SQL Join Rework (#2086)

* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* added the other six index links

* trying different annotations

* Start testing

* Update resources on package install

* Add changelog

* Join rework

* CLean up SQL builder

* Add docs

* SP rework

* Join work

* Work on params

* Work on refactor

* Work on chains

* Work on joins

* Rework queries

* Work on queries

* Many more tests passing

* Refs test

* Work on sorting

* Work on tests

* More joins work

* Work on tests

* Work on queries

* Tests passing

* More test fixes

* Test fixes

* Work on SQL

* Tests passing

* Add some tests

* Add some tests

* License headers

* Use entity manager to get datasourcd

* One more fix

* Model cleanup

* Ongoing work

* Fixes

* Fixes

* Work on joins

* Ongoing fixes

* Merge conflict

* Cleanup

* clean up unused fields

* Work on join

* COmpile fix

* Rework querying

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Resolve fixmes

* Test fix

* Test fixes

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>

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

@@ -208,7 +208,7 @@ public class TokenParam extends BaseParam /*implements IQueryParameterType*/ {
 	}
 
 	public boolean isEmpty() {
-		return StringUtils.isEmpty(myValue);
+		return StringUtils.isBlank(mySystem) && StringUtils.isBlank(myValue) && getMissing() == null;
 	}
 
 	/**

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

@@ -0,0 +1,39 @@
+package ca.uhn.fhir.util;
+
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+public class IoUtil {
+
+	/**
+	 * Replacement for the deprecated commons-lang method of the same name. Use sparingly
+	 * since they are right that most uses of this should be replaced with try-with-resources
+	 */
+	public static void closeQuietly(final AutoCloseable theCloseable) {
+		try {
+			if (theCloseable != null) {
+				theCloseable.close();
+			}
+		} catch (final Exception ioe) {
+			// ignore
+		}
+	}
+
+}

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

@@ -101,6 +101,7 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulCreate=Successfully create
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulUpdate=Successfully updated resource "{0}" in {1}ms
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulDeletes=Successfully deleted {0} resource(s) in {1}ms
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.invalidSearchParameter=Unknown search parameter "{0}" for resource type "{1}". Valid search parameters for this search are: {2}
+ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.invalidSortParameter=Unknown _sort parameter value "{0}" for resource type "{1}" (Note: sort parameters values must use a valid Search Parameter). Valid values for this search are: {2}
 
 ca.uhn.fhir.rest.api.PatchTypeEnum.missingPatchContentType=Missing or invalid content type for PATCH operation
 ca.uhn.fhir.rest.api.PatchTypeEnum.invalidPatchContentType=Invalid Content-Type for PATCH operation: {0}
@@ -115,11 +116,11 @@ ca.uhn.fhir.jpa.patch.FhirPatch.invalidMoveDestinationIndex=Invalid move destina
 ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor.externalReferenceNotAllowed=Resource contains external reference to URL "{0}" but this server is not configured to allow external references
 ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor.failedToExtractPaths=Failed to extract values from resource using FHIRPath "{0}": {1}
 
-ca.uhn.fhir.jpa.dao.SearchBuilder.invalidQuantityPrefix=Unable to handle quantity prefix "{0}" for value: {1}
+ca.uhn.fhir.jpa.dao.LegacySearchBuilder.invalidQuantityPrefix=Unable to handle quantity prefix "{0}" for value: {1}
-ca.uhn.fhir.jpa.dao.SearchBuilder.invalidNumberPrefix=Unable to handle number prefix "{0}" for value: {1}
+ca.uhn.fhir.jpa.dao.LegacySearchBuilder.invalidNumberPrefix=Unable to handle number prefix "{0}" for value: {1}
-ca.uhn.fhir.jpa.dao.SearchBuilder.sourceParamDisabled=The _source parameter is disabled on this server
+ca.uhn.fhir.jpa.dao.LegacySearchBuilder.sourceParamDisabled=The _source parameter is disabled on this server
-ca.uhn.fhir.jpa.dao.SearchBuilder.invalidCodeMissingSystem=Invalid token specified for parameter {0} - No system specified: {1}|{2}
+ca.uhn.fhir.jpa.dao.LegacySearchBuilder.invalidCodeMissingSystem=Invalid token specified for parameter {0} - No system specified: {1}|{2}
-ca.uhn.fhir.jpa.dao.SearchBuilder.invalidCodeMissingCode=Invalid token specified for parameter {0} - No code specified: {1}|{2}
+ca.uhn.fhir.jpa.dao.LegacySearchBuilder.invalidCodeMissingCode=Invalid token specified for parameter {0} - No code specified: {1}|{2}
 
 ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoConceptMapDstu3.matchesFound=Matches found!
 ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoConceptMapDstu3.noMatchesFound=No matches found!

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

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.util;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import static org.mockito.Mockito.doThrow;
+
+@ExtendWith(MockitoExtension.class)
+public class IoUtilTest {
+
+	@Mock
+	private AutoCloseable myCloseable;
+
+	@Test
+	public void testCloseNull() {
+		// Should throw no exception
+		IoUtil.closeQuietly(null);
+	}
+
+	@Test
+	public void testCloseWithException() throws Exception {
+		doThrow(new Exception()).when(myCloseable).close();
+		// Should throw no exception
+		IoUtil.closeQuietly(myCloseable);
+	}
+
+
+}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/changes.yaml

@@ -12,3 +12,17 @@
         <li>MomentJS (Testpage Overlay): 2.15.1 -&gt; 2.27.0</li>
         <li>Select2 (Testpage Overlay): 4.0.3 -&gt; 4.0.13</li>
     </ul>"
+- item:
+     type: "add"
+     title: "The JPA Server SQL generator for handling FHIR search operations has been completely rewritten to
+     no longer depend on the Hibernate QueryBuilder APIs. This rewrite produces much more efficient SQL in many cases
+     and should dramatically increase performance in such cases. For example, a 10x speedup has been observed on
+     Postgresql when searching a very large database where the search URL has multiple chained search params.
+     <br/><br/>
+     This new SQL builder will be disabled by default in HAPI FHIR 5.2.0 and Smile CDR 2020.11.R01, and can be enabled
+     via a setting in the DaoConfig (HAPI FHIR) and Storage Module config (Smile CDR). Snapshot/prerelease builds will
+     ship with this new SQL builder enabled by default, and the intention is to make this the default and ultimately
+     remove the legacy SQL builder in the next quarterly release.
+     <br/><br/>
+     We highly encourage testing of this new feature, and welcome feedback on how it performs in your environment.
+     "

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

@@ -3,7 +3,6 @@ package ca.uhn.fhir.jpa.api.config;
 import ca.uhn.fhir.jpa.api.model.WarmCacheEntry;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
-import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
 import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
 import ca.uhn.fhir.util.HapiExtensions;
 import com.google.common.annotations.VisibleForTesting;
@@ -83,9 +82,8 @@ public class DaoConfig {
 	private static final Integer DEFAULT_MAXIMUM_TRANSACTION_BUNDLE_SIZE = null;
 	private static final Logger ourLog = LoggerFactory.getLogger(DaoConfig.class);
 	private static final int DEFAULT_EXPUNGE_BATCH_SIZE = 800;
-	private IndexEnabledEnum myIndexMissingFieldsEnabled = IndexEnabledEnum.DISABLED;
 	private static final int DEFAULT_MAXIMUM_DELETE_CONFLICT_COUNT = 60;
-
+	private IndexEnabledEnum myIndexMissingFieldsEnabled = IndexEnabledEnum.DISABLED;
 	/**
 	 * Child Configurations
 	 */
@@ -196,6 +194,32 @@ public class DaoConfig {
 	 * @since 5.0.0
 	 */
 	private boolean myDeleteEnabled = true;
+	/**
+	 * @since 5.1.0
+	 */
+	private boolean myLastNEnabled = false;
+	/**
+	 * @since 5.2.0
+	 */
+	private boolean myUseLegacySearchBuilder = false;
+
+	/**
+	 * Constructor
+	 */
+	public DaoConfig() {
+		setSubscriptionEnabled(true);
+		setSubscriptionPollDelay(0);
+		setSubscriptionPurgeInactiveAfterMillis(Long.MAX_VALUE);
+		setMarkResourcesForReindexingUponSearchParameterChange(true);
+		setReindexThreadCount(Runtime.getRuntime().availableProcessors());
+		setExpungeThreadCount(Runtime.getRuntime().availableProcessors());
+		setBundleTypesAllowedForStorage(DEFAULT_BUNDLE_TYPES_ALLOWED_FOR_STORAGE);
+
+		if ("true".equalsIgnoreCase(System.getProperty(DISABLE_STATUS_BASED_REINDEX))) {
+			ourLog.info("Status based reindexing is DISABLED");
+			setStatusBasedReindexingDisabled(true);
+		}
+	}
 
 	/**
 	 * If set to <code>true</code> (default is <code>false</code>) the <code>$lastn</code> operation will be enabled for
@@ -222,26 +246,27 @@ public class DaoConfig {
 	}
 
 	/**
-	 * @since 5.1.0
+	 * This method controls whether to use the new non-hibernate search SQL builder that was introduced in HAPI FHIR 5.2.0.
+	 * By default this will be <code>false</code> meaning that the new SQL builder is used. Set to <code>true</code> to use the
+	 * legacy SQL builder based on Hibernate.
+	 * <p>Note that this method will be removed in HAPI FHIR 5.4.0</p>
+	 *
+	 * @since 5.3.0
 	 */
-	private boolean myLastNEnabled = false;
+	public boolean isUseLegacySearchBuilder() {
+		return myUseLegacySearchBuilder;
+	}
 
 	/**
-	 * Constructor
+	 * This method controls whether to use the new non-hibernate search SQL builder that was introduced in HAPI FHIR 5.2.0.
+	 * By default this will be <code>false</code> meaning that the new SQL builder is used. Set to <code>true</code> to use the
+	 * legacy SQL builder based on Hibernate.
+	 * <p>Note that this method will be removed in HAPI FHIR 5.4.0</p>
+	 *
+	 * @since 5.3.0
 	 */
-	public DaoConfig() {
+	public void setUseLegacySearchBuilder(boolean theUseLegacySearchBuilder) {
-		setSubscriptionEnabled(true);
+		myUseLegacySearchBuilder = theUseLegacySearchBuilder;
-		setSubscriptionPollDelay(0);
-		setSubscriptionPurgeInactiveAfterMillis(Long.MAX_VALUE);
-		setMarkResourcesForReindexingUponSearchParameterChange(true);
-		setReindexThreadCount(Runtime.getRuntime().availableProcessors());
-		setExpungeThreadCount(Runtime.getRuntime().availableProcessors());
-		setBundleTypesAllowedForStorage(DEFAULT_BUNDLE_TYPES_ALLOWED_FOR_STORAGE);
-
-		if ("true".equalsIgnoreCase(System.getProperty(DISABLE_STATUS_BASED_REINDEX))) {
-			ourLog.info("Status based reindexing is DISABLED");
-			setStatusBasedReindexingDisabled(true);
-		}
 	}
 
