Merge branch 'master' into ng_validation_s13n_interceptors

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

@@ -267,6 +267,7 @@ public class Constants {
 	 */
 	public static final String RESOURCE_PARTITION_ID = Constants.class.getName() + "_RESOURCE_PARTITION_ID";
 	public static final String CT_APPLICATION_GZIP = "application/gzip";
+	public static final String[] EMPTY_STRING_ARRAY = new String[0];
 
 	static {
 		CHARSET_UTF8 = StandardCharsets.UTF_8;

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

@@ -0,0 +1,76 @@
+package ca.uhn.fhir.rest.api;
+
+/*
+ * #%L
+ * HAPI FHIR Search Parameters
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.UrlUtil;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public enum SearchContainedModeEnum {
+
+	/**
+	 * default, search on the non-contained (normal) resources
+	 */
+	FALSE("false"),
+
+	/**
+	 * search on the contained resources only
+	 */
+	TRUE("true"),
+
+	/**
+	 * Search on the normal resources and contained resources.
+	 * This option is not supported yet.
+	 */
+	BOTH("both");
+
+	private static volatile Map<String, SearchContainedModeEnum> ourCodeToEnum;
+	private final String myCode;
+
+	SearchContainedModeEnum(String theCode) {
+		myCode = theCode;
+	}
+
+	private String getCode() {
+		return myCode;
+	}
+
+	public static SearchContainedModeEnum fromCode(String theCode) {
+		Map<String, SearchContainedModeEnum> codeToEnum = ourCodeToEnum;
+		if (codeToEnum == null) {
+			codeToEnum = new HashMap<>();
+			for (SearchContainedModeEnum next : values()) {
+				codeToEnum.put(next.getCode(), next);
+			}
+			ourCodeToEnum = codeToEnum;
+		}
+
+		SearchContainedModeEnum retVal = codeToEnum.get(theCode);
+		if (retVal == null) {
+			throw new InvalidRequestException("Invalid contained mode: " + UrlUtil.sanitizeUrlPart(theCode));
+		}
+
+		return retVal;
+	}
+
+}

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

@@ -1,5 +1,10 @@
 package ca.uhn.fhir.rest.param;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+
 import static org.apache.commons.lang3.StringUtils.defaultString;
 
 /*
@@ -22,11 +27,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
  * #L%
  */
 
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.IQueryParameterType;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-
 /**
  * Implementation of the _has method parameter
  */
@@ -55,7 +55,7 @@ public class HasParam extends BaseParam implements IQueryParameterType {
 
 	@Override
 	String doGetQueryParameterQualifier() {
-		return myTargetResourceType + ':' + myParameterName + ':' + myParameterValue;
+		return ':' + myTargetResourceType + ':' + myReferenceFieldName + ':' + myParameterName;
 	}
 	
 	@Override

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java

@@ -25,7 +25,6 @@ import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
 import org.apache.commons.dbcp2.BasicDataSource;
-import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.dialect.H2Dialect;
 import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
 import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
@@ -49,9 +48,6 @@ public class CommonConfig {
 	@Bean
 	public DaoConfig daoConfig() {
 		DaoConfig retVal = new DaoConfig();
-		retVal.setSubscriptionEnabled(true);
-		retVal.setSubscriptionPollDelay(5000);
-		retVal.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);
 		retVal.setAllowMultipleDelete(true);
 		return retVal;
 	}

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java

@@ -59,9 +59,6 @@ public class FhirServerConfig extends BaseJavaConfigDstu2 {
 	@Bean
 	public DaoConfig daoConfig() {
 		DaoConfig retVal = new DaoConfig();
-		retVal.setSubscriptionEnabled(true);
-		retVal.setSubscriptionPollDelay(5000);
-		retVal.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);
 		retVal.setAllowMultipleDelete(true);
 		return retVal;
 	}
@@ -79,7 +76,6 @@ public class FhirServerConfig extends BaseJavaConfigDstu2 {
 
 	/**
 	 * Do some fancy logging to create a nice access log that has details about each incoming request.
-	 * @return
 	 */
 	public LoggingInterceptor loggingInterceptor() {
 		LoggingInterceptor retVal = new LoggingInterceptor();

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/1953-avoid-npe-performing-partitioned-read-for-unknown-id.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 1953
+title: "A crash was fixed when performing a FHIR read on a partitioned server, where the requested ID is not known. Thanks
+   to Umberto Cappellini for reporting!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2403-support-contained-search.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+issue: 2403
+title: "Optionally support '_contained' resource search by enabling the indexing on the contained resources in the ModelConfig."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2446-issues-with-placeholder-reference-targets-need-to-be-resolved-placeholder-extension.yaml

@@ -2,4 +2,4 @@
 type: add
 issue: 2446
 title: "Auto-created placeholder reference targets now have an extension with the URL
-   `http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder` and a value of `true`."
+   `http://hapifhir.io/fhir/StructureDefinition/resource-placeholder` and a value of `true`."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2454-address-cve-2020-27223.yaml

@@ -0,0 +1,9 @@
+---
+type: security
+issue: 2454
+title: "Addressed the following CVE report by bumping the minor version for Jetty in the root POM:
+   <ul>
+      <li>
+         [CVE-2020-27223](https://nvd.nist.gov/vuln/detail/CVE-2020-27223)
+      </li>
+   </ul>"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2458-hasparam-dogetqueryparameterqualifier-returns-malformed-modifier.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 2458
+title: "`HasParam#doGetQueryParameterQualifier()` returned a malformed modifier. For example, the modifier for
+   `_has:Observation:patient:code=123` was returned as `Observation:code:123` when it should be
+   `:Observation:patient:code`. This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/support-contained-searches.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 2441
+title: "Support has been added to the JPA server for indexing and searching using the `_contained` parameter, which
+   allows searching using chained parameters that chain into contained resources. This feature is disabled by default
+   but can be enabled via a setting on the ModelConfig object."

hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java

@@ -118,11 +118,6 @@ public class DaoConfig {
 	 * update setter javadoc if default changes
 	 */
 	private Integer myFetchSizeDefaultMaximum = null;
-	private int myHardTagListLimit = 1000;
-	/**
-	 * update setter javadoc if default changes
-	 */
-	private boolean myIndexContainedResources = true;
 	private int myMaximumExpansionSize = DEFAULT_MAX_EXPANSION_SIZE;
 	private Integer myMaximumSearchResultCountInTransaction = DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION;
 
@@ -209,9 +204,6 @@ public class DaoConfig {
 	 * Constructor
 	 */
 	public DaoConfig() {
-		setSubscriptionEnabled(true);
-		setSubscriptionPollDelay(0);
-		setSubscriptionPurgeInactiveAfterMillis(Long.MAX_VALUE);
 		setMarkResourcesForReindexingUponSearchParameterChange(true);
 		setReindexThreadCount(Runtime.getRuntime().availableProcessors());
 		setExpungeThreadCount(Runtime.getRuntime().availableProcessors());
@@ -580,20 +572,6 @@ public class DaoConfig {
 		myFetchSizeDefaultMaximum = theFetchSizeDefaultMaximum;
 	}
 
-	/**
-	 * Gets the maximum number of results to return in a GetTags query (DSTU1 only)
-	 */
-	public int getHardTagListLimit() {
-		return myHardTagListLimit;
-	}
-
-	/**
-	 * Gets the maximum number of results to return in a GetTags query (DSTU1 only)
-	 */
-	public void setHardTagListLimit(int theHardTagListLimit) {
-		myHardTagListLimit = theHardTagListLimit;
-	}
-
 	/**
 	 * If set to {@link IndexEnabledEnum#DISABLED} (default is {@link IndexEnabledEnum#DISABLED})
 	 * the server will not create search indexes for search parameters with no values in resources.
@@ -1070,7 +1048,7 @@ public class DaoConfig {
 	 * Note however that references containing purely numeric IDs will not be auto-created
 	 * as they are never allowed to be client supplied in HAPI FHIR JPA.
 	 *
-	 * All placeholder resources created in this way have a meta extension
+	 * All placeholder resources created in this way have an extension
 	 * with the URL {@link HapiExtensions#EXT_RESOURCE_PLACEHOLDER} and the value "true".
 	 * </p>
 	 */
@@ -1094,7 +1072,7 @@ public class DaoConfig {
 	 * Note however that references containing purely numeric IDs will not be auto-created
 	 * as they are never allowed to be client supplied in HAPI FHIR JPA.
 	 *
-	 * All placeholder resources created in this way have a meta extension
+	 * All placeholder resources created in this way have an extension
 	 * with the URL {@link HapiExtensions#EXT_RESOURCE_PLACEHOLDER} and the value "true".
 	 * </p>
 	 */
@@ -1442,22 +1420,6 @@ public class DaoConfig {
 		myExpungeBatchSize = theExpungeBatchSize;
 	}
 
-	/**
-	 * Should contained IDs be indexed the same way that non-contained IDs are (default is
-	 * <code>true</code>)
-	 */
-	public boolean isIndexContainedResources() {
-		return myIndexContainedResources;
-	}
-
-	/**
-	 * Should contained IDs be indexed the same way that non-contained IDs are (default is
-	 * <code>true</code>)
-	 */
-	public void setIndexContainedResources(boolean theIndexContainedResources) {
-		myIndexContainedResources = theIndexContainedResources;
-	}
-
 	/**
 	 * Should resources be marked as needing reindexing when a
 	 * SearchParameter resource is added or changed. This should generally
@@ -1591,62 +1553,6 @@ public class DaoConfig {
 		myValidateSearchParameterExpressionsOnSave = theValidateSearchParameterExpressionsOnSave;
 	}
 
-	/**
-	 * Do not call this method, it exists only for legacy reasons. It
-	 * will be removed in a future version. Configure the page size on your
-	 * paging provider instead.
-	 *
-	 * @deprecated This method does not do anything. Configure the page size on your
-	 * paging provider instead. Deprecated in HAPI FHIR 2.3 (Jan 2017)
-	 */
-	@Deprecated
-	public void setHardSearchLimit(int theHardSearchLimit) {
-		// this method does nothing
-	}
-
-	/**
-	 * This is the maximum number of resources that will be added to a single page of returned resources. Because of
-	 * includes with wildcards and other possibilities it is possible for a client to make requests that include very
-	 * large amounts of data, so this hard limit can be imposed to prevent runaway requests.
-	 *
-	 * @deprecated Deprecated in HAPI FHIR 3.2.0 as this method doesn't actually do anything
-	 */
-	@Deprecated
-	public void setIncludeLimit(@SuppressWarnings("unused") int theIncludeLimit) {
-		// nothing
-	}
-
-	/**
-	 * @deprecated As of HAPI FHIR 3.0.0, subscriptions no longer use polling for
-	 * detecting changes, so this setting has no effect
-	 */
-	@Deprecated
-	public void setSubscriptionEnabled(boolean theSubscriptionEnabled) {
-		// nothing
-	}
-
-	/**
-	 * @deprecated As of HAPI FHIR 3.0.0, subscriptions no longer use polling for
-	 * detecting changes, so this setting has no effect
-	 */
-	@Deprecated
-	public void setSubscriptionPollDelay(long theSubscriptionPollDelay) {
-		// ignore
-	}
-
-	/**
-	 * @deprecated As of HAPI FHIR 3.0.0, subscriptions no longer use polling for
-	 * detecting changes, so this setting has no effect
-	 */
-	@Deprecated
-	public void setSubscriptionPurgeInactiveAfterMillis(Long theMillis) {
-		// ignore
-	}
-
-	public void setSubscriptionPurgeInactiveAfterSeconds(int theSeconds) {
-		setSubscriptionPurgeInactiveAfterMillis(theSeconds * DateUtils.MILLIS_PER_SECOND);
-	}
-
 	/**
 	 * This setting sets the number of search results to prefetch. For example, if this list
 	 * is set to [100, 1000, -1] then the server will initially load 100 results and not

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

@@ -54,6 +54,7 @@ import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.jpa.search.cache.SearchCacheStatusEnum;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
 import ca.uhn.fhir.model.api.IQueryParameterType;
@@ -1149,7 +1150,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		BaseHasResource entity = myEntityManager.find(ResourceTable.class, pid.getIdAsLong());
 
 		// Verify that the resource is for the correct partition
-		if (!requestPartitionId.isAllPartitions()) {
+		if (entity != null && !requestPartitionId.isAllPartitions()) {
 			if (entity.getPartitionId() != null && entity.getPartitionId().getPartitionId() != null) {
 				if (!requestPartitionId.hasPartitionId(entity.getPartitionId().getPartitionId())) {
 					ourLog.debug("Performing a read for PartitionId={} but entity has partition: {}", requestPartitionId, entity.getPartitionId());
@@ -1291,6 +1292,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Override
 	public IBundleProvider search(final SearchParameterMap theParams, RequestDetails theRequest, HttpServletResponse theServletResponse) {
 
+		if (theParams.getSearchContainedMode() == SearchContainedModeEnum.BOTH) {
+			throw new MethodNotAllowedException("Contained mode 'both' is not currently supported");
+		}
+		if (theParams.getSearchContainedMode() != SearchContainedModeEnum.FALSE && !myModelConfig.isIndexOnContainedResources()) {
+			throw new MethodNotAllowedException("Searching with _contained mode enabled is not enabled on this server");
+		}
+
 		if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.DISABLED) {
 			for (List<List<IQueryParameterType>> nextAnds : theParams.values()) {
 				for (List<? extends IQueryParameterType> nextOrs : nextAnds) {

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

@@ -52,6 +52,7 @@ import ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder;
 import ca.uhn.fhir.jpa.search.builder.predicate.UriPredicateBuilder;
 import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
 import ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.util.SourceParam;
@@ -109,6 +110,7 @@ import java.util.Collections;
 import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -286,7 +288,7 @@ public class QueryStack {
 		return new PredicateBuilderCacheLookupResult<>(cacheHit, (T) retVal);
 	}
 
-	private Condition createPredicateComposite(@Nullable DbColumn theSourceJoinColumn, String theResourceName, RuntimeSearchParam theParamDef, List<? extends IQueryParameterType> theNextAnd, RequestPartitionId theRequestPartitionId) {
+	private Condition createPredicateComposite(@Nullable DbColumn theSourceJoinColumn, String theResourceName, String theSpnamePrefix, RuntimeSearchParam theParamDef, List<? extends IQueryParameterType> theNextAnd, RequestPartitionId theRequestPartitionId) {
 
 		Condition orCondidtion = null;
 		for (IQueryParameterType next : theNextAnd) {
@@ -298,11 +300,11 @@ public class QueryStack {
 
 			RuntimeSearchParam left = theParamDef.getCompositeOf().get(0);
 			IQueryParameterType leftValue = cp.getLeftValue();
-			Condition leftPredicate = createPredicateCompositePart(theSourceJoinColumn, theResourceName, left, leftValue, theRequestPartitionId);
+			Condition leftPredicate = createPredicateCompositePart(theSourceJoinColumn, theResourceName, theSpnamePrefix, left, leftValue, theRequestPartitionId);
 
 			RuntimeSearchParam right = theParamDef.getCompositeOf().get(1);
 			IQueryParameterType rightValue = cp.getRightValue();
-			Condition rightPredicate = createPredicateCompositePart(theSourceJoinColumn, theResourceName, right, rightValue, theRequestPartitionId);
+			Condition rightPredicate = createPredicateCompositePart(theSourceJoinColumn, theResourceName, theSpnamePrefix, right, rightValue, theRequestPartitionId);
 
 			Condition andCondition = toAndPredicate(leftPredicate, rightPredicate);
 
