	@Override
-	protected void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
-		if (isBlank(theConceptMap.getIdElement().getIdPart())) {
-			String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
-			myConceptMapResourceDao.update(theConceptMap, matchUrl);
-		} else {
-			myConceptMapResourceDao.update(theConceptMap);
-		}
-	}
-
-	@Override
-	protected void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
-		if (isBlank(theValueSet.getIdElement().getIdPart())) {
-			String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
-			myValueSetResourceDao.update(theValueSet, matchUrl);
-		} else {
-			myValueSetResourceDao.update(theValueSet);
-		}
-	}
 
 	@Override
 	public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
@@ -233,7 +195,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
 	}
 
 	@Override
-	protected CodeSystem getCodeSystemFromContext(String theSystem) {
+	public CodeSystem getCodeSystemFromContext(String theSystem) {
 		return myValidationSupport.fetchCodeSystem(myContext, theSystem);
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java

@@ -5,12 +5,11 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
 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.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.r5.model.*;
 import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
@@ -28,7 +27,6 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /*
@@ -51,14 +49,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * #L%
  */
 
-public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements IValidationSupport, IHapiTerminologySvcR5 {
+public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSupport, ITermReadSvcR5 {
 
-	@Autowired
-	@Qualifier("myConceptMapDaoR5")
-	private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
-	@Autowired
-	@Qualifier("myCodeSystemDaoR5")
-	private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
 	@Autowired
 	@Qualifier("myValueSetDaoR5")
 	private IFhirResourceDao<ValueSet> myValueSetResourceDao;
@@ -90,44 +82,6 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
 		return false;
 	}
 
-	@Override
-	protected IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
-		validateCodeSystemForStorage(theCodeSystemResource);
-
-		CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(theCodeSystemResource);
-		if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
-			String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
-			return myCodeSystemResourceDao.update(codeSystemR4, matchUrl).getId();
-		} else {
-			return myCodeSystemResourceDao.update(codeSystemR4).getId();
-		}
-	}
-
-	@Override
-	protected void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
-
-		ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(theConceptMap);
-
-		if (isBlank(theConceptMap.getIdElement().getIdPart())) {
-			String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
-			myConceptMapResourceDao.update(conceptMapR4, matchUrl);
-		} else {
-			myConceptMapResourceDao.update(conceptMapR4);
-		}
-	}
-
-	@Override
-	protected void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
-
-		ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(theValueSet);
-
-		if (isBlank(theValueSet.getIdElement().getIdPart())) {
-			String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
-			myValueSetResourceDao.update(valueSetR4, matchUrl);
-		} else {
-			myValueSetResourceDao.update(valueSetR4);
-		}
-	}
 
 	@Override
 	public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
@@ -244,7 +198,7 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
 	}
 
 	@Override
-	protected org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
+	public org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
 		CodeSystem codeSystemR5 = myValidationSupport.fetchCodeSystem(myContext, theSystem);
 		return org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(codeSystemR5);
 	}

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

@@ -0,0 +1,169 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
+import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.model.sched.FireAtIntervalJob;
+import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
+import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
+import ca.uhn.fhir.util.StopWatch;
+import com.google.common.annotations.VisibleForTesting;
+import com.google.common.collect.ArrayListMultimap;
+import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.time.DateUtils;
+import org.quartz.JobExecutionContext;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+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.TransactionDefinition;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import javax.annotation.PostConstruct;
+import java.util.Collection;
+import java.util.List;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
+public class TermReindexingSvcImpl implements ITermReindexingSvc {
+	private static final Logger ourLog = LoggerFactory.getLogger(TermReindexingSvcImpl.class);
+	private static final long SCHEDULE_INTERVAL_MILLIS = DateUtils.MILLIS_PER_MINUTE;
+	private static boolean ourForceSaveDeferredAlwaysForUnitTest;
+	@Autowired
+	protected ITermConceptDao myConceptDao;
+	private ArrayListMultimap<Long, Long> myChildToParentPidCache;
+	@Autowired
+	private PlatformTransactionManager myTransactionMgr;
+	@Autowired
+	private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
+	@Autowired
+	private ITermCodeSystemStorageSvc myConceptStorageSvc;
+	@Autowired
+	private ITermDeferredStorageSvc myDeferredStorageSvc;
+	@Autowired
+	private ISchedulerService mySchedulerService;
+
+	@Override
+	public void processReindexing() {
+		if (myDeferredStorageSvc.isStorageQueueEmpty() == false && !ourForceSaveDeferredAlwaysForUnitTest) {
+			return;
+		}
+
+		TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
+		tt.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
+		tt.execute(new TransactionCallbackWithoutResult() {
+			private void createParentsString(StringBuilder theParentsBuilder, Long theConceptPid) {
+				Validate.notNull(theConceptPid, "theConceptPid must not be null");
+				List<Long> parents = myChildToParentPidCache.get(theConceptPid);
+				if (parents.contains(-1L)) {
+					return;
+				} else if (parents.isEmpty()) {
+					Collection<Long> parentLinks = myConceptParentChildLinkDao.findAllWithChild(theConceptPid);
+					if (parentLinks.isEmpty()) {
+						myChildToParentPidCache.put(theConceptPid, -1L);
+						ourLog.info("Found {} parent concepts of concept {} (cache has {})", 0, theConceptPid, myChildToParentPidCache.size());
+						return;
+					} else {
+						for (Long next : parentLinks) {
+							myChildToParentPidCache.put(theConceptPid, next);
+						}
+						int parentCount = myChildToParentPidCache.get(theConceptPid).size();
+						ourLog.info("Found {} parent concepts of concept {} (cache has {})", parentCount, theConceptPid, myChildToParentPidCache.size());
+					}
+				}
+
+				for (Long nextParent : parents) {
+					if (theParentsBuilder.length() > 0) {
+						theParentsBuilder.append(' ');
+					}
+					theParentsBuilder.append(nextParent);
+					createParentsString(theParentsBuilder, nextParent);
+				}
+
+			}
+
+
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				int maxResult = 1000;
+				Page<TermConcept> concepts = myConceptDao.findResourcesRequiringReindexing(PageRequest.of(0, maxResult));
+				if (!concepts.hasContent()) {
+					if (myChildToParentPidCache != null) {
+						ourLog.info("Clearing parent concept cache");
+						myChildToParentPidCache = null;
+					}
+					return;
+				}
+
+				if (myChildToParentPidCache == null) {
+					myChildToParentPidCache = ArrayListMultimap.create();
+				}
+
+				ourLog.info("Indexing {} / {} concepts", concepts.getContent().size(), concepts.getTotalElements());
+
+				int count = 0;
+				StopWatch stopwatch = new StopWatch();
+
+				for (TermConcept nextConcept : concepts) {
+
+					if (isBlank(nextConcept.getParentPidsAsString())) {
+						StringBuilder parentsBuilder = new StringBuilder();
+						createParentsString(parentsBuilder, nextConcept.getId());
+						nextConcept.setParentPids(parentsBuilder.toString());
+					}
+
+					myConceptStorageSvc.saveConcept(nextConcept);
+					count++;
+				}
+
+				ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count));
+			}
+		});
+
+	}
+
+	@PostConstruct
+	public void registerScheduledJob() {
+		// Register scheduled job to save deferred concepts
+		// In the future it would be great to make this a cluster-aware task somehow
+		ScheduledJobDefinition jobDefinition = new ScheduledJobDefinition();
+		jobDefinition.setId(TermReindexingSvcImpl.class.getName() + "_reindex");
+		jobDefinition.setJobClass(SaveDeferredJob.class);
+		mySchedulerService.scheduleFixedDelay(SCHEDULE_INTERVAL_MILLIS, false, jobDefinition);
+	}
+
+	public static class SaveDeferredJob extends FireAtIntervalJob {
+
+		@Autowired
+		private ITermDeferredStorageSvc myTerminologySvc;
+
+		/**
+		 * Constructor
+		 */
+		public SaveDeferredJob() {
+			super(SCHEDULE_INTERVAL_MILLIS);
+		}
+
+		@Override
+		protected void doExecute(JobExecutionContext theContext) {
+			myTerminologySvc.saveDeferred();
+		}
+	}
+
+	/**
+	 * This method is present only for unit tests, do not call from client code
+	 */
+	@VisibleForTesting
+	public static void setForceSaveDeferredAlwaysForUnitTest(boolean theForceSaveDeferredAlwaysForUnitTest) {
+		ourForceSaveDeferredAlwaysForUnitTest = theForceSaveDeferredAlwaysForUnitTest;
+	}
+
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu2.java

