Merge branch 'master' into ja_20200206_multitenancy

examples/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

examples/src/main/java/example/ConverterExamples.java

@@ -1,7 +1,7 @@
 package example;
 
-import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
+import org.hl7.fhir.convertors.conv10_30.Observation10_30;
-import org.hl7.fhir.convertors.*;
+import org.hl7.fhir.convertors.conv14_30.Questionnaire14_30;
 import org.hl7.fhir.exceptions.FHIRException;
 
 public class ConverterExamples {
@@ -9,16 +9,12 @@ public class ConverterExamples {
 	@SuppressWarnings("unused")
 	public void c1020() throws FHIRException {
 	//START SNIPPET: 1020
-		// Create a converter
-		NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
-		VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
-		
 		// Create an input resource to convert
 		org.hl7.fhir.dstu2.model.Observation input = new org.hl7.fhir.dstu2.model.Observation();
 		input.setEncounter(new org.hl7.fhir.dstu2.model.Reference("Encounter/123"));
 		
 		// Convert the resource
-		org.hl7.fhir.dstu3.model.Observation output = converter.convertObservation(input);
+		org.hl7.fhir.dstu3.model.Observation output = Observation10_30.convertObservation(input);
 		String context = output.getContext().getReference();
 	//END SNIPPET: 1020
 	}
@@ -31,7 +27,7 @@ public class ConverterExamples {
 		input.setTitle("My title");
 		
 		// Convert the resource
-		org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_30.convertQuestionnaire(input);
+		org.hl7.fhir.dstu3.model.Questionnaire output = Questionnaire14_30.convertQuestionnaire(input);
 		String context = output.getTitle();
 	//END SNIPPET: 1420
 	}

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -22,8 +22,11 @@ package ca.uhn.fhir.context;
 
 import ca.uhn.fhir.util.UrlUtil;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import java.lang.reflect.Constructor;
 import java.util.*;
 
@@ -33,11 +36,11 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 	private final Class<? extends T> myImplementingClass;
 	private final String myName;
 	private final boolean myStandardType;
-	private Map<Class<?>, Constructor<T>> myConstructors = Collections.synchronizedMap(new HashMap<Class<?>, Constructor<T>>());
+	private Map<Class<?>, Constructor<T>> myConstructors = Collections.synchronizedMap(new HashMap<>());
-	private List<RuntimeChildDeclaredExtensionDefinition> myExtensions = new ArrayList<RuntimeChildDeclaredExtensionDefinition>();
+	private List<RuntimeChildDeclaredExtensionDefinition> myExtensions = new ArrayList<>();
-	private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsModifier = new ArrayList<RuntimeChildDeclaredExtensionDefinition>();
+	private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsModifier = new ArrayList<>();
-	private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsNonModifier = new ArrayList<RuntimeChildDeclaredExtensionDefinition>();
+	private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsNonModifier = new ArrayList<>();
-	private Map<String, RuntimeChildDeclaredExtensionDefinition> myUrlToExtension = new HashMap<String, RuntimeChildDeclaredExtensionDefinition>();
+	private Map<String, RuntimeChildDeclaredExtensionDefinition> myUrlToExtension = new HashMap<>();
 	private BaseRuntimeElementDefinition<?> myRootParentDefinition;
 
 	public BaseRuntimeElementDefinition(String theName, Class<? extends T> theImplementingClass, boolean theStandardType) {
@@ -56,19 +59,17 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 		myImplementingClass = theImplementingClass;
 	}
 
-	public void addExtension(RuntimeChildDeclaredExtensionDefinition theExtension) {
+	public void addExtension(@Nonnull RuntimeChildDeclaredExtensionDefinition theExtension) {
-		if (theExtension == null) {
+		Validate.notNull(theExtension, "theExtension must not be null");
-			throw new NullPointerException();
-		}
 		myExtensions.add(theExtension);
 	}
 
 	public abstract ChildTypeEnum getChildType();
 
 	@SuppressWarnings("unchecked")
-	private Constructor<T> getConstructor(Object theArgument) {
+	private Constructor<T> getConstructor(@Nullable Object theArgument) {
 
-		Class<? extends Object> argumentType;
+		Class<?> argumentType;
 		if (theArgument == null) {
 			argumentType = VOID_CLASS;
 		} else {

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

@@ -377,9 +377,8 @@ public class FhirContext {
 	 */
 	public RuntimeResourceDefinition getResourceDefinition(final Class<? extends IBaseResource> theResourceType) {
 		validateInitialized();
-		if (theResourceType == null) {
+		Validate.notNull(theResourceType, "theResourceType can not be null");
-			throw new NullPointerException("theResourceType can not be null");
+
-		}
 		if (Modifier.isAbstract(theResourceType.getModifiers())) {
 			throw new IllegalArgumentException("Can not scan abstract or interface class (resource definitions must be concrete classes): " + theResourceType.getName());
 		}

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

@@ -0,0 +1,21 @@
+package ca.uhn.fhir.rest.param;
+
+import com.google.common.collect.Sets;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class QualifierDetailsTest {
+
+	@Test
+	public void testBlacklist() {
+
+		QualifierDetails details = new QualifierDetails();
+		details.setColonQualifier(":Patient");
+		assertFalse(details.passes(null, Sets.newHashSet(":Patient")));
+		assertTrue(details.passes(null, Sets.newHashSet(":Observation")));
+
+	}
+
+
+}

hapi-fhir-bom/pom.xml

@@ -3,14 +3,14 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>ca.uhn.hapi.fhir</groupId>
     <artifactId>hapi-fhir-bom</artifactId>
-    <version>4.2.0-SNAPSHOT</version>
+    <version>4.3.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 	 <name>HAPI FHIR BOM</name>
 
     <parent>
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-deployable-pom</artifactId>
-      <version>4.2.0-SNAPSHOT</version>
+      <version>4.3.0-SNAPSHOT</version>
       <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
    </parent>
     

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -26,7 +26,6 @@ import org.apache.commons.cli.Options;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVPrinter;
 import org.apache.commons.csv.QuoteMode;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.ConceptMap;
@@ -43,6 +42,7 @@ import java.util.List;
 import java.util.concurrent.ExecutionException;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
 
 public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConceptMapCommand {
 	// TODO: Don't use qualified names for loggers in HAPI CLI.
@@ -114,7 +114,7 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
 
 	private void convertConceptMapToCsv(org.hl7.fhir.dstu3.model.ConceptMap theConceptMap) throws ExecutionException {
 		try {
-			convertConceptMapToCsv(VersionConvertor_30_40.convertConceptMap(theConceptMap));
+			convertConceptMapToCsv(convertConceptMap(theConceptMap));
 		} catch (FHIRException fe) {
 			throw new ExecutionException(fe);
 		}

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

@@ -28,7 +28,6 @@ import org.apache.commons.cli.Options;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVParser;
 import org.apache.commons.csv.CSVRecord;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
@@ -45,7 +44,10 @@ import java.util.Map;
 import java.util.Set;
 import java.util.concurrent.ExecutionException;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
 
 public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConceptMapCommand {
 	// TODO: Don't use qualified names for loggers in HAPI CLI.
@@ -154,7 +156,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 
 	private org.hl7.fhir.dstu3.model.ConceptMap convertCsvToConceptMapDstu3() throws ExecutionException {
 		try {
-			return VersionConvertor_30_40.convertConceptMap(convertCsvToConceptMapR4());
+			return convertConceptMap(convertCsvToConceptMapR4());
 		} catch (FHIRException fe) {
 			throw new ExecutionException(fe);
 		}
@@ -174,7 +176,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 					.withFirstRecordAsHeader()
 					.withIgnoreHeaderCase()
 					.withIgnoreEmptyLines()
-					.withTrim());
+					.withTrim())
 		) {
 			retVal.setUrl(conceptMapUrl);
 

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-converter/src/main/java/ca/uhn/hapi/converters/server/VersionedApiConverterInterceptor.java

@@ -31,7 +31,11 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
 import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
 import org.hl7.fhir.converter.NullVersionConverterAdvisor40;
-import org.hl7.fhir.convertors.*;
+import org.hl7.fhir.convertors.VersionConvertorAdvisor30;
+import org.hl7.fhir.convertors.VersionConvertorAdvisor40;
+import org.hl7.fhir.convertors.VersionConvertor_10_30;
+import org.hl7.fhir.convertors.VersionConvertor_10_40;
+import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -40,7 +44,9 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import java.util.StringTokenizer;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /**
  * <b>This is an experimental interceptor! Use with caution as
@@ -54,16 +60,12 @@ import static org.apache.commons.lang3.StringUtils.*;
 public class VersionedApiConverterInterceptor extends InterceptorAdapter {
 	private final FhirContext myCtxDstu2;
 	private final FhirContext myCtxDstu2Hl7Org;
-	private VersionConvertor_30_40 myVersionConvertor_30_40;
+	private final NullVersionConverterAdvisor40 advisor40;
-	private VersionConvertor_10_40 myVersionConvertor_10_40;
+	private final NullVersionConverterAdvisor30 advisor30;
-	private VersionConvertor_10_30 myVersionConvertor_10_30;
 
 	public VersionedApiConverterInterceptor() {
-		myVersionConvertor_30_40 = new VersionConvertor_30_40();
+		advisor40 = new NullVersionConverterAdvisor40();
-		VersionConvertorAdvisor40 advisor40 = new NullVersionConverterAdvisor40();
+		advisor30 = new NullVersionConverterAdvisor30();
-		myVersionConvertor_10_40 = new VersionConvertor_10_40(advisor40);
-		VersionConvertorAdvisor30 advisor30 = new NullVersionConverterAdvisor30();
-		myVersionConvertor_10_30 = new VersionConvertor_10_30(advisor30);
 
 		myCtxDstu2 = FhirContext.forDstu2();
 		myCtxDstu2Hl7Org = FhirContext.forDstu2Hl7Org();
@@ -104,17 +106,17 @@ public class VersionedApiConverterInterceptor extends InterceptorAdapter {
 		IBaseResource converted = null;
 		try {
 			if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU3) {
-				converted = myVersionConvertor_30_40.convertResource(toDstu3(responseResource), true);
+				converted = VersionConvertor_30_40.convertResource(toDstu3(responseResource), true);
 			} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.R4) {
-				converted = myVersionConvertor_30_40.convertResource(toR4(responseResource), true);
+				converted = VersionConvertor_30_40.convertResource(toR4(responseResource), true);
 			} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.R4) {
-				converted = myVersionConvertor_10_40.convertResource(toR4(responseResource));
+				converted = VersionConvertor_10_40.convertResource(toR4(responseResource), advisor40);
 			} else if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU2) {
-				converted = myVersionConvertor_10_40.convertResource(toDstu2(responseResource));
+				converted = VersionConvertor_10_40.convertResource(toDstu2(responseResource), advisor40);
 			} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.DSTU3) {
-				converted = myVersionConvertor_10_30.convertResource(toDstu3(responseResource));
+				converted = VersionConvertor_10_30.convertResource(toDstu3(responseResource), advisor30);
 			} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.DSTU2) {
-				converted = myVersionConvertor_10_30.convertResource(toDstu2(responseResource));
+				converted = VersionConvertor_10_30.convertResource(toDstu2(responseResource), advisor30);
 			}
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);

hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor50.java

@@ -27,8 +27,12 @@ import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CodeSystem;
 import org.hl7.fhir.r5.model.ValueSet;
 
+import java.util.IdentityHashMap;
+
 public class NullVersionConverterAdvisor50 implements VersionConvertorAdvisor50 {
 
+	private IdentityHashMap<ValueSet, CodeSystem> myCodeSystems = new IdentityHashMap<>();
+
 	@Override
 	public boolean ignoreEntry(Bundle.BundleEntryComponent src) {
 		return false;
@@ -56,11 +60,11 @@ public class NullVersionConverterAdvisor50 implements VersionConvertorAdvisor50
 
 	@Override
 	public void handleCodeSystem(CodeSystem tgtcs, ValueSet source) throws FHIRException {
-
+		myCodeSystems.put(source, tgtcs);
 	}
 
 	@Override
 	public CodeSystem getCodeSystem(ValueSet src) throws FHIRException {
-		return null;
+		return myCodeSystems.get(src);
 	}
 }

hapi-fhir-converter/src/test/java/org/hl7/fhir/converter/VersionConvertor_10_30Test.java

@@ -16,13 +16,10 @@ public class VersionConvertor_10_30Test {
 	@Test
 	public void testConvert() throws FHIRException {
 		
-		NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
-		VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
-		
 		org.hl7.fhir.dstu2.model.Observation input = new org.hl7.fhir.dstu2.model.Observation();
 		input.setEncounter(new org.hl7.fhir.dstu2.model.Reference("Encounter/123"));
 		
-		org.hl7.fhir.dstu3.model.Observation output = converter.convertObservation(input);
+		org.hl7.fhir.dstu3.model.Observation output = (Observation) VersionConvertor_10_30.convertResource(input);
 		String context = output.getContext().getReference();
 		
 		assertEquals("Encounter/123", context);
@@ -31,9 +28,6 @@ public class VersionConvertor_10_30Test {
 	@Test
 	public void testConvertSpecimen() throws FHIRException {
 
-		NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
-		VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
-
 		Specimen spec = new Specimen();
 		CodeableConcept cc = new CodeableConcept();
 		Coding coding = new Coding();
@@ -58,7 +52,7 @@ public class VersionConvertor_10_30Test {
 		Specimen.SpecimenContainerComponent specimenContainerComponent = new Specimen.SpecimenContainerComponent();
 		specimenContainerComponent.getExtension().add(new Extension().setUrl("some_url").setValue(new StringType("some_value")));
 		spec.setContainer(Collections.singletonList(specimenContainerComponent));
-		Resource resource = converter.convertResource(spec);
+		Resource resource = VersionConvertor_10_30.convertResource(spec);
 	}
 
 	

hapi-fhir-converter/src/test/java/org/hl7/fhir/converter/VersionConvertor_14_30Test.java

@@ -3,6 +3,7 @@ package org.hl7.fhir.converter;
 import static org.junit.Assert.assertEquals;
 
 import org.hl7.fhir.convertors.VersionConvertor_14_30;
+import org.hl7.fhir.dstu3.model.Questionnaire;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.junit.Test;
 
@@ -14,7 +15,7 @@ public class VersionConvertor_14_30Test {
 		org.hl7.fhir.dstu2016may.model.Questionnaire input = new org.hl7.fhir.dstu2016may.model.Questionnaire();
 		input.setTitle("My title");
 		
-		org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_30.convertQuestionnaire(input);
+		org.hl7.fhir.dstu3.model.Questionnaire output = (Questionnaire) VersionConvertor_14_30.convertResource(input);
 		String context = output.getTitle();
 		
 		assertEquals("My title", context);

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -73,13 +73,13 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2</artifactId>
-			<version>4.2.0-SNAPSHOT</version>
+			<version>4.3.0-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-subscription</artifactId>
-			<version>4.2.0-SNAPSHOT</version>
+			<version>4.3.0-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -96,7 +96,7 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-testpage-overlay</artifactId>
-			<version>4.2.0-SNAPSHOT</version>
+			<version>4.3.0-SNAPSHOT</version>
 			<classifier>classes</classifier>
 		</dependency>
 		<dependency>