@@ -316,20 +318,20 @@ public class QueryStack {
 		return orCondidtion;
 	}
 
-	private Condition createPredicateCompositePart(@Nullable DbColumn theSourceJoinColumn, String theResourceName, RuntimeSearchParam theParam, IQueryParameterType theParamValue, RequestPartitionId theRequestPartitionId) {
+	private Condition createPredicateCompositePart(@Nullable DbColumn theSourceJoinColumn, String theResourceName, String theSpnamePrefix, RuntimeSearchParam theParam, IQueryParameterType theParamValue, RequestPartitionId theRequestPartitionId) {
 
 		switch (theParam.getParamType()) {
 			case STRING: {
-				return createPredicateString(theSourceJoinColumn, theResourceName, theParam, Collections.singletonList(theParamValue), null, theRequestPartitionId);
+				return createPredicateString(theSourceJoinColumn, theResourceName, theSpnamePrefix, theParam, Collections.singletonList(theParamValue), null, theRequestPartitionId);
 			}
 			case TOKEN: {
-				return createPredicateToken(theSourceJoinColumn, theResourceName, theParam, Collections.singletonList(theParamValue), null, theRequestPartitionId);
+				return createPredicateToken(theSourceJoinColumn, theResourceName, theSpnamePrefix, theParam, Collections.singletonList(theParamValue), null, theRequestPartitionId);
 			}
 			case DATE: {
-				return createPredicateDate(theSourceJoinColumn, theResourceName, theParam, Collections.singletonList(theParamValue), toOperation(((DateParam) theParamValue).getPrefix()), theRequestPartitionId);
+				return createPredicateDate(theSourceJoinColumn, theResourceName, theSpnamePrefix, theParam, Collections.singletonList(theParamValue), toOperation(((DateParam) theParamValue).getPrefix()), theRequestPartitionId);
 			}
 			case QUANTITY: {
-				return createPredicateQuantity(theSourceJoinColumn, theResourceName, theParam, Collections.singletonList(theParamValue), null, theRequestPartitionId);
+				return createPredicateQuantity(theSourceJoinColumn, theResourceName, theSpnamePrefix, theParam, Collections.singletonList(theParamValue), null, theRequestPartitionId);
 			}
 		}
 
@@ -357,15 +359,12 @@ public class QueryStack {
 		return predicateBuilder.combineWithRequestPartitionIdPredicate(theRequestPartitionId, ComboCondition.or(codePredicates.toArray(new Condition[0])));
 	}
 
-	public Condition createPredicateDate(@Nullable DbColumn theSourceJoinColumn,
+	public Condition createPredicateDate(@Nullable DbColumn theSourceJoinColumn, String theResourceName,
-													 String theResourceName,
+			String theSpnamePrefix, RuntimeSearchParam theSearchParam, List<? extends IQueryParameterType> theList,
-													 RuntimeSearchParam theSearchParam,
+			SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
-													 List<? extends IQueryParameterType> theList,
-													 SearchFilterParser.CompareOperation theOperation,
-													 RequestPartitionId theRequestPartitionId) {
-
-		String paramName = theSearchParam.getName();
 
+		String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
+	
 		PredicateBuilderCacheLookupResult<DatePredicateBuilder> predicateBuilderLookupResult = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.DATE, theSourceJoinColumn, paramName, () -> mySqlBuilder.addDatePredicateBuilder(theSourceJoinColumn));
 		DatePredicateBuilder predicateBuilder = predicateBuilderLookupResult.getResult();
 		boolean cacheHit = predicateBuilderLookupResult.isCacheHit();
@@ -440,13 +439,13 @@ public class QueryStack {
 			}
 			RestSearchParameterTypeEnum typeEnum = searchParam.getParamType();
 			if (typeEnum == RestSearchParameterTypeEnum.URI) {
-				return theQueryStack3.createPredicateUri(null, theResourceName, searchParam, Collections.singletonList(new UriParam(theFilter.getValue())), theFilter.getOperation(), theRequest, theRequestPartitionId);
+				return theQueryStack3.createPredicateUri(null, theResourceName, null, searchParam, Collections.singletonList(new UriParam(theFilter.getValue())), theFilter.getOperation(), theRequest, theRequestPartitionId);
 			} else if (typeEnum == RestSearchParameterTypeEnum.STRING) {
-				return theQueryStack3.createPredicateString(null, theResourceName, searchParam, Collections.singletonList(new StringParam(theFilter.getValue())), theFilter.getOperation(), theRequestPartitionId);
+				return theQueryStack3.createPredicateString(null, theResourceName, null, searchParam, Collections.singletonList(new StringParam(theFilter.getValue())), theFilter.getOperation(), theRequestPartitionId);
 			} else if (typeEnum == RestSearchParameterTypeEnum.DATE) {
-				return theQueryStack3.createPredicateDate(null, theResourceName, searchParam, Collections.singletonList(new DateParam(fromOperation(theFilter.getOperation()), theFilter.getValue())), theFilter.getOperation(), theRequestPartitionId);
+				return theQueryStack3.createPredicateDate(null, theResourceName, null, searchParam, Collections.singletonList(new DateParam(fromOperation(theFilter.getOperation()), theFilter.getValue())), theFilter.getOperation(), theRequestPartitionId);
 			} else if (typeEnum == RestSearchParameterTypeEnum.NUMBER) {
-				return theQueryStack3.createPredicateNumber(null, theResourceName, searchParam, Collections.singletonList(new NumberParam(theFilter.getValue())), theFilter.getOperation(), theRequestPartitionId);
+				return theQueryStack3.createPredicateNumber(null, theResourceName, null, searchParam, Collections.singletonList(new NumberParam(theFilter.getValue())), theFilter.getOperation(), theRequestPartitionId);
 			} else if (typeEnum == RestSearchParameterTypeEnum.REFERENCE) {
 				SearchFilterParser.CompareOperation operation = theFilter.getOperation();
 				String resourceType = null; // The value can either have (Patient/123) or not have (123) a resource type, either way it's not needed here
@@ -455,7 +454,7 @@ public class QueryStack {
 				ReferenceParam referenceParam = new ReferenceParam(resourceType, chain, value);
 				return theQueryStack3.createPredicateReference(null, theResourceName, paramName, Collections.singletonList(referenceParam), operation, theRequest, theRequestPartitionId);
 			} else if (typeEnum == RestSearchParameterTypeEnum.QUANTITY) {
-				return theQueryStack3.createPredicateQuantity(null, theResourceName, searchParam, Collections.singletonList(new QuantityParam(theFilter.getValue())), theFilter.getOperation(), theRequestPartitionId);
+				return theQueryStack3.createPredicateQuantity(null, theResourceName, null, searchParam, Collections.singletonList(new QuantityParam(theFilter.getValue())), theFilter.getOperation(), theRequestPartitionId);
 			} else if (typeEnum == RestSearchParameterTypeEnum.COMPOSITE) {
 				throw new InvalidRequestException("Composite search parameters not currently supported with _filter clauses");
 			} else if (typeEnum == RestSearchParameterTypeEnum.TOKEN) {
@@ -464,7 +463,7 @@ public class QueryStack {
 					null,
 					null,
 					theFilter.getValue());
-				return theQueryStack3.createPredicateToken(null, theResourceName, searchParam, Collections.singletonList(param), theFilter.getOperation(), theRequestPartitionId);
+				return theQueryStack3.createPredicateToken(null, theResourceName, null, searchParam, Collections.singletonList(param), theFilter.getOperation(), theRequestPartitionId);
 			}
 		}
 		return null;
@@ -562,7 +561,7 @@ public class QueryStack {
 			List<String> paths = join.createResourceLinkPaths(targetResourceType, paramReference);
 			Condition typePredicate = BinaryCondition.equalTo(join.getColumnTargetResourceType(), mySqlBuilder.generatePlaceholder(theResourceType));
 			Condition pathPredicate = toEqualToOrInPredicate(join.getColumnSourcePath(), mySqlBuilder.generatePlaceholders(paths));
-			Condition linkedPredicate = searchForIdsWithAndOr(join.getColumnSrcResourceId(), targetResourceType, parameterName, Collections.singletonList(orValues), theRequest, theRequestPartitionId);
+			Condition linkedPredicate = searchForIdsWithAndOr(join.getColumnSrcResourceId(), targetResourceType, parameterName, Collections.singletonList(orValues), theRequest, theRequestPartitionId, SearchContainedModeEnum.FALSE);
 			andPredicates.add(toAndPredicate(partitionPredicate, pathPredicate, typePredicate, linkedPredicate));
 		}
 
@@ -607,17 +606,16 @@ public class QueryStack {
 		return toAndPredicate(predicates);
 	}
 
-	public Condition createPredicateNumber(@Nullable DbColumn theSourceJoinColumn,
+	public Condition createPredicateNumber(@Nullable DbColumn theSourceJoinColumn, String theResourceName,
-														String theResourceName,
+			String theSpnamePrefix, RuntimeSearchParam theSearchParam, List<? extends IQueryParameterType> theList,
-														RuntimeSearchParam theSearchParam,
+			SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
-														List<? extends IQueryParameterType> theList,
-														SearchFilterParser.CompareOperation theOperation,
-														RequestPartitionId theRequestPartitionId) {
 
-		NumberPredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.NUMBER, theSourceJoinColumn, theSearchParam.getName(), () -> mySqlBuilder.addNumberPredicateBuilder(theSourceJoinColumn)).getResult();
+		String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
+
+		NumberPredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.NUMBER, theSourceJoinColumn, paramName, () -> mySqlBuilder.addNumberPredicateBuilder(theSourceJoinColumn)).getResult();
 
 		if (theList.get(0).getMissing() != null) {
-			return join.createPredicateParamMissingForNonReference(theResourceName, theSearchParam.getName(), theList.get(0).getMissing(), theRequestPartitionId);
+			return join.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
 		}
 
 		List<Condition> codePredicates = new ArrayList<>();
@@ -636,7 +634,8 @@ public class QueryStack {
 					operation = toOperation(param.getPrefix());
 				}
 
-				Condition predicate = join.createPredicateNumeric(theResourceName, theSearchParam.getName(), operation, value, theRequestPartitionId, nextOr);
+				
+				Condition predicate = join.createPredicateNumeric(theResourceName, paramName, operation, value, theRequestPartitionId, nextOr);
 				codePredicates.add(predicate);
 
 			} else {
@@ -648,16 +647,15 @@ public class QueryStack {
 		return join.combineWithRequestPartitionIdPredicate(theRequestPartitionId, ComboCondition.or(codePredicates.toArray(new Condition[0])));
 	}
 
-	public Condition createPredicateQuantity(@Nullable DbColumn theSourceJoinColumn,
+	public Condition createPredicateQuantity(@Nullable DbColumn theSourceJoinColumn, String theResourceName,
-														  String theResourceName,
+			String theSpnamePrefix, RuntimeSearchParam theSearchParam, List<? extends IQueryParameterType> theList,
-														  RuntimeSearchParam theSearchParam,
+			SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
-														  List<? extends IQueryParameterType> theList,
+
-														  SearchFilterParser.CompareOperation theOperation,
+		String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
-														  RequestPartitionId theRequestPartitionId) {
 
 		if (theList.get(0).getMissing() != null) {
 			QuantityBasePredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.QUANTITY, theSourceJoinColumn, theSearchParam.getName(), () -> mySqlBuilder.addQuantityPredicateBuilder(theSourceJoinColumn)).getResult();
-			return join.createPredicateParamMissingForNonReference(theResourceName, theSearchParam.getName(), theList.get(0).getMissing(), theRequestPartitionId);
+			return join.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
 		}
 
 		List<QuantityParam> quantityParams = theList
@@ -675,18 +673,18 @@ public class QueryStack {
 				.collect(Collectors.toList());
 
 			if (normalizedQuantityParams.size() == quantityParams.size()) {
-				join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.QUANTITY, theSourceJoinColumn, theSearchParam.getName(), () -> mySqlBuilder.addQuantityNormalizedPredicateBuilder(theSourceJoinColumn)).getResult();
+				join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.QUANTITY, theSourceJoinColumn, paramName, () -> mySqlBuilder.addQuantityNormalizedPredicateBuilder(theSourceJoinColumn)).getResult();
 				quantityParams = normalizedQuantityParams;
 			}
 		}
 
 		if (join == null) {
-			join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.QUANTITY, theSourceJoinColumn, theSearchParam.getName(), () -> mySqlBuilder.addQuantityPredicateBuilder(theSourceJoinColumn)).getResult();
+			join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.QUANTITY, theSourceJoinColumn, paramName, () -> mySqlBuilder.addQuantityPredicateBuilder(theSourceJoinColumn)).getResult();
 		}
 
 		List<Condition> codePredicates = new ArrayList<>();
 		for (QuantityParam nextOr : quantityParams) {
-			Condition singleCode = join.createPredicateQuantity(nextOr, theResourceName, theSearchParam.getName(), null, join, theOperation, theRequestPartitionId);
+			Condition singleCode = join.createPredicateQuantity(nextOr, theResourceName, paramName, null, join, theOperation, theRequestPartitionId);
 			codePredicates.add(singleCode);
 		}
 
@@ -720,6 +718,106 @@ public class QueryStack {
 		return predicateBuilder.createPredicate(theRequest, theResourceName, theParamName, theList, theOperation, theRequestPartitionId);
 	}
 
+	private Condition createPredicateReferenceForContainedResource(@Nullable DbColumn theSourceJoinColumn,
+			String theResourceName, String theParamName, RuntimeSearchParam theSearchParam,
+			List<? extends IQueryParameterType> theList, SearchFilterParser.CompareOperation theOperation,
+			RequestDetails theRequest, RequestPartitionId theRequestPartitionId) {
+
+		String spnamePrefix = theParamName;
+
+		String targetChain = null;
+		String targetParamName = null;
+		String targetQualifier = null;
+		String targetValue = null;
+
+		RuntimeSearchParam targetParamDefinition = null;
+
+		ArrayList<IQueryParameterType> orValues = Lists.newArrayList();
+		IQueryParameterType qp = null;
+
+		for (int orIdx = 0; orIdx < theList.size(); orIdx++) {
+
+			IQueryParameterType nextOr = theList.get(orIdx);
+
+			if (nextOr instanceof ReferenceParam) {
+
+				ReferenceParam referenceParam = (ReferenceParam) nextOr;
+
+				// 1. Find out the parameter, qualifier and the value
+				targetChain = referenceParam.getChain();
+				targetParamName = targetChain;
+				targetValue = nextOr.getValueAsQueryToken(myFhirContext);
+
+				int qualifierIndex = targetChain.indexOf(':');
+				if (qualifierIndex != -1) {
+					targetParamName = targetChain.substring(0, qualifierIndex);
+					targetQualifier = targetChain.substring(qualifierIndex);
+				}
+
+				// 2. find out the data type
+				if (targetParamDefinition == null) {
+					Iterator<String> it = theSearchParam.getTargets().iterator();
+					while (it.hasNext()) {
+						targetParamDefinition = mySearchParamRegistry.getActiveSearchParam(it.next(), targetParamName);
+						if (targetParamDefinition != null)
+							break;
+					}
+				}
+
+				if (targetParamDefinition == null) {
+					throw new InvalidRequestException("Unknown search parameter name: " + theSearchParam.getName() + '.' + targetParamName + ".");
+				}
+			
+				qp = toParameterType(targetParamDefinition);
+				qp.setValueAsQueryToken(myFhirContext, targetParamName, targetQualifier, targetValue);
+				orValues.add(qp);
+			}
+		}
+
+		if (targetParamDefinition == null) {
+			throw new InvalidRequestException("Unknown search parameter name: " + theSearchParam.getName() + ".");
+		}
+		
+		// 3. create the query
+		Condition containedCondition = null;
+
+		switch (targetParamDefinition.getParamType()) {
+		case DATE:
+			containedCondition = createPredicateDate(null, theResourceName, spnamePrefix, targetParamDefinition,
+					orValues, theOperation, theRequestPartitionId);
+			break;
+		case NUMBER:
+			containedCondition = createPredicateNumber(null, theResourceName, spnamePrefix, targetParamDefinition,
+					orValues, theOperation, theRequestPartitionId);
+			break;
+		case QUANTITY:
+			containedCondition = createPredicateQuantity(null, theResourceName, spnamePrefix, targetParamDefinition,
+					orValues, theOperation, theRequestPartitionId);
+			break;
+		case STRING:
+			containedCondition = createPredicateString(null, theResourceName, spnamePrefix, targetParamDefinition,
+					orValues, theOperation, theRequestPartitionId);
+			break;
+		case TOKEN:
+			containedCondition = createPredicateToken(null, theResourceName, spnamePrefix, targetParamDefinition,
+					orValues, theOperation, theRequestPartitionId);
+			break;
+		case COMPOSITE:
+			containedCondition = createPredicateComposite(null, theResourceName, spnamePrefix, targetParamDefinition,
+					orValues, theRequestPartitionId);
+			break;
+		case URI:
+			containedCondition = createPredicateUri(null, theResourceName, spnamePrefix, targetParamDefinition,
+					orValues, theOperation, theRequest, theRequestPartitionId);
+			break;
+		default:
+			throw new InvalidRequestException(
+					"The search type:" + targetParamDefinition.getParamType() + " is not supported.");
+		}
+
+		return containedCondition;
+	}
+	
 	@Nullable
 	public Condition createPredicateResourceId(@Nullable DbColumn theSourceJoinColumn, List<List<IQueryParameterType>> theValues, String theResourceName, SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
 		ResourceIdPredicateBuilder builder = mySqlBuilder.newResourceIdBuilder();
@@ -762,22 +860,21 @@ public class QueryStack {
 		return toOrPredicate(orPredicates);
 	}
 