 	/**
@@ -995,43 +1020,6 @@ public class DaoConfig {
 		myModelConfig.setAllowExternalReferences(theAllowExternalReferences);
 	}
 
-	/**
-	 * <p>
-	 * Should searches use the integer field {@code SP_VALUE_LOW_DATE_ORDINAL} and {@code SP_VALUE_HIGH_DATE_ORDINAL} in
-	 * {@link ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate} when resolving searches where all predicates are using
-	 * precision of {@link ca.uhn.fhir.model.api.TemporalPrecisionEnum#DAY}.
-	 *
-	 * For example, if enabled, the search of {@code Observation?date=2020-02-25} will cause the date to be collapsed down to an
-	 * ordinal {@code 20200225}. It would then be compared against {@link ResourceIndexedSearchParamDate#getValueLowDateOrdinal()}
-	 * and {@link ResourceIndexedSearchParamDate#getValueHighDateOrdinal()}
-	 * </p>
-	 * Default is {@literal true} beginning in HAPI FHIR 5.0
-	 * </p>
-	 *
-	 * @since 5.0
-	 */
-	public void setUseOrdinalDatesForDayPrecisionSearches(boolean theUseOrdinalDates) {
-		myModelConfig.setUseOrdinalDatesForDayPrecisionSearches(theUseOrdinalDates);
-	}
-
-	/**
-	 * <p>
-	 * Should searches use the integer field {@code SP_VALUE_LOW_DATE_ORDINAL} and {@code SP_VALUE_HIGH_DATE_ORDINAL} in
-	 * {@link ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate} when resolving searches where all predicates are using
-	 * precision of {@link ca.uhn.fhir.model.api.TemporalPrecisionEnum#DAY}.
-	 *
-	 * For example, if enabled, the search of {@code Observation?date=2020-02-25} will cause the date to be collapsed down to an
-	 *  integer representing the ordinal date {@code 20200225}. It would then be compared against {@link ResourceIndexedSearchParamDate#getValueLowDateOrdinal()}
-	 * and {@link ResourceIndexedSearchParamDate#getValueHighDateOrdinal()}
-	 * </p>
-	 * Default is {@literal true} beginning in HAPI FHIR 5.0
-	 * </p>
-	 *
-	 * @since 5.0
-	 */
-	public boolean getUseOrdinalDatesForDayPrecisionSearches() {
-		return myModelConfig.getUseOrdinalDatesForDayPrecisionSearches();
-	}
 	/**
 	 * @see #setAllowInlineMatchUrlReferences(boolean)
 	 */
@@ -2033,8 +2021,8 @@ public class DaoConfig {
 	 *
 	 * @since 5.0.0
 	 */
-	public void setDeleteEnabled(boolean theDeleteEnabled) {
+	public boolean isDeleteEnabled() {
-		myDeleteEnabled = theDeleteEnabled;
+		return myDeleteEnabled;
 	}
 
 	/**
@@ -2046,11 +2034,60 @@ public class DaoConfig {
 	 *
 	 * @since 5.0.0
 	 */
-	public boolean isDeleteEnabled() {
+	public void setDeleteEnabled(boolean theDeleteEnabled) {
-		return myDeleteEnabled;
+		myDeleteEnabled = theDeleteEnabled;
 	}
 
-    public enum StoreMetaSourceInformationEnum {
+	/**
+	 * <p>
+	 * This determines the maximum number of conflicts that should be fetched and handled while retrying a delete of a resource.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code 60}.
+	 * </p>
+	 *
+	 * @since 5.1.0
+	 */
+	public Integer getMaximumDeleteConflictQueryCount() {
+		return myMaximumDeleteConflictQueryCount;
+	}
+
+	/**
+	 * <p>
+	 * This determines the maximum number of conflicts that should be fetched and handled while retrying a delete of a resource.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code 60}.
+	 * </p>
+	 *
+	 * @since 5.1.0
+	 */
+	public void setMaximumDeleteConflictQueryCount(Integer theMaximumDeleteConflictQueryCount) {
+		myMaximumDeleteConflictQueryCount = theMaximumDeleteConflictQueryCount;
+	}
+
+	/**
+	 * <p>
+	 * This determines whether $binary-access-write operations should first load the InputStream into memory before persisting the
+	 * contents to the database. This needs to be enabled for MS SQL Server as this DB requires that the blob size be known
+	 * in advance.
+	 * </p>
+	 * <p>
+	 * Note that this setting should be enabled with caution as it can lead to significant demands on memory.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code false}.
+	 * </p>
+	 *
+	 * @since 5.1.0
+	 * @deprecated In 5.2.0 this setting no longer does anything
+	 */
+	@Deprecated
+	public void setPreloadBlobFromInputStream(Boolean thePreloadBlobFromInputStream) {
+		// ignore
+	}
+
+	public enum StoreMetaSourceInformationEnum {
 		NONE(false, false),
 		SOURCE_URI(true, false),
 		REQUEST_ID(false, true),
@@ -2120,53 +2157,4 @@ public class DaoConfig {
 		ANY
 	}
 
-	/**
-	 * <p>
-	 * This determines the maximum number of conflicts that should be fetched and handled while retrying a delete of a resource.
-	 * </p>
-	 * <p>
-	 * The default value for this setting is {@code 60}.
-	 * </p>
-	 *
-	 * @since 5.1.0
-	 */
-	public Integer getMaximumDeleteConflictQueryCount() {
-		return myMaximumDeleteConflictQueryCount;
-	}
-
-	/**
-	 * <p>
-	 * This determines the maximum number of conflicts that should be fetched and handled while retrying a delete of a resource.
-	 * </p>
-	 * <p>
-	 * The default value for this setting is {@code 60}.
-	 * </p>
-	 *
-	 * @since 5.1.0
-	 */
-	public void setMaximumDeleteConflictQueryCount(Integer theMaximumDeleteConflictQueryCount) {
-		myMaximumDeleteConflictQueryCount = theMaximumDeleteConflictQueryCount;
-	}
-
-	/**
-	 * <p>
-	 * This determines whether $binary-access-write operations should first load the InputStream into memory before persisting the
-	 * contents to the database. This needs to be enabled for MS SQL Server as this DB requires that the blob size be known
-	 * in advance.
-	 * </p>
-	 * <p>
-	 * Note that this setting should be enabled with caution as it can lead to significant demands on memory.
-	 * </p>
-	 * <p>
-	 * The default value for this setting is {@code false}.
-	 * </p>
-	 *
-	 * @since 5.1.0
-	 * @deprecated In 5.2.0 this setting no longer does anything
-	 */
-	@Deprecated
-	public void setPreloadBlobFromInputStream(Boolean thePreloadBlobFromInputStream) {
-		// ignore
-	}
-
 }

hapi-fhir-jpaserver-base/pom.xml

@@ -183,6 +183,13 @@
 			<artifactId>javassist</artifactId>
 		</dependency>
 
+		<!-- SQL Builder -->
+		<dependency>
+			<groupId>com.healthmarketscience.sqlbuilder</groupId>
+			<artifactId>sqlbuilder</artifactId>
+		</dependency>
+
+
 		<!-- Jackson -->
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>

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

@@ -5,6 +5,7 @@ import ca.uhn.fhir.i18n.HapiLocalizer;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.interceptor.executor.InterceptorService;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IDao;
 import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
@@ -19,7 +20,7 @@ import ca.uhn.fhir.jpa.bulk.svc.BulkDataExportSvcImpl;
 import ca.uhn.fhir.jpa.dao.HistoryBuilder;
 import ca.uhn.fhir.jpa.dao.HistoryBuilderFactory;
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
 import ca.uhn.fhir.jpa.dao.index.DaoResourceLinkResolver;
 import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
@@ -51,6 +52,27 @@ import ca.uhn.fhir.jpa.search.PersistedJpaBundleProviderFactory;
 import ca.uhn.fhir.jpa.search.PersistedJpaSearchFirstPageBundleProvider;
 import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
 import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
+import ca.uhn.fhir.jpa.search.builder.QueryStack;
+import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.CompositeUniqueSearchParameterPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.CoordsPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.DatePredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ForcedIdPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.NumberPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.QuantityPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ResourceIdPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ResourceLinkPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ResourceTablePredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.SearchParamPresentPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.SourcePredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.TagPredicateBuilder;
+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.GeneratedSql;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryExecutor;
+import ca.uhn.fhir.jpa.search.builder.sql.SqlObjectFactory;
 import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
 import ca.uhn.fhir.jpa.search.cache.DatabaseSearchResultCacheSvcImpl;
 import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
@@ -414,33 +436,19 @@ public abstract class BaseConfig {
 		return new PersistedJpaBundleProviderFactory();
 	}
 
-	@Bean(name = PERSISTED_JPA_BUNDLE_PROVIDER)
-	@Scope("prototype")
-	public PersistedJpaBundleProvider persistedJpaBundleProvider(RequestDetails theRequest, String theUuid) {
-		return new PersistedJpaBundleProvider(theRequest, theUuid);
-	}
-
-	@Bean(name = PERSISTED_JPA_BUNDLE_PROVIDER_BY_SEARCH)
-	@Scope("prototype")
-	public PersistedJpaBundleProvider persistedJpaBundleProvider(RequestDetails theRequest, Search theSearch) {
-		return new PersistedJpaBundleProvider(theRequest, theSearch);
-	}
-
-	@Bean(name = PERSISTED_JPA_SEARCH_FIRST_PAGE_BUNDLE_PROVIDER)
-	@Scope("prototype")
-	public PersistedJpaSearchFirstPageBundleProvider persistedJpaSearchFirstPageBundleProvider(RequestDetails theRequest, Search theSearch, SearchCoordinatorSvcImpl.SearchTask theSearchTask, ISearchBuilder theSearchBuilder) {
-		return new PersistedJpaSearchFirstPageBundleProvider(theSearch, theSearchTask, theSearchBuilder, theRequest);
-	}
-
 	@Bean
 	public SearchBuilderFactory searchBuilderFactory() {
 		return new SearchBuilderFactory();
 	}
 