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ConverterExamples.java

@@ -20,9 +20,8 @@ package ca.uhn.hapi.fhir.docs;
  * #L%
  */
 
-import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
+import org.hl7.fhir.convertors.conv10_30.Observation10_30;
-import org.hl7.fhir.convertors.VersionConvertor_10_30;
+import org.hl7.fhir.convertors.conv14_30.Questionnaire14_30;
-import org.hl7.fhir.convertors.VersionConvertor_14_30;
 import org.hl7.fhir.exceptions.FHIRException;
 
 public class ConverterExamples {
@@ -30,16 +29,12 @@ public class ConverterExamples {
 	@SuppressWarnings("unused")
 	public void c1020() throws FHIRException {
 	//START SNIPPET: 1020
-		// Create a converter
-		NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
-		VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
-		
 		// Create an input resource to convert
 		org.hl7.fhir.dstu2.model.Observation input = new org.hl7.fhir.dstu2.model.Observation();
 		input.setEncounter(new org.hl7.fhir.dstu2.model.Reference("Encounter/123"));
 		
 		// Convert the resource
-		org.hl7.fhir.dstu3.model.Observation output = converter.convertObservation(input);
+		org.hl7.fhir.dstu3.model.Observation output = Observation10_30.convertObservation(input);
 		String context = output.getContext().getReference();
 	//END SNIPPET: 1020
 	}
@@ -52,7 +47,7 @@ public class ConverterExamples {
 		input.setTitle("My title");
 		
 		// Convert the resource
-		org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_30.convertQuestionnaire(input);
+		org.hl7.fhir.dstu3.model.Questionnaire output = Questionnaire14_30.convertQuestionnaire(input);
 		String context = output.getTitle();
 	//END SNIPPET: 1420
 	}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/version.yaml

@@ -1,2 +1,3 @@
 ---
-release-date: "TBD"
+release-date: "2020-02-15"
+codename: "Koala"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1693-forcedid-circular-dependency.yaml

@@ -0,0 +1,5 @@
+---
+type: change
+issue: 1693
+title: Adjusted schema definitions for Resource and Resource History tables to eliminate circular
+   dependencies with Forced ID table and to improve performance when expunging large numbers of resources.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1702-includes-perf-fix.yaml

@@ -0,0 +1,4 @@
+---
+type: perf
+issue: 1702
+title: "Loading of _include and _revinclude values has been optimized to be slightly faster"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1715-update-converters.yaml

@@ -0,0 +1,6 @@
+---
+type: change
+issue: 1715
+title: The version converters for all versions except R4/R5 have been reworked to be split into individual
+   classes per resource type (the R4/R5 converters were already organized this way). Thanks to Mark Iantorno
+   for a huge effort to write a Java source parser/serializer to acomplish this task.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1717-avoid-multiterm-in-es.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 1717
+title: ValueSet expansions containing lists of terms did not correctly expand when backed by
+   ElasticSearch due to the use of a feature not supported in ES. Thanks to Jens Villadsen for 
+   reporting!

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1721-dont-thrash-delta-links.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 1721
+title: When performing a terminology delta ADD operation, existing parent-child links were often
+   deleted and recrreated needlessly during operations, which could result in a deadlock. This has
+   been resolved.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1726-collapse-date-joins.yaml

@@ -0,0 +1,6 @@
+---
+type: perf
+issue: 1726
+title: When performing date range searches in the JPA server, the server was generating extra
+  unneccessary joins in the generated SQL. This has been streamlined, which should result in 
+  faster searches when performing date ranges.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1728-index-canonical.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 1728
+title: "Fields of type `canonical` were not previously indexed by the JPA server, meaning that some
+   default search parameters could not be honoured (e.g. StructureDefinition:valueset). This is now corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1732-remove-deleted-from-results.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 1732
+title: In the JPA server, quickly deleting a resource and then performing a query that had recently returned that
+   search result could cause a cached stub resource (containing no data but with an ID and metadata populated) to
+   be returned. This has been corrected.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1736-defer-large-terminology-delta-adds.yaml

@@ -0,0 +1,7 @@
+---
+type: add
+issue: 1736
+title: When performing large terminology concept additions via the delta addition service, concepts will
+  now be added via the deferred storage service, meaning that they will be added in small incremental batches
+  instead of as a part of one large transaction. This helps to avoid timeouts and memory issues when uploading
+  large collections of concepts.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-error-on-missing-profile-validation.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 1742
+title: "When validating a resource, the validator will now report an error if the resource declares conformance
+   to an unknown or invalid profile URL via the `Resource.meta.profile` declaration. Previously this was a warning
+   and did not block successful validation."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-limit-type-on-has.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 1742
+title: "When performing a search in the JPA server where the only parameter was a `_has` parameter,
+   the server did not respect the resource typename being searched for, causing false positive
+   search results. This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-terminology-delta-defer.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 1742
+title: When performing a terminology delta ADD operation, if the number of codes being added is large
+   the codes will be added in small batches via an asynchronous scheduled task in order to avoid overwhelming
+   the database with a large operation.

hapi-fhir-igpacks/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<artifactId>hapi-deployable-pom</artifactId>
 		<groupId>ca.uhn.hapi.fhir</groupId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-example/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>4.2.0-SNAPSHOT</version>
+		<version>4.3.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -48,6 +48,11 @@
 			<artifactId>commons-csv</artifactId>
 		</dependency>
 
+		<dependency>
+			<groupId>co.elastic.apm</groupId>
+			<artifactId>apm-agent-api</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-base</artifactId>

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

@@ -33,6 +33,7 @@ import ca.uhn.fhir.jpa.subscription.dbmatcher.CompositeInMemoryDaoSubscriptionMa
 import ca.uhn.fhir.jpa.subscription.dbmatcher.DaoSubscriptionMatcher;
 import ca.uhn.fhir.jpa.subscription.module.cache.LinkedBlockingQueueSubscribableChannelFactory;
 import ca.uhn.fhir.jpa.subscription.module.channel.ISubscribableChannelFactory;
+import ca.uhn.fhir.jpa.subscription.module.channel.SubscriptionChannelFactory;
 import ca.uhn.fhir.jpa.subscription.module.matcher.ISubscriptionMatcher;
 import ca.uhn.fhir.jpa.subscription.module.matcher.InMemorySubscriptionMatcher;
 import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
@@ -204,10 +205,15 @@ public abstract class BaseConfig {
 	 * Create a @Primary @Bean if you need a different implementation
 	 */
 	@Bean
-	public ISubscribableChannelFactory linkedBlockingQueueSubscribableChannelFactory() {
+	public ISubscribableChannelFactory subscribableChannelFactory() {
 		return new LinkedBlockingQueueSubscribableChannelFactory();
 	}
 
+	@Bean
+	public SubscriptionChannelFactory subscriptionChannelFactory() {
+		return new SubscriptionChannelFactory();
+	}
+
 	@Bean
 	@Primary
 	public ISubscriptionMatcher subscriptionMatcherCompositeInMemoryDatabase() {
@@ -280,6 +286,4 @@ public abstract class BaseConfig {
 	private static HapiFhirHibernateJpaDialect hibernateJpaDialect(HapiLocalizer theLocalizer) {
 		return new HapiFhirHibernateJpaDialect(theLocalizer);
 	}
-
-
 }

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

@@ -153,8 +153,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	@Autowired
 	protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
 	@Autowired
-	protected ISearchParamRegistry mySerarchParamRegistry;
-	@Autowired
 	protected ITermReadSvc myTerminologySvc;
 	@Autowired
 	protected IResourceHistoryTableDao myResourceHistoryTableDao;
@@ -162,8 +160,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	protected IResourceTableDao myResourceTableDao;
 	@Autowired
 	protected IResourceTagDao myResourceTagDao;
-	@Autowired
+
-	protected ISearchParamRegistry mySearchParamRegistry;
 	@Autowired
 	protected DeleteConflictService myDeleteConflictService;
 	@Autowired
@@ -1550,4 +1547,5 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 				"Resource with ID " + theEntity.getIdDt().getIdPart() + " exists but it is not of type " + theResourceName + ", found resource of type " + theEntity.getResourceType());
 		}
 	}
+
 }

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

@@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.dao;
 
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
-import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.delete.DeleteConflictList;
@@ -39,16 +38,12 @@ import ca.uhn.fhir.jpa.util.ExpungeOutcome;
 import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
 import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils;
 import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils;
-import ca.uhn.fhir.model.api.IQueryParameterAnd;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.*;
 import ca.uhn.fhir.rest.api.server.*;
-import ca.uhn.fhir.rest.param.ParameterUtil;
-import ca.uhn.fhir.rest.param.QualifierDetails;
 import ca.uhn.fhir.rest.server.exceptions.*;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
-import ca.uhn.fhir.rest.server.method.SearchMethodBinding;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.ObjectUtil;
 import ca.uhn.fhir.util.OperationOutcomeUtil;
@@ -1164,38 +1159,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return retVal;
 	}
 
-	@Transactional(propagation = Propagation.SUPPORTS)
-	@Override
-	public void translateRawParameters(Map<String, List<String>> theSource, SearchParameterMap theTarget) {
-		if (theSource == null || theSource.isEmpty()) {
-			return;
-		}
-
-		Map<String, RuntimeSearchParam> searchParams = mySerarchParamRegistry.getActiveSearchParams(getResourceName());
-
-		Set<String> paramNames = theSource.keySet();
-		for (String nextParamName : paramNames) {
-			QualifierDetails qualifiedParamName = SearchMethodBinding.extractQualifiersFromParameterName(nextParamName);
-			RuntimeSearchParam param = searchParams.get(qualifiedParamName.getParamName());
-			if (param == null) {
-				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", qualifiedParamName.getParamName(), new TreeSet<>(searchParams.keySet()));
-				throw new InvalidRequestException(msg);
-			}
-
-			// Should not be null since the check above would have caught it
-			RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(myResourceName);
-			RuntimeSearchParam paramDef = mySearchParamRegistry.getSearchParamByName(resourceDef, qualifiedParamName.getParamName());
-
-			for (String nextValue : theSource.get(nextParamName)) {
-				QualifiedParamList qualifiedParam = QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifiedParamName.getWholeQualifier(), nextValue);
-				List<QualifiedParamList> paramList = Collections.singletonList(qualifiedParam);
-				IQueryParameterAnd<?> parsedParam = ParameterUtil.parseQueryParams(getContext(), paramDef, nextParamName, paramList);
-				theTarget.add(qualifiedParamName.getParamName(), parsedParam);
-			}
-
-		}
-	}
-
 	@Override
 	public DaoMethodOutcome update(T theResource) {
 		return update(theResource, null, null);

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

@@ -21,19 +21,24 @@ package ca.uhn.fhir.jpa.dao;
  */
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
-import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
+import ca.uhn.fhir.model.api.IQueryParameterAnd;
-import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
+import ca.uhn.fhir.rest.api.QualifiedParamList;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.*;
-import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
+import ca.uhn.fhir.rest.param.ParameterUtil;
-import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
+import ca.uhn.fhir.rest.param.QualifierDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.rest.server.method.SearchMethodBinding;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.FhirTerser;
@@ -44,12 +49,14 @@ import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.InstantType;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import javax.validation.constraints.NotNull;
-import java.util.List;
+import java.util.*;
-import java.util.Set;
 
 import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_ERROR;
 import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_INFO;
@@ -57,6 +64,8 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public abstract class BaseStorageDao {
+	@Autowired
+	protected ISearchParamRegistry mySearchParamRegistry;
 
 	/**
 	 * May be overridden by subclasses to validate resources prior to storage
@@ -206,4 +215,36 @@ public abstract class BaseStorageDao {
 	 */
 	protected abstract FhirContext getContext();
 
+
+	@Transactional(propagation = Propagation.SUPPORTS)
+	public void translateRawParameters(Map<String, List<String>> theSource, SearchParameterMap theTarget) {
+		if (theSource == null || theSource.isEmpty()) {
+			return;
+		}
+
+		Map<String, RuntimeSearchParam> searchParams = mySearchParamRegistry.getActiveSearchParams(getResourceName());
+
+		Set<String> paramNames = theSource.keySet();
+		for (String nextParamName : paramNames) {
+			QualifierDetails qualifiedParamName = SearchMethodBinding.extractQualifiersFromParameterName(nextParamName);
+			RuntimeSearchParam param = searchParams.get(qualifiedParamName.getParamName());
+			if (param == null) {
+				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", qualifiedParamName.getParamName(), new TreeSet<>(searchParams.keySet()));
+				throw new InvalidRequestException(msg);
+			}
+
+			// Should not be null since the check above would have caught it
+			RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(getResourceName());
+			RuntimeSearchParam paramDef = mySearchParamRegistry.getSearchParamByName(resourceDef, qualifiedParamName.getParamName());
+
+			for (String nextValue : theSource.get(nextParamName)) {
+				QualifiedParamList qualifiedParam = QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifiedParamName.getWholeQualifier(), nextValue);
+				List<QualifiedParamList> paramList = Collections.singletonList(qualifiedParam);
+				IQueryParameterAnd<?> parsedParam = ParameterUtil.parseQueryParams(getContext(), paramDef, nextParamName, paramList);
+				theTarget.add(qualifiedParamName.getParamName(), parsedParam);
+			}
+
+		}
+	}
+
 }

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

@@ -102,7 +102,7 @@ public class DaoConfig {
 	/**
 	 * update setter javadoc if default changes
 	 */
-	private int myDeferIndexingForCodesystemsOfSize = 2000;
+	private int myDeferIndexingForCodesystemsOfSize = 100;
 	private boolean myDeleteStaleSearches = true;
 	private boolean myEnforceReferentialIntegrityOnDelete = true;
 	private boolean myUniqueIndexesEnabled = true;
@@ -397,7 +397,7 @@ public class DaoConfig {
 	 * the code system will be indexed later in an incremental process in order to
 	 * avoid overwhelming Lucene with a huge number of codes in a single operation.
 	 * <p>
-	 * Defaults to 2000
+	 * Defaults to 100
 	 * </p>
 	 */
 	public int getDeferIndexingForCodesystemsOfSize() {
@@ -409,7 +409,7 @@ public class DaoConfig {
 	 * the code system will be indexed later in an incremental process in order to
 	 * avoid overwhelming Lucene with a huge number of codes in a single operation.
 	 * <p>
-	 * Defaults to 2000
+	 * Defaults to 100
 	 * </p>
 	 */
 	public void setDeferIndexingForCodesystemsOfSize(int theDeferIndexingForCodesystemsOfSize) {

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

@@ -29,4 +29,6 @@ public interface IResultIterator extends Iterator<ResourcePersistentId>, Closeab
 
 	int getSkippedCount();
 