-	public Condition createPredicateString(@Nullable DbColumn theSourceJoinColumn,
+	public Condition createPredicateString(@Nullable DbColumn theSourceJoinColumn, String theResourceName,
-														String theResourceName,
+			String theSpnamePrefix, RuntimeSearchParam theSearchParam, List<? extends IQueryParameterType> theList,
-														RuntimeSearchParam theSearchParam,
+			SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
-														List<? extends IQueryParameterType> theList,
-														SearchFilterParser.CompareOperation theOperation,
-														RequestPartitionId theRequestPartitionId) {
 
-		StringPredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.STRING, theSourceJoinColumn, theSearchParam.getName(), () -> mySqlBuilder.addStringPredicateBuilder(theSourceJoinColumn)).getResult();
+		String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
+		
+		StringPredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.STRING, theSourceJoinColumn, paramName, () -> mySqlBuilder.addStringPredicateBuilder(theSourceJoinColumn)).getResult();
 
 		if (theList.get(0).getMissing() != null) {
-			return join.createPredicateParamMissingForNonReference(theResourceName, theSearchParam.getName(), theList.get(0).getMissing(), theRequestPartitionId);
+			return join.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
 		}
 
 		List<Condition> codePredicates = new ArrayList<>();
 		for (IQueryParameterType nextOr : theList) {
-			Condition singleCode = join.createPredicateString(nextOr, theResourceName, theSearchParam, join, theOperation);
+			Condition singleCode = join.createPredicateString(nextOr, theResourceName, theSpnamePrefix, theSearchParam, join, theOperation);
 			codePredicates.add(singleCode);
 		}
 
@@ -873,12 +970,9 @@ public class QueryStack {
 		return toAndPredicate(andPredicates);
 	}
 
-	public Condition createPredicateToken(@Nullable DbColumn theSourceJoinColumn,
+	public Condition createPredicateToken(@Nullable DbColumn theSourceJoinColumn, String theResourceName,
-													  String theResourceName,
+			String theSpnamePrefix, RuntimeSearchParam theSearchParam, List<? extends IQueryParameterType> theList,
-													  RuntimeSearchParam theSearchParam,
+			SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
-													  List<? extends IQueryParameterType> theList,
-													  SearchFilterParser.CompareOperation theOperation,
-													  RequestPartitionId theRequestPartitionId) {
 
 		List<IQueryParameterType> tokens = new ArrayList<>();
 		for (IQueryParameterType nextOr : theList) {
@@ -900,7 +994,7 @@ public class QueryStack {
 							throw new MethodNotAllowedException(msg);
 						}
 
-						return createPredicateString(theSourceJoinColumn, theResourceName, theSearchParam, theList, null, theRequestPartitionId);
+						return createPredicateString(theSourceJoinColumn, theResourceName, theSpnamePrefix, theSearchParam, theList, null, theRequestPartitionId);
 					}
 
 					tokens.add(nextOr);
@@ -917,26 +1011,26 @@ public class QueryStack {
 		if (tokens.isEmpty()) {
 			return null;
 		}
+		
+		String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
 
-		TokenPredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.TOKEN, theSourceJoinColumn, theSearchParam.getName(), () -> mySqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn)).getResult();
+		TokenPredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.TOKEN, theSourceJoinColumn, paramName, () -> mySqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn)).getResult();
 
 		if (theList.get(0).getMissing() != null) {
-			return join.createPredicateParamMissingForNonReference(theResourceName, theSearchParam.getName(), theList.get(0).getMissing(), theRequestPartitionId);
+			return join.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
 		}
 
-		Condition predicate = join.createPredicateToken(tokens, theResourceName, theSearchParam, theOperation, theRequestPartitionId);
+		Condition predicate = join.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theOperation, theRequestPartitionId);
 		return join.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
 	}
 
-	public Condition createPredicateUri(@Nullable DbColumn theSourceJoinColumn,
+	public Condition createPredicateUri(@Nullable DbColumn theSourceJoinColumn, String theResourceName,
-													String theResourceName,
+			String theSpnamePrefix, RuntimeSearchParam theSearchParam, List<? extends IQueryParameterType> theList,
-													RuntimeSearchParam theSearchParam,
+			SearchFilterParser.CompareOperation theOperation, RequestDetails theRequestDetails,
-													List<? extends IQueryParameterType> theList,
+			RequestPartitionId theRequestPartitionId) {
-													SearchFilterParser.CompareOperation theOperation,
-													RequestDetails theRequestDetails,
-													RequestPartitionId theRequestPartitionId) {
 
-		String paramName = theSearchParam.getName();
+		String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
+		
 		UriPredicateBuilder join = mySqlBuilder.addUriPredicateBuilder(theSourceJoinColumn);
 
 		if (theList.get(0).getMissing() != null) {
@@ -952,7 +1046,7 @@ public class QueryStack {
 	}
 
 	@Nullable
-	public Condition searchForIdsWithAndOr(@Nullable DbColumn theSourceJoinColumn, String theResourceName, String theParamName, List<List<IQueryParameterType>> theAndOrParams, RequestDetails theRequest, RequestPartitionId theRequestPartitionId) {
+	public Condition searchForIdsWithAndOr(@Nullable DbColumn theSourceJoinColumn, String theResourceName, String theParamName, List<List<IQueryParameterType>> theAndOrParams, RequestDetails theRequest, RequestPartitionId theRequestPartitionId, SearchContainedModeEnum theSearchContainedMode) {
 
 		if (theAndOrParams.isEmpty()) {
 			return null;
@@ -998,7 +1092,7 @@ public class QueryStack {
 									DateParam param = (DateParam) nextAnd.get(0);
 									operation = toOperation(param.getPrefix());
 								}
-								andPredicates.add(createPredicateDate(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, operation, theRequestPartitionId));
+								andPredicates.add(createPredicateDate(theSourceJoinColumn, theResourceName, null, nextParamDef, nextAnd, operation, theRequestPartitionId));
 								//andPredicates.add(createPredicateDate(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, null, theRequestPartitionId));
 							}
 							break;
@@ -1009,17 +1103,20 @@ public class QueryStack {
 									QuantityParam param = (QuantityParam) nextAnd.get(0);
 									operation = toOperation(param.getPrefix());
 								}
-								andPredicates.add(createPredicateQuantity(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, operation, theRequestPartitionId));
+								andPredicates.add(createPredicateQuantity(theSourceJoinColumn, theResourceName, null, nextParamDef, nextAnd, operation, theRequestPartitionId));
 							}
 							break;
 						case REFERENCE:
 							for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
-								andPredicates.add(createPredicateReference(theSourceJoinColumn, theResourceName, theParamName, nextAnd, null, theRequest, theRequestPartitionId));
+								if (theSearchContainedMode.equals(SearchContainedModeEnum.TRUE))
+									andPredicates.add(createPredicateReferenceForContainedResource(theSourceJoinColumn, theResourceName, theParamName, nextParamDef, nextAnd, null, theRequest, theRequestPartitionId));
+								else 	
+									andPredicates.add(createPredicateReference(theSourceJoinColumn, theResourceName, theParamName, nextAnd, null, theRequest, theRequestPartitionId));
 							}
 							break;
 						case STRING:
 							for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
-								andPredicates.add(createPredicateString(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, SearchFilterParser.CompareOperation.sw, theRequestPartitionId));
+								andPredicates.add(createPredicateString(theSourceJoinColumn, theResourceName, null, nextParamDef, nextAnd, SearchFilterParser.CompareOperation.sw, theRequestPartitionId));
 							}
 							break;
 						case TOKEN:
@@ -1027,23 +1124,23 @@ public class QueryStack {
 								if ("Location.position".equals(nextParamDef.getPath())) {
 									andPredicates.add(createPredicateCoords(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, theRequestPartitionId));
 								} else {
-									andPredicates.add(createPredicateToken(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, null, theRequestPartitionId));
+									andPredicates.add(createPredicateToken(theSourceJoinColumn, theResourceName, null, nextParamDef, nextAnd, null, theRequestPartitionId));
 								}
 							}
 							break;
 						case NUMBER:
 							for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
-								andPredicates.add(createPredicateNumber(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, null, theRequestPartitionId));
+								andPredicates.add(createPredicateNumber(theSourceJoinColumn, theResourceName, null, nextParamDef, nextAnd, null, theRequestPartitionId));
 							}
 							break;
 						case COMPOSITE:
 							for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
-								andPredicates.add(createPredicateComposite(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, theRequestPartitionId));
+								andPredicates.add(createPredicateComposite(theSourceJoinColumn, theResourceName, null, nextParamDef, nextAnd, theRequestPartitionId));
 							}
 							break;
 						case URI:
 							for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
-								andPredicates.add(createPredicateUri(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, SearchFilterParser.CompareOperation.eq, theRequest, theRequestPartitionId));
+								andPredicates.add(createPredicateUri(theSourceJoinColumn, theResourceName, null, nextParamDef, nextAnd, SearchFilterParser.CompareOperation.eq, theRequest, theRequestPartitionId));
 							}
 							break;
 						case HAS:
@@ -1246,4 +1343,48 @@ public class QueryStack {
 		return parameter.substring(parameter.indexOf(".") + 1);
 	}
 
+	private IQueryParameterType toParameterType(RuntimeSearchParam theParam) {
+		
+		IQueryParameterType qp;
+		switch (theParam.getParamType()) {
+			case DATE:
+				qp = new DateParam();
+				break;
+			case NUMBER:
+				qp = new NumberParam();
+				break;
+			case QUANTITY:
+				qp = new QuantityParam();
+				break;
+			case STRING:
+				qp = new StringParam();
+				break;
+			case TOKEN:
+				qp = new TokenParam();
+				break;
+			case COMPOSITE:
+				List<RuntimeSearchParam> compositeOf = theParam.getCompositeOf();
+				if (compositeOf.size() != 2) {
+					throw new InternalErrorException("Parameter " + theParam.getName() + " has " + compositeOf.size() + " composite parts. Don't know how handlt this.");
+				}
+				IQueryParameterType leftParam = toParameterType(compositeOf.get(0));
+				IQueryParameterType rightParam = toParameterType(compositeOf.get(1));
+				qp = new CompositeParam<>(leftParam, rightParam);
+				break;
+			case URI:
+				qp = new UriParam();
+				break;
+			default:
+				throw new InvalidRequestException("The search type: " + theParam.getParamType() + " is not supported.");
+		}
+		return qp;
+	}
+
+	public static String getParamNameWithPrefix(String theSpnamePrefix, String theParamName) {
+		
+		if (isBlank(theSpnamePrefix))
+			return theParamName;
+		
+		return theSpnamePrefix + "." + theParamName;
+	}
 }

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

@@ -60,6 +60,7 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.util.Dstu3DistanceHelper;
 import ca.uhn.fhir.jpa.searchparam.util.LastNParameterHelper;
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
 import ca.uhn.fhir.jpa.util.BaseIterator;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
 import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
@@ -91,7 +92,6 @@ import com.healthmarketscience.sqlbuilder.Condition;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.IdType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -216,6 +216,8 @@ public class SearchBuilder implements ISearchBuilder {
 			attemptCompositeUniqueSpProcessing(theQueryStack, theParams, theRequest);
 		}
 
+		SearchContainedModeEnum searchContainedMode = theParams.getSearchContainedMode();
+		
 		// Handle each parameter
 		List<String> paramNames = new ArrayList<>(myParams.keySet());
 		for (String nextParamName : paramNames) {
@@ -224,7 +226,7 @@ public class SearchBuilder implements ISearchBuilder {
 				continue;
 			}
 			List<List<IQueryParameterType>> andOrParams = myParams.get(nextParamName);
-			Condition predicate = theQueryStack.searchForIdsWithAndOr(null, myResourceName, nextParamName, andOrParams, theRequest, myRequestPartitionId);
+			Condition predicate = theQueryStack.searchForIdsWithAndOr(null, myResourceName, nextParamName, andOrParams, theRequest, myRequestPartitionId, searchContainedMode);
 			if (predicate != null) {
 				theSearchSqlBuilder.addPredicate(predicate);
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java

@@ -43,6 +43,7 @@ import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
 import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
 import ca.uhn.fhir.model.api.IQueryParameterType;
@@ -394,7 +395,7 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
 			List<Condition> andPredicates = new ArrayList<>();
 
 			List<List<IQueryParameterType>> chainParamValues = Collections.singletonList(orValues);
-			andPredicates.add(childQueryFactory.searchForIdsWithAndOr(myColumnTargetResourceId, subResourceName, chain, chainParamValues, theRequest, theRequestPartitionId));
+			andPredicates.add(childQueryFactory.searchForIdsWithAndOr(myColumnTargetResourceId, subResourceName, chain, chainParamValues, theRequest, theRequestPartitionId, SearchContainedModeEnum.FALSE));
 
 			orPredicates.add(toAndPredicate(andPredicates));
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/StringPredicateBuilder.java

@@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import ca.uhn.fhir.jpa.search.builder.QueryStack;
 import ca.uhn.fhir.model.api.IPrimitiveDatatype;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.param.StringParam;
@@ -75,11 +76,13 @@ public class StringPredicateBuilder extends BaseSearchParamPredicateBuilder {
 
 	public Condition createPredicateString(IQueryParameterType theParameter,
 														String theResourceName,
+														String theSpnamePrefix,
 														RuntimeSearchParam theSearchParam,
 														StringPredicateBuilder theFrom,
 														SearchFilterParser.CompareOperation operation) {
 		String rawSearchTerm;
-		String paramName = theSearchParam.getName();
+		String paramName = QueryStack.getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
+		
 		if (theParameter instanceof TokenParam) {
 			TokenParam id = (TokenParam) theParameter;
 			if (!id.isText()) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/TokenPredicateBuilder.java

@@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
 import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
+import ca.uhn.fhir.jpa.search.builder.QueryStack;
 import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.model.api.IQueryParameterType;
@@ -93,11 +94,13 @@ public class TokenPredicateBuilder extends BaseSearchParamPredicateBuilder {
 
 	public Condition createPredicateToken(Collection<IQueryParameterType> theParameters,
 													  String theResourceName,
+													  String theSpnamePrefix,
 													  RuntimeSearchParam theSearchParam,
 													  RequestPartitionId theRequestPartitionId) {
 		return createPredicateToken(
 			theParameters,
 			theResourceName,
+			theSpnamePrefix,
 			theSearchParam,
 			null,
 			theRequestPartitionId);
@@ -105,11 +108,15 @@ public class TokenPredicateBuilder extends BaseSearchParamPredicateBuilder {
 
 	public Condition createPredicateToken(Collection<IQueryParameterType> theParameters,
 													  String theResourceName,
+													  String theSpnamePrefix,
 													  RuntimeSearchParam theSearchParam,
 													  SearchFilterParser.CompareOperation theOperation,
 													  RequestPartitionId theRequestPartitionId) {
+		
+		
 		final List<FhirVersionIndependentConcept> codes = new ArrayList<>();
-		String paramName = theSearchParam.getName();
+		
+		String paramName = QueryStack.getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
 