@@ -0,0 +1,26 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+
+public class TermVersionAdapterSvcDstu2 implements ITermVersionAdapterSvc {
+
+	@Override
+	public IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource) {
+		throw new UnsupportedOperationException();
+	}
+
+	@Override
+	public void createOrUpdateConceptMap(ConceptMap theNextConceptMap) {
+		throw new UnsupportedOperationException();
+	}
+
+	@Override
+	public void createOrUpdateValueSet(ValueSet theValueSet) {
+		throw new UnsupportedOperationException();
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu3.java

@@ -0,0 +1,101 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.util.UrlUtil;
+import org.hl7.fhir.convertors.VersionConvertor_30_40;
+import org.hl7.fhir.dstu3.model.CodeSystem;
+import org.hl7.fhir.dstu3.model.ConceptMap;
+import org.hl7.fhir.dstu3.model.ValueSet;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.event.ContextRefreshedEvent;
+import org.springframework.context.event.ContextStartedEvent;
+import org.springframework.context.event.EventListener;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
+public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
+
+	private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
+	private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
+	private IFhirResourceDao<ValueSet> myValueSetResourceDao;
+
+	@Autowired
+	private ApplicationContext myAppCtx;
+
+	public TermVersionAdapterSvcDstu3() {
+		super();
+	}
+
+
+	/**
+	 * Initialize the beans that are used by this service.
+	 *
+	 * Note: There is a circular dependency here where the CodeSystem DAO
+	 * needs terminology services, and the term services need the CodeSystem DAO.
+	 * So we look these up in a refresh event instead of just autowiring them
+	 * in order to avoid weird circular reference errors.
+	 */
+	@SuppressWarnings({"unchecked", "unused"})
+	@EventListener
+	public void start(ContextRefreshedEvent theEvent) {
+		myCodeSystemResourceDao = (IFhirResourceDao<CodeSystem>) myAppCtx.getBean("myCodeSystemDaoDstu3");
+		myValueSetResourceDao = (IFhirResourceDao<ValueSet>) myAppCtx.getBean("myValueSetDaoDstu3");
+		myConceptMapResourceDao = (IFhirResourceDao<ConceptMap>) myAppCtx.getBean("myConceptMapDaoDstu3");
+	}
+
+		@Override
+	public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
+		CodeSystem resourceToStore;
+		try {
+			resourceToStore = VersionConvertor_30_40.convertCodeSystem(theCodeSystemResource);
+		} catch (FHIRException e) {
+			throw new InternalErrorException(e);
+		}
+		validateCodeSystemForStorage(theCodeSystemResource);
+		if (isBlank(resourceToStore.getIdElement().getIdPart())) {
+			String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
+			return myCodeSystemResourceDao.update(resourceToStore, matchUrl).getId();
+		} else {
+			return myCodeSystemResourceDao.update(resourceToStore).getId();
+		}
+	}
+
+	@Override
+	public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
+		ConceptMap resourceToStore;
+		try {
+			resourceToStore = VersionConvertor_30_40.convertConceptMap(theConceptMap);
+		} catch (FHIRException e) {
+			throw new InternalErrorException(e);
+		}
+		if (isBlank(resourceToStore.getIdElement().getIdPart())) {
+			String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
+			myConceptMapResourceDao.update(resourceToStore, matchUrl);
+		} else {
+			myConceptMapResourceDao.update(resourceToStore);
+		}
+	}
+
+	@Override
+	public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
+		ValueSet valueSetDstu3;
+		try {
+			valueSetDstu3 = VersionConvertor_30_40.convertValueSet(theValueSet);
+		} catch (FHIRException e) {
+			throw new InternalErrorException(e);
+		}
+
+		if (isBlank(valueSetDstu3.getIdElement().getIdPart())) {
+			String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
+			myValueSetResourceDao.update(valueSetDstu3, matchUrl);
+		} else {
+			myValueSetResourceDao.update(valueSetDstu3);
+		}
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR4.java