+    int getNonSkippedCount();
+
 }

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

@@ -29,17 +29,29 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
-import ca.uhn.fhir.jpa.dao.predicate.*;
+import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilder;
+import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderFactory;
+import ca.uhn.fhir.jpa.dao.predicate.QueryRoot;
+import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinEnum;
+import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinKey;
 import ca.uhn.fhir.jpa.entity.ResourceSearchView;
 import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
 import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
-import ca.uhn.fhir.jpa.model.entity.*;
+import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
+import ca.uhn.fhir.jpa.model.entity.ResourceLink;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.entity.ResourceTag;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
 import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
 import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
-import ca.uhn.fhir.jpa.util.*;
+import ca.uhn.fhir.jpa.util.BaseIterator;
+import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
+import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
+import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
+import ca.uhn.fhir.jpa.util.SqlQueryList;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.Include;
@@ -80,10 +92,27 @@ import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.persistence.PersistenceContextType;
 import javax.persistence.TypedQuery;
-import javax.persistence.criteria.*;
+import javax.persistence.criteria.CriteriaBuilder;
-import java.util.*;
+import javax.persistence.criteria.CriteriaQuery;
+import javax.persistence.criteria.From;
+import javax.persistence.criteria.Join;
+import javax.persistence.criteria.JoinType;
+import javax.persistence.criteria.Order;
+import javax.persistence.criteria.Predicate;
+import javax.persistence.criteria.Root;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /**
  * The SearchBuilder is responsible for actually forming the SQL query that handles
@@ -103,8 +132,9 @@ public class SearchBuilder implements ISearchBuilder {
 	private static final List<ResourcePersistentId> EMPTY_LONG_LIST = Collections.unmodifiableList(new ArrayList<>());
 	private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilder.class);
 	private static ResourcePersistentId NO_MORE = new ResourcePersistentId(-1L);
-	@Autowired
+	private final QueryRoot myQueryRoot = new QueryRoot();
-	private DaoConfig myDaoConfig;
+	private final String myResourceName;
+	private final Class<? extends IBaseResource> myResourceType;
 	@Autowired
 	protected IInterceptorBroadcaster myInterceptorBroadcaster;
 	@Autowired
@@ -112,6 +142,8 @@ public class SearchBuilder implements ISearchBuilder {
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	protected EntityManager myEntityManager;
 	@Autowired
+	private DaoConfig myDaoConfig;
+	@Autowired
 	private IResourceSearchViewDao myResourceSearchViewDao;
 	@Autowired
 	private FhirContext myContext;
@@ -123,7 +155,6 @@ public class SearchBuilder implements ISearchBuilder {
 	private ISearchParamRegistry mySearchParamRegistry;
 	@Autowired
 	private PredicateBuilderFactory myPredicateBuilderFactory;
-
 	private List<ResourcePersistentId> myAlsoIncludePids;
 	private CriteriaBuilder myBuilder;
 	private IDao myCallingDao;
@@ -133,9 +164,6 @@ public class SearchBuilder implements ISearchBuilder {
 	private Integer myMaxResultsToFetch;
 	private Set<ResourcePersistentId> myPidSet;
 	private PredicateBuilder myPredicateBuilder;
-	private final QueryRoot myQueryRoot = new QueryRoot();
-	private final String myResourceName;
-	private final Class<? extends IBaseResource> myResourceType;
 
 	/**
 	 * Constructor
@@ -254,7 +282,8 @@ public class SearchBuilder implements ISearchBuilder {
 				outerQuery.multiselect(myBuilder.countDistinct(myQueryRoot.getRoot()));
 			} else {
 				outerQuery.multiselect(myQueryRoot.get("myId").as(Long.class));
-				outerQuery.distinct(true);
+				// KHS This distinct call is causing performance issues in large installations
+//				outerQuery.distinct(true);
 			}
 
 		}
@@ -475,6 +504,9 @@ public class SearchBuilder implements ISearchBuilder {
 
 		ResourcePersistentId resourceId;
 		for (ResourceSearchView next : resourceSearchViewList) {
+			if (next.getDeleted() != null) {
+				continue;
+			}
 
 			Class<? extends IBaseResource> resourceType = myContext.getResourceDefinition(next.getResourceType()).getImplementingClass();
 
@@ -594,6 +626,7 @@ public class SearchBuilder implements ISearchBuilder {
 			return new HashSet<>();
 		}
 		String searchFieldName = theReverseMode ? "myTargetResourcePid" : "mySourceResourcePid";
+		String findFieldName = theReverseMode ? "mySourceResourcePid" : "myTargetResourcePid";
 
 		Collection<ResourcePersistentId> nextRoundMatches = theMatches;
 		HashSet<ResourcePersistentId> allAdded = new HashSet<>();
@@ -618,17 +651,17 @@ public class SearchBuilder implements ISearchBuilder {
 				boolean matchAll = "*".equals(nextInclude.getValue());
 				if (matchAll) {
 					String sql;
-					sql = "SELECT r FROM ResourceLink r WHERE r." + searchFieldName + " IN (:target_pids) ";
+					sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r." + searchFieldName + " IN (:target_pids) ";
 					List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, MAXIMUM_PAGE_SIZE);
 					for (Collection<ResourcePersistentId> nextPartition : partitions) {
-						TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
+						TypedQuery<Long> q = theEntityManager.createQuery(sql, Long.class);
 						q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
-						List<ResourceLink> results = q.getResultList();
+						List<Long> results = q.getResultList();
-						for (ResourceLink resourceLink : results) {
+						for (Long resourceLink : results) {
 							if (theReverseMode) {
-								pidsToInclude.add(new ResourcePersistentId(resourceLink.getSourceResourcePid()));
+								pidsToInclude.add(new ResourcePersistentId(resourceLink));
 							} else {
-								pidsToInclude.add(new ResourcePersistentId(resourceLink.getTargetResourcePid()));
+								pidsToInclude.add(new ResourcePersistentId(resourceLink));
 							}
 						}
 					}
@@ -665,16 +698,16 @@ public class SearchBuilder implements ISearchBuilder {
 
 						boolean haveTargetTypesDefinedByParam = param.hasTargets();
 						if (targetResourceType != null) {
-							sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType = :target_resource_type";
+							sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType = :target_resource_type";
 						} else if (haveTargetTypesDefinedByParam) {
-							sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType in (:target_resource_types)";
+							sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType in (:target_resource_types)";
 						} else {
-							sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
+							sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
 						}
 
 						List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, MAXIMUM_PAGE_SIZE);
 						for (Collection<ResourcePersistentId> nextPartition : partitions) {
-							TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
+							TypedQuery<Long> q = theEntityManager.createQuery(sql, Long.class);
 							q.setParameter("src_path", nextPath);
 							q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
 							if (targetResourceType != null) {
@@ -682,18 +715,10 @@ public class SearchBuilder implements ISearchBuilder {
 							} else if (haveTargetTypesDefinedByParam) {
 								q.setParameter("target_resource_types", param.getTargets());
 							}
-							List<ResourceLink> results = q.getResultList();
+							List<Long> results = q.getResultList();
-							for (ResourceLink resourceLink : results) {
+							for (Long resourceLink : results) {
-								if (theReverseMode) {
+								if (resourceLink != null) {
-									Long pid = resourceLink.getSourceResourcePid();
+									pidsToInclude.add(new ResourcePersistentId(resourceLink));
-									if (pid != null) {
-										pidsToInclude.add(new ResourcePersistentId(pid));
-									}
-								} else {
-									Long pid = resourceLink.getTargetResourcePid();
-									if (pid != null) {
-										pidsToInclude.add(new ResourcePersistentId(pid));
-									}
 								}
 							}
 						}
@@ -965,6 +990,7 @@ public class SearchBuilder implements ISearchBuilder {
 		private SortSpec mySort;
 		private boolean myStillNeedToFetchIncludes;
 		private int mySkipCount = 0;
+		private int myNonSkipCount = 0;
 
 		private QueryIterator(SearchRuntimeDetails theSearchRuntimeDetails, RequestDetails theRequest) {
 			mySearchRuntimeDetails = theSearchRuntimeDetails;
@@ -994,14 +1020,7 @@ public class SearchBuilder implements ISearchBuilder {
 						myMaxResultsToFetch = myDaoConfig.getFetchSizeDefaultMaximum();
 					}
 
-					final TypedQuery<Long> query = createQuery(mySort, myMaxResultsToFetch, false, myRequest);
+					initializeIteratorQuery(myMaxResultsToFetch);
-
-					mySearchRuntimeDetails.setQueryStopwatch(new StopWatch());
-
-					Query<Long> hibernateQuery = (Query<Long>) query;
-					hibernateQuery.setFetchSize(myFetchSize);
-					ScrollableResults scroll = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
-					myResultsIterator = new ScrollableResultsIterator<>(scroll);
 
 					// If the query resulted in extra results being requested
 					if (myAlsoIncludePids != null) {
@@ -1036,11 +1055,32 @@ public class SearchBuilder implements ISearchBuilder {
 								ResourcePersistentId next = new ResourcePersistentId(nextLong);
 								if (myPidSet.add(next)) {
 									myNext = next;
+									myNonSkipCount++;
 									break;
 								} else {
 									mySkipCount++;
 								}
 							}
+
+							if (!myResultsIterator.hasNext()) {
+								if (myMaxResultsToFetch != null && (mySkipCount + myNonSkipCount == myMaxResultsToFetch)) {
+									if (mySkipCount > 0 && myNonSkipCount == 0) {
+										myMaxResultsToFetch += 1000;
+
+										StorageProcessingMessage message = new StorageProcessingMessage();
+										String msg = "Pass completed with no matching results. This indicates an inefficient query! Retrying with new max count of " + myMaxResultsToFetch;
+										ourLog.warn(msg);
+										message.setMessage(msg);
+										HookParams params = new HookParams()
+											.add(RequestDetails.class, myRequest)
+											.addIfMatchesType(ServletRequestDetails.class, myRequest)
+											.add(StorageProcessingMessage.class, message);
+										JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, myRequest, Pointcut.JPA_PERFTRACE_WARNING, params);
+
+										initializeIteratorQuery(myMaxResultsToFetch);
+									}
+								}
+							}
 						}
 					}
 
@@ -1100,6 +1140,20 @@ public class SearchBuilder implements ISearchBuilder {
 
 		}
 
+		private void initializeIteratorQuery(Integer theMaxResultsToFetch) {
+			final TypedQuery<Long> query = createQuery(mySort, theMaxResultsToFetch, false, myRequest);
+
+			mySearchRuntimeDetails.setQueryStopwatch(new StopWatch());
+
+			Query<Long> hibernateQuery = (Query<Long>) query;
+			hibernateQuery.setFetchSize(myFetchSize);
+			ScrollableResults scroll = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
+			myResultsIterator = new ScrollableResultsIterator<>(scroll);
+
+			mySkipCount = 0;
+			myNonSkipCount = 0;
+		}
+
 		@Override
 		public boolean hasNext() {
 			if (myNext == null) {
@@ -1122,6 +1176,11 @@ public class SearchBuilder implements ISearchBuilder {
 			return mySkipCount;
 		}
 
+		@Override
+		public int getNonSkippedCount() {
+			return myNonSkipCount;
+		}
+
 		@Override
 		public void close() {
 			if (myResultsIterator != null) {

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

@@ -50,4 +50,8 @@ public interface ITermConceptDao extends JpaRepository<TermConcept, Long> {
 	@Query("SELECT t FROM TermConcept t WHERE t.myIndexStatus = null")
 	Page<TermConcept> findResourcesRequiringReindexing(Pageable thePageRequest);
 
+	@Modifying
+	@Query("DELETE FROM TermConcept t WHERE t.myId = :pid")
+	void deleteByPid(@Param("pid") Long theId);
+
 }

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

@@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Slice;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.query.Param;
 
@@ -39,4 +40,9 @@ public interface ITermConceptParentChildLinkDao extends JpaRepository<TermConcep
 
 	@Query("SELECT t.myPid FROM TermConceptParentChildLink t WHERE t.myCodeSystem.myId = :cs_pid")
 	Slice<Long> findIdsByCodeSystemVersion(Pageable thePage, @Param("cs_pid") Long thePid);
+
+	@Modifying
+	@Query("DELETE FROM TermConceptParentChildLink t WHERE t.myChildPid = :pid OR t.myParentPid = :pid")
+	void deleteByConceptPid(@Param("pid") Long theId);
+
 }

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

@@ -24,10 +24,10 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
-import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
-import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
@@ -35,7 +35,6 @@ import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
@@ -53,6 +52,7 @@ import java.util.List;
 import java.util.Set;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
 
 @Transactional
 public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
@@ -147,7 +147,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 
 			CodeSystem csDstu3 = (CodeSystem) theResource;
 
-			org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
+			org.hl7.fhir.r4.model.CodeSystem cs = convertCodeSystem(csDstu3);
 			addPidToResource(theEntity, cs);
 
 			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, (ResourceTable) theEntity);

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

@@ -22,21 +22,24 @@ package ca.uhn.fhir.jpa.dao.dstu3;
 
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 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.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.TranslationMatch;
 import ca.uhn.fhir.jpa.term.TranslationRequest;
 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.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;
 import org.hl7.fhir.dstu3.model.ConceptMap;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.CodeType;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.model.UriType;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import java.util.Date;
@@ -44,6 +47,8 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
+
 public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
 	@Autowired
 	private ITermReadSvc myHapiTerminologySvc;
@@ -166,7 +171,7 @@ public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<Conc
 			if (retVal.getDeleted() == null) {
 				try {
 					ConceptMap conceptMap = (ConceptMap) theResource;
-					org.hl7.fhir.r4.model.ConceptMap converted = VersionConvertor_30_40.convertConceptMap(conceptMap);
+					org.hl7.fhir.r4.model.ConceptMap converted = convertConceptMap(conceptMap);
 					myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, converted);
 				} catch (FHIRException fe) {
 					throw new InternalErrorException(fe);

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

@@ -33,12 +33,15 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.ElementUtil;
 import org.apache.commons.codec.binary.StringUtils;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
 import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
 import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
-import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.CodeSystem;
+import org.hl7.fhir.dstu3.model.CodeableConcept;
+import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
+import org.hl7.fhir.dstu3.model.IntegerType;
+import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
 import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
@@ -51,7 +54,6 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
 
 import java.util.Collections;
 import java.util.Date;
@@ -59,6 +61,7 @@ import java.util.List;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
 
 public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
 	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
@@ -420,7 +423,7 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
 			if (retVal.getDeleted() == null) {
 				try {
 					ValueSet valueSet = (ValueSet) theResource;
-					org.hl7.fhir.r4.model.ValueSet converted = VersionConvertor_30_40.convertValueSet(valueSet);
+					org.hl7.fhir.r4.model.ValueSet converted = convertValueSet(valueSet);
 					myHapiTerminologySvc.storeTermValueSet(retVal, converted);
 				} catch (FHIRException fe) {
 					throw new InternalErrorException(fe);

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

@@ -78,8 +78,6 @@ public class ExpungeEverythingService {
 		ourLog.info("BEGINNING GLOBAL $expunge");
 		myTxTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 		myTxTemplate.execute(t -> {
-			counter.addAndGet(doExpungeEverythingQuery("UPDATE " + ResourceHistoryTable.class.getSimpleName() + " d SET d.myForcedId = null"));
-			counter.addAndGet(doExpungeEverythingQuery("UPDATE " + ResourceTable.class.getSimpleName() + " d SET d.myForcedId = null"));
 			counter.addAndGet(doExpungeEverythingQuery("UPDATE " + TermCodeSystem.class.getSimpleName() + " d SET d.myCurrentVersion = null"));
 			return null;
 		});

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

@@ -39,13 +39,17 @@ import javax.persistence.criteria.Join;
 import javax.persistence.criteria.Predicate;
 import java.util.ArrayList;
 import java.util.Date;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 @Component
 @Scope("prototype")
 public class PredicateBuilderDate extends BasePredicateBuilder implements IPredicateBuilder {
 	private static final Logger ourLog = LoggerFactory.getLogger(PredicateBuilderDate.class);
 