 		SearchFilterParser.CompareOperation operation = theOperation;
 
@@ -197,12 +204,12 @@ public class TokenPredicateBuilder extends BaseSearchParamPredicateBuilder {
 			long hashIdentity = BaseResourceIndexedSearchParam.calculateHashIdentity(getPartitionSettings(), theRequestPartitionId, theResourceName, paramName);
 			Condition hashIdentityPredicate = BinaryCondition.equalTo(getColumnHashIdentity(), generatePlaceholder(hashIdentity));
 
-			Condition hashValuePredicate = createPredicateOrList(theResourceName, theSearchParam.getName(), sortedCodesList, false);
+			Condition hashValuePredicate = createPredicateOrList(theResourceName, paramName, sortedCodesList, false);
 			predicate = toAndPredicate(hashIdentityPredicate, hashValuePredicate);
 
 		} else {
 
-			predicate = createPredicateOrList(theResourceName, theSearchParam.getName(), sortedCodesList, true);
+			predicate = createPredicateOrList(theResourceName, paramName, sortedCodesList, true);
 
 		}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java

@@ -244,9 +244,6 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 
 	@BeforeEach
 	public void beforeResetConfig() {
-		myDaoConfig.setHardSearchLimit(1000);
-		myDaoConfig.setHardTagListLimit(1000);
-		myDaoConfig.setIncludeLimit(2000);
 		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
 	}
 

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

@@ -396,9 +396,6 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 
 	@BeforeEach
 	public void beforeResetConfig() {
-		myDaoConfig.setHardSearchLimit(1000);
-		myDaoConfig.setHardTagListLimit(1000);
-		myDaoConfig.setIncludeLimit(2000);
 		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ContainedTest.java

@@ -3,12 +3,10 @@ package ca.uhn.fhir.jpa.dao.dstu3;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.TokenParamModifier;
-import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.dstu3.model.Observation;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.Reference;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Test;
 
 import static org.hamcrest.MatcherAssert.assertThat;
@@ -18,23 +16,17 @@ public class FhirResourceDaoDstu3ContainedTest extends BaseJpaDstu3Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3ContainedTest.class);
 
 
-
-	@Test
-	public void before() {
-		myDaoConfig.setIndexContainedResources(true);
-	}
-	
 	@Test
 	public void testIndexContained() {
 		Patient p = new Patient();
 		p.setId("#some_patient");
 		p.addName().setFamily("MYFAMILY").addGiven("MYGIVEN");
-		
+
 		Observation o1 = new Observation();
 		o1.getCode().setText("Some Observation");
 		o1.setSubject(new Reference(p));
 		IIdType oid1 = myObservationDao.create(o1, mySrd).getId().toUnqualifiedVersionless();
-		
+
 		Observation o2 = new Observation();
 		o2.getCode().setText("Some Observation");
 		o2.setSubject(new Reference(p));
@@ -43,16 +35,16 @@ public class FhirResourceDaoDstu3ContainedTest extends BaseJpaDstu3Test {
 		Patient p2 = new Patient();
 		p2.addName().setFamily("MYFAMILY").addGiven("MYGIVEN");
 		IIdType pid2 = myPatientDao.create(p2, mySrd).getId().toUnqualifiedVersionless();
-		
+
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(o2));
-		
+
-		
+
 		SearchParameterMap map = new SearchParameterMap();
 		map.add(Observation.SP_CODE, new TokenParam(null, "some observation").setModifier(TokenParamModifier.TEXT));
 		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(oid1, oid2)));
 	}
 
-	
+
 	// TODO: make sure match URLs don't delete
-	
+
 }

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

@@ -476,7 +476,6 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 	@Autowired
 	private IValidationSupport myJpaValidationSupportChainR4;
 	private PerformanceTracingLoggingInterceptor myPerformanceTracingLoggingInterceptor;
-	private List<Object> mySystemInterceptors;
 	@Autowired
 	private IBulkDataExportSvc myBulkDataExportSvc;
 	@Autowired
@@ -524,8 +523,6 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 
 	@BeforeEach
 	public void beforeCreateInterceptor() {
-		mySystemInterceptors = myInterceptorRegistry.getAllRegisteredInterceptors();
-
 		myInterceptor = mock(IServerInterceptor.class);
 
 		myPerformanceTracingLoggingInterceptor = new PerformanceTracingLoggingInterceptor();
@@ -558,9 +555,6 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 
 	@BeforeEach
 	public void beforeResetConfig() {
-		myDaoConfig.setHardSearchLimit(1000);
-		myDaoConfig.setHardTagListLimit(1000);
-		myDaoConfig.setIncludeLimit(2000);
 		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
 		myValidationSettings.setLocalReferenceValidationDefaultPolicy(new ValidationSettings().getLocalReferenceValidationDefaultPolicy());
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ContainedTest.java

@@ -1,57 +1,309 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import org.hl7.fhir.r4.model.Observation;
+import static org.hamcrest.MatcherAssert.assertThat;
-import org.hl7.fhir.r4.model.Patient;
+import static org.hamcrest.Matchers.containsInAnyOrder;
-import org.hl7.fhir.r4.model.Reference;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.fail;
+
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
+import org.hl7.fhir.r4.model.Address;
+import org.hl7.fhir.r4.model.Address.AddressUse;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.DateTimeType;
+import org.hl7.fhir.r4.model.Encounter;
+import org.hl7.fhir.r4.model.Encounter.EncounterParticipantComponent;
+import org.hl7.fhir.r4.model.Encounter.EncounterStatus;
+import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Organization;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Practitioner;
+import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.ServiceRequest;
+import org.hl7.fhir.r4.model.ServiceRequest.ServiceRequestIntent;
+import org.hl7.fhir.r4.model.ServiceRequest.ServiceRequestStatus;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.ReferenceParam;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
 public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ContainedTest.class);
 
-
+	@BeforeEach
-
+	public void before() throws Exception {
-	@Test
+		myModelConfig.setIndexOnContainedResources(true);
-	public void before() {
-		myDaoConfig.setIndexContainedResources(true);
 	}
-	
-	@Test
-	public void testIndexContained() {
-		Patient p = new Patient();
-		p.setId("#some_patient");
-		p.addName().setFamily("MYFAMILY").addGiven("MYGIVEN");
-		
-		Observation o1 = new Observation();
-		o1.getCode().setText("Some Observation");
-		o1.setSubject(new Reference(p));
-		IIdType oid1 = myObservationDao.create(o1, mySrd).getId().toUnqualifiedVersionless();
-		
-		Observation o2 = new Observation();
-		o2.getCode().setText("Some Observation");
-		o2.setSubject(new Reference(p));
-		IIdType oid2 = myObservationDao.create(o2, mySrd).getId().toUnqualifiedVersionless();
 
-		Patient p2 = new Patient();
+	@AfterEach
-		p2.addName().setFamily("MYFAMILY").addGiven("MYGIVEN");
+	public void after() throws Exception {
-		IIdType pid2 = myPatientDao.create(p2, mySrd).getId().toUnqualifiedVersionless();
+		myModelConfig.setIndexOnContainedResources(false);
+	}
+
+	@Test
+	public void testCreateSimpleContainedResourceIndexWithGeneratedId() {
+
+		Patient p = new Patient();
+		p.addName().setFamily("Smith").addGiven("John");
 		
-		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(o2));
+		Observation obs = new Observation();
+		obs.getCode().setText("Some Observation");
+		obs.setSubject(new Reference(p));
+		 				
+		ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+
+		IIdType id = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+		Observation createdObs = myObservationDao.read(id);
 		
+		ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
+		
+		runInTransaction(()->{
+			Long i = myEntityManager
+				.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamString s WHERE s.myParamName = 'subject.family' AND s.myResourceType = 'Observation'", Long.class)
+				.getSingleResult();
+			assertEquals(1L, i.longValue());
+		});
 		
 		SearchParameterMap map;
+
+		map = new SearchParameterMap();
+		map.add("subject", new ReferenceParam("name", "Smith"));
+		map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
 		
-//		map = new SearchParameterMap();
+		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id)));
-//		map.add(Observation.SP_CODE, new TokenParam(null, "some observation").setModifier(TokenParamModifier.TEXT));
-//		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1, id2)));
-
 	}
+	
+	@Test
+	public void testCreateSimpleContainedResourceIndexUserDefinedId() {
 
+		Patient p = new Patient();
+		p.setId("fooId");
+		p.addName().setFamily("Smith").addGiven("John");
+		
+		Observation obs = new Observation();
+		obs.getCode().setText("Some Observation");
+		obs.getContained().add(p);
+		obs.getSubject().setReference("#fooId");
+		
+		ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+
+		IIdType id = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+		Observation createdObs = myObservationDao.read(id);
+		
+		ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
+		
+		runInTransaction(()->{
+			Long i = myEntityManager
+				.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamString s WHERE s.myParamName = 'subject.family' AND s.myResourceType = 'Observation'", Long.class)
+				.getSingleResult();
+			assertEquals(1L, i.longValue());
+		});
+		
+		SearchParameterMap map;
+
+		map = new SearchParameterMap();
+		map.add("subject", new ReferenceParam("name", "Smith"));
+		map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
+		
+		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id)));
+	}
 	
-	// TODO: make sure match URLs don't delete
 	
+	@Test
+	public void testCreateMultipleContainedResourceIndex() {
+
+		Practitioner prac1 = new Practitioner();
+		prac1.setId("prac1");
+		prac1.setActive(true);
+		prac1.setGender(AdministrativeGender.FEMALE);
+		prac1.addName().setFamily("Smith").addGiven("John");
+		Address address = prac1.addAddress();
+		address.setUse(AddressUse.WORK);
+		address.addLine("534 Erewhon St");
+		address.setCity("PleasantVille");
+		address.setState("NY");
+		address.setPostalCode("12345");
+		
+		Organization org1 = new Organization();
+		org1.setId("org1");
+		org1.setActive(true);
+		org1.setName("org name 1");
+
+		Organization org2 = new Organization();
+		org2.setId("org2");
+		org2.setActive(false);
+		org2.setName("org name 2");
+
+		Patient patient = new Patient();
+		patient.getContained().add(prac1);
+		patient.getContained().add(org1);
+		patient.getContained().add(org2);
+		patient.addName().setFamily("Doe").addGiven("Jane");
+		patient.addGeneralPractitioner().setReference("#prac1");
+		patient.addGeneralPractitioner().setReference("#org1");
+		patient.getManagingOrganization().setReference("#org2");
+				
+		ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
+
+		IIdType id = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+
+		Patient createdPatient = myPatientDao.read(id);
+		
+		ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdPatient));
+		
+		runInTransaction(()->{
+			Long i = myEntityManager
+				.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamString s WHERE s.myParamName = 'general-practitioner.family' AND s.myResourceType = 'Patient'", Long.class)
+				.getSingleResult();
+			assertEquals(1L, i.longValue());
+
+			i = myEntityManager
+				.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamString s WHERE s.myParamName = 'general-practitioner.name' AND s.myResourceType = 'Patient'", Long.class)
+				.getSingleResult();
+			assertEquals(3L, i.longValue());
+
+			i = myEntityManager
+					.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamString s WHERE s.myParamName = 'organization.name' AND s.myResourceType = 'Patient'", Long.class)
+					.getSingleResult();
+		    assertEquals(1L, i.longValue());
+		});
+		
+		SearchParameterMap map;
+
+		map = new SearchParameterMap();
+		map.add("general-practitioner", new ReferenceParam("family", "Smith"));
+		map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
+		
+		assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(map)), containsInAnyOrder(toValues(id)));
+	}
+	
+	@Test
+	public void testCreateComplexContainedResourceIndex() {
+
+		Encounter encounter = new Encounter();
+		encounter.setStatus(EncounterStatus.ARRIVED);
+		
+		Patient patient = new Patient();
+		patient.setId("patient1");
+		patient.addName().setFamily("Doe").addGiven("Jane");
+		encounter.getSubject().setReference("#patient1");
+		encounter.getContained().add(patient);
+		
+		ServiceRequest serviceRequest = new ServiceRequest();
+		serviceRequest.setId("serviceRequest1");
+		serviceRequest.setStatus(ServiceRequestStatus.ACTIVE);
+		serviceRequest.setIntent(ServiceRequestIntent.ORDER);
+		serviceRequest.setAuthoredOnElement(new DateTimeType("2021-02-23"));
+		encounter.addBasedOn().setReference("#serviceRequest1");
+		encounter.getContained().add(serviceRequest);
+
+		Practitioner prac1 = new Practitioner();
+		prac1.setId("prac1");
+		prac1.setActive(true);
+		prac1.setGender(AdministrativeGender.FEMALE);
+		prac1.addName().setFamily("Smith").addGiven("John");
+		EncounterParticipantComponent participient = encounter.addParticipant();
+		participient.getIndividual().setReference("#prac1");
+		encounter.getContained().add(prac1);
+		
+		Observation obs = new Observation();
+		obs.setId("obs1");
+		obs.addIdentifier().setSystem("urn:system").setValue("FOO");
+		obs.getSubject().setReference("#patient1");
+		CodeableConcept cc = obs.getCode();
+		cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
+		encounter.addReasonReference().setReference("#obs1");
+		encounter.getContained().add(obs);
+		
+		ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
+
+		IIdType id = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
+
+		Encounter createdEncounter = myEncounterDao.read(id);
+		
+		ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
+		
+		runInTransaction(()->{
+			// The practitioner
+			Long i = myEntityManager
+				.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamString s WHERE s.myParamName = 'participant.family' AND s.myResourceType = 'Encounter'", Long.class)
+				.getSingleResult();
+			assertEquals(1L, i.longValue());
+
+			// The Patient
+			i = myEntityManager
+				.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamString s WHERE s.myParamName = 'subject.family' AND s.myResourceType = 'Encounter'", Long.class)
+				.getSingleResult();
+			assertEquals(1L, i.longValue());
+
+			// The Observation
+			i = myEntityManager
+					.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamToken s WHERE s.myParamName = 'reason-reference.code' AND s.myResourceType = 'Encounter'", Long.class)
+					.getSingleResult();
+		    assertEquals(1L, i.longValue());
+			i = myEntityManager
+					.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamToken s WHERE s.myParamName = 'reason-reference.combo-code' AND s.myResourceType = 'Encounter'", Long.class)
+					.getSingleResult();
+		    assertEquals(1L, i.longValue());
+		    
+		    // The ServiceRequest
+			i = myEntityManager
+					.createQuery("SELECT count(s) FROM ResourceIndexedSearchParamDate s WHERE s.myParamName = 'based-on.authored' AND s.myResourceType = 'Encounter'", Long.class)
+					.getSingleResult();
+		    assertEquals(1L, i.longValue());
+		});
+		
+		SearchParameterMap map;
+
+		map = new SearchParameterMap();
+		map.add("based-on", new ReferenceParam("authored", "2021-02-23"));
+		map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
+		
+		assertThat(toUnqualifiedVersionlessIdValues(myEncounterDao.search(map)), containsInAnyOrder(toValues(id)));
+	}
+	
+	@Test
+	public void testSearchWithNotSupportedSearchType() {
+
+		SearchParameterMap map;
+
+		map = new SearchParameterMap();
+		map.add("subject", new ReferenceParam("near", "toronto"));
+		map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
+		
+		try {
+			IBundleProvider outcome = myObservationDao.search(map);
+			outcome.getResources(0, 1).get(0);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals(e.getMessage(), "The search type: SPECIAL is not supported.");
+		}
+		
+	}
+	
+	@Test
+	public void testSearchWithNotSupportedSearchParameter() {
+
+		SearchParameterMap map;
+
+		map = new SearchParameterMap();
+		map.add("subject", new ReferenceParam("marital-status", "M"));
+		map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
+		
+		try {
+			IBundleProvider outcome = myObservationDao.search(map);
+			outcome.getResources(0, 1).get(0);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals(e.getMessage(), "Unknown search parameter name: subject.marital-status.");
+		}
+		
+	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java