-	@Bean(name = SEARCH_BUILDER)
+	@Bean
-	@Scope("prototype")
+	public SqlObjectFactory sqlBuilderFactory() {
-	public SearchBuilder persistedJpaSearchFirstPageBundleProvider(IDao theDao, String theResourceName, Class<? extends IBaseResource> theResourceType) {
+		return new SqlObjectFactory();
-		return new SearchBuilder(theDao, theResourceName, theResourceType);
+	}
+
+	@Bean
+	public HibernateDialectProvider hibernateDialectProvider() {
+		return new HibernateDialectProvider();
 	}
 
 	@Bean
@@ -448,9 +456,136 @@ public abstract class BaseConfig {
 		return new HistoryBuilderFactory();
 	}
 
+	/* **************************************************************** *
+	 * Prototype Beans Below                                            *
+	 * **************************************************************** */
+
+	@Bean(name = PERSISTED_JPA_BUNDLE_PROVIDER)
+	@Scope("prototype")
+	public PersistedJpaBundleProvider newPersistedJpaBundleProvider(RequestDetails theRequest, String theUuid) {
+		return new PersistedJpaBundleProvider(theRequest, theUuid);
+	}
+
+	@Bean(name = PERSISTED_JPA_BUNDLE_PROVIDER_BY_SEARCH)
+	@Scope("prototype")
+	public PersistedJpaBundleProvider newPersistedJpaBundleProvider(RequestDetails theRequest, Search theSearch) {
+		return new PersistedJpaBundleProvider(theRequest, theSearch);
+	}
+
+	@Bean(name = PERSISTED_JPA_SEARCH_FIRST_PAGE_BUNDLE_PROVIDER)
+	@Scope("prototype")
+	public PersistedJpaSearchFirstPageBundleProvider newPersistedJpaSearchFirstPageBundleProvider(RequestDetails theRequest, Search theSearch, SearchCoordinatorSvcImpl.SearchTask theSearchTask, ISearchBuilder theSearchBuilder) {
+		return new PersistedJpaSearchFirstPageBundleProvider(theSearch, theSearchTask, theSearchBuilder, theRequest);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public CompositeUniqueSearchParameterPredicateBuilder newCompositeUniqueSearchParameterPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		return new CompositeUniqueSearchParameterPredicateBuilder(theSearchSqlBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public CoordsPredicateBuilder newCoordsPredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new CoordsPredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public DatePredicateBuilder newDatePredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new DatePredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public ForcedIdPredicateBuilder newForcedIdPredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new ForcedIdPredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public NumberPredicateBuilder newNumberPredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new NumberPredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public QuantityPredicateBuilder newQuantityPredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new QuantityPredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public ResourceLinkPredicateBuilder newResourceLinkPredicateBuilder(QueryStack theQueryStack, SearchQueryBuilder theSearchBuilder, boolean theReversed) {
+		return new ResourceLinkPredicateBuilder(theQueryStack, theSearchBuilder, theReversed);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public ResourceTablePredicateBuilder newResourceTablePredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new ResourceTablePredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public TagPredicateBuilder newTagPredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new TagPredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public ResourceIdPredicateBuilder newResourceIdPredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new ResourceIdPredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public SearchParamPresentPredicateBuilder newSearchParamPresentPredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new SearchParamPresentPredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public StringPredicateBuilder newStringPredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new StringPredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public TokenPredicateBuilder newTokenPredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new TokenPredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public SourcePredicateBuilder newSourcePredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new SourcePredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public UriPredicateBuilder newUriPredicateBuilder(SearchQueryBuilder theSearchBuilder) {
+		return new UriPredicateBuilder(theSearchBuilder);
+	}
+
+	@Bean
+	@Scope("prototype")
+	public SearchQueryExecutor newSearchQueryExecutor(GeneratedSql theGeneratedSql, Integer theMaxResultsToFetch) {
+		return new SearchQueryExecutor(theGeneratedSql, theMaxResultsToFetch);
+	}
+
+	@Bean(name = SEARCH_BUILDER)
+	@Scope("prototype")
+	public ISearchBuilder newSearchBuilder(IDao theDao, String theResourceName, Class<? extends IBaseResource> theResourceType, DaoConfig theDaoConfig) {
+		if (theDaoConfig.isUseLegacySearchBuilder()) {
+			return new LegacySearchBuilder(theDao, theResourceName, theResourceType);
+		}
+		return new SearchBuilder(theDao, theResourceName, theResourceType);
+	}
+
 	@Bean(name = HISTORY_BUILDER)
 	@Scope("prototype")
-	public HistoryBuilder persistedJpaSearchFirstPageBundleProvider(@Nullable String theResourceType, @Nullable Long theResourceId, @Nullable Date theRangeStartInclusive, @Nullable Date theRangeEndInclusive) {
+	public HistoryBuilder newPersistedJpaSearchFirstPageBundleProvider(@Nullable String theResourceType, @Nullable Long theResourceId, @Nullable Date theRangeStartInclusive, @Nullable Date theRangeEndInclusive) {
 		return new HistoryBuilder(theResourceType, theResourceId, theRangeStartInclusive, theRangeEndInclusive);
 	}
 

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

@@ -0,0 +1,46 @@
+package ca.uhn.fhir.jpa.config;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.util.ReflectionUtil;
+import org.apache.commons.lang3.Validate;
+import org.hibernate.dialect.Dialect;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+
+public class HibernateDialectProvider {
+
+	@Autowired
+	private LocalContainerEntityManagerFactoryBean myEntityManagerFactory;
+	private Dialect myDialect;
+
+	public Dialect getDialect() {
+		Dialect dialect = myDialect;
+		if (dialect == null) {
+			String dialectClass = (String) myEntityManagerFactory.getJpaPropertyMap().get("hibernate.dialect");
+			dialect = ReflectionUtil.newInstanceOrReturnNull(dialectClass, Dialect.class);
+			Validate.notNull(dialect, "Unable to create instance of class: %s", dialectClass);
+			myDialect = dialect;
+		}
+		return dialect;
+	}
+
+}

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

@@ -65,11 +65,11 @@ import org.springframework.transaction.annotation.Transactional;
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import javax.validation.constraints.NotNull;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.TreeSet;
 
 import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_ERROR;
 import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_INFO;
@@ -248,7 +248,8 @@ public abstract class BaseStorageDao {
 			QualifierDetails qualifiedParamName = QualifierDetails.extractQualifiersFromParameterName(nextParamName);
 			RuntimeSearchParam param = searchParams.get(qualifiedParamName.getParamName());
 			if (param == null) {
-				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", qualifiedParamName.getParamName(), new TreeSet<>(searchParams.keySet()));
+				Collection<String> validNames = mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(getResourceName());
+				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", qualifiedParamName.getParamName(), getResourceName(), validNames);
 				throw new InvalidRequestException(msg);
 			}
 

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

@@ -49,7 +49,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 
-import static ca.uhn.fhir.jpa.dao.SearchBuilder.toPredicateArray;
+import static ca.uhn.fhir.jpa.dao.LegacySearchBuilder.toPredicateArray;
 
 /**
  * The HistoryBuilder is responsible for building history queries

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

@@ -116,6 +116,7 @@ import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
 
+import static ca.uhn.fhir.jpa.search.builder.SearchBuilder.getMaximumPageSize;
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -124,19 +125,10 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * The SearchBuilder is responsible for actually forming the SQL query that handles
  * searches for resources
  */
-public class SearchBuilder implements ISearchBuilder {
+public class LegacySearchBuilder implements ISearchBuilder {
-
-	/**
-	 * See loadResourcesByPid
-	 * for an explanation of why we use the constant 800
-	 */
-	// NB: keep public
-	public static final int MAXIMUM_PAGE_SIZE = 800;
-	public static final int MAXIMUM_PAGE_SIZE_FOR_TESTING = 50;
-	public static boolean myUseMaxPageSize50ForTest = false;
 
 	private static final List<ResourcePersistentId> EMPTY_LONG_LIST = Collections.unmodifiableList(new ArrayList<>());
-	private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilder.class);
+	private static final Logger ourLog = LoggerFactory.getLogger(LegacySearchBuilder.class);
 	private static final ResourcePersistentId NO_MORE = new ResourcePersistentId(-1L);
 	private final String myResourceName;
 	private final Class<? extends IBaseResource> myResourceType;
@@ -179,24 +171,12 @@ public class SearchBuilder implements ISearchBuilder {
 	/**
 	 * Constructor
 	 */
-	public SearchBuilder(IDao theDao, String theResourceName, Class<? extends IBaseResource> theResourceType) {
+	public LegacySearchBuilder(IDao theDao, String theResourceName, Class<? extends IBaseResource> theResourceType) {
 		myCallingDao = theDao;
 		myResourceName = theResourceName;
 		myResourceType = theResourceType;
 	}
 
-	public static int getMaximumPageSize() {
-		if (myUseMaxPageSize50ForTest) {
-			return MAXIMUM_PAGE_SIZE_FOR_TESTING;
-		} else {
-			return MAXIMUM_PAGE_SIZE;
-		}
-	}
-
-	public static void setMaxPageSize50ForTest(boolean theIsTest) {
-		myUseMaxPageSize50ForTest = theIsTest;
-	}
-
 	@Override
 	public void setMaxResultsToFetch(Integer theMaxResultsToFetch) {
 		myMaxResultsToFetch = theMaxResultsToFetch;
@@ -1408,7 +1388,7 @@ public class SearchBuilder implements ISearchBuilder {
 		List<Predicate> lastUpdatedPredicates = createLastUpdatedPredicates(theLastUpdated, builder, from);
 		lastUpdatedPredicates.add(from.get("myId").as(Long.class).in(ResourcePersistentId.toLongList(thePids)));
 
-		cq.where(SearchBuilder.toPredicateArray(lastUpdatedPredicates));
+		cq.where(LegacySearchBuilder.toPredicateArray(lastUpdatedPredicates));
 		TypedQuery<Long> query = theEntityManager.createQuery(cq);
 
 		return ResourcePersistentId.fromLongList(query.getResultList());

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

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.IDao;
 import ca.uhn.fhir.jpa.config.BaseConfig;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -30,9 +31,11 @@ public class SearchBuilderFactory {
 