+	private Map<String, Join<ResourceTable, ResourceIndexedSearchParamDate>> myJoinMap;
+
 	PredicateBuilderDate(SearchBuilder theSearchBuilder) {
 		super(theSearchBuilder);
 	}
@@ -56,7 +60,18 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
 											List<? extends IQueryParameterType> theList,
 											SearchFilterParser.CompareOperation operation) {
 
-		Join<ResourceTable, ResourceIndexedSearchParamDate> join = createJoin(SearchBuilderJoinEnum.DATE, theParamName);
+		boolean newJoin = false;
+		if (myJoinMap == null) {
+			myJoinMap = new HashMap<>();
+		}
+		String key = theResourceName + " " + theParamName;
+
+		Join<ResourceTable, ResourceIndexedSearchParamDate> join = myJoinMap.get(key);
+		if (join == null) {
+			join = createJoin(SearchBuilderJoinEnum.DATE, theParamName);
+			myJoinMap.put(key, join);
+			newJoin = true;
+		}
 
 		if (theList.get(0).getMissing() != null) {
 			Boolean missing = theList.get(0).getMissing();
@@ -77,7 +92,14 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
 		}
 
 		Predicate orPredicates = myBuilder.or(toArray(codePredicates));
+
+		if (newJoin) {
+			Predicate identityAndValuePredicate = combineParamIndexPredicateWithParamNamePredicate(theResourceName, theParamName, join, orPredicates);
+			myQueryRoot.addPredicate(identityAndValuePredicate);
+		} else {
 			myQueryRoot.addPredicate(orPredicates);
+		}
+
 		return orPredicates;
 	}
 
@@ -86,12 +108,13 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
 													 String theParamName,
 													 CriteriaBuilder theBuilder,
 													 From<?, ResourceIndexedSearchParamDate> theFrom) {
-		return createPredicateDate(theParam,
+		Predicate predicateDate = createPredicateDate(theParam,
 			theResourceName,
 			theParamName,
 			theBuilder,
 			theFrom,
 			null);
+		return combineParamIndexPredicateWithParamNamePredicate(theResourceName, theParamName, theFrom, predicateDate);
 	}
 
 	private Predicate createPredicateDate(IQueryParameterType theParam,
@@ -99,7 +122,7 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
 													  String theParamName,
 													  CriteriaBuilder theBuilder,
 													  From<?, ResourceIndexedSearchParamDate> theFrom,
-													  SearchFilterParser.CompareOperation operation) {
+													  SearchFilterParser.CompareOperation theOperation) {
 
 		Predicate p;
 		if (theParam instanceof DateParam) {
@@ -109,7 +132,7 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
 				p = createPredicateDateFromRange(theBuilder,
 					theFrom,
 					range,
-					operation);
+					theOperation);
 			} else {
 				// TODO: handle missing date param?
 				p = null;
@@ -119,12 +142,12 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
 			p = createPredicateDateFromRange(theBuilder,
 				theFrom,
 				range,
-				operation);
+				theOperation);
 		} else {
 			throw new IllegalArgumentException("Invalid token type: " + theParam.getClass());
 		}
 
-		return combineParamIndexPredicateWithParamNamePredicate(theResourceName, theParamName, theFrom, p);
+		return p;
 	}
 
 	private Predicate createPredicateDateFromRange(CriteriaBuilder theBuilder,

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

@@ -430,7 +430,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
 				break;
 
 			case Constants.PARAM_HAS:
-				addPredicateHas(theAndOrParams, theRequest);
+				addPredicateHas(theResourceName, theAndOrParams, theRequest);
 				break;
 
 			case Constants.PARAM_TAG:
@@ -756,7 +756,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
 		return retVal;
 	}
 
-	private void addPredicateHas(List<List<IQueryParameterType>> theHasParameters, RequestDetails theRequest) {
+	private void addPredicateHas(String theResourceType, List<List<IQueryParameterType>> theHasParameters, RequestDetails theRequest) {
 
 		for (List<? extends IQueryParameterType> nextOrList : theHasParameters) {
 
@@ -811,8 +811,9 @@ class PredicateBuilderReference extends BasePredicateBuilder {
 
 			Join<ResourceTable, ResourceLink> join = myQueryRoot.join("myResourceLinksAsTarget", JoinType.LEFT);
 			Predicate pathPredicate = myPredicateBuilder.createResourceLinkPathPredicate(targetResourceType, paramReference, join);
-			Predicate pidPredicate = join.get("mySourceResourcePid").in(subQ);
+			Predicate sourceTypePredicate = myBuilder.equal(join.get("myTargetResourceType"), theResourceType);
-			Predicate andPredicate = myBuilder.and(pathPredicate, pidPredicate);
+			Predicate sourcePidPredicate = join.get("mySourceResourcePid").in(subQ);
+			Predicate andPredicate = myBuilder.and(pathPredicate, sourcePidPredicate, sourceTypePredicate);
 			myQueryRoot.addPredicate(andPredicate);
 		}
 	}

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

@@ -148,7 +148,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 			CodeSystem cs = (CodeSystem) theResource;
 			addPidToResource(theEntity, theResource);
 
-			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), (ResourceTable) theEntity);
+			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(cs), (ResourceTable) theEntity);
 		}
 
 		return retVal;

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

@@ -166,7 +166,7 @@ public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<Concept
 
 			if (retVal.getDeleted() == null) {
 				ConceptMap conceptMap = (ConceptMap) theResource;
-				myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(conceptMap));
+				myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap40_50.convertConceptMap(conceptMap));
 			} else {
 				myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
 			}

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

@@ -415,7 +415,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
 		if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
 			if (retVal.getDeleted() == null) {
 				ValueSet valueSet = (ValueSet) theResource;
-				myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet));
+				myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSet));
 			} else {
 				myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
 			}

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

@@ -47,7 +47,7 @@ public class TermCodeSystem implements Serializable {
 	@Column(name = "CODE_SYSTEM_URI", nullable = false, length = MAX_URL_LENGTH)
 	private String myCodeSystemUri;
 
-	@OneToOne()
+	@OneToOne(fetch = FetchType.LAZY)
 	@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)
@@ -57,7 +57,7 @@ public class TermCodeSystem implements Serializable {
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CODESYSTEM_PID")
 	@Column(name = "PID")
 	private Long myPid;
-	@OneToOne()
+	@OneToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_RES"))
 	private ResourceTable myResource;
 	@Column(name = "RES_ID", insertable = false, updatable = false)

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

@@ -50,7 +50,7 @@ public class TermCodeSystemVersion implements Serializable {
 	@Column(name = "PID")
 	private Long myId;
 
-	@OneToOne()
+	@OneToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_CODESYSVER_RES_ID"))
 	private ResourceTable myResource;
 
@@ -64,7 +64,7 @@ public class TermCodeSystemVersion implements Serializable {
 	 * This was added in HAPI FHIR 3.3.0 and is nullable just to avoid migration
 	 * issued. It should be made non-nullable at some point.
 	 */
-	@ManyToOne
+	@ManyToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", nullable = true, foreignKey = @ForeignKey(name = "FK_CODESYSVER_CS_ID"))
 	private TermCodeSystem myCodeSystem;
 
@@ -72,7 +72,7 @@ public class TermCodeSystemVersion implements Serializable {
 	private Long myCodeSystemPid;
 
 	@SuppressWarnings("unused")
-	@OneToOne(mappedBy = "myCurrentVersion", optional = true)
+	@OneToOne(mappedBy = "myCurrentVersion", optional = true, fetch = FetchType.LAZY)
 	private TermCodeSystem myCodeSystemHavingThisVersionAsCurrentVersionIfAny;
 
 	@Column(name = "CS_DISPLAY", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)

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

@@ -65,7 +65,7 @@ public class TermConcept implements Serializable {
 	@Temporal(TemporalType.TIMESTAMP)
 	@Column(name = "CONCEPT_UPDATED", nullable = true)
 	private Date myUpdated;
-	@ManyToOne()
+	@ManyToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPT_PID_CS_PID"))
 	private TermCodeSystemVersion myCodeSystem;
 	@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
@@ -79,11 +79,11 @@ public class TermConcept implements Serializable {
 		@Field(name = "myDisplayPhonetic", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompletePhoneticAnalyzer"))
 	})
 	private String myDisplay;
-	@OneToMany(mappedBy = "myConcept", orphanRemoval = false)
+	@OneToMany(mappedBy = "myConcept", orphanRemoval = false, fetch = FetchType.LAZY)
 	@Field(name = "PROPmyProperties", analyzer = @Analyzer(definition = "termConceptPropertyAnalyzer"))
 	@FieldBridge(impl = TermConceptPropertyFieldBridge.class)
 	private Collection<TermConceptProperty> myProperties;
-	@OneToMany(mappedBy = "myConcept", orphanRemoval = false)
+	@OneToMany(mappedBy = "myConcept", orphanRemoval = false, fetch = FetchType.LAZY)
 	private Collection<TermConceptDesignation> myDesignations;
 	@Id()
 	@SequenceGenerator(name = "SEQ_CONCEPT_PID", sequenceName = "SEQ_CONCEPT_PID")

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

@@ -39,7 +39,7 @@ public class TermConceptDesignation implements Serializable {
 	public static final int MAX_LENGTH = 500;
 	public static final int MAX_VAL_LENGTH = 2000;
 
-	@ManyToOne
+	@ManyToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTDESIG_CONCEPT"))
 	private TermConcept myConcept;
 	@Id()
@@ -62,7 +62,7 @@ public class TermConceptDesignation implements Serializable {
 	 *
 	 * @since 3.5.0
 	 */
-	@ManyToOne
+	@ManyToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "CS_VER_PID", nullable = true, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTDESIG_CSV"))
 	private TermCodeSystemVersion myCodeSystemVersion;
 

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

@@ -32,14 +32,14 @@ import java.io.Serializable;
 public class TermConceptParentChildLink implements Serializable {
 	private static final long serialVersionUID = 1L;
 
-	@ManyToOne()
+	@ManyToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "CHILD_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CHILD"))
 	private TermConcept myChild;
 
 	@Column(name = "CHILD_PID", insertable = false, updatable = false)
 	private Long myChildPid;
 
-	@ManyToOne()
+	@ManyToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "CODESYSTEM_PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CS"))
 	private TermCodeSystemVersion myCodeSystem;
 
@@ -47,7 +47,7 @@ public class TermConceptParentChildLink implements Serializable {
 	@Fields({@Field(name = "myCodeSystemVersionPid")})
 	private long myCodeSystemVersionPid;
 
-	@ManyToOne(cascade = {})
+	@ManyToOne(fetch = FetchType.LAZY, 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/entity/TermConceptProperty.java

@@ -44,7 +44,7 @@ public class TermConceptProperty implements Serializable {
 	private static final int MAX_LENGTH = 500;
 	static final int MAX_PROPTYPE_ENUM_LENGTH = 6;
 
-	@ManyToOne
+	@ManyToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CONCEPT"))
 	private TermConcept myConcept;
 	/**
@@ -52,7 +52,7 @@ public class TermConceptProperty implements Serializable {
 	 *
 	 * @since 3.5.0
 	 */
-	@ManyToOne
+	@ManyToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "CS_VER_PID", nullable = true, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CSV"))
 	private TermCodeSystemVersion myCodeSystemVersion;
 	@Id()

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

@@ -39,7 +39,6 @@ import ca.uhn.fhir.util.ValidateUtil;
 import com.google.common.base.Charsets;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Multimap;
-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;
@@ -61,6 +60,7 @@ import java.util.Map;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.apache.commons.lang3.StringUtils.trim;
+import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
 
 public class TerminologyUploaderProvider extends BaseJpaProvider {
 
@@ -272,10 +272,10 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 		CodeSystem nextCodeSystem;
 		switch (getContext().getVersion().getVersion()) {
 			case DSTU3:
-				nextCodeSystem = VersionConvertor_30_40.convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theCodeSystem);
+				nextCodeSystem = convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theCodeSystem);
 				break;
 			case R5:
-				nextCodeSystem = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem);
+				nextCodeSystem = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem);
 				break;
 			default:
 				nextCodeSystem = (CodeSystem) theCodeSystem;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderConceptMapDstu3.java

@@ -21,9 +21,9 @@ package ca.uhn.fhir.jpa.provider.dstu3;
  */
 
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.term.TranslationRequest;
 import ca.uhn.fhir.jpa.term.TranslationResult;
-import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
@@ -31,11 +31,21 @@ 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 org.hl7.fhir.convertors.VersionConvertor_30_40;
-import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.BooleanType;
+import org.hl7.fhir.dstu3.model.CodeType;
+import org.hl7.fhir.dstu3.model.CodeableConcept;
+import org.hl7.fhir.dstu3.model.Coding;
+import org.hl7.fhir.dstu3.model.ConceptMap;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.Parameters;
+import org.hl7.fhir.dstu3.model.StringType;
+import org.hl7.fhir.dstu3.model.UriType;
 import org.hl7.fhir.exceptions.FHIRException;
 
 import javax.servlet.http.HttpServletRequest;
 
+import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
+
 public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderDstu3<ConceptMap> {
 	@Operation(name = JpaConstants.OPERATION_TRANSLATE, idempotent = true, returnParameters = {
 		@OperationParam(name = "result", type = BooleanType.class, min = 1, max = 1),
@@ -129,7 +139,7 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
 			TranslationResult result = dao.translate(translationRequest, theRequestDetails);
 
 			// Convert from R4 to DSTU3
-			return VersionConvertor_30_40.convertParameters(result.toParameters());
+			return convertParameters(result.toParameters());
 		} catch (FHIRException fe) {
 			throw new InternalErrorException(fe);
 		} finally {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaResourceProviderDstu3.java

@@ -21,17 +21,28 @@ package ca.uhn.fhir.jpa.provider.dstu3;
  */
 
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
-import ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
-import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider;
+import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
+import ca.uhn.fhir.rest.annotation.Create;
+import ca.uhn.fhir.rest.annotation.Delete;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.annotation.ResourceParam;
+import ca.uhn.fhir.rest.annotation.Update;
+import ca.uhn.fhir.rest.annotation.Validate;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
 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 org.hl7.fhir.convertors.VersionConvertor_30_40;
+import org.hl7.fhir.dstu3.model.BooleanType;
-import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.IntegerType;
+import org.hl7.fhir.dstu3.model.Meta;
+import org.hl7.fhir.dstu3.model.Parameters;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -41,6 +52,7 @@ import javax.servlet.http.HttpServletRequest;
 import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META;
 import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META_ADD;
 import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META_DELETE;
+import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
 
 public class JpaResourceProviderDstu3<T extends IAnyResource> extends BaseJpaResourceProvider<T> {
 
@@ -91,7 +103,7 @@ public class JpaResourceProviderDstu3<T extends IAnyResource> extends BaseJpaRes
 		RequestDetails theRequest) {
 		org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(theIdParam, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
 		try {
-			return VersionConvertor_30_40.convertParameters(retVal);
+			return convertParameters(retVal);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}
@@ -107,7 +119,7 @@ public class JpaResourceProviderDstu3<T extends IAnyResource> extends BaseJpaRes
 		RequestDetails theRequest) {
 		org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(null, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
 		try {
-			return VersionConvertor_30_40.convertParameters(retVal);
+			return convertParameters(retVal);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaSystemProviderDstu3.java