@@ -148,13 +148,6 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
 		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
 	}
 
-	@BeforeEach
-	public void beforeResetConfig() {
-		myDaoConfig.setHardSearchLimit(1000);
-		myDaoConfig.setHardTagListLimit(1000);
-		myDaoConfig.setIncludeLimit(2000);
-	}
-
 	@Override
 	protected PlatformTransactionManager getTxManager() {
 		return myTxManager;
@@ -171,7 +164,7 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
 
 		Organization org = new Organization();
 		org.setName(methodName);
-		IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
+		myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
 
 		SearchParameterMap map = new SearchParameterMap();
 		map.add(ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT, new StringParam(methodName));
@@ -189,7 +182,7 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
 
 		Organization org = new Organization();
 		org.setName(methodName);
-		IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
+		myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
 
 		SearchParameterMap map = new SearchParameterMap();
 		map.add(Organization.SP_NAME, new StringParam(methodName));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java

@@ -975,6 +975,58 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 		}
 	}
 
+
+	@Test
+	public void testRead_PidId_UnknownResourceId() {
+		// Read in specific Partition
+		{
+			addReadPartition(1);
+			try {
+				myPatientDao.read(new IdType("Patient/1"), mySrd);
+				fail();
+			} catch (ResourceNotFoundException e) {
+				// expected
+			}
+		}
+
+		// Read in null Partition
+		{
+			addReadDefaultPartition();
+			try {
+				myPatientDao.read(new IdType("Patient/1"), mySrd);
+				fail();
+			} catch (ResourceNotFoundException e) {
+				// expected
+			}
+		}
+	}
+
+	@Test
+	public void testRead_PidId_ResourceIdOnlyExistsInDifferentPartition() {
+		IIdType id = createPatient(withPartition(2), withActiveTrue());
+		// Read in specific Partition
+		{
+			addReadPartition(1);
+			try {
+				myPatientDao.read(id, mySrd);
+				fail();
+			} catch (ResourceNotFoundException e) {
+				// expected
+			}
+		}
+
+		// Read in null Partition
+		{
+			addReadDefaultPartition();
+			try {
+				myPatientDao.read(id, mySrd);
+				fail();
+			} catch (ResourceNotFoundException e) {
+				// expected
+			}
+		}
+	}
+
 	@Test
 	public void testRead_ForcedId_SpecificPartition() {
 		IIdType patientIdNull = createPatient(withPutPartition(null), withActiveTrue(), withId("NULL"));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchParamExtractorR4Test.java

@@ -284,7 +284,7 @@ public class SearchParamExtractorR4Test {
 		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new ModelConfig(), new PartitionSettings(), ourCtx, mySearchParamRegistry);
 		RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam("Encounter", "location");
 		assertNotNull(param);
-		ISearchParamExtractor.SearchParamSet<PathAndRef> links = extractor.extractResourceLinks(enc);
+		ISearchParamExtractor.SearchParamSet<PathAndRef> links = extractor.extractResourceLinks(enc, false);
 		assertEquals(1, links.size());
 		assertEquals("location", links.iterator().next().getSearchParamName());
 		assertEquals("Encounter.location.location", links.iterator().next().getPath());
@@ -299,7 +299,7 @@ public class SearchParamExtractorR4Test {
 		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new ModelConfig(), new PartitionSettings(), ourCtx, mySearchParamRegistry);
 		RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam("Consent", Consent.SP_SOURCE_REFERENCE);
 		assertNotNull(param);
-		ISearchParamExtractor.SearchParamSet<PathAndRef> links = extractor.extractResourceLinks(consent);
+		ISearchParamExtractor.SearchParamSet<PathAndRef> links = extractor.extractResourceLinks(consent, false);
 		assertEquals(1, links.size());
 		assertEquals("Consent.source", links.iterator().next().getPath());
 		assertEquals("Consent/999", ((Reference) links.iterator().next().getRef()).getReference());
@@ -334,7 +334,7 @@ public class SearchParamExtractorR4Test {
 		patient.addExtension("http://patext", new Reference("Organization/AAA"));
 
 		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new ModelConfig(), new PartitionSettings(), ourCtx, mySearchParamRegistry);
-		ISearchParamExtractor.SearchParamSet<PathAndRef> links = extractor.extractResourceLinks(patient);
+		ISearchParamExtractor.SearchParamSet<PathAndRef> links = extractor.extractResourceLinks(patient, false);
 		assertEquals(1, links.size());
 
 	}

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

@@ -3,7 +3,6 @@ package ca.uhn.fhir.jpa.dao.r4;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.param.HasParam;
 import ca.uhn.fhir.test.BaseTest;
 import org.junit.jupiter.api.Test;
@@ -19,6 +18,6 @@ public class SearchParameterMapTest extends BaseTest {
 		SearchParameterMap params = new SearchParameterMap();
 		params.add("_has", new HasParam("Observation", "subject", "identifier", "urn:system|FOO"));
 		String criteria = params.toNormalizedQueryString(myContext);
-		assertEquals(criteria, "?_has:Observation:identifier:urn:system|FOO=urn%3Asystem%7CFOO");
+		assertEquals(criteria, "?_has:Observation:subject:identifier=urn%3Asystem%7CFOO");
 	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java

@@ -480,7 +480,6 @@ public abstract class BaseJpaR5Test extends BaseJpaTest {
 
 	@BeforeEach
 	public void beforeResetConfig() {
-		myDaoConfig.setHardTagListLimit(1000);
 		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -309,9 +309,6 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 
 	@Test
 	public void testCountParam() {
-		// NB this does not get used- The paging provider has its own limits built in
-		myDaoConfig.setHardSearchLimit(100);
-
 		List<IBaseResource> resources = new ArrayList<IBaseResource>();
 		for (int i = 0; i < 100; i++) {
 			Organization org = new Organization();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderHasParamR4Test.java

@@ -108,12 +108,14 @@ public class ResourceProviderHasParamR4Test extends BaseResourceProviderR4Test {
 			obs.addIdentifier().setSystem("urn:system").setValue("NOLINK");
 			obs.setDevice(new Reference(devId));
 			myObservationDao.create(obs, mySrd);
+			
+			ourLog.info("Observation: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
+		
 		String uri = ourServerBase + "/Patient?_has:Observation:subject:identifier=" + UrlUtil.escapeUrlParam("urn:system|FOO");
 		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
 		assertThat(ids, contains(pid0.getValue()));
-
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4SearchContainedTest.java