 	@Autowired
 	private ApplicationContext myApplicationContext;
+	@Autowired
+	private DaoConfig myDaoConfig;
 
 	public ISearchBuilder newSearchBuilder(IDao theDao, String theResourceName, Class<? extends IBaseResource> theResourceType) {
-		return (ISearchBuilder) myApplicationContext.getBean(BaseConfig.SEARCH_BUILDER, theDao, theResourceName, theResourceType);
+		return (ISearchBuilder) myApplicationContext.getBean(BaseConfig.SEARCH_BUILDER, theDao, theResourceName, theResourceType, myDaoConfig);
 	}
 
 }

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

@@ -23,7 +23,7 @@ package ca.uhn.fhir.jpa.dao.predicate;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.dao.predicate.querystack.QueryStack;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.BasePartitionable;
@@ -63,7 +63,7 @@ abstract class BasePredicateBuilder {
 	@Autowired
 	private PartitionSettings myPartitionSettings;
 
-	BasePredicateBuilder(SearchBuilder theSearchBuilder) {
+	BasePredicateBuilder(LegacySearchBuilder theSearchBuilder) {
 		myCriteriaBuilder = theSearchBuilder.getBuilder();
 		myQueryStack = theSearchBuilder.getQueryStack();
 		myResourceType = theSearchBuilder.getResourceType();
@@ -172,7 +172,7 @@ abstract class BasePredicateBuilder {
 			case ENDS_BEFORE:
 			case STARTS_AFTER:
 			default:
-				String msg = myContext.getLocalizer().getMessage(SearchBuilder.class, invalidMessageName, thePrefix.getValue(), theParam.getValueAsQueryToken(myContext));
+				String msg = myContext.getLocalizer().getMessage(LegacySearchBuilder.class, invalidMessageName, thePrefix.getValue(), theParam.getValueAsQueryToken(myContext));
 				throw new InvalidRequestException(msg);
 		}
 

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

@@ -22,7 +22,7 @@ package ca.uhn.fhir.jpa.dao.predicate;
 
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
@@ -52,7 +52,7 @@ public class PredicateBuilder {
 	private final PredicateBuilderToken myPredicateBuilderToken;
 	private final PredicateBuilderUri myPredicateBuilderUri;
 
-	public PredicateBuilder(SearchBuilder theSearchBuilder, PredicateBuilderFactory thePredicateBuilderFactory) {
+	public PredicateBuilder(LegacySearchBuilder theSearchBuilder, PredicateBuilderFactory thePredicateBuilderFactory) {
 		myPredicateBuilderCoords = thePredicateBuilderFactory.newPredicateBuilderCoords(theSearchBuilder);
 		myPredicateBuilderDate = thePredicateBuilderFactory.newPredicateBuilderDate(theSearchBuilder);
 		myPredicateBuilderNumber = thePredicateBuilderFactory.newPredicateBuilderNumber(theSearchBuilder);

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

@@ -22,8 +22,9 @@ package ca.uhn.fhir.jpa.dao.predicate;
 
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamCoords;
+import ca.uhn.fhir.jpa.model.entity.ResourceLink;
 import ca.uhn.fhir.jpa.util.CoordCalculator;
 import ca.uhn.fhir.jpa.util.SearchBox;
 import ca.uhn.fhir.model.api.IQueryParameterType;
@@ -50,7 +51,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 public class PredicateBuilderCoords extends BasePredicateBuilder implements IPredicateBuilder {
 	private static final Logger ourLog = LoggerFactory.getLogger(PredicateBuilderCoords.class);
 
-	PredicateBuilderCoords(SearchBuilder theSearchBuilder) {
+	PredicateBuilderCoords(LegacySearchBuilder theSearchBuilder) {
 		super(theSearchBuilder);
 	}
 

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

@@ -22,7 +22,7 @@ package ca.uhn.fhir.jpa.dao.predicate;
 
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
@@ -50,7 +50,7 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
 	private static final Logger ourLog = LoggerFactory.getLogger(PredicateBuilderDate.class);
 
 
-	PredicateBuilderDate(SearchBuilder theSearchBuilder) {
+	PredicateBuilderDate(LegacySearchBuilder theSearchBuilder) {
 		super(theSearchBuilder);
 	}
 

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

@@ -20,30 +20,30 @@ package ca.uhn.fhir.jpa.dao.predicate;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import org.springframework.beans.factory.annotation.Lookup;
 import org.springframework.stereotype.Service;
 
 @Service
 public abstract class PredicateBuilderFactory {
 	@Lookup
-	public abstract PredicateBuilderCoords newPredicateBuilderCoords(SearchBuilder theSearchBuilder);
+	public abstract PredicateBuilderCoords newPredicateBuilderCoords(LegacySearchBuilder theSearchBuilder);
 	@Lookup
-	public abstract PredicateBuilderDate newPredicateBuilderDate(SearchBuilder theSearchBuilder);
+	public abstract PredicateBuilderDate newPredicateBuilderDate(LegacySearchBuilder theSearchBuilder);
 	@Lookup
-	public abstract PredicateBuilderNumber newPredicateBuilderNumber(SearchBuilder theSearchBuilder);
+	public abstract PredicateBuilderNumber newPredicateBuilderNumber(LegacySearchBuilder theSearchBuilder);
 	@Lookup
-	public abstract PredicateBuilderQuantity newPredicateBuilderQuantity(SearchBuilder theSearchBuilder);
+	public abstract PredicateBuilderQuantity newPredicateBuilderQuantity(LegacySearchBuilder theSearchBuilder);
 	@Lookup
-	public abstract PredicateBuilderReference newPredicateBuilderReference(SearchBuilder theSearchBuilder, PredicateBuilder thePredicateBuilder);
+	public abstract PredicateBuilderReference newPredicateBuilderReference(LegacySearchBuilder theSearchBuilder, PredicateBuilder thePredicateBuilder);
 	@Lookup
-	public abstract PredicateBuilderResourceId newPredicateBuilderResourceId(SearchBuilder theSearchBuilder);
+	public abstract PredicateBuilderResourceId newPredicateBuilderResourceId(LegacySearchBuilder theSearchBuilder);
 	@Lookup
-	public abstract PredicateBuilderString newPredicateBuilderString(SearchBuilder theSearchBuilder);
+	public abstract PredicateBuilderString newPredicateBuilderString(LegacySearchBuilder theSearchBuilder);
 	@Lookup
-	public abstract PredicateBuilderTag newPredicateBuilderTag(SearchBuilder theSearchBuilder);
+	public abstract PredicateBuilderTag newPredicateBuilderTag(LegacySearchBuilder theSearchBuilder);
 	@Lookup
-	public abstract PredicateBuilderToken newPredicateBuilderToken(SearchBuilder theSearchBuilder, PredicateBuilder thePredicateBuilder);
+	public abstract PredicateBuilderToken newPredicateBuilderToken(LegacySearchBuilder theSearchBuilder, PredicateBuilder thePredicateBuilder);
 	@Lookup
-	public abstract PredicateBuilderUri newPredicateBuilderUri(SearchBuilder theSearchBuilder);
+	public abstract PredicateBuilderUri newPredicateBuilderUri(LegacySearchBuilder theSearchBuilder);
 }

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

@@ -22,8 +22,9 @@ package ca.uhn.fhir.jpa.dao.predicate;
 
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
+import ca.uhn.fhir.jpa.model.entity.ResourceLink;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.param.NumberParam;
 import ca.uhn.fhir.rest.param.ParamPrefixEnum;
@@ -46,7 +47,7 @@ import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
 class PredicateBuilderNumber extends BasePredicateBuilder implements IPredicateBuilder {
 	private static final Logger ourLog = LoggerFactory.getLogger(PredicateBuilderNumber.class);
 
-	PredicateBuilderNumber(SearchBuilder theSearchBuilder) {
+	PredicateBuilderNumber(LegacySearchBuilder theSearchBuilder) {
 		super(theSearchBuilder);
 	}
 

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

@@ -22,9 +22,10 @@ package ca.uhn.fhir.jpa.dao.predicate;
 
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
+import ca.uhn.fhir.jpa.model.entity.ResourceLink;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.base.composite.BaseQuantityDt;
 import ca.uhn.fhir.rest.param.ParamPrefixEnum;
@@ -47,7 +48,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 @Scope("prototype")
 class PredicateBuilderQuantity extends BasePredicateBuilder implements IPredicateBuilder {
 
-	PredicateBuilderQuantity(SearchBuilder theSearchBuilder) {
+	PredicateBuilderQuantity(LegacySearchBuilder theSearchBuilder) {
 		super(theSearchBuilder);
 	}
 

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

@@ -35,7 +35,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IDao;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ResourceHistoryProvenanceEntity;
@@ -109,6 +109,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
 
 @Component
 @Scope("prototype")
+public
 class PredicateBuilderReference extends BasePredicateBuilder {
 	private static final Logger ourLog = LoggerFactory.getLogger(PredicateBuilderReference.class);
 	private final PredicateBuilder myPredicateBuilder;
@@ -125,7 +126,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
 	@Autowired
 	private IInterceptorBroadcaster myInterceptorBroadcaster;
 
-	PredicateBuilderReference(SearchBuilder theSearchBuilder, PredicateBuilder thePredicateBuilder) {
+	PredicateBuilderReference(LegacySearchBuilder theSearchBuilder, PredicateBuilder thePredicateBuilder) {
 		super(theSearchBuilder);
 		myPredicateBuilder = thePredicateBuilder;
 	}
@@ -682,7 +683,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
 						}
 
 					} else {
-						String validNames = new TreeSet<>(mySearchParamRegistry.getActiveSearchParams(theResourceName).keySet()).toString();
+						Collection<String> validNames = mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(theResourceName);
 						String msg = myContext.getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", theParamName, theResourceName, validNames);
 						throw new InvalidRequestException(msg);
 					}
@@ -881,7 +882,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
 		assert theOperation == SearchFilterParser.CompareOperation.eq;
 
 		if (myDaoConfig.getStoreMetaSourceInformation() == DaoConfig.StoreMetaSourceInformationEnum.NONE) {
-			String msg = myContext.getLocalizer().getMessage(SearchBuilder.class, "sourceParamDisabled");
+			String msg = myContext.getLocalizer().getMessage(LegacySearchBuilder.class, "sourceParamDisabled");
 			throw new InvalidRequestException(msg);
 		}
 

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

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.dao.predicate;
  */
 
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
@@ -51,7 +51,7 @@ class PredicateBuilderResourceId extends BasePredicateBuilder {
 	@Autowired
 	IdHelperService myIdHelperService;
 