@@ -0,0 +1,75 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.util.UrlUtil;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.event.ContextRefreshedEvent;
+import org.springframework.context.event.EventListener;
+
+import javax.annotation.PostConstruct;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
+public class TermVersionAdapterSvcR4 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
+	private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
+	private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
+	private IFhirResourceDao<ValueSet> myValueSetResourceDao;
+
+	@Autowired
+	private ApplicationContext myAppCtx;
+
+	/**
+	 * Initialize the beans that are used by this service.
+	 *
+	 * Note: There is a circular dependency here where the CodeSystem DAO
+	 * needs terminology services, and the term services need the CodeSystem DAO.
+	 * So we look these up in a refresh event instead of just autowiring them
+	 * in order to avoid weird circular reference errors.
+	 */
+	@SuppressWarnings({"unchecked", "unused"})
+	@EventListener
+	public void start(ContextRefreshedEvent theEvent) {
+		myCodeSystemResourceDao = (IFhirResourceDao<CodeSystem>) myAppCtx.getBean("myCodeSystemDaoR4");
+		myValueSetResourceDao = (IFhirResourceDao<ValueSet>) myAppCtx.getBean("myValueSetDaoR4");
+		myConceptMapResourceDao = (IFhirResourceDao<ConceptMap>) myAppCtx.getBean("myConceptMapDaoR4");
+	}
+
+	@Override
+	public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
+		validateCodeSystemForStorage(theCodeSystemResource);
+		if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
+			String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
+			return myCodeSystemResourceDao.update(theCodeSystemResource, matchUrl).getId();
+		} else {
+			return myCodeSystemResourceDao.update(theCodeSystemResource).getId();
+		}
+	}
+
+	@Override
+	public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
+		if (isBlank(theConceptMap.getIdElement().getIdPart())) {
+			String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
+			myConceptMapResourceDao.update(theConceptMap, matchUrl);
+		} else {
+			myConceptMapResourceDao.update(theConceptMap);
+		}
+	}
+
+	@Override
+	public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
+		if (isBlank(theValueSet.getIdElement().getIdPart())) {
+			String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
+			myValueSetResourceDao.update(theValueSet, matchUrl);
+		} else {
+			myValueSetResourceDao.update(theValueSet);
+		}
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR5.java

@@ -0,0 +1,80 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.util.UrlUtil;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r5.model.CodeSystem;
+import org.hl7.fhir.r5.model.ConceptMap;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.event.ContextRefreshedEvent;
+import org.springframework.context.event.EventListener;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
+public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
+	private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
+	private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
+	private IFhirResourceDao<ValueSet> myValueSetResourceDao;
+
+	@Autowired
+	private ApplicationContext myAppCtx;
+
+	/**
+	 * Initialize the beans that are used by this service.
+	 *
+	 * Note: There is a circular dependency here where the CodeSystem DAO
+	 * needs terminology services, and the term services need the CodeSystem DAO.
+	 * So we look these up in a refresh event instead of just autowiring them
+	 * in order to avoid weird circular reference errors.
+	 */
+	@SuppressWarnings({"unchecked", "unused"})
+	@EventListener
+	public void start(ContextRefreshedEvent theEvent) {
+		myCodeSystemResourceDao = (IFhirResourceDao<CodeSystem>) myAppCtx.getBean("myCodeSystemDaoR5");
+		myValueSetResourceDao = (IFhirResourceDao<ValueSet>) myAppCtx.getBean("myValueSetDaoR5");
+		myConceptMapResourceDao = (IFhirResourceDao<ConceptMap>) myAppCtx.getBean("myConceptMapDaoR5");
+	}
+
+	@Override
+	public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
+		validateCodeSystemForStorage(theCodeSystemResource);
+
+		CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(theCodeSystemResource);
+		if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
+			String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
+			return myCodeSystemResourceDao.update(codeSystemR4, matchUrl).getId();
+		} else {
+			return myCodeSystemResourceDao.update(codeSystemR4).getId();
+		}
+	}
+
+	@Override
+	public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
+
+		ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(theConceptMap);
+
+		if (isBlank(theConceptMap.getIdElement().getIdPart())) {
+			String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
+			myConceptMapResourceDao.update(conceptMapR4, matchUrl);
+		} else {
+			myConceptMapResourceDao.update(conceptMapR4);
+		}
+	}
+
+	@Override
+	public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
+
+		ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(theValueSet);
+
+		if (isBlank(theValueSet.getIdElement().getIdPart())) {
+			String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
+			myValueSetResourceDao.update(valueSetR4, matchUrl);
+		} else {
+			myValueSetResourceDao.update(valueSetR4);
+		}
+	}
+
+}

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

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.jpa.term;
+
+import org.hl7.fhir.instance.model.api.IIdType;
+
+public class UploadStatistics {
+	private final IIdType myTarget;
+	private int myUpdatedConceptCount;
+
+	public UploadStatistics(IIdType theTarget) {
+		this(0, theTarget);
+	}
+
+	public UploadStatistics(int theUpdatedConceptCount, IIdType theTarget) {
+		myUpdatedConceptCount = theUpdatedConceptCount;
+		myTarget = theTarget;
+	}
+
+	public void incrementUpdatedConceptCount() {
+		myUpdatedConceptCount++;
+	}
+
+	public int getUpdatedConceptCount() {
+		return myUpdatedConceptCount;
+	}
+
+	public IIdType getTarget() {
+		return myTarget;
+	}
+
+}

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

@@ -0,0 +1,39 @@
+package ca.uhn.fhir.jpa.term.api;
+
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.term.UploadStatistics;
+import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ValueSet;
+
+import java.util.List;
+
+/**
+ * This service handles writes to the CodeSystem/Concept tables within the terminology services
+ */
+public interface ITermCodeSystemStorageSvc {
+
+	void deleteCodeSystem(TermCodeSystem theCodeSystem);
+
+	void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable);
+
+	/**
+	 * @return Returns the ID of the created/updated code system
+	 */
+	IIdType storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets, List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps);
+
+	void storeNewCodeSystemVersionIfNeeded(CodeSystem theCodeSystem, ResourceTable theResourceEntity);
+
+	UploadStatistics applyDeltaCodeSystemsAdd(String theSystem, CustomTerminologySet theAdditions);
+
+	UploadStatistics applyDeltaCodeSystemsRemove(String theSystem, CustomTerminologySet theRemovals);
+
+	int saveConcept(TermConcept theNextConcept);
+
+	Long getValueSetResourcePid(IIdType theIdElement);
+}

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

@@ -0,0 +1,33 @@
+package ca.uhn.fhir.jpa.term.api;
+
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+
+import java.util.List;
+
+/**
+ * This service handles processing "deferred" concept writes, meaning concepts that have neen
+ * queued for storage because there are too many of them to handle in a single transaction.
+ */
+public interface ITermDeferredStorageSvc {
+
+	void saveDeferred();
+
+	boolean isStorageQueueEmpty();
+
+	/**
+	 * This is mostly for unit tests - we can disable processing of deferred concepts
+	 * by changing this flag
+	 */
+	void setProcessDeferred(boolean theProcessDeferred);
+
+	void addConceptToStorageQueue(TermConcept theConcept);
+
+	void addConceptLinkToStorageQueue(TermConceptParentChildLink theConceptLink);
+
+	void addConceptMapsToStorageQueue(List<ConceptMap> theConceptMaps);
+
+	void addValueSetsToStorageQueue(List<ValueSet> theValueSets);
+}

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

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.term;
+package ca.uhn.fhir.jpa.term.api;
 
 /*
  * #%L
@@ -20,13 +20,18 @@ package ca.uhn.fhir.jpa.term;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.term.UploadStatistics;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
-import org.hl7.fhir.instance.model.api.IIdType;
 