@@ -0,0 +1,994 @@
+package ca.uhn.fhir.jpa.provider.r4;
+
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.parser.StrictErrorHandler;
+import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
+import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
+import ca.uhn.fhir.util.UrlUtil;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.CarePlan;
+import org.hl7.fhir.r4.model.CarePlan.CarePlanIntent;
+import org.hl7.fhir.r4.model.CarePlan.CarePlanStatus;
+import org.hl7.fhir.r4.model.ClinicalImpression;
+import org.hl7.fhir.r4.model.ClinicalImpression.ClinicalImpressionStatus;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.DecimalType;
+import org.hl7.fhir.r4.model.Encounter;
+import org.hl7.fhir.r4.model.Encounter.EncounterStatus;
+import org.hl7.fhir.r4.model.HumanName;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Quantity;
+import org.hl7.fhir.r4.model.Resource;
+import org.hl7.fhir.r4.model.RiskAssessment;
+import org.hl7.fhir.r4.model.RiskAssessment.RiskAssessmentStatus;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+
+public class ResourceProviderR4SearchContainedTest extends BaseResourceProviderR4Test {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4SearchContainedTest.class);
+	@Autowired
+	@Qualifier("myClinicalImpressionDaoR4")
+	protected IFhirResourceDao<ClinicalImpression> myClinicalImpressionDao;
+	private CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
+
+	@Override
+	@AfterEach
+	public void after() throws Exception {
+		super.after();
+
+		myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
+		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
+		myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
+		myDaoConfig.setCountSearchResultsUpTo(new DaoConfig().getCountSearchResultsUpTo());
+		myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
+		myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
+		myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
+
+		myClient.unregisterInterceptor(myCapturingInterceptor);
+		myModelConfig.setIndexOnContainedResources(false);
+		myModelConfig.setIndexOnContainedResources(new ModelConfig().isIndexOnContainedResources());
+	}
+
+	@BeforeEach
+	@Override
+	public void before() throws Exception {
+		super.before();
+		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
+
+		myDaoConfig.setAllowMultipleDelete(true);
+		myClient.registerInterceptor(myCapturingInterceptor);
+		myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
+		myModelConfig.setIndexOnContainedResources(true);
+		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
+	}
+
+	@Test
+	public void testContainedDisabled() throws Exception {
+		myModelConfig.setIndexOnContainedResources(false);
+
+		String uri = ourServerBase + "/Observation?subject.name=Smith&_contained=true";
+		try (CloseableHttpResponse response = ourHttpClient.execute(new HttpGet(uri))) {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			assertEquals(MethodNotAllowedException.STATUS_CODE, response.getStatusLine().getStatusCode());
+			assertThat(resp, containsString(">Searching with _contained mode enabled is not enabled on this server"));
+		}
+	}
+
+	@Test
+	public void testContainedBoth() throws Exception {
+		String uri = ourServerBase + "/Observation?subject.name=Smith&_contained=both";
+		try (CloseableHttpResponse response = ourHttpClient.execute(new HttpGet(uri))) {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			assertEquals(MethodNotAllowedException.STATUS_CODE, response.getStatusLine().getStatusCode());
+			assertThat(resp, containsString("Contained mode 'both' is not currently supported"));
+		}
+	}
+
+	@Test
+	public void testContainedSearchByName() throws Exception {
+
+		IIdType oid1;
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Smith").addGiven("John");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient1");
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+		}
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Doe").addGiven("Jane");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 2");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient1");
+
+			myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+		}
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Jones").addGiven("Peter");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 2");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient1");
+
+			myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+		}
+
+
+		//-- Simple name match
+		String uri = ourServerBase + "/Observation?subject.name=Smith&_contained=true";
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getValue()));
+
+		//-- Simple name match with or
+		uri = ourServerBase + "/Observation?subject.name=Smith,Jane&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(2L, oids.size());
+		//assertEquals(oids.toString(), "[Observation/1, Observation/2]");
+
+		//-- Simple name match with qualifier
+		uri = ourServerBase + "/Observation?subject.name:exact=Smith&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getValue()));
+
+		//-- Simple name match with and
+		uri = ourServerBase + "/Observation?subject.family=Smith&subject.given=John&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getValue()));
+
+	}
+
+	@Test
+	public void testContainedSearchByDate() throws Exception {
+
+		IIdType oid1;
+		IIdType oid3;
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getBirthDateElement().setValueAsString("2000-01-01");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient1");
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+		}
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Doe").addGiven("Jane");
+			p.getBirthDateElement().setValueAsString("2000-02-01");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 2");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient1");
+
+			myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+		}
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Jones").addGiven("Peter");
+			p.getBirthDateElement().setValueAsString("2000-03-01");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 2");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient1");
+
+			oid3 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+		}
+
+		//-- Search by date default op
+		String uri = ourServerBase + "/Observation?subject.birthdate=2000-01-01&_contained=true";
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getValue()));
+
+		//-- Search by date op=eq
+		uri = ourServerBase + "/Observation?subject.birthdate=eq2000-01-01&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getValue()));
+
+		//-- Search by date op=eq, with or
+		uri = ourServerBase + "/Observation?subject.birthdate=2000-01-01,2000-02-01&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(2L, oids.size());
+		//assertEquals(oids.toString(), "[Observation/1, Observation/2]");
+
+		//-- Simple name match with op = gt
+		uri = ourServerBase + "/Observation?subject.birthdate=gt2000-02-10&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid3.getValue()));
+
+		//-- Simple name match with AND
+		uri = ourServerBase + "/Observation?subject.family=Smith&subject.birthdate=eq2000-01-01&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getValue()));
+
+		//-- Simple name match with AND - not found
+		uri = ourServerBase + "/Observation?subject.family=Smith&subject.birthdate=eq2000-02-01&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(0L, oids.size());
+	}
+
+
+	@Test
+	public void testContainedSearchByNumber() throws Exception {
+
+		IIdType cid1;
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getBirthDateElement().setValueAsString("2000-01-01");
+
+
+			RiskAssessment risk = new RiskAssessment();
+			risk.setId("risk1");
+			risk.setStatus(RiskAssessmentStatus.CORRECTED);
+			risk.getSubject().setReference("#patient1");
+			risk.getPredictionFirstRep().setProbability(new DecimalType(2));
+
+			ClinicalImpression imp = new ClinicalImpression();
+			imp.setStatus(ClinicalImpressionStatus.COMPLETED);
+
+			imp.getContained().add(p);
+			imp.getSubject().setReference("#patient1");
+
+			imp.getContained().add(risk);
+			imp.getInvestigationFirstRep().getItemFirstRep().setReference("#risk1");
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(imp));
+
+			cid1 = myClinicalImpressionDao.create(imp, mySrd).getId().toUnqualifiedVersionless();
+
+			ClinicalImpression createdImp = myClinicalImpressionDao.read(cid1);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdImp));
+		}
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getBirthDateElement().setValueAsString("2000-01-01");
+
+
+			RiskAssessment risk = new RiskAssessment();
+			risk.setId("risk1");
+			risk.setStatus(RiskAssessmentStatus.CORRECTED);
+			risk.getSubject().setReference("#patient1");
+			risk.getPredictionFirstRep().setProbability(new DecimalType(5));
+
+			ClinicalImpression imp = new ClinicalImpression();
+			imp.setStatus(ClinicalImpressionStatus.COMPLETED);
+
+			imp.getContained().add(p);
+			imp.getSubject().setReference("#patient1");
+
+			imp.getContained().add(risk);
+			imp.getInvestigationFirstRep().getItemFirstRep().setReference("#risk1");
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(imp));
+
+			IIdType cid2 = myClinicalImpressionDao.create(imp, mySrd).getId().toUnqualifiedVersionless();
+
+			ClinicalImpression createdImp = myClinicalImpressionDao.read(cid2);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdImp));
+		}
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getBirthDateElement().setValueAsString("2000-01-01");
+
+
+			RiskAssessment risk = new RiskAssessment();
+			risk.setId("risk1");
+			risk.setStatus(RiskAssessmentStatus.CORRECTED);
+			risk.getSubject().setReference("#patient1");
+			risk.getPredictionFirstRep().setProbability(new DecimalType(10));
+
+			ClinicalImpression imp = new ClinicalImpression();
+			imp.setStatus(ClinicalImpressionStatus.COMPLETED);
+
+			imp.getContained().add(p);
+			imp.getSubject().setReference("#patient1");
+
+			imp.getContained().add(risk);
+			imp.getInvestigationFirstRep().getItemFirstRep().setReference("#risk1");
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(imp));
+
+			IIdType cid3 = myClinicalImpressionDao.create(imp, mySrd).getId().toUnqualifiedVersionless();
+
+			ClinicalImpression createdImp = myClinicalImpressionDao.read(cid3);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdImp));
+		}
+
+		//-- Search by number
+		String uri = ourServerBase + "/ClinicalImpression?investigation.probability=2&_contained=true";
+		List<String> cids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, cids.size());
+		assertThat(cids, contains(cid1.getValue()));
+
+
+		//-- Search by number with op = eq
+		uri = ourServerBase + "/ClinicalImpression?investigation.probability=eq2&_contained=true";
+		cids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, cids.size());
+		assertThat(cids, contains(cid1.getValue()));
+
+
+		//-- Search by number with op = eq and or
+		uri = ourServerBase + "/ClinicalImpression?investigation.probability=eq2,10&_contained=true";
+		cids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+		assertEquals(2L, cids.size());
+
+		//-- Search by number with op = lt 
+		uri = ourServerBase + "/ClinicalImpression?investigation.probability=lt4&_contained=true";
+		cids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, cids.size());
+		assertThat(cids, contains(cid1.getValue()));
+	}
+
+	@Test
+	public void testContainedSearchByQuantity() throws Exception {
+
+		IIdType eid1;
+		{
+			Encounter encounter = new Encounter();
+			encounter.setStatus(EncounterStatus.ARRIVED);
+
+			Patient patient = new Patient();
+			patient.setId("patient1");
+			patient.addName().setFamily("Doe").addGiven("Jane");
+			encounter.getSubject().setReference("#patient1");
+			encounter.getContained().add(patient);
+
+			Observation obs = new Observation();
+			obs.setId("obs1");
+			obs.addIdentifier().setSystem("urn:system").setValue("FOO");
+			obs.getSubject().setReference("#patient1");
+			CodeableConcept cc = obs.getCode();
+			cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
+			Quantity quantity = obs.getValueQuantity();
+			quantity.setValue(200);
+			encounter.addReasonReference().setReference("#obs1");
+			encounter.getContained().add(obs);
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
+
+			eid1 = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
+
+			Encounter createdEncounter = myEncounterDao.read(eid1);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
+		}
+
+
+		{
+			Encounter encounter = new Encounter();
+			encounter.setStatus(EncounterStatus.ARRIVED);
+
+			Patient patient = new Patient();
+			patient.setId("patient1");
+			patient.addName().setFamily("Doe").addGiven("Jane");
+			encounter.getSubject().setReference("#patient1");
+			encounter.getContained().add(patient);
+
+			Observation obs = new Observation();
+			obs.setId("obs1");
+			obs.addIdentifier().setSystem("urn:system").setValue("FOO");
+			obs.getSubject().setReference("#patient1");
+			CodeableConcept cc = obs.getCode();
+			cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
+			Quantity quantity = obs.getValueQuantity();
+			quantity.setValue(300);
+			encounter.addReasonReference().setReference("#obs1");
+			encounter.getContained().add(obs);
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
+
+			IIdType eid2 = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
+
+			Encounter createdEncounter = myEncounterDao.read(eid2);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
+		}
+
+		{
+			Encounter encounter = new Encounter();
+			encounter.setStatus(EncounterStatus.ARRIVED);
+
+			Patient patient = new Patient();
+			patient.setId("patient1");
+			patient.addName().setFamily("Doe").addGiven("Jane");
+			encounter.getSubject().setReference("#patient1");
+			encounter.getContained().add(patient);
+
+			Observation obs = new Observation();
+			obs.setId("obs1");
+			obs.addIdentifier().setSystem("urn:system").setValue("FOO");
+			obs.getSubject().setReference("#patient1");
+			CodeableConcept cc = obs.getCode();
+			cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
+			Quantity quantity = obs.getValueQuantity();
+			quantity.setValue(400);
+			encounter.addReasonReference().setReference("#obs1");
+			encounter.getContained().add(obs);
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
+
+			IIdType eid3 = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
+
+			Encounter createdEncounter = myEncounterDao.read(eid3);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
+		}
+
+		//-- Search by quantity
+		String uri = ourServerBase + "/Encounter?reason-reference.combo-value-quantity=200&_contained=true";
+		List<String> eids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, eids.size());
+		assertThat(eids, contains(eid1.getValue()));
+
+
+		//-- Search by quantity
+		uri = ourServerBase + "/Encounter?reason-reference.combo-value-quantity=le400&_contained=true";
+		eids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(3L, eids.size());
+
+	}
+
+	@Test
+	public void testContainedSearchByToken() throws Exception {
+
+		IIdType eid1;
+		{
+			Encounter encounter = new Encounter();
+			encounter.setStatus(EncounterStatus.ARRIVED);
+
+			Patient patient = new Patient();
+			patient.setId("patient1");
+			patient.addName().setFamily("Doe").addGiven("Jane");
+			encounter.getSubject().setReference("#patient1");
+			encounter.getContained().add(patient);
+
+			Observation obs = new Observation();
+			obs.setId("obs1");
+			obs.addIdentifier().setSystem("urn:system").setValue("FOO");
+			obs.getSubject().setReference("#patient1");
+			CodeableConcept cc = obs.getCode();
+			cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
+			Quantity quantity = obs.getValueQuantity();
+			quantity.setValue(200);
+			encounter.addReasonReference().setReference("#obs1");
+			encounter.getContained().add(obs);
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
+
+			eid1 = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
+
+			Encounter createdEncounter = myEncounterDao.read(eid1);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
+		}
+
+
+		{
+			Encounter encounter = new Encounter();
+			encounter.setStatus(EncounterStatus.ARRIVED);
+
+			Patient patient = new Patient();
+			patient.setId("patient1");
+			patient.addName().setFamily("Doe").addGiven("Jane");
+			encounter.getSubject().setReference("#patient1");
+			encounter.getContained().add(patient);
+
+			Observation obs = new Observation();
+			obs.setId("obs1");
+			obs.addIdentifier().setSystem("urn:system").setValue("FOO");
+			obs.getSubject().setReference("#patient1");
+			CodeableConcept cc = obs.getCode();
+			cc.addCoding().setCode("2345-8").setSystem("http://loinc.org");
+			Quantity quantity = obs.getValueQuantity();
+			quantity.setValue(300);
+			encounter.addReasonReference().setReference("#obs1");
+			encounter.getContained().add(obs);
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
+
+			IIdType eid2 = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
+
+			Encounter createdEncounter = myEncounterDao.read(eid2);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
+		}
+
+		{
+			Encounter encounter = new Encounter();
+			encounter.setStatus(EncounterStatus.ARRIVED);
+
+			Patient patient = new Patient();
+			patient.setId("patient1");
+			patient.addName().setFamily("Doe").addGiven("Jane");
+			encounter.getSubject().setReference("#patient1");
+			encounter.getContained().add(patient);
+
+			Observation obs = new Observation();
+			obs.setId("obs1");
+			obs.addIdentifier().setSystem("urn:system").setValue("FOO");
+			obs.getSubject().setReference("#patient1");
+			CodeableConcept cc = obs.getCode();
+			cc.addCoding().setCode("2345-9").setSystem("http://loinc.org");
+			Quantity quantity = obs.getValueQuantity();
+			quantity.setValue(400);
+			encounter.addReasonReference().setReference("#obs1");
+			encounter.getContained().add(obs);
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
+
+			IIdType eid3 = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
+
+			Encounter createdEncounter = myEncounterDao.read(eid3);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
+		}
+
+		//-- Search by code
+		String uri = ourServerBase + "/Encounter?reason-reference.code=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7") + "&_contained=true";
+		List<String> eids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, eids.size());
+		assertThat(eids, contains(eid1.getValue()));
+
+	}
+
+	@Test
+	public void testContainedSearchByComposite() throws Exception {
+
+		IIdType eid2;
+		{
+			Encounter encounter = new Encounter();
+			encounter.setStatus(EncounterStatus.ARRIVED);
+
+			Patient patient = new Patient();
+			patient.setId("patient1");
+			patient.addName().setFamily("Doe").addGiven("Jane");
+			encounter.getSubject().setReference("#patient1");
+			encounter.getContained().add(patient);
+
+			Observation obs = new Observation();
+			obs.setId("obs1");
+			obs.addIdentifier().setSystem("urn:system").setValue("FOO");
+			obs.getSubject().setReference("#patient1");
+			CodeableConcept cc = obs.getCode();
+			cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
+			Quantity quantity = obs.getValueQuantity();
+			quantity.setValue(200);
+			encounter.addReasonReference().setReference("#obs1");
+			encounter.getContained().add(obs);
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
+
+			IIdType eid1 = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
+
+			Encounter createdEncounter = myEncounterDao.read(eid1);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
+		}
+
+
+		{
+			Encounter encounter = new Encounter();
+			encounter.setStatus(EncounterStatus.ARRIVED);
+
+			Patient patient = new Patient();
+			patient.setId("patient1");
+			patient.addName().setFamily("Doe").addGiven("Jane");
+			encounter.getSubject().setReference("#patient1");
+			encounter.getContained().add(patient);
+
+			Observation obs = new Observation();
+			obs.setId("obs1");
+			obs.addIdentifier().setSystem("urn:system").setValue("FOO");
+			obs.getSubject().setReference("#patient1");
+			CodeableConcept cc = obs.getCode();
+			cc.addCoding().setCode("2345-8").setSystem("http://loinc.org");
+			Quantity quantity = obs.getValueQuantity();
+			quantity.setValue(300);
+			encounter.addReasonReference().setReference("#obs1");
+			encounter.getContained().add(obs);
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
+
+			eid2 = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
+
+			Encounter createdEncounter = myEncounterDao.read(eid2);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
+		}
+
+		{
+			Encounter encounter = new Encounter();
+			encounter.setStatus(EncounterStatus.ARRIVED);
+
+			Patient patient = new Patient();
+			patient.setId("patient1");
+			patient.addName().setFamily("Doe").addGiven("Jane");
+			encounter.getSubject().setReference("#patient1");
+			encounter.getContained().add(patient);
+
+			Observation obs = new Observation();
+			obs.setId("obs1");
+			obs.addIdentifier().setSystem("urn:system").setValue("FOO");
+			obs.getSubject().setReference("#patient1");
+			CodeableConcept cc = obs.getCode();
+			cc.addCoding().setCode("2345-9").setSystem("http://loinc.org");
+			Quantity quantity = obs.getValueQuantity();
+			quantity.setValue(400);
+			encounter.addReasonReference().setReference("#obs1");
+			encounter.getContained().add(obs);
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
+
+			IIdType eid3 = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
+
+			Encounter createdEncounter = myEncounterDao.read(eid3);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
+		}
+
+		//-- Search by composite
+		String uri = ourServerBase + "/Encounter?reason-reference.combo-code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-8$300") + "&_contained=true";
+		List<String> eids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, eids.size());
+		assertThat(eids, contains(eid2.getValue()));
+
+		//-- Search by composite - not found
+		uri = ourServerBase + "/Encounter?reason-reference.combo-code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$300") + "&_contained=true";
+		eids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(0L, eids.size());
+
+	}
+
+
+	@Test
+	public void testContainedSearchByUri() throws Exception {
+
+		IIdType oid1;
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getBirthDateElement().setValueAsString("2000-01-01");
+
+			CarePlan carePlan = new CarePlan();
+			carePlan.setId("carePlan1");
+			carePlan.setStatus(CarePlanStatus.ACTIVE);
+			carePlan.setIntent(CarePlanIntent.ORDER);
+			carePlan.getSubject().setReference("#patient1");
+			carePlan.addInstantiatesUri("http://www.hl7.com");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient1");
+			obs.getContained().add(carePlan);
+			obs.getBasedOnFirstRep().setReference("#carePlan1");
+
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+
+			Observation createdObs = myObservationDao.read(oid1);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
+		}
+
+		{
+			Patient p = new Patient();
+			p.setId("patient2");
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getBirthDateElement().setValueAsString("2000-01-01");
+
+			CarePlan carePlan = new CarePlan();
+			carePlan.setId("carePlan2");
+			carePlan.setStatus(CarePlanStatus.ACTIVE);
+			carePlan.setIntent(CarePlanIntent.ORDER);
+			carePlan.getSubject().setReference("#patient2");
+			carePlan.addInstantiatesUri("http://www2.hl7.com");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 2");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient2");
+			obs.getContained().add(carePlan);
+			obs.getBasedOnFirstRep().setReference("#carePlan2");
+
+			myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+		}
+
+		{
+			Patient p = new Patient();
+			p.setId("patient3");
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getBirthDateElement().setValueAsString("2000-01-01");
+
+			CarePlan carePlan = new CarePlan();
+			carePlan.setId("carePlan3");
+			carePlan.setStatus(CarePlanStatus.ACTIVE);
+			carePlan.setIntent(CarePlanIntent.ORDER);
+			carePlan.getSubject().setReference("#patient3");
+			carePlan.addInstantiatesUri("http://www2.hl7.com");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 3");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient3");
+			obs.getContained().add(carePlan);
+			obs.getBasedOnFirstRep().setReference("#carePlan3");
+
+			myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+		}
+
+		//-- Search by uri
+		String uri = ourServerBase + "/Observation?based-on.instantiates-uri=http://www.hl7.com&_contained=true";
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getValue()));
+
+		//-- Search by uri more than 1 results
+		uri = ourServerBase + "/Observation?based-on.instantiates-uri=http://www2.hl7.com&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(2L, oids.size());
+
+		//-- Search by uri with 'or'
+		uri = ourServerBase + "/Observation?based-on.instantiates-uri=http://www.hl7.com,http://www2.hl7.com&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(3L, oids.size());
+
+	}
+
+	@Test
+	public void testUpdateContainedResource() throws Exception {
+
+		IIdType oid1;
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Smith").addGiven("John");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient1");
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+
+			Observation createdObs = myObservationDao.read(oid1);
+
+			//-- changed the last name to Doe
+			List<Resource> containedResources = createdObs.getContained();
+
+			for (Resource res : containedResources) {
+				if (res instanceof Patient) {
+					Patient p1 = (Patient) res;
+					HumanName name = p1.getNameFirstRep();
+					name.setFamily("Doe");
+					break;
+				}
+			}
+
+			// -- update
+			oid1 = myObservationDao.update(createdObs, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Doe").addGiven("Jane");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 2");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient1");
+
+			myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+		}
+
+		{
+			Patient p = new Patient();
+			p.setId("patient1");
+			p.addName().setFamily("Jones").addGiven("Peter");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 2");
+			obs.getContained().add(p);
+			obs.getSubject().setReference("#patient1");
+
+			myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+		}
+
+
+		//-- No Obs with Patient Smith
+		String uri = ourServerBase + "/Observation?subject.family=Smith&_contained=true";
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(0L, oids.size());
+
+		//-- Two Obs with Patient Doe
+		uri = ourServerBase + "/Observation?subject.family=Doe&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(2L, oids.size());
+	}
+
+
+	@Test
+	public void testDeleteContainedResource() throws Exception {
+
+		IIdType oid1;
+
+		{
+			Patient p1 = new Patient();
+			p1.setId("patient1");
+			p1.addName().setFamily("Smith").addGiven("John");
+
+			Patient p2 = new Patient();
+			p2.setId("patient2");
+			p2.addName().setFamily("Doe").addGiven("Jane");
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getContained().add(p1);
+			obs.getSubject().setReference("#patient1");
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			// -- remove contained resource
+			obs.getContained().remove(p1);
+			// -- add new contained resource
+			obs.getContained().add(p2);
+			obs.getSubject().setReference("#patient2");
+
+			ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+
+			// -- update
+			oid1 = myObservationDao.update(obs, mySrd).getId().toUnqualifiedVersionless();
+
+			Observation updatedObs = myObservationDao.read(oid1);
+
+			ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedObs));
+		}
+
+		//-- No Obs with Patient Smith
+		String uri = ourServerBase + "/Observation?subject.family=Smith&_contained=true";
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(0L, oids.size());
+
+		//-- 1 Obs with Patient Doe
+		uri = ourServerBase + "/Observation?subject.family=Doe&_contained=true";
+		oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getValue()));
+
+	}
+
+	private List<String> searchAndReturnUnqualifiedVersionlessIdValues(String uri) throws IOException {
+		List<String> ids;
+		HttpGet get = new HttpGet(uri);
+
+		try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, resp);
+			ids = toUnqualifiedVersionlessIdValues(bundle);
+		}
+		return ids;
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookWithEventDefinitionR4Test.java

@@ -7,7 +7,12 @@ import ca.uhn.fhir.jpa.subscription.SubscriptionTestUtil;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import com.google.common.collect.Lists;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.EventDefinition;
+import org.hl7.fhir.r4.model.Expression;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Subscription;
+import org.hl7.fhir.r4.model.TriggerDefinition;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
@@ -36,6 +41,7 @@ import java.util.List;
  * 6. Execute the 'sendObservation' test
  * 7. Look in the 'attachWebSocket' terminal execution and wait for your ping with the subscription id
  */
+
 /**
  * Ignored because this feature isn't implemented yet
  */
@@ -77,15 +83,6 @@ public class RestHookWithEventDefinitionR4Test extends BaseResourceProviderR4Tes
 		mySubscriptionTestUtil.unregisterSubscriptionInterceptor();
 	}
 