-	PredicateBuilderResourceId(SearchBuilder theSearchBuilder) {
+	PredicateBuilderResourceId(LegacySearchBuilder theSearchBuilder) {
 		super(theSearchBuilder);
 	}
 

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

@@ -22,8 +22,9 @@ package ca.uhn.fhir.jpa.dao.predicate;
 
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
+import ca.uhn.fhir.jpa.model.entity.ResourceLink;
 import ca.uhn.fhir.model.api.IPrimitiveDatatype;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.param.StringParam;
@@ -43,7 +44,7 @@ import java.util.List;
 @Component
 @Scope("prototype")
 class PredicateBuilderString extends BasePredicateBuilder implements IPredicateBuilder {
-	PredicateBuilderString(SearchBuilder theSearchBuilder) {
+	PredicateBuilderString(LegacySearchBuilder theSearchBuilder) {
 		super(theSearchBuilder);
 	}
 

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

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.dao.predicate;
  */
 
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.model.entity.ResourceTag;
 import ca.uhn.fhir.jpa.model.entity.TagDefinition;
 import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
@@ -53,7 +53,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 class PredicateBuilderTag extends BasePredicateBuilder {
 	private static final Logger ourLog = LoggerFactory.getLogger(PredicateBuilderTag.class);
 
-	PredicateBuilderTag(SearchBuilder theSearchBuilder) {
+	PredicateBuilderTag(LegacySearchBuilder theSearchBuilder) {
 		super(theSearchBuilder);
 	}
 

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

@@ -25,7 +25,7 @@ import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
@@ -65,6 +65,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 @Component
 @Scope("prototype")
+public
 class PredicateBuilderToken extends BasePredicateBuilder implements IPredicateBuilder {
 	private final PredicateBuilder myPredicateBuilder;
 	@Autowired
@@ -72,7 +73,7 @@ class PredicateBuilderToken extends BasePredicateBuilder implements IPredicateBu
 	@Autowired
 	private ModelConfig myModelConfig;
 
-	PredicateBuilderToken(SearchBuilder theSearchBuilder, PredicateBuilder thePredicateBuilder) {
+	PredicateBuilderToken(LegacySearchBuilder theSearchBuilder, PredicateBuilder thePredicateBuilder) {
 		super(theSearchBuilder);
 		myPredicateBuilder = thePredicateBuilder;
 	}
@@ -105,13 +106,13 @@ class PredicateBuilderToken extends BasePredicateBuilder implements IPredicateBu
 						String msg;
 						if (myModelConfig.isSuppressStringIndexingInTokens()) {
 							msg = myContext.getLocalizer().getMessage(PredicateBuilderToken.class, "textModifierDisabledForServer");
-						}else{
+						} else {
 							msg = myContext.getLocalizer().getMessage(PredicateBuilderToken.class, "textModifierDisabledForSearchParam");
 						}
 						throw new MethodNotAllowedException(msg);
 					}
 
-					myPredicateBuilder.addPredicateString(theResourceName, theSearchParam, theList, theRequestPartitionId);
+					myPredicateBuilder.addPredicateString(theResourceName, theSearchParam, theList, theOperation, theRequestPartitionId);
 					break;
 				}
 			}
@@ -289,11 +290,11 @@ class PredicateBuilderToken extends BasePredicateBuilder implements IPredicateBu
 		String systemDesc = defaultIfBlank(theSystem, "(missing)");
 		String codeDesc = defaultIfBlank(theCode, "(missing)");
 		if (isBlank(theCode)) {
-			String msg = myContext.getLocalizer().getMessage(SearchBuilder.class, "invalidCodeMissingSystem", theParamName, systemDesc, codeDesc);
+			String msg = myContext.getLocalizer().getMessage(LegacySearchBuilder.class, "invalidCodeMissingSystem", theParamName, systemDesc, codeDesc);
 			throw new InvalidRequestException(msg);
 		}
 		if (isBlank(theSystem)) {
-			String msg = myContext.getLocalizer().getMessage(SearchBuilder.class, "invalidCodeMissingCode", theParamName, systemDesc, codeDesc);
+			String msg = myContext.getLocalizer().getMessage(LegacySearchBuilder.class, "invalidCodeMissingCode", theParamName, systemDesc, codeDesc);
 			throw new InvalidRequestException(msg);
 		}
 	}

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

@@ -22,7 +22,7 @@ package ca.uhn.fhir.jpa.dao.predicate;
 
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
 import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
@@ -48,7 +48,7 @@ class PredicateBuilderUri extends BasePredicateBuilder implements IPredicateBuil
 	@Autowired
 	private IResourceIndexedSearchParamUriDao myResourceIndexedSearchParamUriDao;
 
-	PredicateBuilderUri(SearchBuilder theSearchBuilder) {
+	PredicateBuilderUri(LegacySearchBuilder theSearchBuilder) {
 		super(theSearchBuilder);
 	}
 

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

@@ -386,7 +386,10 @@ public class SearchFilterParser {
 		ss,
 		sb,
 		in,
-		re
+		re,
+		ap,
+		sa,
+		eb
 	}
 
 	public enum FilterLogicalOperation {
@@ -508,7 +511,7 @@ public class SearchFilterParser {
 		private String FValue;
 		private FilterValueType FValueType;
 
-		FilterParameterPath getParamPath() {
+		public FilterParameterPath getParamPath() {
 
 			return FParamPath;
 		}
@@ -566,7 +569,7 @@ public class SearchFilterParser {
 		private Filter FFilter2;
 
 
-		Filter getFilter1() {
+		public Filter getFilter1() {
 
 			return FFilter1;
 		}
@@ -586,7 +589,7 @@ public class SearchFilterParser {
 			this.FOperation = FOperation;
 		}
 
-		Filter getFilter2() {
+		public Filter getFilter2() {
 
 			return FFilter2;
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSearchParameterR4.java

@@ -166,7 +166,7 @@ public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<Se
 							try {
 								theContext.newFluentPath().evaluate(temporaryInstance, nextPath, IBase.class);
 							} catch (Exception e) {
-								String msg = theContext.getLocalizer().getMessage(FhirResourceDaoSearchParameterR4.class, "invalidSearchParamExpression", nextPath, e.getMessage());
+								String msg = theContext.getLocalizer().getMessageSanitized(FhirResourceDaoSearchParameterR4.class, "invalidSearchParamExpression", nextPath, e.getMessage());
 								throw new UnprocessableEntityException(msg, e);
 							}
 						}

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

@@ -91,7 +91,7 @@ import java.util.Map;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import static ca.uhn.fhir.jpa.dao.SearchBuilder.toPredicateArray;
+import static ca.uhn.fhir.jpa.dao.LegacySearchBuilder.toPredicateArray;
 import static ca.uhn.fhir.util.StringUtil.toUtf8String;
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;

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

@@ -90,6 +90,7 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionSynchronizationManager;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.Nonnull;
@@ -535,8 +536,11 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			 * individually for pages as we return them to clients
 			 */
 			final Set<ResourcePersistentId> includedPids = new HashSet<>();
+			if (theParams.getEverythingMode() == null) {
+				includedPids.addAll(theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated(), "(synchronous)", theRequestDetails));
+			}
 			includedPids.addAll(theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated(), "(synchronous)", theRequestDetails));
-			includedPids.addAll(theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated(), "(synchronous)", theRequestDetails));
+
 			List<ResourcePersistentId> includedPidsList = new ArrayList<>(includedPids);
 
 			List<IBaseResource> resources = new ArrayList<>();
@@ -945,6 +949,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				// Create an initial search in the DB and give it an ID
 				saveSearch();
 
+				assert !TransactionSynchronizationManager.isActualTransactionActive();
+
 				TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
 				txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 

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

@@ -0,0 +1,99 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.NotCondition;
+import com.healthmarketscience.sqlbuilder.UnaryCondition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbTable;
+import org.apache.commons.lang3.Validate;
+
+import javax.annotation.Nullable;
+import java.util.List;
+
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toAndPredicate;
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toEqualToOrInPredicate;
+
+public abstract class BaseJoiningPredicateBuilder extends BasePredicateBuilder {
+
+	private final DbTable myTable;
+	private final DbColumn myColumnPartitionId;
+
+	BaseJoiningPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder, DbTable theTable) {
+		super(theSearchSqlBuilder);
+		myTable = theTable;
+		myColumnPartitionId = theTable.addColumn("PARTITION_ID");
+	}
+
+	public DbTable getTable() {
+		return myTable;
+	}
+
+	public abstract DbColumn getResourceIdColumn();
+
+	DbColumn getPartitionIdColumn() {
+		return myColumnPartitionId;
+	}
+
+	public Condition combineWithRequestPartitionIdPredicate(RequestPartitionId theRequestPartitionId, Condition theCondition) {
+		Condition partitionIdPredicate = createPartitionIdPredicate(theRequestPartitionId);
+		if (partitionIdPredicate == null) {
+			return theCondition;
+		}
+		return toAndPredicate(partitionIdPredicate, theCondition);
+	}
+
+
+	@Nullable
+	public Condition createPartitionIdPredicate(RequestPartitionId theRequestPartitionId) {
+		if (theRequestPartitionId != null && !theRequestPartitionId.isAllPartitions()) {
+			Condition condition;
+			Integer partitionId = theRequestPartitionId.getPartitionId();
+			if (partitionId != null) {
+				Object placeholder = generatePlaceholder(partitionId);
+				condition = BinaryCondition.equalTo(getPartitionIdColumn(), placeholder);
+			} else {
+				condition = UnaryCondition.isNull(getPartitionIdColumn());
+			}
+			return condition;
+		} else {
+			return null;
+		}
+	}
+
+	public Condition createPredicateResourceIds(boolean theInverse, List<Long> theResourceIds) {
+		Validate.notNull(theResourceIds, "theResourceIds must not be null");
+
+		// Handle the _id parameter by adding it to the tail
+		Condition inResourceIds = toEqualToOrInPredicate(getResourceIdColumn(), generatePlaceholders(theResourceIds));
+		if (theInverse) {
+			inResourceIds = new NotCondition(inResourceIds);
+		}
+		return inResourceIds;
+
+	}
+
+
+}