@@ -3,17 +3,26 @@ package ca.uhn.fhir.jpa.provider.dstu3;
 import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl.Suggestion;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
-import ca.uhn.fhir.jpa.provider.BaseJpaSystemProviderDstu2Plus;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.provider.BaseJpaSystemProviderDstu2Plus;
 import ca.uhn.fhir.model.api.annotation.Description;
-import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.annotation.Transaction;
+import ca.uhn.fhir.rest.annotation.TransactionParam;
 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.servlet.ServletRequestDetails;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
+import org.hl7.fhir.dstu3.model.BooleanType;
-import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.DecimalType;
+import org.hl7.fhir.dstu3.model.IntegerType;
+import org.hl7.fhir.dstu3.model.Meta;
+import org.hl7.fhir.dstu3.model.Parameters;
 import org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent;
+import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -29,6 +38,7 @@ import java.util.TreeMap;
 
 import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
 import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
 
 /*
  * #%L
@@ -72,7 +82,7 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
 	) {
 		org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
 		try {
-			return VersionConvertor_30_40.convertParameters(retVal);
+			return convertParameters(retVal);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}
@@ -90,7 +100,7 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
 	) {
 		org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
 		try {
-			return VersionConvertor_30_40.convertParameters(retVal);
+			return convertParameters(retVal);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderConceptMapR5.java

@@ -122,7 +122,7 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5<C
 			IFhirResourceDaoConceptMap<ConceptMap> dao = (IFhirResourceDaoConceptMap<ConceptMap>) getDao();
 			TranslationResult result = dao.translate(translationRequest, theRequestDetails);
 			org.hl7.fhir.r4.model.Parameters parameters = result.toParameters();
-			return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
+			return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
 		} finally {
 			endRequest(theServletRequest);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/JpaResourceProviderR5.java

@@ -86,7 +86,7 @@ public class JpaResourceProviderR5<T extends IAnyResource> extends BaseJpaResour
 		RequestDetails theRequest) {
 
 		org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(theIdParam, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
-		return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
+		return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
 
 	}
 
@@ -99,7 +99,7 @@ public class JpaResourceProviderR5<T extends IAnyResource> extends BaseJpaResour
 		@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_PREVIOUS_VERSIONS) BooleanType theExpungeOldVersions,
 		RequestDetails theRequest) {
 		org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(null, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
-		return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
+		return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
 	}
 
 	@Operation(name = OPERATION_META, idempotent = true, returnParameters = {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/JpaSystemProviderR5.java

@@ -68,7 +68,7 @@ public class JpaSystemProviderR5 extends BaseJpaSystemProviderDstu2Plus<Bundle,
 		RequestDetails theRequestDetails
 	) {
 		org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
-		return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
+		return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
 	}
 
 	@Operation(name = JpaConstants.OPERATION_EXPUNGE, idempotent = false, returnParameters = {
@@ -82,7 +82,7 @@ public class JpaSystemProviderR5 extends BaseJpaSystemProviderDstu2Plus<Bundle,
 		RequestDetails theRequestDetails
 	) {
 		org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
-		return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
+		return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
 	}
 
 	// This is generated by hand:

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

@@ -227,10 +227,14 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		template.execute(new TransactionCallbackWithoutResult() {
 			@Override
 			protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
-				ensureSearchEntityLoaded();
+				boolean entityLoaded = ensureSearchEntityLoaded();
+				assert entityLoaded;
 			}
 		});
 
+		assert mySearchEntity != null;
+		assert mySearchEntity.getSearchType() != null;
+
 		switch (mySearchEntity.getSearchType()) {
 			case HISTORY:
 				return template.execute(theStatus -> doHistoryInTransaction(theFromIndex, theToIndex));

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

@@ -56,6 +56,9 @@ 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 co.elastic.apm.api.ElasticApm;
+import co.elastic.apm.api.Span;
+import co.elastic.apm.api.Transaction;
 import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.exception.ExceptionUtils;
@@ -601,7 +604,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		private List<ResourcePersistentId> myPreviouslyAddedResourcePids;
 		private Integer myMaxResultsToFetch;
 		private SearchRuntimeDetails mySearchRuntimeDetails;
-
+		private Transaction myParentTransaction;
 		/**
 		 * Constructor
 		 */
@@ -614,6 +617,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			mySearchRuntimeDetails = new SearchRuntimeDetails(theRequest, mySearch.getUuid());
 			mySearchRuntimeDetails.setQueryString(theParams.toNormalizedQueryString(theCallingDao.getContext()));
 			myRequest = theRequest;
+			myParentTransaction = ElasticApm.currentTransaction();
 		}
 
 		/**
@@ -774,10 +778,11 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 						if (theResultIter.hasNext() == false) {
 							int skippedCount = theResultIter.getSkippedCount();
+							int nonSkippedCount = theResultIter.getNonSkippedCount();
 							int totalFetched = skippedCount + myCountSavedThisPass + myCountBlockedThisPass;
 							ourLog.trace("MaxToFetch[{}] SkippedCount[{}] CountSavedThisPass[{}] CountSavedThisTotal[{}] AdditionalPrefetchRemaining[{}]", myMaxResultsToFetch, skippedCount, myCountSavedThisPass, myCountSavedTotal, myAdditionalPrefetchThresholdsRemaining);
 
-							if (myMaxResultsToFetch != null && totalFetched < myMaxResultsToFetch) {
+							if (nonSkippedCount == 0 || (myMaxResultsToFetch != null && totalFetched < myMaxResultsToFetch)) {
 								ourLog.trace("Setting search status to FINISHED");
 								mySearch.setStatus(SearchStatusEnum.FINISHED);
 								mySearch.setTotalCount(myCountSavedTotal);
@@ -840,7 +845,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		@Override
 		public Void call() {
 			StopWatch sw = new StopWatch();
-
+			Span span = myParentTransaction.startSpan("db", "query", "search");
+			span.setName("FHIR Database Search");
 			try {
 				// Create an initial search in the DB and give it an ID
 				saveSearch();
@@ -896,7 +902,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 					ourLog.error("Failed during search loading after {}ms", sw.getMillis(), t);
 				}
 				myUnsyncedPids.clear();
-
 				Throwable rootCause = ExceptionUtils.getRootCause(t);
 				rootCause = defaultIfNull(rootCause, t);
 
@@ -923,12 +928,13 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, myRequest, Pointcut.JPA_PERFTRACE_SEARCH_FAILED, params);
 
 				saveSearch();
-
+				span.captureException(t);
 			} finally {
 
 				myIdToSearchTask.remove(mySearch.getUuid());
 				myInitialCollectionLatch.countDown();
 				markComplete();
+				span.end();
 
 			}
 			return null;

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

@@ -66,6 +66,7 @@ import org.apache.lucene.search.BooleanQuery;
 import org.apache.lucene.search.MultiPhraseQuery;
 import org.apache.lucene.search.Query;
 import org.apache.lucene.search.RegexpQuery;
+import org.apache.lucene.search.TermQuery;
 import org.hibernate.ScrollMode;
 import org.hibernate.ScrollableResults;
 import org.hibernate.search.jpa.FullTextEntityManager;
@@ -600,11 +601,16 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 					.map(t -> new Term("myCode", t))
 					.collect(Collectors.toList());
 				if (codes.size() > 0) {
-					MultiPhraseQuery query = new MultiPhraseQuery();
+
-					query.add(codes.toArray(new Term[0]));
+					BooleanQuery.Builder builder = new BooleanQuery.Builder();
+					builder.setMinimumNumberShouldMatch(1);
+					for (Term nextCode : codes) {
+						builder.add(new TermQuery(nextCode), BooleanClause.Occur.SHOULD);
+					}
+
 					luceneQuery = new BooleanQuery.Builder()
 						.add(luceneQuery, BooleanClause.Occur.MUST)
-						.add(query, BooleanClause.Occur.MUST)
+						.add(builder.build(), BooleanClause.Occur.MUST)
 						.build();
 				}
 
@@ -1240,6 +1246,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 		return retVal;
 	}
 
+	@Transactional
 	@Override
 	public List<VersionIndependentConcept> findCodesAbove(String theSystem, String theCode) {
 		TermCodeSystem cs = getCodeSystem(theSystem);
@@ -1271,6 +1278,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 		return retVal;
 	}
 
+	@Transactional
 	@Override
 	public List<VersionIndependentConcept> findCodesBelow(String theSystem, String theCode) {
 		TermCodeSystem cs = getCodeSystem(theSystem);

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

@@ -45,7 +45,6 @@ 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.Constants;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -53,11 +52,7 @@ 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;
@@ -78,11 +73,6 @@ 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;
@@ -165,11 +155,12 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		IIdType codeSystemId = cs.getResource().getIdDt();
 
 		UploadStatistics retVal = new UploadStatistics(codeSystemId);
+		HashMap<String, TermConcept> codeToConcept = new HashMap<>();
 
 		// Add root concepts
 		for (TermConcept nextRootConcept : theAdditions.getRootConcepts()) {
 			List<String> parentCodes = Collections.emptyList();
-			addConcept(csv, parentCodes, nextRootConcept, retVal, true, 0);
+			addConceptInHierarchy(csv, parentCodes, nextRootConcept, retVal, codeToConcept, 0);
 		}
 
 		return retVal;
@@ -232,8 +223,16 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		 * save parent concepts first (it's way too slow to do that)
 		 */
 		if (theConcept.getId() == null) {
+			boolean needToSaveParents = false;
+			for (TermConceptParentChildLink next : theConcept.getParents()) {
+				if (next.getParent().getId() == null) {
+					needToSaveParents = true;
+				}
+			}
+			if (needToSaveParents) {
 				retVal += ensureParentsSaved(theConcept.getParents());
 			}
+		}
 
 		if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
 			retVal++;
@@ -445,66 +444,68 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		Validate.isTrue(myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3), "Terminology operations only supported in DSTU3+ mode");
 	}
 
-	private void addConcept(TermCodeSystemVersion theCsv, Collection<String> theParentCodes, TermConcept theConceptToAdd, UploadStatistics theStatisticsTracker, boolean theRootConcept, int theSequence) {
+	private void addConceptInHierarchy(TermCodeSystemVersion theCsv, Collection<String> theParentCodes, TermConcept theConceptToAdd, UploadStatistics theStatisticsTracker, Map<String, TermConcept> theCodeToConcept, int theSequence) {
 		TermConcept conceptToAdd = theConceptToAdd;
 		List<TermConceptParentChildLink> childrenToAdd = theConceptToAdd.getChildren();
 
 		String nextCodeToAdd = conceptToAdd.getCode();
 		String parentDescription = "(root concept)";
-		Set<TermConcept> parentConcepts = new HashSet<>();
-
-		if (!theParentCodes.isEmpty()) {
-			parentDescription = "[" + String.join(", ", theParentCodes) + "]";
-			for (String nextParentCode : theParentCodes) {
-				Optional<TermConcept> nextParentOpt = myConceptDao.findByCodeSystemAndCode(theCsv, nextParentCode);
-				if (nextParentOpt.isPresent() == false) {
-					throw new InvalidRequestException("Unable to add code \"" + nextCodeToAdd + "\" to unknown parent: " + nextParentCode);
-				}
-				parentConcepts.add(nextParentOpt.get());
-			}
-		}
 
 		ourLog.info("Saving concept {} with parent {}", theStatisticsTracker.getUpdatedConceptCount(), parentDescription);
 
 		Optional<TermConcept> existingCodeOpt = myConceptDao.findByCodeSystemAndCode(theCsv, nextCodeToAdd);
+		List<TermConceptParentChildLink> existingParentLinks;
 		if (existingCodeOpt.isPresent()) {
 			TermConcept existingCode = existingCodeOpt.get();
 			existingCode.setIndexStatus(null);
 			existingCode.setDisplay(conceptToAdd.getDisplay());
 			conceptToAdd = existingCode;
+			existingParentLinks = conceptToAdd.getParents();
+		} else {
+			existingParentLinks = Collections.emptyList();
+		}
+
+		Set<TermConcept> parentConceptsWeShouldLinkTo = new HashSet<>();
+		for (String nextParentCode : theParentCodes) {
+
+			// Don't add parent links that already exist for the code
+			if (existingParentLinks.stream().anyMatch(t -> t.getParent().getCode().equals(nextParentCode))) {
+				continue;
+			}
+
+			TermConcept nextParentOpt = theCodeToConcept.get(nextParentCode);
+			if (nextParentOpt == null) {
+				nextParentOpt = myConceptDao.findByCodeSystemAndCode(theCsv, nextParentCode).orElse(null);
+			}
+			if (nextParentOpt == null) {
+				throw new InvalidRequestException("Unable to add code \"" + nextCodeToAdd + "\" to unknown parent: " + nextParentCode);
+			}
+			parentConceptsWeShouldLinkTo.add(nextParentOpt);
 		}
 
 		if (conceptToAdd.getSequence() == null) {
 			conceptToAdd.setSequence(theSequence);
 		}
 
-		// Drop any old parent-child links if they aren't explicitly specified in the
-		// hierarchy being added
-		if (!theRootConcept) {
-			for (Iterator<TermConceptParentChildLink> iter = conceptToAdd.getParents().iterator(); iter.hasNext(); ) {
-				TermConceptParentChildLink nextLink = iter.next();
-				String parentCode = nextLink.getParent().getCode();
-				ourLog.info("Dropping existing parent/child link from {} -> {}", parentCode, nextCodeToAdd);
-				myConceptParentChildLinkDao.delete(nextLink);
-				iter.remove();
-
-				List<TermConceptParentChildLink> parentChildrenList = nextLink.getParent().getChildren();
-				parentChildrenList.remove(nextLink);
-			}
-		}
-
 		// Null out the hierarchy PIDs for this concept always. We do this because we're going to
 		// force a reindex, and it'll be regenerated then
 		conceptToAdd.setParentPids(null);
 		conceptToAdd.setCodeSystemVersion(theCsv);
-		conceptToAdd = myConceptDao.save(conceptToAdd);
 
+		if (theStatisticsTracker.getUpdatedConceptCount() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
+			saveConcept(conceptToAdd);
 			Long nextConceptPid = conceptToAdd.getId();
 			Validate.notNull(nextConceptPid);
+		} else {
+			myDeferredStorageSvc.addConceptToStorageQueue(conceptToAdd);
+		}
+
+		theCodeToConcept.put(conceptToAdd.getCode(), conceptToAdd);
+
 		theStatisticsTracker.incrementUpdatedConceptCount();
 
 		// Add link to new child to the parent
-		for (TermConcept nextParentConcept : parentConcepts) {
+		for (TermConcept nextParentConcept : parentConceptsWeShouldLinkTo) {
 			TermConceptParentChildLink parentLink = new TermConceptParentChildLink();
 			parentLink.setParent(nextParentConcept);
 			parentLink.setChild(conceptToAdd);
@@ -513,7 +514,13 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 			nextParentConcept.getChildren().add(parentLink);
 			conceptToAdd.getParents().add(parentLink);
 			ourLog.info("Saving parent/child link - Parent[{}] Child[{}]", parentLink.getParent().getCode(), parentLink.getChild().getCode());
+
+			if (theStatisticsTracker.getUpdatedConceptCount() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
 				myConceptParentChildLinkDao.save(parentLink);
+			} else {
+				myDeferredStorageSvc.addConceptLinkToStorageQueue(parentLink);
+			}
+
 		}
 
 		ourLog.trace("About to save parent-child links");
@@ -527,13 +534,20 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 			for (int i = 0; i < nextChild.getParents().size(); i++) {
 				if (nextChild.getParents().get(i).getId() == null) {
 					String parentCode = nextChild.getParents().get(i).getParent().getCode();
-					TermConcept parentConcept = myConceptDao.findByCodeSystemAndCode(theCsv, parentCode).orElseThrow(() -> new IllegalArgumentException("Unknown parent code: " + parentCode));
+					TermConcept parentConcept = theCodeToConcept.get(parentCode);
+					if (parentConcept == null) {
+						parentConcept = myConceptDao.findByCodeSystemAndCode(theCsv, parentCode).orElse(null);
+					}
+					if (parentConcept == null) {
+						throw new IllegalArgumentException("Unknown parent code: " + parentCode);
+					}
+
 					nextChild.getParents().get(i).setParent(parentConcept);
 				}
 			}
 