-	@Override
-	@BeforeEach
-	public void before() throws Exception {
-		super.before();
-
-		myDaoConfig.setSubscriptionEnabled(true);
-
-	}
-
 	@Test
 	public void testSubscriptionAddedTrigger() {
 		/*

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/websocket/WebsocketWithSubscriptionIdDstu3Test.java

@@ -9,7 +9,12 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
 import org.eclipse.jetty.websocket.api.Session;
 import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
 import org.eclipse.jetty.websocket.client.WebSocketClient;
-import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.CodeableConcept;
+import org.hl7.fhir.dstu3.model.Coding;
+import org.hl7.fhir.dstu3.model.Observation;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.Reference;
+import org.hl7.fhir.dstu3.model.Subscription;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -20,8 +25,8 @@ import java.net.URI;
 import java.util.concurrent.Future;
 import java.util.concurrent.TimeUnit;
 
-import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.contains;
 
 /**
  * Adds a FHIR subscription with criteria through the rest interface. Then creates a websocket with the id of the
@@ -71,9 +76,6 @@ public class WebsocketWithSubscriptionIdDstu3Test extends BaseResourceProviderDs
 	public void before() throws Exception {
 		super.before();
 
-		myDaoConfig.setSubscriptionEnabled(true);
-		myDaoConfig.setSubscriptionPollDelay(0L);
-
 		mySubscriptionTestUtil.registerWebSocketInterceptor();
 
 		/*

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ModelConfig.java

@@ -98,6 +98,8 @@ public class ModelConfig {
 	private Set<String> myAutoVersionReferenceAtPaths = Collections.emptySet();
 	private Map<String, Set<String>> myTypeToAutoVersionReferenceAtPaths = Collections.emptyMap();
 	private boolean myRespectVersionsForSearchIncludes;
+	
+	private boolean myIndexOnContainedResources = false;
 
 	/**
 	 * Constructor
@@ -730,6 +732,27 @@ public class ModelConfig {
 		myRespectVersionsForSearchIncludes = theRespectVersionsForSearchIncludes;
 	}
 	
+	
+	/**
+	 * Should indexing and searching on contained resources be enabled on this server.
+	 * This may have performance impacts, and should be enabled only if it is needed. Default is <code>false</code>.
+	 * 
+	 * @since 5.4.0
+	 */
+	public boolean isIndexOnContainedResources() {
+		return myIndexOnContainedResources;
+	}
+	
+	/**
+	 * Should indexing and searching on contained resources be enabled on this server.
+	 * This may have performance impacts, and should be enabled only if it is needed. Default is <code>false</code>.
+	 *
+	 * @since 5.4.0
+	 */
+	public void setIndexOnContainedResources(boolean theIndexOnContainedResources) {
+		myIndexOnContainedResources = theIndexOnContainedResources;
+	}
+	
 	private static void validateTreatBaseUrlsAsLocal(String theUrl) {
 		Validate.notBlank(theUrl, "Base URL must not be null or empty");
 

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/SearchParameterMap.java

@@ -6,6 +6,7 @@ import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
 import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
 import ca.uhn.fhir.rest.api.SortOrderEnum;
 import ca.uhn.fhir.rest.api.SortSpec;
@@ -79,7 +80,8 @@ public class SearchParameterMap implements Serializable {
 	private boolean myLastN;
 	private Integer myLastNMax;
 	private boolean myDeleteExpunge;
-
+	private SearchContainedModeEnum mySearchContainedMode = SearchContainedModeEnum.FALSE;
+	
 	/**
 	 * Constructor
 	 */
@@ -413,10 +415,6 @@ public class SearchParameterMap implements Serializable {
 				IQueryParameterType firstValue = nextValuesAnd.get(0);
 				b.append(UrlUtil.escapeUrlParam(nextKey));
 
-				if (nextKey.equals(Constants.PARAM_HAS)) {
-					b.append(':');
-				}
-
 				if (firstValue.getMissing() != null) {
 					b.append(Constants.PARAMQUALIFIER_MISSING);
 					b.append('=');
@@ -738,4 +736,17 @@ public class SearchParameterMap implements Serializable {
 		return retVal;
 	}
 
+	public SearchContainedModeEnum getSearchContainedMode() {
+		return mySearchContainedMode;
+	}
+
+	public void setSearchContainedMode(SearchContainedModeEnum theSearchContainedMode) {
+		if (theSearchContainedMode == null) {
+			mySearchContainedMode = SearchContainedModeEnum.FALSE;
+		} else {
+			this.mySearchContainedMode = theSearchContainedMode;
+		}
+	}
+
+	
 }

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java

@@ -171,9 +171,9 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 	}
 
 	@Override
-	public SearchParamSet<PathAndRef> extractResourceLinks(IBaseResource theResource) {
+	public SearchParamSet<PathAndRef> extractResourceLinks(IBaseResource theResource, boolean theWantLocalReferences) {
 		IExtractor<PathAndRef> extractor = createReferenceExtractor();
-		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.REFERENCE);
+		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.REFERENCE, theWantLocalReferences);
 	}
 
 	private IExtractor<PathAndRef> createReferenceExtractor() {
@@ -231,7 +231,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 
 	private List<String> extractReferenceParamsAsQueryTokens(RuntimeSearchParam theSearchParam, IBaseResource theResource, IExtractor<PathAndRef> theExtractor) {
 		SearchParamSet<PathAndRef> params = new SearchParamSet<>();
-		extractSearchParam(theSearchParam, theResource, theExtractor, params);
+		extractSearchParam(theSearchParam, theResource, theExtractor, params, false);
 		return refsToStringList(params);
 	}
 
@@ -244,7 +244,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 
 	private <T extends BaseResourceIndexedSearchParam> List<String> extractParamsAsQueryTokens(RuntimeSearchParam theSearchParam, IBaseResource theResource, IExtractor<T> theExtractor) {
 		SearchParamSet<T> params = new SearchParamSet<>();
-		extractSearchParam(theSearchParam, theResource, theExtractor, params);
+		extractSearchParam(theSearchParam, theResource, theExtractor, params, false);
 		return toStringList(params);
 	}
 
@@ -257,14 +257,14 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 	@Override
 	public SearchParamSet<BaseResourceIndexedSearchParam> extractSearchParamTokens(IBaseResource theResource) {
 		IExtractor<BaseResourceIndexedSearchParam> extractor = createTokenExtractor(theResource);
-		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.TOKEN);
+		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.TOKEN, false);
 	}
 
 	@Override
 	public SearchParamSet<BaseResourceIndexedSearchParam> extractSearchParamTokens(IBaseResource theResource, RuntimeSearchParam theSearchParam) {
 		IExtractor<BaseResourceIndexedSearchParam> extractor = createTokenExtractor(theResource);
 		SearchParamSet<BaseResourceIndexedSearchParam> setToPopulate = new SearchParamSet<>();
-		extractSearchParam(theSearchParam, theResource, extractor, setToPopulate);
+		extractSearchParam(theSearchParam, theResource, extractor, setToPopulate, false);
 		return setToPopulate;
 	}
 
@@ -293,11 +293,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 	public SearchParamSet<BaseResourceIndexedSearchParam> extractSearchParamSpecial(IBaseResource theResource) {
 		String resourceTypeName = toRootTypeName(theResource);
 		IExtractor<BaseResourceIndexedSearchParam> extractor = createSpecialExtractor(resourceTypeName);
-		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.SPECIAL);
+		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.SPECIAL, false);
 	}
 
 	private IExtractor<BaseResourceIndexedSearchParam> createSpecialExtractor(String theResourceTypeName) {
-		return (params, searchParam, value, path) -> {
+		return (params, searchParam, value, path, theWantLocalReferences) -> {
 			if (COORDS_INDEX_PATHS.contains(path)) {
 				addCoords_Position(theResourceTypeName, params, searchParam, value);
 			}
@@ -311,11 +311,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 	@Override
 	public SearchParamSet<ResourceIndexedSearchParamUri> extractSearchParamUri(IBaseResource theResource) {
 		IExtractor<ResourceIndexedSearchParamUri> extractor = createUriExtractor(theResource);
-		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.URI);
+		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.URI, false);
 	}
 
 	private IExtractor<ResourceIndexedSearchParamUri> createUriExtractor(IBaseResource theResource) {
-		return (params, searchParam, value, path) -> {
+		return (params, searchParam, value, path, theWantLocalReferences) -> {
 			String nextType = toRootTypeName(value);
 			String resourceType = toRootTypeName(theResource);
 			switch (nextType) {
@@ -336,7 +336,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 	@Override
 	public SearchParamSet<ResourceIndexedSearchParamDate> extractSearchParamDates(IBaseResource theResource) {
 		IExtractor<ResourceIndexedSearchParamDate> extractor = createDateExtractor(theResource);
-		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.DATE);
+		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.DATE, false);
 	}
 
 	private IExtractor<ResourceIndexedSearchParamDate> createDateExtractor(IBaseResource theResource) {
@@ -346,17 +346,17 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 	@Override
 	public Date extractDateFromResource(IBase theValue, String thePath) {
 		DateExtractor extractor = new DateExtractor("DateType");
-		return extractor.get(theValue, thePath).getValueHigh();
+		return extractor.get(theValue, thePath, false).getValueHigh();
 	}
 
 	@Override
 	public SearchParamSet<ResourceIndexedSearchParamNumber> extractSearchParamNumber(IBaseResource theResource) {
 		IExtractor<ResourceIndexedSearchParamNumber> extractor = createNumberExtractor(theResource);
-		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.NUMBER);
+		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.NUMBER, false);
 	}
 
 	private IExtractor<ResourceIndexedSearchParamNumber> createNumberExtractor(IBaseResource theResource) {
-		return (params, searchParam, value, path) -> {
+		return (params, searchParam, value, path, theWantLocalReferences) -> {
 			String nextType = toRootTypeName(value);
 			String resourceType = toRootTypeName(theResource);
 			switch (nextType) {
@@ -384,18 +384,18 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 	@Override
 	public SearchParamSet<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(IBaseResource theResource) {
 		IExtractor<ResourceIndexedSearchParamQuantity> extractor = createQuantityExtractor(theResource);
-		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.QUANTITY);
+		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.QUANTITY, false);
 	}
 
 
 	@Override
 	public SearchParamSet<ResourceIndexedSearchParamQuantityNormalized> extractSearchParamQuantityNormalized(IBaseResource theResource) {
 		IExtractor<ResourceIndexedSearchParamQuantityNormalized> extractor = createQuantityNormalizedExtractor(theResource);
-		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.QUANTITY);
+		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.QUANTITY, false);
 	}
 
 	private IExtractor<ResourceIndexedSearchParamQuantity> createQuantityExtractor(IBaseResource theResource) {
-		return (params, searchParam, value, path) -> {
+		return (params, searchParam, value, path, theWantLocalReferences) -> {
 			if (value.getClass().equals(myLocationPositionDefinition.getImplementingClass())) {
 				return;
 			}
@@ -421,7 +421,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 
 	private IExtractor<ResourceIndexedSearchParamQuantityNormalized> createQuantityNormalizedExtractor(IBaseResource theResource) {
 
-		return (params, searchParam, value, path) -> {
+		return (params, searchParam, value, path, theWantLocalReferences) -> {
 			if (value.getClass().equals(myLocationPositionDefinition.getImplementingClass())) {
 				return;
 			}
@@ -449,11 +449,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 	public SearchParamSet<ResourceIndexedSearchParamString> extractSearchParamStrings(IBaseResource theResource) {
 		IExtractor<ResourceIndexedSearchParamString> extractor = createStringExtractor(theResource);
 
-		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.STRING);
+		return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.STRING, false);
 	}
 
 	private IExtractor<ResourceIndexedSearchParamString> createStringExtractor(IBaseResource theResource) {
-		return (params, searchParam, value, path) -> {
+		return (params, searchParam, value, path, theWantLocalReferences) -> {
 			String resourceType = toRootTypeName(theResource);
 
 			if (value instanceof IPrimitiveType) {
@@ -934,7 +934,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 
 	}
 
-	private <T> SearchParamSet<T> extractSearchParams(IBaseResource theResource, IExtractor<T> theExtractor, RestSearchParameterTypeEnum theSearchParamType) {
+	private <T> SearchParamSet<T> extractSearchParams(IBaseResource theResource, IExtractor<T> theExtractor, RestSearchParameterTypeEnum theSearchParamType, boolean theWantLocalReferences) {
 		SearchParamSet<T> retVal = new SearchParamSet<>();
 
 		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
@@ -943,12 +943,12 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 				continue;
 			}
 
-			extractSearchParam(nextSpDef, theResource, theExtractor, retVal);
+			extractSearchParam(nextSpDef, theResource, theExtractor, retVal, theWantLocalReferences);
 		}
 		return retVal;
 	}
 
-	private <T> void extractSearchParam(RuntimeSearchParam theSearchParameterDef, IBaseResource theResource, IExtractor<T> theExtractor, SearchParamSet<T> theSetToPopulate) {
+	private <T> void extractSearchParam(RuntimeSearchParam theSearchParameterDef, IBaseResource theResource, IExtractor<T> theExtractor, SearchParamSet<T> theSetToPopulate, boolean theWantLocalReferences) {
 		String nextPathUnsplit = theSearchParameterDef.getPath();
 		if (isBlank(nextPathUnsplit)) {
 			return;
@@ -961,7 +961,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 				if (nextObject != null) {
 					String typeName = toRootTypeName(nextObject);
 					if (!myIgnoredForSearchDatatypes.contains(typeName)) {
-						theExtractor.extract(theSetToPopulate, theSearchParameterDef, nextObject, nextPath);
+						theExtractor.extract(theSetToPopulate, theSearchParameterDef, nextObject, nextPath, theWantLocalReferences);
 					}
 				}
 			}
@@ -1181,7 +1181,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 	@FunctionalInterface
 	private interface IExtractor<T> {
 
-		void extract(SearchParamSet<T> theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath);
+		void extract(SearchParamSet<T> theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath, boolean theWantLocalReferences);
 
 	}
 
@@ -1196,9 +1196,9 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		}
 
 		@Override
-		public void extract(SearchParamSet<T> theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath) {
+		public void extract(SearchParamSet<T> theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath, boolean theWantLocalReferences) {
-			myExtractor0.extract(theParams, theSearchParam, theValue, thePath);
+			myExtractor0.extract(theParams, theSearchParam, theValue, thePath, theWantLocalReferences);
-			myExtractor1.extract(theParams, theSearchParam, theValue, thePath);
+			myExtractor1.extract(theParams, theSearchParam, theValue, thePath, theWantLocalReferences);
 		}
 	}
 
@@ -1207,7 +1207,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		private PathAndRef myPathAndRef = null;
 
 		@Override
-		public void extract(SearchParamSet<PathAndRef> theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath) {
+		public void extract(SearchParamSet<PathAndRef> theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath, boolean theWantLocalReferences) {
 			if (theValue instanceof IBaseResource) {
 				return;
 			}
@@ -1257,10 +1257,13 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 					}
 
 					if (nextId == null ||
-						nextId.isEmpty() ||
+							nextId.isEmpty() ||
-						nextId.getValue().startsWith("#") ||
+							nextId.getValue().startsWith("urn:")) {
-						nextId.getValue().startsWith("urn:")) {
+							return;
-						return;
+					}
+					if (!theWantLocalReferences) {
+						if (nextId.getValue().startsWith("#"))
+							return;
 					}
 
 					myPathAndRef = new PathAndRef(theSearchParam.getName(), thePath, valueRef, false);
@@ -1275,7 +1278,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		public PathAndRef get(IBase theValue, String thePath) {
 			extract(new SearchParamSet<>(),
 				new RuntimeSearchParam(null, null, "Reference", null, null, null, null, null, null, null),
-				theValue, thePath);
+				theValue, thePath, false);
 			return myPathAndRef;
 		}
 	}
@@ -1294,7 +1297,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		}
 