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

@@ -0,0 +1,93 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import ca.uhn.fhir.rest.param.ParamPrefixEnum;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbTable;
+
+import javax.annotation.Nonnull;
+import java.util.Collection;
+import java.util.List;
+
+public class BasePredicateBuilder {
+
+	private final SearchQueryBuilder mySearchSqlBuilder;
+
+	public BasePredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		mySearchSqlBuilder = theSearchSqlBuilder;
+	}
+
+
+	PartitionSettings getPartitionSettings() {
+		return mySearchSqlBuilder.getPartitionSettings();
+	}
+
+	RequestPartitionId getRequestPartitionId() {
+		return mySearchSqlBuilder.getRequestPartitionId();
+	}
+
+	String getResourceType() {
+		return mySearchSqlBuilder.getResourceType();
+	}
+
+	ModelConfig getModelConfig() {
+		return mySearchSqlBuilder.getModelConfig();
+	}
+
+	@Nonnull
+	String generatePlaceholder(Object theInput) {
+		return mySearchSqlBuilder.generatePlaceholder(theInput);
+	}
+
+	@Nonnull
+	List<String> generatePlaceholders(Collection<?> theValues) {
+		return mySearchSqlBuilder.generatePlaceholders(theValues);
+	}
+
+	protected FhirContext getFhirContext() {
+		return mySearchSqlBuilder.getFhirContext();
+	}
+
+	protected void setMatchNothing() {
+		mySearchSqlBuilder.setMatchNothing();
+	}
+
+
+	protected BinaryCondition createConditionForValueWithComparator(ParamPrefixEnum theComparator, DbColumn theColumn, Object theValue) {
+		return mySearchSqlBuilder.createConditionForValueWithComparator(theComparator, theColumn, theValue);
+	}
+
+	protected BaseJoiningPredicateBuilder getOrCreateQueryRootTable() {
+		return mySearchSqlBuilder.getOrCreateFirstPredicateBuilder();
+	}
+
+	public void addJoin(DbTable theFromTable, DbTable theToTable, DbColumn theFromColumn, DbColumn theToColumn) {
+		mySearchSqlBuilder.addJoin(theFromTable, theToTable, theFromColumn, theToColumn);
+	}
+
+}

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

@@ -0,0 +1,103 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.ComboCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbTable;
+
+import javax.annotation.Nonnull;
+import java.util.ArrayList;
+import java.util.List;
+
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toAndPredicate;
+
+public abstract class BaseSearchParamPredicateBuilder extends BaseJoiningPredicateBuilder {
+
+	private final DbColumn myColumnMissing;
+	private final DbColumn myColumnResType;
+	private final DbColumn myColumnParamName;
+	private final DbColumn myColumnResId;
+	private final DbColumn myColumnHashIdentity;
+
+	public BaseSearchParamPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder, DbTable theTable) {
+		super(theSearchSqlBuilder, theTable);
+
+		myColumnResId = getTable().addColumn("RES_ID");
+		myColumnMissing = theTable.addColumn("SP_MISSING");
+		myColumnResType = theTable.addColumn("RES_TYPE");
+		myColumnParamName = theTable.addColumn("SP_NAME");
+		myColumnHashIdentity = theTable.addColumn("HASH_IDENTITY");
+	}
+
+	public DbColumn getColumnHashIdentity() {
+		return myColumnHashIdentity;
+	}
+
+	public DbColumn getResourceTypeColumn() {
+		return myColumnResType;
+	}
+
+	public DbColumn getColumnParamName() {
+		return myColumnParamName;
+	}
+
+	public DbColumn getMissingColumn() {
+		return myColumnMissing;
+	}
+
+	@Override
+	public DbColumn getResourceIdColumn() {
+		return myColumnResId;
+	}
+
+	public Condition combineWithHashIdentityPredicate(String theResourceName, String theParamName, Condition thePredicate) {
+		List<Condition> andPredicates = new ArrayList<>();
+
+		Condition hashIdentityPredicate = createHashIdentityPredicate(theResourceName, theParamName);
+		andPredicates.add(hashIdentityPredicate);
+		andPredicates.add(thePredicate);
+
+		return toAndPredicate(andPredicates);
+	}
+
+	@Nonnull
+	public Condition createHashIdentityPredicate(String theResourceType, String theParamName) {
+		long hashIdentity = BaseResourceIndexedSearchParam.calculateHashIdentity(getPartitionSettings(), getRequestPartitionId(), theResourceType, theParamName);
+		String hashIdentityVal = generatePlaceholder(hashIdentity);
+		return BinaryCondition.equalTo(myColumnHashIdentity, hashIdentityVal);
+	}
+
+	public Condition createPredicateParamMissingForNonReference(String theResourceName, String theParamName, Boolean theMissing, RequestPartitionId theRequestPartitionId) {
+		ComboCondition condition = ComboCondition.and(
+			BinaryCondition.equalTo(getResourceTypeColumn(), generatePlaceholder(theResourceName)),
+			BinaryCondition.equalTo(getColumnParamName(), generatePlaceholder(theParamName)),
+			BinaryCondition.equalTo(getMissingColumn(), generatePlaceholder(theMissing))
+		);
+		return combineWithRequestPartitionIdPredicate(theRequestPartitionId, condition);
+
+	}
+}

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

@@ -0,0 +1,47 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+
+public class CompositeUniqueSearchParameterPredicateBuilder extends BaseSearchParamPredicateBuilder {
+
+	private final DbColumn myColumnString;
+
+	/**
+	 * Constructor
+	 */
+	public CompositeUniqueSearchParameterPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_IDX_CMP_STRING_UNIQ"));
+
+		myColumnString = getTable().addColumn("IDX_STRING");
+	}
+
+
+	public Condition createPredicateIndexString(RequestPartitionId theRequestPartitionId, String theIndexString) {
+		BinaryCondition predicate = BinaryCondition.equalTo(myColumnString, generatePlaceholder(theIndexString));
+		return combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
+	}
+}

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

@@ -0,0 +1,154 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.util.CoordCalculator;
+import ca.uhn.fhir.jpa.util.SearchBox;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.model.dstu2.resource.Location;
+import ca.uhn.fhir.rest.param.QuantityParam;
+import ca.uhn.fhir.rest.param.SpecialParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.ComboCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
+public class CoordsPredicateBuilder extends BaseSearchParamPredicateBuilder {
+
+	private final DbColumn myColumnLatitude;
+	private final DbColumn myColumnLongitude;
+
+	/**
+	 * Constructor
+	 */
+	public CoordsPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_SPIDX_COORDS"));
+
+		myColumnLatitude = getTable().addColumn("SP_LATITUDE");
+		myColumnLongitude = getTable().addColumn("SP_LONGITUDE");
+	}
+
+
+	public Condition createPredicateCoords(SearchParameterMap theParams,
+														IQueryParameterType theParam,
+														String theResourceName,
+														RuntimeSearchParam theSearchParam,
+														CoordsPredicateBuilder theFrom,
+														RequestPartitionId theRequestPartitionId) {
+		String latitudeValue;
+		String longitudeValue;
+		double distanceKm = 0.0;
+
+		if (theParam instanceof TokenParam) { // DSTU3
+			TokenParam param = (TokenParam) theParam;
+			String value = param.getValue();
+			String[] parts = value.split(":");
+			if (parts.length != 2) {
+				throw new IllegalArgumentException("Invalid position format '" + value + "'.  Required format is 'latitude:longitude'");
+			}
+			latitudeValue = parts[0];
+			longitudeValue = parts[1];
+			if (isBlank(latitudeValue) || isBlank(longitudeValue)) {
+				throw new IllegalArgumentException("Invalid position format '" + value + "'.  Both latitude and longitude must be provided.");
+			}
+			QuantityParam distanceParam = theParams.getNearDistanceParam();
+			if (distanceParam != null) {
+				distanceKm = distanceParam.getValue().doubleValue();
+			}
+		} else if (theParam instanceof SpecialParam) { // R4
+			SpecialParam param = (SpecialParam) theParam;
+			String value = param.getValue();
+			String[] parts = value.split("\\|");
+			if (parts.length < 2 || parts.length > 4) {
+				throw new IllegalArgumentException("Invalid position format '" + value + "'.  Required format is 'latitude|longitude' or 'latitude|longitude|distance' or 'latitude|longitude|distance|units'");
+			}
+			latitudeValue = parts[0];
+			longitudeValue = parts[1];
+			if (isBlank(latitudeValue) || isBlank(longitudeValue)) {
+				throw new IllegalArgumentException("Invalid position format '" + value + "'.  Both latitude and longitude must be provided.");
+			}
+			if (parts.length >= 3) {
+				String distanceString = parts[2];
+				if (!isBlank(distanceString)) {
+					distanceKm = Double.parseDouble(distanceString);
+				}
+			}
+		} else {
+			throw new IllegalArgumentException("Invalid position type: " + theParam.getClass());
+		}
+
+		Condition latitudePredicate;
+		Condition longitudePredicate;
+		if (distanceKm == 0.0) {
+			latitudePredicate = theFrom.createPredicateLatitudeExact(latitudeValue);
+			longitudePredicate = theFrom.createPredicateLongitudeExact(longitudeValue);
+		} else if (distanceKm < 0.0) {
+			throw new IllegalArgumentException("Invalid " + Location.SP_NEAR_DISTANCE + " parameter '" + distanceKm + "' must be >= 0.0");
+		} else if (distanceKm > CoordCalculator.MAX_SUPPORTED_DISTANCE_KM) {
+			throw new IllegalArgumentException("Invalid " + Location.SP_NEAR_DISTANCE + " parameter '" + distanceKm + "' must be <= " + CoordCalculator.MAX_SUPPORTED_DISTANCE_KM);
+		} else {
+			double latitudeDegrees = Double.parseDouble(latitudeValue);
+			double longitudeDegrees = Double.parseDouble(longitudeValue);
+
+			SearchBox box = CoordCalculator.getBox(latitudeDegrees, longitudeDegrees, distanceKm);
+			latitudePredicate = theFrom.createLatitudePredicateFromBox(box);
+			longitudePredicate = theFrom.createLongitudePredicateFromBox(box);
+		}
+		ComboCondition singleCode = ComboCondition.and(latitudePredicate, longitudePredicate);
+		return combineWithHashIdentityPredicate(theResourceName, theSearchParam.getName(), singleCode);
+	}
+
+
+	public Condition createPredicateLatitudeExact(String theLatitudeValue) {
+		return BinaryCondition.equalTo(myColumnLatitude, generatePlaceholder(theLatitudeValue));
+	}
+
+	public Condition createPredicateLongitudeExact(String theLongitudeValue) {
+		return BinaryCondition.equalTo(myColumnLongitude, generatePlaceholder(theLongitudeValue));
+	}
+
+	public Condition createLatitudePredicateFromBox(SearchBox theBox) {
+		return ComboCondition.and(
+			BinaryCondition.greaterThanOrEq(myColumnLatitude, generatePlaceholder(theBox.getSouthWest().getLatitude())),
+			BinaryCondition.lessThanOrEq(myColumnLatitude, generatePlaceholder(theBox.getNorthEast().getLatitude()))
+		);
+	}
+
+	public Condition createLongitudePredicateFromBox(SearchBox theBox) {
+		if (theBox.crossesAntiMeridian()) {
+			return ComboCondition.or(
+				BinaryCondition.greaterThanOrEq(myColumnLongitude, generatePlaceholder(theBox.getNorthEast().getLongitude())),
+				BinaryCondition.lessThanOrEq(myColumnLongitude, generatePlaceholder(theBox.getSouthWest().getLongitude()))
+			);
+		}
+		return ComboCondition.and(
+			BinaryCondition.greaterThanOrEq(myColumnLongitude, generatePlaceholder(theBox.getSouthWest().getLongitude())),
+			BinaryCondition.lessThanOrEq(myColumnLongitude, generatePlaceholder(theBox.getNorthEast().getLongitude()))
+		);
+	}
+}