+import java.io.ByteArrayInputStream;
 import java.io.InputStream;
 import java.util.List;
 
-public interface IHapiTerminologyLoaderSvc {
+/**
+ * This service handles bulk loading concepts into the terminology service concept tables
+ * using any of several predefined input formats
+ */
+public interface ITermLoaderSvc {
 
 	String IMGTHLA_URI = "http://www.ebi.ac.uk/ipd/imgt/hla";
 	String LOINC_URI = "http://loinc.org";
@@ -39,9 +44,15 @@ public interface IHapiTerminologyLoaderSvc {
 
 	UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
 
-	// FIXME: remove the default implementation before 4.0.0
+	// FIXME: remove the default implementation before 4.1.0
 	default UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) { return null; };
 
+	// FIXME: remove the default implementation before 4.1.0
+	default UploadStatistics loadDeltaAdd(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) { return null; };
+
+	// FIXME: remove the default implementation before 4.1.0
+	default UploadStatistics loadDeltaRemove(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) { return null; };
+
 	interface FileDescriptor {
 
 		String getFilename();
@@ -50,23 +61,25 @@ public interface IHapiTerminologyLoaderSvc {
 
 	}
 
-	class UploadStatistics {
-		private final int myConceptCount;
-		private final IIdType myTarget;
+	class ByteArrayFileDescriptor implements FileDescriptor {
 
-		public UploadStatistics(int theConceptCount, IIdType theTarget) {
-			myConceptCount = theConceptCount;
-			myTarget = theTarget;
+		private final String myNextUrl;
+		private final byte[] myNextData;
+
+		public ByteArrayFileDescriptor(String theNextUrl, byte[] theNextData) {
+			myNextUrl = theNextUrl;
+			myNextData = theNextData;
 		}
 
-		public int getConceptCount() {
-			return myConceptCount;
+		@Override
+		public String getFilename() {
+			return myNextUrl;
 		}
 
-		public IIdType getTarget() {
-			return myTarget;
+		@Override
+		public InputStream getInputStream() {
+			return new ByteArrayInputStream(myNextData);
 		}
-
 	}
 
 }

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

@@ -1,20 +1,25 @@
-package ca.uhn.fhir.jpa.term;
+package ca.uhn.fhir.jpa.term.api;
 
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
-import ca.uhn.fhir.jpa.entity.*;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
+import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import org.hl7.fhir.instance.model.api.*;
+import ca.uhn.fhir.jpa.term.IValueSetConceptAccumulator;
+import ca.uhn.fhir.jpa.term.TranslationRequest;
+import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
+import org.hl7.fhir.instance.model.api.IBaseDatatype;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ValueSet;
 
-import javax.annotation.Nullable;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
-import java.util.concurrent.atomic.AtomicInteger;
 
 /*
  * #%L
@@ -36,9 +41,17 @@ import java.util.concurrent.atomic.AtomicInteger;
  * #L%
  */
 
-public interface IHapiTerminologySvc {
-
-	void deleteCodeSystem(TermCodeSystem theCodeSystem);
+/**
+ * This interface is the "read" interface for the terminology service. It handles things like
+ * lookups, code validations, expansions, concept mappings, etc.
+ * <p>
+ * It is intended to only handle read operations, leaving various write operations to
+ * other services within the terminology service APIs.
+ * (Note that at present, a few write operations remain here- they should be moved but haven't
+ * been moved yet)
+ * </p>
+ */
+public interface ITermReadSvc {
 
 	ValueSet expandValueSet(ValueSet theValueSetToExpand);
 
@@ -74,22 +87,7 @@ public interface IHapiTerminologySvc {
 
 	List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode);
 
-	void saveDeferred();
-
-	/**
-	 * This is mostly for unit tests - we can disable processing of deferred concepts
-	 * by changing this flag
-	 */
-	void setProcessDeferred(boolean theProcessDeferred);
-
-	void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable);
-
-	/**
-	 * @return Returns the ID of the created/updated code system
-	 */
-	IIdType storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<org.hl7.fhir.r4.model.ValueSet> theValueSets, List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps);
-
-	void storeNewCodeSystemVersionIfNeeded(CodeSystem theCodeSystem, ResourceTable theResourceEntity);
+	CodeSystem getCodeSystemFromContext(String theSystem);
 
 	void deleteConceptMapAndChildren(ResourceTable theResourceTable);
 
@@ -107,10 +105,6 @@ public interface IHapiTerminologySvc {
 
 	IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB);
 
-	AtomicInteger applyDeltaCodesystemsAdd(String theSystem, @Nullable String theParent, CodeSystem theValue);
-
-	AtomicInteger applyDeltaCodesystemsRemove(String theSystem, CodeSystem theDelta);
-
 	void preExpandDeferredValueSetsToTerminologyTables();
 
 	/**
@@ -124,4 +118,6 @@ public interface IHapiTerminologySvc {
 	 * Version independent
 	 */
 	boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet);
+
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvcDstu3.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.term;
+package ca.uhn.fhir.jpa.term.api;
 
 /*
  * #%L
@@ -22,6 +22,6 @@ package ca.uhn.fhir.jpa.term;
 
 import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
 
-public interface IHapiTerminologySvcDstu3 extends IHapiTerminologySvc, IValidationSupport {
+public interface ITermReadSvcDstu3 extends ITermReadSvc, IValidationSupport {
 	// nothing
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvcR4.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.term;
+package ca.uhn.fhir.jpa.term.api;
 
 /*-
  * #%L
@@ -22,6 +22,6 @@ package ca.uhn.fhir.jpa.term;
 
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
 
-public interface IHapiTerminologySvcR4 extends IHapiTerminologySvc, IValidationSupport {
+public interface ITermReadSvcR4 extends ITermReadSvc, IValidationSupport {
 	// nothing
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvcR5.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.term;
+package ca.uhn.fhir.jpa.term.api;
 
 /*-
  * #%L
@@ -22,6 +22,6 @@ package ca.uhn.fhir.jpa.term;
 
 import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
 
-public interface IHapiTerminologySvcR5 extends IHapiTerminologySvc, IValidationSupport {
+public interface ITermReadSvcR5 extends ITermReadSvc, IValidationSupport {
 	// nothing
 }

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

@@ -0,0 +1,7 @@
+package ca.uhn.fhir.jpa.term.api;
+
+public interface ITermReindexingSvc {
+
+	void processReindexing();
+
+}

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

@@ -0,0 +1,21 @@
+package ca.uhn.fhir.jpa.term.api;
+
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+
+/**
+ * This interface is used to handle differences in versions of FHIR for the terminology
+ * server. It is really just an internal interface used by the
+ * {@link ITermReadSvc terminology read service}.
+ */
+public interface ITermVersionAdapterSvc {
+
+	IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource);
+
+	void createOrUpdateConceptMap(ConceptMap theNextConceptMap);
+
+	void createOrUpdateValueSet(ValueSet theValueSet);
+
+}