 			Collection<String> parentCodes = nextChild.getParents().stream().map(t -> t.getParent().getCode()).collect(Collectors.toList());
-			addConcept(theCsv, parentCodes, nextChild, theStatisticsTracker, false, childIndex);
+			addConceptInHierarchy(theCsv, parentCodes, nextChild, theStatisticsTracker, theCodeToConcept, childIndex);
 
 			childIndex++;
 		}
@@ -649,12 +663,15 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 	private void deleteConceptChildrenAndConcept(TermConcept theConcept, AtomicInteger theRemoveCounter) {
 		for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
 			deleteConceptChildrenAndConcept(nextChildLink.getChild(), theRemoveCounter);
-			myConceptParentChildLinkDao.delete(nextChildLink);
 		}
 
+		myConceptParentChildLinkDao.deleteByConceptPid(theConcept.getId());
+
 		myConceptDesignationDao.deleteAll(theConcept.getDesignations());
 		myConceptPropertyDao.deleteAll(theConcept.getProperties());
-		myConceptDao.delete(theConcept);
+
+		ourLog.info("Deleting concept {} - Code {}", theConcept.getId(), theConcept.getCode());
+		myConceptDao.deleteByPid(theConcept.getId());
 		theRemoveCounter.incrementAndGet();
 	}
 

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

@@ -98,6 +98,13 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 		myDeferredValueSets.addAll(theValueSets);
 	}
 
+	@Override
+	public void saveAllDeferred() {
+		while (!isStorageQueueEmpty()) {
+			saveDeferred();
+		}
+	}
+
 	@Override
 	public void setProcessDeferred(boolean theProcessDeferred) {
 		myProcessDeferred = theProcessDeferred;

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

@@ -9,10 +9,13 @@ 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.ValidateUtil;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
-import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
+import org.hl7.fhir.dstu3.model.CodeableConcept;
+import org.hl7.fhir.dstu3.model.Coding;
+import org.hl7.fhir.dstu3.model.StructureDefinition;
+import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
 import org.hl7.fhir.exceptions.FHIRException;
@@ -31,6 +34,9 @@ import java.util.List;
 import java.util.Optional;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
+import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
+import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSetExpansionComponent;
 
 /*
  * #%L
@@ -104,7 +110,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
 			org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
 			valueSetToExpandR4 = toCanonicalValueSet(valueSetToExpand);
 			org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent expandedR4 = super.expandValueSetInMemory(valueSetToExpandR4, null).getExpansion();
-			return VersionConvertor_30_40.convertValueSetExpansionComponent(expandedR4);
+			return convertValueSetExpansionComponent(expandedR4);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}
@@ -118,7 +124,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
 			org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
 			valueSetToExpandR4 = toCanonicalValueSet(valueSetToExpand);
 			org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSetInMemory(valueSetToExpandR4, null);
-			return VersionConvertor_30_40.convertValueSet(expandedR4);
+			return convertValueSet(expandedR4);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}
@@ -127,7 +133,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
 	@Override
 	protected org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(IBaseResource theValueSet) throws FHIRException {
 		org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
-		valueSetToExpandR4 = VersionConvertor_30_40.convertValueSet((ValueSet) theValueSet);
+		valueSetToExpandR4 = convertValueSet((ValueSet) theValueSet);
 		return valueSetToExpandR4;
 	}
 
@@ -139,7 +145,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
 			org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
 			valueSetToExpandR4 = toCanonicalValueSet(valueSetToExpand);
 			org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(valueSetToExpandR4, theOffset, theCount);
-			return VersionConvertor_30_40.convertValueSet(expandedR4);
+			return convertValueSet(expandedR4);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}
@@ -256,7 +262,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
 	public org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
 		CodeSystem codeSystem = myValidationSupport.fetchCodeSystem(myContext, theSystem);
 		try {
-			return VersionConvertor_30_40.convertCodeSystem(codeSystem);
+			return convertCodeSystem(codeSystem);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}
@@ -323,7 +329,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
 	public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
 		ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
 		ValueSet valueSet = (ValueSet) theValueSet;
-		org.hl7.fhir.r4.model.ValueSet valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
+		org.hl7.fhir.r4.model.ValueSet valueSetR4 = convertValueSet(valueSet);
 
 		Coding coding = (Coding) theCoding;
 		org.hl7.fhir.r4.model.Coding codingR4 = null;
@@ -347,7 +353,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
 	public boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet) {
 		ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
 		ValueSet valueSet = (ValueSet) theValueSet;
-		org.hl7.fhir.r4.model.ValueSet valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
+		org.hl7.fhir.r4.model.ValueSet valueSetR4 = convertValueSet(valueSet);
 		return super.isValueSetPreExpandedForCodeValidation(valueSetR4);
 	}
 }

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

@@ -90,21 +90,21 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
 			super.throwInvalidValueSet(theValueSet);
 		}
 
-		return expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR5), null);
+		return expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR5), null);
 	}
 
 	@Override
 	public IBaseResource expandValueSet(IBaseResource theInput) {
 		org.hl7.fhir.r4.model.ValueSet valueSetToExpand = toCanonicalValueSet(theInput);
 		org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSetInMemory(valueSetToExpand, null);
-		return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
+		return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR4);
 	}
 
 	@Override
 	public IBaseResource expandValueSet(IBaseResource theInput, int theOffset, int theCount) {
 		org.hl7.fhir.r4.model.ValueSet valueSetToExpand = toCanonicalValueSet(theInput);
 		org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSet(valueSetToExpand, theOffset, theCount);
-		return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
+		return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR4);
 	}
 
 	@Override
@@ -117,8 +117,8 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
 	public ValueSetExpander.ValueSetExpansionOutcome expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
 		ValueSet valueSetToExpand = new ValueSet();
 		valueSetToExpand.getCompose().addInclude(theInclude);
-		org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSetInMemory(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetToExpand), null);
+		org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSetInMemory(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetToExpand), null);
-		return new ValueSetExpander.ValueSetExpansionOutcome(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(expandedR4));
+		return new ValueSetExpander.ValueSetExpansionOutcome(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(expandedR4));
 	}
 
 	@Override
@@ -199,13 +199,13 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
 	@Override
 	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);
+		return org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(codeSystemR5);
 	}
 
 	@Override
 	protected org.hl7.fhir.r4.model.ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
 		ValueSet valueSetR5 = myValueSetResourceDao.toResource(ValueSet.class, theResourceTable, null, false);
-		return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR5);
+		return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR5);
 	}
 
 	@Override
@@ -277,7 +277,7 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
 
 	@Override
 	protected org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(IBaseResource theValueSet) throws org.hl7.fhir.exceptions.FHIRException {
-		return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theValueSet);
+		return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet((ValueSet) theValueSet);
 	}
 
 	@Override

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

@@ -37,6 +37,9 @@ import org.springframework.context.event.ContextStartedEvent;
 import org.springframework.context.event.EventListener;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
+import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
+import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
 
 public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
 
@@ -72,7 +75,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
 	public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
 		CodeSystem resourceToStore;
 		try {
-			resourceToStore = VersionConvertor_30_40.convertCodeSystem(theCodeSystemResource);
+			resourceToStore = convertCodeSystem(theCodeSystemResource);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}
@@ -89,7 +92,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
 	public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
 		ConceptMap resourceToStore;
 		try {
-			resourceToStore = VersionConvertor_30_40.convertConceptMap(theConceptMap);
+			resourceToStore = convertConceptMap(theConceptMap);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}
@@ -105,7 +108,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
 	public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
 		ValueSet valueSetDstu3;
 		try {
-			valueSetDstu3 = VersionConvertor_30_40.convertValueSet(theValueSet);
+			valueSetDstu3 = convertValueSet(theValueSet);
 		} catch (FHIRException e) {
 			throw new InternalErrorException(e);
 		}

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

@@ -62,7 +62,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
 	public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
 		validateCodeSystemForStorage(theCodeSystemResource);
 
-		CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(theCodeSystemResource);
+		CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(theCodeSystemResource);
 		if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
 			String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
 			return myCodeSystemResourceDao.update(codeSystemR4, matchUrl).getId();
@@ -74,7 +74,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
 	@Override
 	public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
 
-		ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(theConceptMap);
+		ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap40_50.convertConceptMap(theConceptMap);
 
 		if (isBlank(theConceptMap.getIdElement().getIdPart())) {
 			String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
@@ -87,7 +87,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
 	@Override
 	public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
 
-		ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(theValueSet);
+		ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(theValueSet);
 
 		if (isBlank(theValueSet.getIdElement().getIdPart())) {
 			String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());

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

@@ -50,4 +50,9 @@ public interface ITermDeferredStorageSvc {
 	void addConceptMapsToStorageQueue(List<ConceptMap> theConceptMaps);
 
 	void addValueSetsToStorageQueue(List<ValueSet> theValueSets);
+
+	/**
+	 * This is mostly here for unit tests - Saves any and all deferred concepts and links
+	 */
+	void saveAllDeferred();
 }

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

@@ -39,11 +39,10 @@ public class SearchBuilderTest {
 
 		TypedQuery mockQuery = mock(TypedQuery.class);
 		when(mockEntityManager.createQuery(any(), any())).thenReturn(mockQuery);
-		List<ResourceLink> resultList = new ArrayList<>();
+		List<Long> resultList = new ArrayList<>();
-		ResourceLink link = new ResourceLink();
+		Long link = 1L;
 		ResourceTable target = new ResourceTable();
 		target.setId(1L);
-		link.setTargetResource(target);
 		resultList.add(link);
 		when(mockQuery.getResultList()).thenReturn(resultList);
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2ValidateTest.java

@@ -1,9 +1,5 @@
 package ca.uhn.fhir.jpa.dao.dstu2;
 
-import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.fail;
-
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
@@ -32,7 +28,11 @@ import org.junit.Before;
 import org.junit.Test;
 
 import java.io.IOException;
-import java.util.Arrays;
+import java.util.Collections;
+
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
 
 public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2ValidateTest.class);
@@ -94,15 +94,14 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
 		myStructureDefinitionDao.create(sd, mySrd);
 
 		Observation input = new Observation();
-		ResourceMetadataKeyEnum.PROFILES.put(input, Arrays.asList(new IdDt(sd.getUrl())));
+		ResourceMetadataKeyEnum.PROFILES.put(input, Collections.singletonList(new IdDt(sd.getUrl())));
 
 		input.addIdentifier().setSystem("http://acme").setValue("12345");
 		input.getEncounter().setReference("http://foo.com/Encounter/9");
 		input.setStatus(ObservationStatusEnum.FINAL);
 		input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
 
-		String encoded = null;
+		String encoded;
-		MethodOutcome outcome = null;
 		ValidationModeEnum mode = ValidationModeEnum.CREATE;
 		switch (enc) {
 		case JSON:
@@ -130,12 +129,12 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
 	}
 
 	@Test
-	public void testValidateResourceContainingProfileDeclarationInvalid() throws Exception {
+	public void testValidateResourceContainingProfileDeclarationInvalid() {
 		String methodName = "testValidateResourceContainingProfileDeclarationInvalid";
 
 		Observation input = new Observation();
 		String profileUri = "http://example.com/StructureDefinition/" + methodName;
-		ResourceMetadataKeyEnum.PROFILES.put(input, Arrays.asList(new IdDt(profileUri)));
+		ResourceMetadataKeyEnum.PROFILES.put(input, Collections.singletonList(new IdDt(profileUri)));
 
 		input.addIdentifier().setSystem("http://acme").setValue("12345");
 		input.getEncounter().setReference("http://foo.com/Encounter/9");
@@ -148,7 +147,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
 
 		String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome());
 		ourLog.info(ooString);
-		assertThat(ooString, containsString("StructureDefinition reference \\\"" + profileUri + "\\\" could not be resolved"));
+		assertThat(ooString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
 
 	}
 

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

@@ -35,7 +35,6 @@ import ca.uhn.fhir.util.UrlUtil;
 import org.apache.commons.io.IOUtils;
 import org.hibernate.search.jpa.FullTextEntityManager;
 import org.hibernate.search.jpa.Search;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.exceptions.FHIRException;
@@ -60,6 +59,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.util.Map;
 
+import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
 import static org.junit.Assert.fail;
 
 @RunWith(SpringJUnit4ClassRunner.class)
@@ -386,7 +386,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	 */
 	public static ConceptMap createConceptMap() {
 		try {
-			return VersionConvertor_30_40.convertConceptMap(BaseJpaR4Test.createConceptMap());
+			return convertConceptMap(BaseJpaR4Test.createConceptMap());
 		} catch (FHIRException fe) {
 			throw new InternalErrorException(fe);
 		}

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

@@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.TokenParamModifier;
@@ -134,8 +135,13 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		}
 
 		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
+
+		myTermDeferredStorageSvc.saveAllDeferred();
 	}
 
+	@Autowired
+	private ITermDeferredStorageSvc myTermDeferredStorageSvc;
+
 	private void createExternalCsAndLocalVs() {
 		CodeSystem codeSystem = createExternalCs();
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java

@@ -326,11 +326,11 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
 			myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
 			fail();
 		} catch (PreconditionFailedException e) {
-			String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome());
+			OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
-			ourLog.info(ooString);
+			String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
-			assertThat(ooString, containsString("StructureDefinition reference \\\"" + profileUri + "\\\" could not be resolved"));
+			ourLog.info(outputString);
+			assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
 		}
-
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -162,6 +162,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Qualifier("myConditionDaoR4")
 	protected IFhirResourceDao<Condition> myConditionDao;
 	@Autowired
+	@Qualifier("myEpisodeOfCareDaoR4")
+	protected IFhirResourceDao<EpisodeOfCare> myEpisodeOfCareDao;
+	@Autowired
 	protected DaoConfig myDaoConfig;
 	@Autowired
 	protected ModelConfig myModelConfig;
@@ -169,6 +172,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Qualifier("myDeviceDaoR4")
 	protected IFhirResourceDao<Device> myDeviceDao;
 	@Autowired
+	@Qualifier("myProvenanceDaoR4")
+	protected IFhirResourceDao<Provenance> myProvenanceDao;
+	@Autowired
 	@Qualifier("myDiagnosticReportDaoR4")
 	protected IFhirResourceDao<DiagnosticReport> myDiagnosticReportDao;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java

@@ -133,6 +133,38 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
 		assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
 	}
 