 		@Override
-		public void extract(SearchParamSet theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath) {
+		public void extract(SearchParamSet theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath, boolean theWantLocalReferences) {
 			String nextType = toRootTypeName(theValue);
 			switch (nextType) {
 				case "date":
@@ -1389,10 +1392,10 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 			}
 		}
 
-		public ResourceIndexedSearchParamDate get(IBase theValue, String thePath) {
+		public ResourceIndexedSearchParamDate get(IBase theValue, String thePath, boolean theWantLocalReferences) {
 			extract(new SearchParamSet<>(),
 				new RuntimeSearchParam(null, null, "date", null, null, null, null, null, null, null),
-				theValue, thePath);
+				theValue, thePath, theWantLocalReferences);
 			return myIndexedSearchParamDate;
 		}
 	}
@@ -1407,7 +1410,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		}
 
 		@Override
-		public void extract(SearchParamSet<BaseResourceIndexedSearchParam> params, RuntimeSearchParam searchParam, IBase value, String path) {
+		public void extract(SearchParamSet<BaseResourceIndexedSearchParam> params, RuntimeSearchParam searchParam, IBase value, String path, boolean theWantLocalReferences) {
 
 			// DSTU3+
 			if (value instanceof IBaseEnumeration<?>) {

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamExtractor.java

@@ -61,7 +61,7 @@ public interface ISearchParamExtractor {
 
 	SearchParamSet<ResourceIndexedSearchParamUri> extractSearchParamUri(IBaseResource theResource);
 
-	SearchParamSet<PathAndRef> extractResourceLinks(IBaseResource theResource);
+	SearchParamSet<PathAndRef> extractResourceLinks(IBaseResource theResource, boolean theWantLocalReferences);
 
 	String[] split(String theExpression);
 

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceIndexedSearchParams.java

@@ -42,9 +42,7 @@ import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
 import ca.uhn.fhir.rest.param.QuantityParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
-import com.google.common.collect.Lists;
+
-import com.google.common.collect.Sets;
-import com.google.common.collect.Streams;
 import org.apache.commons.lang3.StringUtils;
 
 import java.util.ArrayList;
@@ -57,7 +55,7 @@ import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
 import java.util.function.Predicate;
-import java.util.stream.Stream;
+import javax.annotation.Nonnull;
 
 import static org.apache.commons.lang3.StringUtils.compare;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -144,6 +142,17 @@ public final class ResourceIndexedSearchParams {
 		theEntity.setResourceLinks(myLinks);
 	}
 
+	public void updateSpnamePrefixForIndexedOnContainedResource(String theSpnamePrefix) {
+		updateSpnamePrefixForIndexedOnContainedResource(myNumberParams, theSpnamePrefix);
+		updateSpnamePrefixForIndexedOnContainedResource(myQuantityParams, theSpnamePrefix);
+		updateSpnamePrefixForIndexedOnContainedResource(myQuantityNormalizedParams, theSpnamePrefix);
+		updateSpnamePrefixForIndexedOnContainedResource(myDateParams, theSpnamePrefix);
+		updateSpnamePrefixForIndexedOnContainedResource(myUriParams, theSpnamePrefix);
+		updateSpnamePrefixForIndexedOnContainedResource(myTokenParams, theSpnamePrefix);
+		updateSpnamePrefixForIndexedOnContainedResource(myStringParams, theSpnamePrefix);
+		updateSpnamePrefixForIndexedOnContainedResource(myCoordsParams, theSpnamePrefix);
+	}
+	
 	void setUpdatedTime(Date theUpdateTime) {
 		setUpdatedTime(myStringParams, theUpdateTime);
 		setUpdatedTime(myNumberParams, theUpdateTime);
@@ -161,6 +170,14 @@ public final class ResourceIndexedSearchParams {
 		}
 	}
 
+	private void updateSpnamePrefixForIndexedOnContainedResource(Collection<? extends BaseResourceIndexedSearchParam> theParams, @Nonnull String theSpnamePrefix) {
+		
+		for (BaseResourceIndexedSearchParam param : theParams) {
+			param.setParamName(theSpnamePrefix + "." + param.getParamName());
+			param.calculateHashes(); // re-calculuteHashes
+		}
+	}
+	
 	public Set<String> getPopulatedResourceLinkParameters() {
 		return myPopulatedResourceLinkParameters;
 	}

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java

@@ -52,6 +52,10 @@ import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.util.FhirTerser;
+import ca.uhn.fhir.util.ResourceReferenceInfo;
+import ca.uhn.fhir.util.StringUtil;
+
 import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBaseReference;
@@ -96,14 +100,87 @@ public class SearchParamExtractorService {
 		IBaseResource resource = normalizeResource(theResource);
 
 		// All search parameter types except Reference
-		extractSearchIndexParameters(theRequestDetails, theParams, resource, theEntity);
+		ResourceIndexedSearchParams normalParams = new ResourceIndexedSearchParams();
+		extractSearchIndexParameters(theRequestDetails, normalParams, resource, theEntity);
+		mergeParams(normalParams, theParams);
 
+		if (myModelConfig.isIndexOnContainedResources()) {
+			ResourceIndexedSearchParams containedParams = new ResourceIndexedSearchParams();
+			extractSearchIndexParametersForContainedResources(theRequestDetails, containedParams, resource, theEntity);
+			mergeParams(containedParams, theParams);
+		}
+		
+		// Do this after, because we add to strings during both string and token processing, and contained resource if any
+		populateResourceTables(theParams, theEntity);
+		
 		// Reference search parameters
 		extractResourceLinks(theRequestPartitionId, theParams, theEntity, resource, theTransactionDetails, theFailOnInvalidReference, theRequestDetails);
 
 		theParams.setUpdatedTime(theTransactionDetails.getTransactionDate());
 	}
 
+	private void extractSearchIndexParametersForContainedResources(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, IBaseResource theResource, ResourceTable theEntity) {		
+		
+		FhirTerser terser = myContext.newTerser();
+
+		// 1. get all contained resources
+		Collection<IBaseResource> containedResources = terser.getAllEmbeddedResources(theResource, false);
+
+		// 2. Find referenced search parameters
+		ISearchParamExtractor.SearchParamSet<PathAndRef> referencedSearchParamSet = mySearchParamExtractor.extractResourceLinks(theResource, true);
+		
+		String spnamePrefix = null;
+		ResourceIndexedSearchParams currParams;
+		// 3. for each referenced search parameter, create an index
+		for (PathAndRef nextPathAndRef : referencedSearchParamSet) {
+			
+			// 3.1 get the search parameter name as spname prefix
+			spnamePrefix = nextPathAndRef.getSearchParamName();
+			
+			if (spnamePrefix == null || nextPathAndRef.getRef() == null)
+				continue;
+			
+			// 3.2 find the contained resource
+			IBaseResource containedResource = findContainedResource(containedResources, nextPathAndRef.getRef());
+			if (containedResource == null)
+				continue;
+			
+			currParams = new ResourceIndexedSearchParams();
+			
+			// 3.3 create indexes for the current contained resource
+			extractSearchIndexParameters(theRequestDetails, currParams, containedResource, theEntity);
+			
+			// 3.4 added reference name as a prefix for the contained resource if any
+			// e.g. for Observation.subject contained reference
+			// the SP_NAME = subject.family
+			currParams.updateSpnamePrefixForIndexedOnContainedResource(spnamePrefix);
+			
+			// 3.5 merge to the mainParams
+			// NOTE: the spname prefix is different
+			mergeParams(currParams, theParams); 
+		}
+	}
+	
+	private IBaseResource findContainedResource(Collection<IBaseResource> resources, IBaseReference reference) {
+		for (IBaseResource resource : resources) {
+			if (resource.getIdElement().equals(reference.getReferenceElement()))
+				return resource;
+		}		
+		return null;
+	}
+	
+	private void mergeParams(ResourceIndexedSearchParams theSrcParams, ResourceIndexedSearchParams theTargetParams) {
+	
+		theTargetParams.myNumberParams.addAll(theSrcParams.myNumberParams);
+		theTargetParams.myQuantityParams.addAll(theSrcParams.myQuantityParams);
+		theTargetParams.myQuantityNormalizedParams.addAll(theSrcParams.myQuantityNormalizedParams);
+		theTargetParams.myDateParams.addAll(theSrcParams.myDateParams);
+		theTargetParams.myUriParams.addAll(theSrcParams.myUriParams);
+		theTargetParams.myTokenParams.addAll(theSrcParams.myTokenParams);
+		theTargetParams.myStringParams.addAll(theSrcParams.myStringParams);
+		theTargetParams.myCoordsParams.addAll(theSrcParams.myCoordsParams);
+	}
+	
 	private void extractSearchIndexParameters(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, IBaseResource theResource, ResourceTable theEntity) {
 		
 		// Strings
@@ -156,7 +233,10 @@ public class SearchParamExtractorService {
 			}
 		}
 
-		// Do this after, because we add to strings during both string and token processing
+	}
+		
+	private void populateResourceTables(ResourceIndexedSearchParams theParams, ResourceTable theEntity) {
+		
 		populateResourceTable(theParams.myNumberParams, theEntity);
 		populateResourceTable(theParams.myQuantityParams, theEntity);
 		populateResourceTable(theParams.myQuantityNormalizedParams, theEntity);
@@ -165,7 +245,6 @@ public class SearchParamExtractorService {
 		populateResourceTable(theParams.myTokenParams, theEntity);
 		populateResourceTable(theParams.myStringParams, theEntity);
 		populateResourceTable(theParams.myCoordsParams, theEntity);
-
 	}
 
 	/**
@@ -186,7 +265,7 @@ public class SearchParamExtractorService {
 	private void extractResourceLinks(RequestPartitionId theRequestPartitionId, ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource, TransactionDetails theTransactionDetails, boolean theFailOnInvalidReference, RequestDetails theRequest) {
 		String resourceName = myContext.getResourceType(theResource);
 
-		ISearchParamExtractor.SearchParamSet<PathAndRef> refs = mySearchParamExtractor.extractResourceLinks(theResource);
+		ISearchParamExtractor.SearchParamSet<PathAndRef> refs = mySearchParamExtractor.extractResourceLinks(theResource, false);
 		SearchParamExtractorService.handleWarnings(theRequest, myInterceptorBroadcaster, refs);
 
 		for (PathAndRef nextPathAndRef : refs) {

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -79,6 +79,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		retVal.setWebsocketContextPath("/");
 		retVal.setFilterParameterEnabled(true);
 		retVal.setDefaultSearchParamsCanBeOverridden(false);
+		retVal.getModelConfig().setIndexOnContainedResources(true);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -77,6 +77,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		retVal.setExpungeEnabled(true);
 		retVal.setFilterParameterEnabled(true);
 		retVal.setDefaultSearchParamsCanBeOverridden(false);
+		retVal.getModelConfig().setIndexOnContainedResources(true);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java

@@ -78,6 +78,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 		retVal.setExpungeEnabled(true);
 		retVal.setFilterParameterEnabled(true);
 		retVal.setDefaultSearchParamsCanBeOverridden(false);
+		retVal.getModelConfig().setIndexOnContainedResources(true);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR5Config.java

@@ -77,6 +77,7 @@ public class TestR5Config extends BaseJavaConfigR5 {
 		retVal.setExpungeEnabled(true);
 		retVal.setFilterParameterEnabled(true);
 		retVal.setDefaultSearchParamsCanBeOverridden(false);
+		retVal.getModelConfig().setIndexOnContainedResources(true);
 		return retVal;
 	}
 

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleBuilder.java

@@ -44,7 +44,6 @@ import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
 
 public class RuleBuilder implements IAuthRuleBuilder {
 
-	private static final String[] EMPTY_STRING_ARRAY = new String[0];
 	private static final ConcurrentHashMap<Class<? extends IBaseResource>, String> ourTypeToName = new ConcurrentHashMap<>();
 	private ArrayList<IAuthRule> myRules;
 	private IAuthRuleBuilderRule myAllow;
@@ -144,7 +143,7 @@ public class RuleBuilder implements IAuthRuleBuilder {
 
 		@Override
 		public IAuthRuleBuilderRuleOpClassifierFinishedWithTenantId forTenantIds(String... theTenantIds) {
-			return forTenantIds(Arrays.asList(defaultIfNull(theTenantIds, EMPTY_STRING_ARRAY)));
+			return forTenantIds(Arrays.asList(defaultIfNull(theTenantIds, Constants.EMPTY_STRING_ARRAY)));
 		}
 
 		@Override
@@ -162,7 +161,7 @@ public class RuleBuilder implements IAuthRuleBuilder {
 
 		@Override
 		public IAuthRuleBuilderRuleOpClassifierFinishedWithTenantId notForTenantIds(String... theTenantIds) {
-			return notForTenantIds(Arrays.asList(defaultIfNull(theTenantIds, EMPTY_STRING_ARRAY)));
+			return notForTenantIds(Arrays.asList(defaultIfNull(theTenantIds, Constants.EMPTY_STRING_ARRAY)));
 		}
 
 		@Override

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/MethodUtil.java

@@ -131,6 +131,8 @@ public class MethodUtil {
 				param = new SummaryEnumParameter();
 			} else if (parameterType.equals(PatchTypeEnum.class)) {
 				param = new PatchTypeParameter();
+			} else if (parameterType.equals(SearchContainedModeEnum.class)) {
+				param = new SearchContainedModeParameter();
 			} else if (parameterType.equals(SearchTotalModeEnum.class)) {
 				param = new SearchTotalModeParameter();
 			} else {

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/SearchContainedModeParameter.java

@@ -0,0 +1,34 @@
+package ca.uhn.fhir.rest.server.method;
+
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
+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 java.lang.reflect.Method;
+import java.util.Collection;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+class SearchContainedModeParameter implements IParameter {
+
+	@Override
+	public Object translateQueryParametersIntoServerArgument(RequestDetails theRequest, BaseMethodBinding<?> theMethodBinding) throws InternalErrorException, InvalidRequestException {
+		return getTypeForRequestOrThrowInvalidRequestException(theRequest);
+	}
+
+	@Override
+	public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
+		// ignore
+	}
+
+	public static SearchContainedModeEnum getTypeForRequestOrThrowInvalidRequestException(RequestDetails theRequest) {
+		String[] paramValues = theRequest.getParameters().getOrDefault(Constants.PARAM_CONTAINED, Constants.EMPTY_STRING_ARRAY);
+		if (paramValues.length > 0 && isNotBlank(paramValues[0])) {
+			return SearchContainedModeEnum.fromCode(paramValues[0]);
+		}
+		return null;
+	}
+
+}

hapi-tinder-plugin/src/main/resources/vm/jpa_resource_provider.vm

@@ -20,6 +20,7 @@ import ca.uhn.fhir.rest.param.*;
 import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.api.SummaryEnum;
 import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
 
 public class ${className}ResourceProvider extends 
 ## We have specialized base classes for RPs that handle certain resource types. These
@@ -138,7 +139,9 @@ public class ${className}ResourceProvider extends
 
 			SummaryEnum theSummaryMode,
 
-			SearchTotalModeEnum theSearchTotalMode
+			SearchTotalModeEnum theSearchTotalMode,
+
+			SearchContainedModeEnum theSearchContainedMode
 
 			) {
 		startRequest(theServletRequest);
@@ -165,6 +168,7 @@ public class ${className}ResourceProvider extends
 			paramMap.setOffset(theOffset);
 			paramMap.setSummaryMode(theSummaryMode);
 			paramMap.setSearchTotalMode(theSearchTotalMode);
+			paramMap.setSearchContainedMode(theSearchContainedMode);
 
 			getDao().translateRawParameters(theAdditionalRawParams, paramMap);
 

pom.xml

@@ -782,7 +782,7 @@
 		<jena_version>3.16.0</jena_version>
 		<jersey_version>3.0.0</jersey_version>
 		<!-- 9.4.17 seems to have issues -->
-		<jetty_version>9.4.35.v20201120</jetty_version>
+		<jetty_version>9.4.38.v20210224</jetty_version>
 		<jsr305_version>3.0.2</jsr305_version>
 		<junit_version>5.7.0</junit_version>
 		<flyway_version>6.5.4</flyway_version>