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

@@ -20,10 +20,9 @@ package ca.uhn.fhir.jpa.term.custom;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
-import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
+import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
 import org.apache.commons.csv.CSVRecord;
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;
@@ -40,11 +39,9 @@ public class ConceptHandler implements IRecordHandler {
 	public static final String CODE = "CODE";
 	public static final String DISPLAY = "DISPLAY";
 	private final Map<String, TermConcept> myCode2Concept;
-	private final TermCodeSystemVersion myCodeSystemVersion;
 
-	public ConceptHandler(Map<String, TermConcept> theCode2concept, TermCodeSystemVersion theCodeSystemVersion) {
+	public ConceptHandler(Map<String, TermConcept> theCode2concept) {
 		myCode2Concept = theCode2concept;
-		myCodeSystemVersion = theCodeSystemVersion;
 	}
 
 	@Override
@@ -55,7 +52,7 @@ public class ConceptHandler implements IRecordHandler {
 
 			Validate.isTrue(!myCode2Concept.containsKey(code), "The code %s has appeared more than once", code);
 
-			TermConcept concept = TerminologyLoaderSvcImpl.getOrCreateConcept(myCodeSystemVersion, myCode2Concept, code);
+			TermConcept concept = TermLoaderSvcImpl.getOrCreateConcept(myCode2Concept, code);
 			concept.setCode(code);
 			concept.setDisplay(display);
 

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

@@ -0,0 +1,158 @@
+package ca.uhn.fhir.jpa.term.custom;
+
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.term.IRecordHandler;
+import ca.uhn.fhir.jpa.term.LoadedFileDescriptors;
+import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import com.google.common.collect.ArrayListMultimap;
+import com.google.common.collect.ListMultimap;
+import com.google.common.collect.Multimaps;
+import org.apache.commons.csv.QuoteMode;
+import org.apache.commons.lang3.Validate;
+
+import javax.annotation.Nonnull;
+import java.util.*;
+
+public class CustomTerminologySet {
+
+	private final int mySize;
+	private final ListMultimap<TermConcept, String> myUnanchoredChildConceptsToParentCodes;
+	private final List<TermConcept> myRootConcepts;
+
+	/**
+	 * Constructor for an empty object
+	 */
+	public CustomTerminologySet() {
+		this(0, ArrayListMultimap.create(), new ArrayList<>());
+	}
+
+	/**
+	 * Constructor
+	 */
+	private CustomTerminologySet(int theSize, ListMultimap<TermConcept, String> theUnanchoredChildConceptsToParentCodes, Collection<TermConcept> theRootConcepts) {
+		this(theSize, theUnanchoredChildConceptsToParentCodes, new ArrayList<>(theRootConcepts));
+	}
+
+	/**
+	 * Constructor
+	 */
+	private CustomTerminologySet(int theSize, ListMultimap<TermConcept, String> theUnanchoredChildConceptsToParentCodes, List<TermConcept> theRootConcepts) {
+		mySize = theSize;
+		myUnanchoredChildConceptsToParentCodes = theUnanchoredChildConceptsToParentCodes;
+		myRootConcepts = theRootConcepts;
+	}
+
+	public void addRootConcept(String theCode) {
+		addRootConcept(theCode, null);
+	}
+
+	public TermConcept addRootConcept(String theCode, String theDisplay) {
+		Validate.notBlank(theCode, "theCode must not be blank");
+		Validate.isTrue(myRootConcepts.stream().noneMatch(t -> t.getCode().equals(theCode)), "Already have code %s", theCode);
+		TermConcept retVal = new TermConcept();
+		retVal.setCode(theCode);
+		retVal.setDisplay(theDisplay);
+		myRootConcepts.add(retVal);
+		return retVal;
+	}
+
+
+	public ListMultimap<TermConcept, String> getUnanchoredChildConceptsToParentCodes() {
+		return Multimaps.unmodifiableListMultimap(myUnanchoredChildConceptsToParentCodes);
+	}
+
+	public int getSize() {
+		return mySize;
+	}
+
+	public TermCodeSystemVersion toCodeSystemVersion() {
+		TermCodeSystemVersion csv = new TermCodeSystemVersion();
+
+		for (TermConcept next : myRootConcepts) {
+			csv.getConcepts().add(next);
+		}
+
+		populateVersionToChildCodes(csv, myRootConcepts);
+
+		return csv;
+	}
+
+	private void populateVersionToChildCodes(TermCodeSystemVersion theCsv, List<TermConcept> theConcepts) {
+		for (TermConcept next : theConcepts) {
+			next.setCodeSystemVersion(theCsv);
+			populateVersionToChildCodes(theCsv, next.getChildCodes());
+		}
+	}
+
+	public List<TermConcept> getRootConcepts() {
+		return Collections.unmodifiableList(myRootConcepts);
+	}
+
+	public void addUnanchoredChildConcept(String theParentCode, String theCode, String theDisplay) {
+		Validate.notBlank(theParentCode);
+		Validate.notBlank(theCode);
+
+		TermConcept code = new TermConcept()
+			.setCode(theCode)
+			.setDisplay(theDisplay);
+		myUnanchoredChildConceptsToParentCodes.put(code, theParentCode);
+	}
+
+	public void validateNoCycleOrThrowInvalidRequest() {
+		Set<String> codes = new HashSet<>();
+		validateNoCycleOrThrowInvalidRequest(codes, getRootConcepts());
+		for (TermConcept next : myUnanchoredChildConceptsToParentCodes.keySet()) {
+			validateNoCycleOrThrowInvalidRequest(codes, next);
+		}
+	}
+
+	private void validateNoCycleOrThrowInvalidRequest(Set<String> theCodes, List<TermConcept> theRootConcepts) {
+		for (TermConcept next : theRootConcepts) {
+			validateNoCycleOrThrowInvalidRequest(theCodes, next);
+		}
+	}
+
+	private void validateNoCycleOrThrowInvalidRequest(Set<String> theCodes, TermConcept next) {
+		if (!theCodes.add(next.getCode())) {
+			throw new InvalidRequestException("Cycle detected around code " + next.getCode());
+		}
+		validateNoCycleOrThrowInvalidRequest(theCodes, next.getChildCodes());
+	}
+
+
+	@Nonnull
+	public static CustomTerminologySet load(LoadedFileDescriptors theDescriptors, boolean theFlat) {
+
+		final Map<String, TermConcept> code2concept = new LinkedHashMap<>();
+		ArrayListMultimap<TermConcept, String> unanchoredChildConceptsToParentCodes = ArrayListMultimap.create();
+
+		// Concepts
+		IRecordHandler conceptHandler = new ConceptHandler(code2concept);
+		TermLoaderSvcImpl.iterateOverZipFile(theDescriptors, TermLoaderSvcImpl.CUSTOM_CONCEPTS_FILE, conceptHandler, ',', QuoteMode.NON_NUMERIC, false);
+		if (theFlat) {
+
+			return new CustomTerminologySet(code2concept.size(), ArrayListMultimap.create(), code2concept.values());
+
+		} else {
+
+			// Hierarchy
+			if (theDescriptors.hasFile(TermLoaderSvcImpl.CUSTOM_HIERARCHY_FILE)) {
+				IRecordHandler hierarchyHandler = new HierarchyHandler(code2concept, unanchoredChildConceptsToParentCodes);
+				TermLoaderSvcImpl.iterateOverZipFile(theDescriptors, TermLoaderSvcImpl.CUSTOM_HIERARCHY_FILE, hierarchyHandler, ',', QuoteMode.NON_NUMERIC, false);
+			}
+
+			// Find root concepts
+			List<TermConcept> rootConcepts = new ArrayList<>();
+			for (TermConcept nextConcept : code2concept.values()) {
+				if (nextConcept.getParents().isEmpty()) {
+					rootConcepts.add(nextConcept);
+				}
+			}
+
+			return new CustomTerminologySet(code2concept.size(), unanchoredChildConceptsToParentCodes, rootConcepts);
+		}
+	}
+
+}