+
+	@Test
+	public void testCreateWithClientAssignedId() {
+		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
+
+		runInTransaction(() -> {
+			Patient p = new Patient();
+			p.getMaritalStatus().setText("123");
+			return myPatientDao.create(p).getId().toUnqualified();
+		});
+
+		myCaptureQueriesListener.clear();
+
+		runInTransaction(() -> {
+			Patient p = new Patient();
+			p.setId("AAA");
+			p.getMaritalStatus().setText("123");
+			return myPatientDao.update(p).getId().toUnqualified();
+		});
+
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+		assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
+		myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
+		assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
+		myCaptureQueriesListener.logInsertQueriesForCurrentThread();
+		assertEquals(4, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
+		myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
+		assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
+	}
+
+
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java

@@ -3,7 +3,14 @@ package ca.uhn.fhir.jpa.dao.r4;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.entity.Search;
-import ca.uhn.fhir.jpa.model.entity.*;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
+import ca.uhn.fhir.jpa.model.entity.ResourceLink;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap.EverythingModeEnum;
@@ -33,7 +40,11 @@ import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.r4.model.Observation.ObservationStatus;
 import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
 import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
-import org.junit.*;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
@@ -44,12 +55,30 @@ import javax.servlet.http.HttpServletRequest;
 import java.io.IOException;
 import java.math.BigDecimal;
 import java.nio.charset.StandardCharsets;
-import java.util.*;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
 import java.util.stream.Collectors;
 
 import static org.hamcrest.CoreMatchers.is;
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.contains;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.endsWith;
+import static org.hamcrest.Matchers.hasItem;
+import static org.hamcrest.Matchers.hasItems;
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.not;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 import static org.mockito.Mockito.mock;
 
 @SuppressWarnings({"unchecked", "Duplicates"})
@@ -73,6 +102,28 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
 	}
 
+	@Test
+	public void testCanonicalReference() {
+		StructureDefinition sd = new StructureDefinition();
+		sd.getSnapshot().addElement().getBinding().setValueSet("http://foo");
+		String id = myStructureDefinitionDao.create(sd).getId().toUnqualifiedVersionless().getValue();
+
+		{
+			SearchParameterMap map = new SearchParameterMap();
+			map.setLoadSynchronous(true);
+			map.add(StructureDefinition.SP_VALUESET, new ReferenceParam("http://foo"));
+			List<String> ids = toUnqualifiedVersionlessIdValues(myStructureDefinitionDao.search(map));
+			assertThat(ids, contains(id));
+		}
+		{
+			SearchParameterMap map = new SearchParameterMap();
+			map.setLoadSynchronous(true);
+			map.add(StructureDefinition.SP_VALUESET, new ReferenceParam("http://foo2"));
+			List<String> ids = toUnqualifiedVersionlessIdValues(myStructureDefinitionDao.search(map));
+			assertThat(ids, empty());
+		}
+	}
+
 	@Test
 	public void testHasConditionAgeCompare() {
 		Patient patient = new Patient();
@@ -569,6 +620,41 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testHasLimitsByType() {
+
+		Patient patient = new Patient();
+		patient.setActive(true);
+		IIdType patientId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
+
+		Encounter encounter = new Encounter();
+		encounter.setStatus(Encounter.EncounterStatus.ARRIVED);
+		IIdType encounterId = myEncounterDao.create(encounter).getId().toUnqualifiedVersionless();
+
+		Device device = new Device();
+		device.setManufacturer("Acme");
+		IIdType deviceId = myDeviceDao.create(device).getId().toUnqualifiedVersionless();
+
+		Provenance provenance = new Provenance();
+		provenance.addTarget().setReferenceElement(patientId);
+		provenance.addTarget().setReferenceElement(encounterId);
+		provenance.addAgent().setWho(new Reference(deviceId));
+		myProvenanceDao.create(provenance);
+
+		String criteria = "_has:Provenance:target:agent=" + deviceId.getValue();
+		SearchParameterMap map = myMatchUrlService.translateMatchUrl(criteria, myFhirCtx.getResourceDefinition(Encounter.class));
+
+		map.setLoadSynchronous(true);
+
+		myCaptureQueriesListener.clear();
+		IBundleProvider results = myEncounterDao.search(map);
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+
+		List<String> ids = toUnqualifiedVersionlessIdValues(results);
+		assertThat(ids, containsInAnyOrder(encounterId.getValue()));
+
+	}
+
 	@Test
 	public void testHasParameter() {
 		IIdType pid0;
@@ -3258,6 +3344,105 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		}
 	}
 
+	@Test
+	public void testSearchWithDateAndReusesExistingJoin() {
+		// Add a search parameter to Observation.issued, so that between that one
+		// and the existing one on Observation.effective, we have 2 date search parameters
+		// on the same resource
+		{
+			SearchParameter sp = new SearchParameter();
+			sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+			sp.addBase("Observation");
+			sp.setType(Enumerations.SearchParamType.DATE);
+			sp.setCode("issued");
+			sp.setExpression("Observation.issued");
+			mySearchParameterDao.create(sp);
+			mySearchParamRegistry.forceRefresh();
+		}
+
+		// Dates are reversed on these two observations
+		IIdType obsId1;
+		{
+			Observation obs = new Observation();
+			obs.setIssuedElement(new InstantType("2020-06-06T12:00:00Z"));
+			obs.setEffective(new InstantType("2019-06-06T12:00:00Z"));
+			obsId1 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+		}
+		IIdType obsId2;
+		{
+			Observation obs = new Observation();
+			obs.setIssuedElement(new InstantType("2019-06-06T12:00:00Z"));
+			obs.setEffective(new InstantType("2020-06-06T12:00:00Z"));
+			obsId2 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+		}
+
+		// Add two with a period
+		IIdType obsId3;
+		{
+			Observation obs = new Observation();
+			obs.setEffective(new Period().setStartElement(new DateTimeType("2000-06-06T12:00:00Z")).setEndElement(new DateTimeType("2001-06-06T12:00:00Z")));
+			obsId3 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+		}
+		IIdType obsId4;
+		{
+			Observation obs = new Observation();
+			obs.setEffective(new Period().setStartElement(new DateTimeType("2001-01-01T12:00:00Z")).setEndElement(new DateTimeType("2002-01-01T12:00:00Z")));
+			obsId4 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+		}
+
+		// Two AND instances of 1 SP
+		{
+			myCaptureQueriesListener.clear();
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			params.add("issued", new DateParam("ge2020-06-05"));
+			params.add("issued", new DateParam("lt2020-06-07"));
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+			assertThat(patients.toString(), patients, contains(obsId1));
+			String searchQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+			ourLog.info("Search query:\n{}", searchQuery);
+			assertEquals(searchQuery, 1, StringUtils.countMatches(searchQuery.toLowerCase(), "join"));
+			assertEquals(searchQuery, 1, StringUtils.countMatches(searchQuery.toLowerCase(), "hash_identity"));
+			assertEquals(searchQuery, 2, StringUtils.countMatches(searchQuery.toLowerCase(), "sp_value_low"));
+		}
+
+		// Two AND instances of 1 SP and 1 instance of another
+		{
+			myCaptureQueriesListener.clear();
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			params.add("issued", new DateParam("ge2020-06-05"));
+			params.add("issued", new DateParam("lt2020-06-07"));
+			params.add("date", new DateParam("gt2019-06-05"));
+			params.add("date", new DateParam("lt2019-06-07"));
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+			assertThat(patients.toString(), patients, contains(obsId1));
+			String searchQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+			ourLog.info("Search query:\n{}", searchQuery);
+			assertEquals(searchQuery, 2, StringUtils.countMatches(searchQuery.toLowerCase(), "join"));
+			assertEquals(searchQuery, 2, StringUtils.countMatches(searchQuery.toLowerCase(), "hash_identity"));
+			assertEquals(searchQuery, 4, StringUtils.countMatches(searchQuery.toLowerCase(), "sp_value_low"));
+		}
+
+		// Period search
+		{
+			myCaptureQueriesListener.clear();
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			params.add("date", new DateParam("lt2002-01-01T12:00:00Z"));
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+			assertThat(patients.toString(), patients, containsInAnyOrder(obsId3, obsId4));
+			String searchQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+			ourLog.info("Search query:\n{}", searchQuery);
+			assertEquals(searchQuery, 1, StringUtils.countMatches(searchQuery.toLowerCase(), "join"));
+			assertEquals(searchQuery, 1, StringUtils.countMatches(searchQuery.toLowerCase(), "hash_identity"));
+			assertEquals(searchQuery, 1, StringUtils.countMatches(searchQuery.toLowerCase(), "sp_value_low"));
+		}
+
+	}
+
+
+
 	@Test
 	public void testSearchWithFetchSizeDefaultMaximum() {
 		myDaoConfig.setFetchSizeDefaultMaximum(5);
@@ -4228,6 +4413,44 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		}
 	}
 
+	@Test
+	public void testCircularReferencesDontBreakRevIncludes() {
+
+		Patient p = new Patient();
+		p.setActive(true);
+		IIdType patientId = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+
+		Encounter enc = new Encounter();
+		enc.setStatus(Encounter.EncounterStatus.ARRIVED);
+		enc.getSubject().setReference(patientId.getValue());
+		IIdType encId = myEncounterDao.create(enc).getId().toUnqualifiedVersionless();
+
+		Condition cond = new Condition();
+		cond.addIdentifier().setSystem("http://foo").setValue("123");
+		IIdType conditionId = myConditionDao.create(cond).getId().toUnqualifiedVersionless();
+
+		EpisodeOfCare ep = new EpisodeOfCare();
+		ep.setStatus(EpisodeOfCare.EpisodeOfCareStatus.ACTIVE);
+		IIdType epId = myEpisodeOfCareDao.create(ep).getId().toUnqualifiedVersionless();
+
+		enc.getEpisodeOfCareFirstRep().setReference(ep.getId());
+		myEncounterDao.update(enc);
+		cond.getEncounter().setReference(enc.getId());
+		myConditionDao.update(cond);
+		ep.getDiagnosisFirstRep().getCondition().setReference(cond.getId());
+		myEpisodeOfCareDao.update(ep);
+
+		// Search time
+		SearchParameterMap params = new SearchParameterMap();
+		params.setLoadSynchronous(true);
+		params.addRevInclude(new Include("*").setRecurse(true));
+		IBundleProvider results = myPatientDao.search(params);
+		List<String> values = toUnqualifiedVersionlessIdValues(results);
+		assertThat(values.toString(), values, containsInAnyOrder(patientId.getValue(), encId.getValue(), conditionId.getValue(), epId.getValue()));
+
+	}
+
+
 	private String toStringMultiline(List<?> theResults) {
 		StringBuilder b = new StringBuilder();
 		for (Object next : theResults) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java

@@ -30,7 +30,6 @@ import org.junit.Test;
 import org.springframework.aop.framework.AopProxyUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.scheduling.concurrent.ThreadPoolExecutorFactoryBean;
-import org.springframework.test.context.TestPropertySource;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -163,7 +162,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testFetchTotalAccurateForSlowLoading() throws InterruptedException {
+	public void testFetchTotalAccurateForSlowLoading() {
 		create200Patients();
 
 		mySearchCoordinatorSvcImpl.setLoadingThrottleForUnitTests(25);
@@ -836,8 +835,6 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
-		// Because of the forced ID's bidirectional link HFJ_RESOURCE <-> HFJ_FORCED_ID
-		assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
 		runInTransaction(() -> {
 			assertEquals(1, myResourceTableDao.count());
 			assertEquals(1, myResourceHistoryTableDao.count());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchTest.java

@@ -23,6 +23,7 @@ import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.ValidationResult;
+import org.hamcrest.Matchers;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.*;
 import org.junit.AfterClass;
@@ -37,8 +38,10 @@ import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.PlatformTransactionManager;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Collectors;
 
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.junit.Assert.assertEquals;
@@ -146,6 +149,53 @@ public class FhirResourceDaoR4SearchWithElasticSearchTest extends BaseJpaTest {
 
 	}
 
+
+	@Test
+	public void testExpandVsWithMultiInclude_All() throws IOException {
+		CodeSystem cs = loadResource(myFhirCtx, CodeSystem.class, "/r4/expand-multi-cs.json");
+		myCodeSystemDao.update(cs);
+
+		ValueSet vs = loadResource(myFhirCtx, ValueSet.class, "/r4/expand-multi-vs-all.json");
+		ValueSet expanded = myValueSetDao.expand(vs, null);
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
+
+		// All codes
+		List<String> codes = expanded
+			.getExpansion()
+			.getContains()
+			.stream()
+			.map(t -> t.getCode())
+			.sorted()
+			.collect(Collectors.toList());
+		assertThat(codes.toString(), codes, Matchers.contains("advice", "message", "note", "notification"));
+	}
+
+
+	@Test
+	public void testExpandVsWithMultiInclude_Some() throws IOException {
+		CodeSystem cs = loadResource(myFhirCtx, CodeSystem.class, "/r4/expand-multi-cs.json");
+		myCodeSystemDao.update(cs);
+
+		ValueSet vs = loadResource(myFhirCtx, ValueSet.class, "/r4/expand-multi-vs-all.json");
+		vs.getCompose().getInclude().get(0).getConcept().remove(0);
+		vs.getCompose().getInclude().get(0).getConcept().remove(0);
+
+		ValueSet expanded = myValueSetDao.expand(vs, null);
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
+
+		// All codes
+		List<String> codes = expanded
+			.getExpansion()
+			.getContains()
+			.stream()
+			.map(t -> t.getCode())
+			.sorted()
+			.collect(Collectors.toList());
+		assertThat(codes.toString(), codes, Matchers.contains("advice", "note"));
+	}
+
 	private CodeSystem createExternalCs() {
 		CodeSystem codeSystem = new CodeSystem();
 		codeSystem.setUrl(URL_MY_CODE_SYSTEM);

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

@@ -164,6 +164,8 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		}
 
 		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+
+		myTerminologyDeferredStorageSvc.saveAllDeferred();
 	}
 
 	private void createLocalCsAndVs() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -147,6 +147,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		}
 		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://loinc.org", codesToAdd);
 
+		myTerminologyDeferredStorageSvc.saveAllDeferred();
+
 		// Create a valueset
 		ValueSet vs = new ValueSet();
 		vs.setUrl("http://example.com/fhir/ValueSet/observation-vitalsignresult");
@@ -399,12 +401,11 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 			myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
 			fail();
 		} catch (PreconditionFailedException e) {
-			String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome());
+			org.hl7.fhir.r4.model.OperationOutcome oo = (org.hl7.fhir.r4.model.OperationOutcome) e.getOperationOutcome();
-			ourLog.info(ooString);
+			String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
-			assertThat(ooString, containsString("StructureDefinition reference \\\"" + profileUri + "\\\" could not be resolved"));
+			ourLog.info(outputString);
+			assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
 		}
-
-
 	}
 
 	@Test
@@ -618,6 +619,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		upload("/r4/uscore/ValueSet-omb-race-category.json");
 		upload("/r4/uscore/ValueSet-us-core-usps-state.json");
 
+		myTerminologyDeferredStorageSvc.saveAllDeferred();
+
 		{
 			String resource = loadResource("/r4/uscore/patient-resource-badcode.json");
 			IBaseResource parsedResource = myFhirCtx.newJsonParser().parseResource(resource);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CacheTest.java