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

@@ -0,0 +1,247 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
+import ca.uhn.fhir.rest.param.DateParam;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.ParamPrefixEnum;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import com.healthmarketscience.sqlbuilder.ComboCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.Date;
+
+public class DatePredicateBuilder extends BaseSearchParamPredicateBuilder {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(DatePredicateBuilder.class);
+	private final DbColumn myColumnValueHigh;
+	private final DbColumn myColumnValueLow;
+	private final DbColumn myColumnValueLowDateOrdinal;
+	private final DbColumn myColumnValueHighDateOrdinal;
+
+	@Autowired
+	private DaoConfig myDaoConfig;
+
+	/**
+	 * Constructor
+	 */
+	public DatePredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_SPIDX_DATE"));
+
+		myColumnValueLow = getTable().addColumn("SP_VALUE_LOW");
+		myColumnValueHigh = getTable().addColumn("SP_VALUE_HIGH");
+		myColumnValueLowDateOrdinal = getTable().addColumn("SP_VALUE_LOW_DATE_ORDINAL");
+		myColumnValueHighDateOrdinal = getTable().addColumn("SP_VALUE_HIGH_DATE_ORDINAL");
+	}
+
+
+	public Condition createPredicateDateWithoutIdentityPredicate(IQueryParameterType theParam,
+																					 String theResourceName,
+																					 String theParamName,
+																					 DatePredicateBuilder theFrom,
+																					 SearchFilterParser.CompareOperation theOperation,
+																					 RequestPartitionId theRequestPartitionId) {
+
+		Condition p;
+		if (theParam instanceof DateParam) {
+			DateParam date = (DateParam) theParam;
+			if (!date.isEmpty()) {
+				DateRangeParam range = new DateRangeParam(date);
+				p = createPredicateDateFromRange(theFrom, range, theOperation);
+			} else {
+				// TODO: handle missing date param?
+				p = null;
+			}
+		} else if (theParam instanceof DateRangeParam) {
+			DateRangeParam range = (DateRangeParam) theParam;
+			p = createPredicateDateFromRange(
+				theFrom,
+				range,
+				theOperation);
+		} else {
+			throw new IllegalArgumentException("Invalid token type: " + theParam.getClass());
+		}
+
+		return p;
+	}
+
+	private Condition createPredicateDateFromRange(DatePredicateBuilder theFrom,
+																  DateRangeParam theRange,
+																  SearchFilterParser.CompareOperation theOperation) {
+		Date lowerBoundInstant = theRange.getLowerBoundAsInstant();
+		Date upperBoundInstant = theRange.getUpperBoundAsInstant();
+
+		DateParam lowerBound = theRange.getLowerBound();
+		DateParam upperBound = theRange.getUpperBound();
+		Integer lowerBoundAsOrdinal = theRange.getLowerBoundAsDateInteger();
+		Integer upperBoundAsOrdinal = theRange.getUpperBoundAsDateInteger();
+		Comparable genericLowerBound;
+		Comparable genericUpperBound;
+		/**
+		 * If all present search parameters are of DAY precision, and {@link ca.uhn.fhir.jpa.model.entity.ModelConfig#getUseOrdinalDatesForDayPrecisionSearches()} is true,
+		 * then we attempt to use the ordinal field for date comparisons instead of the date field.
+		 */
+		boolean isOrdinalComparison = isNullOrDayPrecision(lowerBound) && isNullOrDayPrecision(upperBound) && myDaoConfig.getModelConfig().getUseOrdinalDatesForDayPrecisionSearches();
+
+		Condition lt;
+		Condition gt = null;
+		Condition lb = null;
+		Condition ub = null;
+		DatePredicateBuilder.ColumnEnum lowValueField;
+		DatePredicateBuilder.ColumnEnum highValueField;
+
+		if (isOrdinalComparison) {
+			lowValueField = DatePredicateBuilder.ColumnEnum.LOW_DATE_ORDINAL;
+			highValueField = DatePredicateBuilder.ColumnEnum.HIGH_DATE_ORDINAL;
+			genericLowerBound = lowerBoundAsOrdinal;
+			genericUpperBound = upperBoundAsOrdinal;
+		} else {
+			lowValueField = DatePredicateBuilder.ColumnEnum.LOW;
+			highValueField = DatePredicateBuilder.ColumnEnum.HIGH;
+			genericLowerBound = lowerBoundInstant;
+			genericUpperBound = upperBoundInstant;
+		}
+
+		if (theOperation == SearchFilterParser.CompareOperation.lt) {
+			if (lowerBoundInstant == null) {
+				throw new InvalidRequestException("lowerBound value not correctly specified for compare theOperation");
+			}
+			//im like 80% sure this should be ub and not lb, as it is an UPPER bound.
+			lb = theFrom.createPredicate(lowValueField, ParamPrefixEnum.LESSTHAN, genericLowerBound);
+		} else if (theOperation == SearchFilterParser.CompareOperation.le) {
+			if (upperBoundInstant == null) {
+				throw new InvalidRequestException("upperBound value not correctly specified for compare theOperation");
+			}
+			//im like 80% sure this should be ub and not lb, as it is an UPPER bound.
+			lb = theFrom.createPredicate(highValueField, ParamPrefixEnum.LESSTHAN_OR_EQUALS, genericUpperBound);
+		} else if (theOperation == SearchFilterParser.CompareOperation.gt) {
+			if (upperBoundInstant == null) {
+				throw new InvalidRequestException("upperBound value not correctly specified for compare theOperation");
+			}
+			lb = theFrom.createPredicate(highValueField, ParamPrefixEnum.GREATERTHAN, genericUpperBound);
+		} else if (theOperation == SearchFilterParser.CompareOperation.ge) {
+			if (lowerBoundInstant == null) {
+				throw new InvalidRequestException("lowerBound value not correctly specified for compare theOperation");
+			}
+			lb = theFrom.createPredicate(lowValueField, ParamPrefixEnum.GREATERTHAN_OR_EQUALS, genericLowerBound);
+		} else if (theOperation == SearchFilterParser.CompareOperation.ne) {
+			if ((lowerBoundInstant == null) ||
+				(upperBoundInstant == null)) {
+				throw new InvalidRequestException("lowerBound and/or upperBound value not correctly specified for compare theOperation");
+			}
+			lt = theFrom.createPredicate(lowValueField, ParamPrefixEnum.LESSTHAN, genericLowerBound);
+			gt = theFrom.createPredicate(highValueField, ParamPrefixEnum.GREATERTHAN, genericUpperBound);
+			lb = ComboCondition.or(lt, gt);
+		} else if ((theOperation == SearchFilterParser.CompareOperation.eq) || (theOperation == null)) {
+			if (lowerBoundInstant != null) {
+				gt = theFrom.createPredicate(lowValueField, ParamPrefixEnum.GREATERTHAN_OR_EQUALS, genericLowerBound);
+				lt = theFrom.createPredicate(highValueField, ParamPrefixEnum.GREATERTHAN_OR_EQUALS, genericLowerBound);
+
+				if (lowerBound.getPrefix() == ParamPrefixEnum.STARTS_AFTER || lowerBound.getPrefix() == ParamPrefixEnum.EQUAL) {
+					lb = gt;
+				} else {
+					lb = ComboCondition.or(gt, lt);
+				}
+			}
+
+			if (upperBoundInstant != null) {
+				gt = theFrom.createPredicate(lowValueField, ParamPrefixEnum.LESSTHAN_OR_EQUALS, genericUpperBound);
+				lt = theFrom.createPredicate(highValueField, ParamPrefixEnum.LESSTHAN_OR_EQUALS, genericUpperBound);
+
+
+				if (theRange.getUpperBound().getPrefix() == ParamPrefixEnum.ENDS_BEFORE || theRange.getUpperBound().getPrefix() == ParamPrefixEnum.EQUAL) {
+					ub = lt;
+				} else {
+					ub = ComboCondition.or(gt, lt);
+				}
+			}
+		} else {
+			throw new InvalidRequestException(String.format("Unsupported operator specified, operator=%s",
+				theOperation.name()));
+		}
+		if (isOrdinalComparison) {
+			ourLog.trace("Ordinal date range is {} - {} ", lowerBoundAsOrdinal, upperBoundAsOrdinal);
+		} else {
+			ourLog.trace("Date range is {} - {}", lowerBoundInstant, upperBoundInstant);
+		}
+
+		if (lb != null && ub != null) {
+			return (ComboCondition.and(lb, ub));
+		} else if (lb != null) {
+			return (lb);
+		} else {
+			return (ub);
+		}
+	}
+
+	public DbColumn getColumnValueLow() {
+		return myColumnValueLow;
+	}
+
+	private boolean isNullOrDayPrecision(DateParam theDateParam) {
+		return theDateParam == null || theDateParam.getPrecision().ordinal() == TemporalPrecisionEnum.DAY.ordinal();
+	}
+
+	private Condition createPredicate(ColumnEnum theColumn, ParamPrefixEnum theComparator, Object theValue) {
+
+		DbColumn column;
+		switch (theColumn) {
+			case LOW:
+				column = myColumnValueLow;
+				break;
+			case LOW_DATE_ORDINAL:
+				column = myColumnValueLowDateOrdinal;
+				break;
+			case HIGH:
+				column = myColumnValueHigh;
+				break;
+			case HIGH_DATE_ORDINAL:
+				column = myColumnValueHighDateOrdinal;
+				break;
+			default:
+				throw new IllegalArgumentException();
+		}
+
+		return createConditionForValueWithComparator(theComparator, column, theValue);
+
+	}
+
+
+	public enum ColumnEnum {
+
+		LOW,
+		LOW_DATE_ORDINAL,
+		HIGH,
+		HIGH_DATE_ORDINAL
+
+	}
+
+}