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

@@ -24,9 +24,8 @@ import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import ca.uhn.fhir.util.ValidateUtil;
+import com.google.common.collect.ArrayListMultimap;
 import org.apache.commons.csv.CSVRecord;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import java.util.Map;
 
@@ -36,9 +35,11 @@ import static org.apache.commons.lang3.StringUtils.trim;
 public class HierarchyHandler implements IRecordHandler {
 
 	private final Map<String, TermConcept> myCode2Concept;
+	private final ArrayListMultimap<TermConcept, String> myUnanchoredChildConceptsToParentCodes;
 
-	public HierarchyHandler(Map<String, TermConcept> theCode2concept) {
+	public HierarchyHandler(Map<String, TermConcept> theCode2concept, ArrayListMultimap<TermConcept, String> theunanchoredChildConceptsToParentCodes) {
 		myCode2Concept = theCode2concept;
+		myUnanchoredChildConceptsToParentCodes = theunanchoredChildConceptsToParentCodes;
 	}
 
 	@Override
@@ -47,12 +48,15 @@ public class HierarchyHandler implements IRecordHandler {
 		String child = trim(theRecord.get("CHILD"));
 		if (isNotBlank(parent) && isNotBlank(child)) {
 
-			TermConcept parentConcept = myCode2Concept.get(parent);
-			ValidateUtil.isNotNullOrThrowUnprocessableEntity(parentConcept, "Parent code %s not found", parent);
 			TermConcept childConcept = myCode2Concept.get(child);
 			ValidateUtil.isNotNullOrThrowUnprocessableEntity(childConcept, "Child code %s not found", child);
 
-			parentConcept.addChild(childConcept, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
+			TermConcept parentConcept = myCode2Concept.get(parent);
+			if (parentConcept == null) {
+				myUnanchoredChildConceptsToParentCodes.put(childConcept, parent);
+			} else {
+				parentConcept.addChild(childConcept, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
+			}
 		}
 	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincTop2000LabResultsHandler.java

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
  */
 
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import org.apache.commons.csv.CSVRecord;
 import org.hl7.fhir.r4.model.ConceptMap;
@@ -52,7 +52,7 @@ public class BaseLoincTop2000LabResultsHandler extends BaseLoincHandler implemen
 		String displayName = trim(theRecord.get("Long Common Name"));
 
 		ValueSet valueSet = getValueSet(myValueSetId, myValueSetUri, myValueSetName, null);
-		addCodeAsIncludeToValueSet(valueSet, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, displayName);
+		addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, displayName);
 	}
 
 }

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

@@ -22,7 +22,7 @@ package ca.uhn.fhir.jpa.term.loinc;
 
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import org.apache.commons.csv.CSVRecord;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ValueSet;
@@ -96,7 +96,7 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
 			vs
 				.getCompose()
 				.getIncludeFirstRep()
-				.setSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
+				.setSystem(ITermLoaderSvc.LOINC_URI)
 				.addConcept()
 				.setCode(answerString)
 				.setDisplay(displayText);

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

@@ -20,18 +20,14 @@ package ca.uhn.fhir.jpa.term.loinc;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import org.apache.commons.csv.CSVRecord;
-import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.ValueSet;
 
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;

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

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
  */
 
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.csv.CSVRecord;
@@ -58,7 +58,7 @@ public class LoincDocumentOntologyHandler extends BaseLoincHandler implements IR
 
 		// RSNA Codes VS
 		ValueSet vs = getValueSet(DOCUMENT_ONTOLOGY_CODES_VS_ID, DOCUMENT_ONTOLOGY_CODES_VS_URI, DOCUMENT_ONTOLOGY_CODES_VS_NAME, null);
-		addCodeAsIncludeToValueSet(vs, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, null);
+		addCodeAsIncludeToValueSet(vs, ITermLoaderSvc.LOINC_URI, loincNumber, null);
 
 		// Part Properties
 		String loincCodePropName;
@@ -84,7 +84,7 @@ public class LoincDocumentOntologyHandler extends BaseLoincHandler implements IR
 
 		TermConcept code = myCode2Concept.get(loincNumber);
 		if (code != null) {
-			code.addPropertyCoding(loincCodePropName, IHapiTerminologyLoaderSvc.LOINC_URI, partNumber, partName);
+			code.addPropertyCoding(loincCodePropName, ITermLoaderSvc.LOINC_URI, partNumber, partName);
 		}
 
 	}

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

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
  */
 
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import org.apache.commons.csv.CSVRecord;
 import org.hl7.fhir.r4.model.ConceptMap;
@@ -46,7 +46,7 @@ public class LoincGroupTermsFileHandler extends BaseLoincHandler implements IRec
 		String loincNumber = trim(theRecord.get("LoincNumber"));
 
 		ValueSet valueSet = getValueSet(groupId, LoincGroupFileHandler.VS_URI_PREFIX + groupId, null, null);
-		addCodeAsIncludeToValueSet(valueSet, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, null);
+		addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, null);
 	}
 
 

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

@@ -22,9 +22,9 @@ package ca.uhn.fhir.jpa.term.loinc;
 
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
-import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
+import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.csv.CSVRecord;
 import org.apache.commons.lang3.Validate;
@@ -58,7 +58,7 @@ public class LoincHandler implements IRecordHandler {
 			String longCommonName = trim(theRecord.get("LONG_COMMON_NAME"));
 			String shortName = trim(theRecord.get("SHORTNAME"));
 			String consumerName = trim(theRecord.get("CONSUMER_NAME"));
-			String display = TerminologyLoaderSvcImpl.firstNonBlank(longCommonName, shortName, consumerName);
+			String display = TermLoaderSvcImpl.firstNonBlank(longCommonName, shortName, consumerName);
 