@@ -9,20 +9,29 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Patient;
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import java.util.Date;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.blankOrNullString;
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.greaterThan;
+import static org.hamcrest.Matchers.lessThan;
 import static org.hamcrest.core.IsNot.not;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
 
 public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 
+	private static final Logger ourLog = LoggerFactory.getLogger(ResourceProviderR4CacheTest.class);
 	private CapturingInterceptor myCapturingInterceptor;
 	@Autowired
 	private ISearchDao mySearchEntityDao;
@@ -184,6 +193,39 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
 		assertEquals(results1.getId(), results2.getId());
 	}
 
+	@Test
+	public void testDeletedSearchResultsNotReturnedFromCache() {
+		Patient p = new Patient();
+		p.addName().setFamily("Foo");
+		String p1Id = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
+
+		p = new Patient();
+		p.addName().setFamily("Foo");
+		String p2Id = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
+
+		Bundle resp1 = ourClient
+			.search()
+			.forResource("Patient")
+			.where(Patient.NAME.matches().value("foo"))
+			.returnBundle(Bundle.class)
+			.execute();
+		assertEquals(2, resp1.getEntry().size());
+
+		ourClient.delete().resourceById(new IdType(p1Id)).execute();
+
+		Bundle resp2 = ourClient
+			.search()
+			.forResource("Patient")
+			.where(Patient.NAME.matches().value("foo"))
+			.returnBundle(Bundle.class)
+			.execute();
+
+		assertEquals(resp1.getId(), resp2.getId());
+
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp2));
+		assertEquals(1, resp2.getEntry().size());
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -15,6 +15,7 @@ import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.parser.StrictErrorHandler;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.*;
+import ca.uhn.fhir.rest.client.apache.ResourceEntity;
 import ca.uhn.fhir.rest.client.api.IClientInterceptor;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.IHttpRequest;
@@ -26,6 +27,9 @@ import ca.uhn.fhir.rest.server.exceptions.*;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.UrlUtil;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import ca.uhn.fhir.validation.SingleValidationMessage;
+import ca.uhn.fhir.validation.ValidationResult;
 import com.google.common.base.Charsets;
 import com.google.common.collect.Lists;
 import org.apache.commons.io.IOUtils;
@@ -52,6 +56,7 @@ import org.hl7.fhir.r4.model.Observation.ObservationStatus;
 import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType;
 import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
 import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
+import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.junit.*;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.test.util.AopTestUtils;
@@ -2260,6 +2265,28 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		}
 	}
 
+
+	@Test
+	public void testValidateResourceContainingProfileDeclarationDoesntResolve() throws IOException {
+		Observation input = new Observation();
+		input.getText().setDiv(new XhtmlNode().setValue("<div>AA</div>")).setStatus(Narrative.NarrativeStatus.GENERATED);
+		input.getMeta().addProfile("http://foo/structuredefinition/myprofile");
+
+		input.getCode().setText("Hello");
+		input.setStatus(ObservationStatus.FINAL);
+
+		HttpPost post = new HttpPost(ourServerBase + "/Observation/$validate?_pretty=true");
+		post.setEntity(new ResourceEntity(myFhirCtx, input));
+
+		try (CloseableHttpResponse resp = ourHttpClient.execute(post)) {
+			String respString = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
+			ourLog.info(respString);
+			assertEquals(412, resp.getStatusLine().getStatusCode());
+			assertThat(respString, containsString("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked"));
+		}
+	}
+
+
 	@SuppressWarnings("unused")
 	@Test
 	public void testFullTextSearch() throws Exception {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java

@@ -182,33 +182,11 @@ public class SearchCoordinatorSvcImplTest {
 		when(mySearchBuilder.createQuery(any(), any(), any())).thenReturn(iter);
 		doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
 
-		when(mySearchResultCacheSvc.fetchResultPids(any(), anyInt(), anyInt())).thenAnswer(t -> {
-			List<ResourcePersistentId> returnedValues = iter.getReturnedValues();
-			int offset = t.getArgument(1, Integer.class);
-			int end = t.getArgument(2, Integer.class);
-			end = Math.min(end, returnedValues.size());
-			offset = Math.min(offset, returnedValues.size());
-			ourLog.info("findWithSearchUuid {} - {} out of {} values", offset, end, returnedValues.size());
-			return returnedValues.subList(offset, end);
-		});
-
-		when(mySearchResultCacheSvc.fetchAllResultPids(any())).thenReturn(allResults);
-
-		when(mySearchCacheSvc.tryToMarkSearchAsInProgress(any())).thenAnswer(t->{
-			Search search = t.getArgument(0, Search.class);
-			assertEquals(SearchStatusEnum.PASSCMPLET, search.getStatus());
-			search.setStatus(SearchStatusEnum.LOADING);
-			return Optional.of(search);
-		});
-		
 		when(mySearchCacheSvc.save(any())).thenAnswer(t -> {
 			Search search = t.getArgument(0, Search.class);
 			myCurrentSearch = search;
 			return search;
 		});
-		when(mySearchCacheSvc.fetchByUuid(any())).thenAnswer(t -> Optional.ofNullable(myCurrentSearch));
-		IFhirResourceDao dao = myCallingDao;
-		when(myDaoRegistry.getResourceDao(any(String.class))).thenReturn(dao);
 
 		IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null);
 		assertNotNull(result.getUuid());
@@ -602,6 +580,11 @@ public class SearchCoordinatorSvcImplTest {
 			return myWrap.getSkippedCount();
 		}
 
+		@Override
+		public int getNonSkippedCount() {
+			return myCount;
+		}
+
 		@Override
 		public void close() {
 			// nothing
@@ -611,6 +594,7 @@ public class SearchCoordinatorSvcImplTest {
 	public static class ResultIterator extends BaseIterator<ResourcePersistentId> implements IResultIterator {
 
 		private final Iterator<ResourcePersistentId> myWrap;
+		private int myCount;
 
 		ResultIterator(Iterator<ResourcePersistentId> theWrap) {
 			myWrap = theWrap;
@@ -623,6 +607,7 @@ public class SearchCoordinatorSvcImplTest {
 
 		@Override
 		public ResourcePersistentId next() {
+			myCount++;
 			return myWrap.next();
 		}
 
@@ -631,6 +616,11 @@ public class SearchCoordinatorSvcImplTest {
 			return 0;
 		}
 
+		@Override
+		public int getNonSkippedCount() {
+			return myCount;
+		}
+
 		@Override
 		public void close() {
 			// nothing
@@ -697,6 +687,11 @@ public class SearchCoordinatorSvcImplTest {
 			}
 		}
 
+		@Override
+		public int getNonSkippedCount() {
+			return 0;
+		}
+
 		@Override
 		public void close() {
 			// nothing

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

@@ -1,10 +1,12 @@
 package ca.uhn.fhir.jpa.term;
 
 import ca.uhn.fhir.context.support.IContextValidationSupport;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
 import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.UriParam;
@@ -16,25 +18,36 @@ import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
 import java.util.stream.Collectors;
 
+import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.apache.commons.lang3.StringUtils.leftPad;
 import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.Matchers.matchesPattern;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.fail;
 
 public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 	private static final Logger ourLog = LoggerFactory.getLogger(TerminologySvcDeltaR4Test.class);
 
+	@After
+	public void after() {
+		myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
+	}
+
 
 	@Test
 	public void testAddRootConcepts() {
@@ -115,17 +128,23 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 			ourLog.info("All concepts: {}", myTermConceptDao.findAll());
 		});
 
+		myCaptureQueriesListener.clear();
+
 		delta = new CustomTerminologySet();
 		TermConcept root = delta.addRootConcept("RootA", "Root A");
 		root.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA");
 		root.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAB").setDisplay("Child AB");
 		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
+
+		myCaptureQueriesListener.logAllQueriesForCurrentThread();
+
 		assertHierarchyContains(
 			"RootA seq=0",
 			" ChildAA seq=0",
 			" ChildAB seq=1",
 			"RootB seq=0"
 		);
+
 	}
 
 	@Test
@@ -156,12 +175,86 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 		outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
 		assertHierarchyContains(
 			"RootA seq=0",
+			" ChildAA seq=0",
+			"  ChildAAA seq=0",
 			"RootB seq=0",
 			" ChildAA seq=0",
 			"  ChildAAA seq=0"
 		);
 		assertEquals(2, outcome.getUpdatedConceptCount());
 
+		runInTransaction(() -> {
+			TermConcept concept = myTermSvc.findCode("http://foo/cs", "ChildAA").orElseThrow(() -> new IllegalStateException());
+			assertEquals(2, concept.getParents().size());
+			assertThat(concept.getParentPidsAsString(), matchesPattern("^[0-9]+ [0-9]+$"));
+		});
+
+	}
+
+	@Test
+	public void testReAddingConceptsDoesntRecreateExistingLinks() {
+		createNotPresentCodeSystem();
+		assertHierarchyContains();
+
+		UploadStatistics outcome;
+		CustomTerminologySet delta;
+
+		myCaptureQueriesListener.clear();
+
+		delta = new CustomTerminologySet();
+		delta.addRootConcept("RootA", "Root A")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA");
+		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
+		assertHierarchyContains(
+			"RootA seq=0",
+			" ChildAA seq=0"
+		);
+
+		myCaptureQueriesListener.logDeleteQueries();
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+		myCaptureQueriesListener.logInsertQueries();
+		// 2 concepts, 1 link
+		assertEquals(3, myCaptureQueriesListener.countInsertQueries());
+		myCaptureQueriesListener.clear();
+
+		delta = new CustomTerminologySet();
+		delta.addRootConcept("RootA", "Root A")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAAA").setDisplay("Child AAA");
+		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
+		assertHierarchyContains(
+			"RootA seq=0",
+			" ChildAA seq=0",
+			"  ChildAAA seq=0"
+		);
+
+		myCaptureQueriesListener.logDeleteQueries();
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+		myCaptureQueriesListener.logInsertQueries();
+		// 1 concept, 1 link
+		assertEquals(2, myCaptureQueriesListener.countInsertQueries());
+		myCaptureQueriesListener.clear();
+
+		delta = new CustomTerminologySet();
+		delta.addRootConcept("RootA", "Root A")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAAA").setDisplay("Child AAA")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAAAA").setDisplay("Child AAAA");
+		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
+		assertHierarchyContains(
+			"RootA seq=0",
+			" ChildAA seq=0",
+			"  ChildAAA seq=0",
+			"   ChildAAAA seq=0"
+		);
+
+		myCaptureQueriesListener.logDeleteQueries();
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+		myCaptureQueriesListener.logInsertQueries();
+		// 1 concept, 1 link
+		assertEquals(2, myCaptureQueriesListener.countInsertQueries());
+		myCaptureQueriesListener.clear();
+
 	}
 
 	@Test
@@ -281,6 +374,49 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 	}
 
 
+	@Test
+	public void testAddLargeHierarchy() {
+		myDaoConfig.setDeferIndexingForCodesystemsOfSize(5);
+
+		createNotPresentCodeSystem();
+		ValueSet vs;
+		vs = expandNotPresentCodeSystem();
+		assertEquals(0, vs.getExpansion().getContains().size());
+
+		CustomTerminologySet delta = new CustomTerminologySet();
+
+		// Create a nice deep hierarchy
+		TermConcept concept = delta.addRootConcept("Root", "Root");
+		int nestedDepth = 10;
+		for (int i = 0; i < nestedDepth; i++) {
+			String name = concept.getCode();
+			concept = concept.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode(name + "0").setDisplay(name + "0");
+		}
+
+		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
+
+		assertFalse(myTermDeferredStorageSvc.isStorageQueueEmpty());
+		while (!myTermDeferredStorageSvc.isStorageQueueEmpty()) {
+			myTermDeferredStorageSvc.saveDeferred();
+		}
+
+		List<String> expectedHierarchy = new ArrayList<>();
+		for (int i = 0; i < nestedDepth + 1; i++) {
+			String expected = leftPad("", i, " ") +
+				"Root" +
+				leftPad("", i, "0") +
+				" seq=0";
+			expectedHierarchy.add(expected);
+		}
+
+		assertHierarchyContains(expectedHierarchy.toArray(new String[0]));
+
+	}
+
+	@Autowired
+	private ITermDeferredStorageSvc myTermDeferredStorageSvc;
+
+
 	@Test
 	public void testAddModifiesExistingCodesInPlace() {
 
@@ -307,54 +443,6 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 		assertEquals("CODEA1", myTermSvc.lookupCode(myFhirCtx, "http://foo", "codea").getCodeDisplay());
 	}
 
-	@Test
-	public void testAddRelocateHierarchy() {
-		createNotPresentCodeSystem();
-
-		// Add code hierarchy
-		CustomTerminologySet delta = new CustomTerminologySet();
-		TermConcept codeA = delta.addRootConcept("CodeA", "Code A");
-		TermConcept codeAA = codeA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAA").setDisplay("Code AA");
-		codeAA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAAA").setDisplay("Code AAA");
-		codeAA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAAB").setDisplay("Code AAB");
-		TermConcept codeB = delta.addRootConcept("CodeB", "Code B");
-		TermConcept codeBA = codeB.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeBA").setDisplay("Code BA");
-		codeBA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeBAA").setDisplay("Code BAA");
-		codeBA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeBAB").setDisplay("Code BAB");
-		UploadStatistics outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
-		assertEquals(8, outcome.getUpdatedConceptCount());
-		assertHierarchyContains(
-			"CodeA seq=0",
-			" CodeAA seq=0",
-			"  CodeAAA seq=0",
-			"  CodeAAB seq=1",
-			"CodeB seq=0",
-			" CodeBA seq=0",
-			"  CodeBAA seq=0",
-			"  CodeBAB seq=1"
-		);
-
-		// Move a single child code to a new spot and make sure the hierarchy comes along
-		// for the ride..
-		delta = new CustomTerminologySet();
-		delta
-			.addRootConcept("CodeB", "Code B")
-			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAA").setDisplay("Code AA");
-		outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
-		assertEquals(2, outcome.getUpdatedConceptCount());
-		assertHierarchyContains(
-			"CodeA seq=0",
-			"CodeB seq=0",
-			" CodeBA seq=0",
-			"  CodeBAA seq=0",
-			"  CodeBAB seq=1",
-			" CodeAA seq=0", // <-- CodeAA got added here so it comes second
-			"  CodeAAA seq=0",
-			"  CodeAAB seq=1"
-		);
-
-	}
-
 	@Test
 	@Ignore
 	public void testAddWithPropertiesAndDesignations() {
@@ -464,9 +552,15 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 		assertEquals(true, runInTransaction(() -> myTermSvc.findCode("http://foo/cs", "codeAAA").isPresent()));
 
 		// Remove CodeA
-		delta = new CustomTerminologySet();
+		myCaptureQueriesListener.clear();
-		delta.addRootConcept("codeA");
+		runInTransaction(()->{
-		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsRemove("http://foo/cs", delta);
+			CustomTerminologySet delta2 = new CustomTerminologySet();
+			delta2.addRootConcept("codeA");
+			myTermCodeSystemStorageSvc.applyDeltaCodeSystemsRemove("http://foo/cs", delta2);
+		});
+		myCaptureQueriesListener.logAllQueriesForCurrentThread();
+
+		ourLog.info("*** Done removing");
 
 		assertEquals(false, runInTransaction(() -> myTermSvc.findCode("http://foo/cs", "codeB").isPresent()));
 		assertEquals(false, runInTransaction(() -> myTermSvc.findCode("http://foo/cs", "codeA").isPresent()));