 			TermConcept concept = new TermConcept(myCodeSystemVersion, code);
 			concept.setDisplay(display);
@@ -117,7 +117,7 @@ public class LoincHandler implements IRecordHandler {
 							}
 
 							if (isNotBlank(partNumber)) {
-								concept.addPropertyCoding(nextPropertyName, IHapiTerminologyLoaderSvc.LOINC_URI, partNumber, nextPropertyValue);
+								concept.addPropertyCoding(nextPropertyName, ITermLoaderSvc.LOINC_URI, partNumber, nextPropertyValue);
 							} else {
 								String msg = "Unable to find part code with TYPE[" + key.getPartType() + "] and NAME[" + nextPropertyValue + "] (using name " + propertyValue + ")";
 								ourLog.warn(msg);

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

@@ -23,7 +23,7 @@ package ca.uhn.fhir.jpa.term.loinc;
 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.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import org.apache.commons.csv.CSVRecord;
 
@@ -56,13 +56,13 @@ public class LoincHierarchyHandler implements IRecordHandler {
 
          parent.addPropertyCoding(
          	"child",
-				IHapiTerminologyLoaderSvc.LOINC_URI,
+				ITermLoaderSvc.LOINC_URI,
 				child.getCode(),
 				child.getDisplay());
 
          child.addPropertyCoding(
          	"parent",
-				IHapiTerminologyLoaderSvc.LOINC_URI,
+				ITermLoaderSvc.LOINC_URI,
 				parent.getCode(),
 				parent.getDisplay());
       }

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

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
  */
 
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import org.apache.commons.csv.CSVRecord;
 import org.hl7.fhir.r4.model.ConceptMap;
@@ -57,8 +57,8 @@ public class LoincIeeeMedicalDeviceCodeHandler extends BaseLoincHandler implemen
 		String ieeeDisplayName = trim(theRecord.get("IEEE_REFID"));
 
 		// LOINC Part -> IEEE 11073:10101 Mappings
-		String sourceCodeSystemUri = IHapiTerminologyLoaderSvc.LOINC_URI;
-		String targetCodeSystemUri = IHapiTerminologyLoaderSvc.IEEE_11073_10101_URI;
+		String sourceCodeSystemUri = ITermLoaderSvc.LOINC_URI;
+		String targetCodeSystemUri = ITermLoaderSvc.IEEE_11073_10101_URI;
 		addConceptMapEntry(
 			new ConceptMapping()
 				.setConceptMapId(LOINC_IEEE_CM_ID)

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

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
  */
 
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import org.apache.commons.csv.CSVRecord;
 import org.hl7.fhir.r4.model.ConceptMap;
@@ -49,7 +49,7 @@ public class LoincImagingDocumentCodeHandler extends BaseLoincHandler implements
 		String displayName = trim(theRecord.get("LONG_COMMON_NAME"));
 
 		ValueSet valueSet = getValueSet(VS_ID, VS_URI, VS_NAME,null);
-		addCodeAsIncludeToValueSet(valueSet, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, displayName);
+		addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, displayName);
 	}
 
 

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

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
  */
 
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.csv.CSVRecord;
@@ -101,7 +101,7 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
 		String loincPartMapUri;
 		String loincPartMapName;
 		switch (extCodeSystem) {
-			case IHapiTerminologyLoaderSvc.SCT_URI:
+			case ITermLoaderSvc.SCT_URI:
 				loincPartMapId = LOINC_SCT_PART_MAP_ID;
 				loincPartMapUri = LOINC_SCT_PART_MAP_URI;
 				loincPartMapName = LOINC_SCT_PART_MAP_NAME;
@@ -133,7 +133,7 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
 				.setConceptMapId(loincPartMapId)
 				.setConceptMapUri(loincPartMapUri)
 				.setConceptMapName(loincPartMapName)
-				.setSourceCodeSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
+				.setSourceCodeSystem(ITermLoaderSvc.LOINC_URI)
 				.setSourceCode(partNumber)
 				.setSourceDisplay(partName)
 				.setTargetCodeSystem(extCodeSystem)

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

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
  */
 
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.csv.CSVRecord;
@@ -98,7 +98,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
 			vs
 				.getCompose()
 				.getIncludeFirstRep()
-				.setSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
+				.setSystem(ITermLoaderSvc.LOINC_URI)
 				.addConcept()
 				.setCode(loincNumber)
 				.setDisplay(longCommonName);
@@ -167,7 +167,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
 
 		TermConcept code = myCode2Concept.get(loincNumber);
 		if (code != null) {
-			code.addPropertyCoding(loincCodePropName, IHapiTerminologyLoaderSvc.LOINC_URI, partNumber, partName);
+			code.addPropertyCoding(loincCodePropName, ITermLoaderSvc.LOINC_URI, partNumber, partName);
 		}
 
 		// LOINC Part -> Radlex RID code mappings
@@ -177,7 +177,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
 					.setConceptMapId(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_ID)
 					.setConceptMapUri(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_URI)
 					.setConceptMapName(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_NAME)
-					.setSourceCodeSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
+					.setSourceCodeSystem(ITermLoaderSvc.LOINC_URI)
 					.setSourceCode(partNumber)
 					.setSourceDisplay(partName)
 					.setTargetCodeSystem(RID_CS_URI)
@@ -194,7 +194,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
 					.setConceptMapId(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_ID)
 					.setConceptMapUri(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_URI)
 					.setConceptMapName(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_NAME)
-					.setSourceCodeSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
+					.setSourceCodeSystem(ITermLoaderSvc.LOINC_URI)
 					.setSourceCode(loincNumber)
 					.setSourceDisplay(longCommonName)
 					.setTargetCodeSystem(RPID_CS_URI)

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

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
  */
 
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import org.apache.commons.csv.CSVRecord;
 import org.hl7.fhir.r4.model.ConceptMap;
@@ -48,7 +48,7 @@ public class LoincUniversalOrderSetHandler extends BaseLoincHandler implements I
 		String orderObs = trim(theRecord.get("ORDER_OBS"));
 
 		ValueSet valueSet = getValueSet(VS_ID, VS_URI, VS_NAME, null);
-		addCodeAsIncludeToValueSet(valueSet, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, displayName);
+		addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, displayName);
 	}
 
 

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

@@ -23,7 +23,7 @@ package ca.uhn.fhir.jpa.term.snomedct;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
-import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
+import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
 import org.apache.commons.csv.CSVRecord;
 
 import java.util.Map;
@@ -56,9 +56,10 @@ public final class SctHandlerDescription implements IRecordHandler {
 
       String term = theRecord.get("term");
 
-      TermConcept concept = TerminologyLoaderSvcImpl.getOrCreateConcept(myCodeSystemVersion, myId2concept, id);
+      TermConcept concept = TermLoaderSvcImpl.getOrCreateConcept(myId2concept, id);
       concept.setCode(conceptId);
       concept.setDisplay(term);
+      concept.setCodeSystemVersion(myCodeSystemVersion);
       myCode2concept.put(conceptId, concept);
    }
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChainDstu3.java

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.validation;
  */
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvcDstu3;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
 import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
 import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
 import org.hl7.fhir.dstu3.hapi.validation.SnapshotGeneratingValidationSupport;
@@ -41,7 +41,7 @@ public class JpaValidationSupportChainDstu3 extends ValidationSupportChain {
 	@Autowired
 	private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
 	@Autowired
-	private IHapiTerminologySvcDstu3 myTerminologyService;
+	private ITermReadSvcDstu3 myTerminologyService;
 	@Autowired
 	private FhirContext myFhirContext;
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChainR4.java

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.validation;
  */
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
 import org.hl7.fhir.r4.hapi.validation.SnapshotGeneratingValidationSupport;
@@ -46,7 +46,7 @@ public class JpaValidationSupportChainR4 extends ValidationSupportChain {
 	public ca.uhn.fhir.jpa.dao.r4.IJpaValidationSupportR4 myJpaValidationSupportR4;
 	
 	@Autowired
-	private IHapiTerminologySvcR4 myTerminologyService;
+	private ITermReadSvcR4 myTerminologyService;
 	
 	public JpaValidationSupportChainR4() {
 		super();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChainR5.java

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.validation;
  */
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR5;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.hapi.ctx.DefaultProfileValidationSupport;
 import org.hl7.fhir.r5.hapi.validation.SnapshotGeneratingValidationSupport;
@@ -46,7 +46,7 @@ public class JpaValidationSupportChainR5 extends ValidationSupportChain {
 	public ca.uhn.fhir.jpa.dao.r5.IJpaValidationSupportR5 myJpaValidationSupportR5;
 	
 	@Autowired
-	private IHapiTerminologySvcR5 myTerminologyService;
+	private ITermReadSvcR5 myTerminologyService;
 	
 	public JpaValidationSupportChainR5() {
 		super();

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

@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.interceptor.executor.InterceptorService;
+import ca.uhn.fhir.jpa.BaseTest;
 import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
@@ -66,7 +67,7 @@ import static org.junit.Assert.fail;
 import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.when;
 
-public abstract class BaseJpaTest {
+public abstract class BaseJpaTest extends BaseTest {
 
 	protected static final String CM_URL = "http://example.com/my_concept_map";
 	protected static final String CS_URL = "http://example.com/my_code_system";

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java

@@ -921,7 +921,6 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 			Patient patient = new Patient();
 			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addFamily("testSearchNameParam01Fam").addGiven("testSearchNameParam01Giv");
-			ResourceMetadataKeyEnum.TITLE.put(patient, "P1TITLE");
 			id1 = myPatientDao.create(patient, mySrd).getId();
 		}
 		{

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -7,7 +7,6 @@ import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.dao.data.*;
 import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
-import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -18,8 +17,11 @@ import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
-import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
-import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
+import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
@@ -67,6 +69,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	private static JpaValidationSupportChainDstu3 ourJpaValidationSupportChainDstu3;
 	private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
 
+	@Autowired
+	protected ITermDeferredStorageSvc myTerminologyDeferredStorageSvc;
 	@Autowired
 	@Qualifier("myResourceCountsCache")
 	protected ResourceCountCache myResourceCountsCache;
@@ -243,7 +247,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Autowired
 	protected ITermCodeSystemDao myTermCodeSystemDao;
 	@Autowired
-	protected IHapiTerminologySvc myTermSvc;
+	protected ITermReadSvc myTermSvc;
 	@Autowired
 	protected PlatformTransactionManager myTransactionMgr;
 	@Autowired
@@ -262,6 +266,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	private JpaValidationSupportChainDstu3 myJpaValidationSupportChainDstu3;
 	@Autowired
 	private IBulkDataExportSvc myBulkDataExportSvc;
+	@Autowired
+	protected ITermCodeSystemStorageSvc myTermCodeSystemStorageSvc;
 
 	@After()
 	public void afterCleanupDao() {
@@ -278,12 +284,13 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 
 	@After
 	public void afterClearTerminologyCaches() {
-		BaseHapiTerminologySvcImpl baseHapiTerminologySvc = AopTestUtils.getTargetObject(myTermSvc);
+		BaseTermReadSvcImpl baseHapiTerminologySvc = AopTestUtils.getTargetObject(myTermSvc);
 		baseHapiTerminologySvc.clearTranslationCache();
 		baseHapiTerminologySvc.clearTranslationWithReverseCache();
-		baseHapiTerminologySvc.clearDeferred();
-		BaseHapiTerminologySvcImpl.clearOurLastResultsFromTranslationCache();
-		BaseHapiTerminologySvcImpl.clearOurLastResultsFromTranslationWithReverseCache();
+		BaseTermReadSvcImpl.clearOurLastResultsFromTranslationCache();
+		BaseTermReadSvcImpl.clearOurLastResultsFromTranslationWithReverseCache();
+		TermDeferredStorageSvcImpl deferredSvc = AopTestUtils.getTargetObject(myTerminologyDeferredStorageSvc);
+		deferredSvc.clearDeferred();
 	}
 
 	@After()

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java

@@ -1,34 +1,30 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
-import static org.hamcrest.Matchers.greaterThan;
-import static org.junit.Assert.*;
-
-import java.nio.charset.StandardCharsets;
-
-import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
+import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
+import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.Enumerations;
-import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Test;
 
-import ca.uhn.fhir.util.TestUtil;
+import java.nio.charset.StandardCharsets;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
 
 public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3CodeSystemTest.class);
-
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();
-		BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
+		TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
 	}
 
 	
 	@Test
 	public void testIndexContained() throws Exception {
-		BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
+		TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
 		
 		String input = IOUtils.toString(getClass().getResource("/dstu3_codesystem_complete.json"), StandardCharsets.UTF_8);
 		CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);
@@ -39,13 +35,13 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
 		int outcome= myResourceReindexingSvc.forceReindexingPass();
 		assertNotEquals(-1, outcome); // -1 means there was a failure
 		
-		myTermSvc.saveDeferred();
+		myTerminologyDeferredStorageSvc.saveDeferred();
 		
 	}
 
 	@Test
 	public void testDeleteCodeSystemComplete() {
-		BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
+		TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
 
 		// Create the code system
 		CodeSystem cs = new CodeSystem();