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

@@ -0,0 +1,56 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class ForcedIdPredicateBuilder extends BaseJoiningPredicateBuilder {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ForcedIdPredicateBuilder.class);
+	private final DbColumn myColumnResourceId;
+	private final DbColumn myColumnForcedId;
+
+	/**
+	 * Constructor
+	 */
+	public ForcedIdPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_FORCED_ID"));
+
+		myColumnResourceId = getTable().addColumn("RESOURCE_PID");
+		myColumnForcedId = getTable().addColumn("FORCED_ID");
+	}
+
+	@Override
+	public DbColumn getResourceIdColumn() {
+		return myColumnResourceId;
+	}
+
+
+	public DbColumn getColumnForcedId() {
+		return myColumnForcedId;
+	}
+
+
+}
+

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

@@ -0,0 +1,113 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
+import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
+import ca.uhn.fhir.jpa.dao.predicate.SearchFuzzUtil;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.rest.param.ParamPrefixEnum;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.ComboCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.math.BigDecimal;
+import java.math.MathContext;
+
+import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
+
+public class NumberPredicateBuilder extends BaseSearchParamPredicateBuilder {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(NumberPredicateBuilder.class);
+	private final DbColumn myColumnValue;
+	@Autowired
+	private FhirContext myFhirContext;
+
+	/**
+	 * Constructor
+	 */
+	public NumberPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_SPIDX_NUMBER"));
+
+		myColumnValue = getTable().addColumn("SP_VALUE");
+	}
+
+	public Condition createPredicateNumeric(String theResourceName, String theParamName, SearchFilterParser.CompareOperation theOperation, BigDecimal theValue, RequestPartitionId theRequestPartitionId, IQueryParameterType theActualParam) {
+		Condition numericPredicate = createPredicateNumeric(this, theOperation, theValue, myColumnValue, "invalidNumberPrefix", myFhirContext, theActualParam);
+		return combineWithHashIdentityPredicate(theResourceName, theParamName, numericPredicate);
+	}
+
+	public DbColumn getColumnValue() {
+		return myColumnValue;
+	}
+
+
+	static Condition createPredicateNumeric(BaseSearchParamPredicateBuilder theIndexTable, SearchFilterParser.CompareOperation theOperation, BigDecimal theValue, DbColumn theColumn, String theInvalidValueKey, FhirContext theFhirContext, IQueryParameterType theActualParam) {
+		Condition num;
+
+		// Per discussions with Grahame Grieve and James Agnew on 11/13/19, modified logic for EQUAL and NOT_EQUAL operators below so as to
+		//   use exact value matching.  The "fuzz amount" matching is still used with the APPROXIMATE operator.
+		SearchFilterParser.CompareOperation operation = defaultIfNull(theOperation, SearchFilterParser.CompareOperation.eq);
+		switch (operation) {
+			case gt:
+				num = BinaryCondition.greaterThan(theColumn, theIndexTable.generatePlaceholder(theValue));
+				break;
+			case ge:
+				num = BinaryCondition.greaterThanOrEq(theColumn, theIndexTable.generatePlaceholder(theValue));
+				break;
+			case lt:
+				num = BinaryCondition.lessThan(theColumn, theIndexTable.generatePlaceholder(theValue));
+				break;
+			case le:
+				num = BinaryCondition.lessThanOrEq(theColumn, theIndexTable.generatePlaceholder(theValue));
+				break;
+			case eq:
+				num = BinaryCondition.equalTo(theColumn, theIndexTable.generatePlaceholder(theValue));
+				break;
+			case ne:
+				num = BinaryCondition.notEqualTo(theColumn, theIndexTable.generatePlaceholder(theValue));
+				break;
+			case ap:
+				BigDecimal mul = SearchFuzzUtil.calculateFuzzAmount(ParamPrefixEnum.APPROXIMATE, theValue);
+				BigDecimal low = theValue.subtract(mul, MathContext.DECIMAL64);
+				BigDecimal high = theValue.add(mul, MathContext.DECIMAL64);
+				Condition lowPred = BinaryCondition.greaterThanOrEq(theColumn, theIndexTable.generatePlaceholder(low));
+				Condition highPred = BinaryCondition.lessThanOrEq(theColumn, theIndexTable.generatePlaceholder(high));
+				num = ComboCondition.and(lowPred, highPred);
+				ourLog.trace("Searching for {} <= val <= {}", low, high);
+				break;
+			default:
+				String paramValue = theActualParam.getValueAsQueryToken(theFhirContext);
+				String msg = theIndexTable.getFhirContext().getLocalizer().getMessage(LegacySearchBuilder.class, theInvalidValueKey, operation, paramValue);
+				throw new InvalidRequestException(msg);
+		}
+
+		return num;
+	}
+}

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

@@ -0,0 +1,115 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
+import ca.uhn.fhir.jpa.search.builder.QueryStack;
+import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.model.base.composite.BaseQuantityDt;
+import ca.uhn.fhir.rest.param.ParamPrefixEnum;
+import ca.uhn.fhir.rest.param.QuantityParam;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.ComboCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.persistence.criteria.CriteriaBuilder;
+import java.math.BigDecimal;
+
+import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
+public class QuantityPredicateBuilder extends BaseSearchParamPredicateBuilder {
+
+	private final DbColumn myColumnHashIdentitySystemUnits;
+	private final DbColumn myColumnHashIdentityUnits;
+	private final DbColumn myColumnValue;
+	@Autowired
+	private FhirContext myFhirContext;
+
+	/**
+	 * Constructor
+	 */
+	public QuantityPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_SPIDX_QUANTITY"));
+
+		myColumnHashIdentitySystemUnits = getTable().addColumn("HASH_IDENTITY_SYS_UNITS");
+		myColumnHashIdentityUnits = getTable().addColumn("HASH_IDENTITY_AND_UNITS");
+		myColumnValue = getTable().addColumn("SP_VALUE");
+	}
+
+
+	public Condition createPredicateQuantity(IQueryParameterType theParam, String theResourceName, String theParamName, CriteriaBuilder theBuilder, QuantityPredicateBuilder theFrom, SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
+
+		String systemValue;
+		String unitsValue;
+		ParamPrefixEnum cmpValue;
+		BigDecimal valueValue;
+
+		if (theParam instanceof BaseQuantityDt) {
+			BaseQuantityDt param = (BaseQuantityDt) theParam;
+			systemValue = param.getSystemElement().getValueAsString();
+			unitsValue = param.getUnitsElement().getValueAsString();
+			cmpValue = ParamPrefixEnum.forValue(param.getComparatorElement().getValueAsString());
+			valueValue = param.getValueElement().getValue();
+		} else if (theParam instanceof QuantityParam) {
+			QuantityParam param = (QuantityParam) theParam;
+			systemValue = param.getSystem();
+			unitsValue = param.getUnits();
+			cmpValue = param.getPrefix();
+			valueValue = param.getValue();
+		} else {
+			throw new IllegalArgumentException("Invalid quantity type: " + theParam.getClass());
+		}
+
+		Condition hashPredicate;
+		if (!isBlank(systemValue) && !isBlank(unitsValue)) {
+			long hash = ResourceIndexedSearchParamQuantity.calculateHashSystemAndUnits(getPartitionSettings(), theRequestPartitionId, theResourceName, theParamName, systemValue, unitsValue);
+			hashPredicate = BinaryCondition.equalTo(myColumnHashIdentitySystemUnits, generatePlaceholder(hash));
+		} else if (!isBlank(unitsValue)) {
+			long hash = ResourceIndexedSearchParamQuantity.calculateHashUnits(getPartitionSettings(), theRequestPartitionId, theResourceName, theParamName, unitsValue);
+			hashPredicate = BinaryCondition.equalTo(myColumnHashIdentityUnits, generatePlaceholder(hash));
+		} else {
+			long hash = BaseResourceIndexedSearchParam.calculateHashIdentity(getPartitionSettings(), theRequestPartitionId, theResourceName, theParamName);
+			hashPredicate = BinaryCondition.equalTo(getColumnHashIdentity(), generatePlaceholder(hash));
+		}
+
+		SearchFilterParser.CompareOperation operation = theOperation;
+		if (operation == null && cmpValue != null) {
+			operation = QueryStack.toOperation(cmpValue);
+		}
+		operation = defaultIfNull(operation, SearchFilterParser.CompareOperation.eq);
+		Condition numericPredicate = NumberPredicateBuilder.createPredicateNumeric(this, operation, valueValue, myColumnValue, "invalidQuantityPrefix", myFhirContext, theParam);
+
+		return ComboCondition.and(hashPredicate, numericPredicate);
+	}
+
+
+	public DbColumn getColumnValue() {
+		return myColumnValue;
+	}
+}

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

@@ -0,0 +1,135 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.dao.index.IdHelperService;
+import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
+import ca.uhn.fhir.jpa.search.builder.QueryStack;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.TokenParamModifier;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.hl7.fhir.r4.model.IdType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.annotation.Nullable;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
+	private static final Logger ourLog = LoggerFactory.getLogger(ResourceIdPredicateBuilder.class);
+
+	@Autowired
+	private IdHelperService myIdHelperService;
+
+	/**
+	 * Constructor
+	 */
+	public ResourceIdPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder);
+	}
+
+
+	@Nullable
+	public Condition createPredicateResourceId(@Nullable DbColumn theSourceJoinColumn, String theResourceName, List<List<IQueryParameterType>> theValues, SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
+
+		Set<ResourcePersistentId> allOrPids = null;
+		SearchFilterParser.CompareOperation defaultOperation = SearchFilterParser.CompareOperation.eq;
+
+		for (List<? extends IQueryParameterType> nextValue : theValues) {
+			Set<ResourcePersistentId> orPids = new HashSet<>();
+			boolean haveValue = false;
+			for (IQueryParameterType next : nextValue) {
+				String value = next.getValueAsQueryToken(getFhirContext());
+				if (value != null && value.startsWith("|")) {
+					value = value.substring(1);
+				}
+
+				IdType valueAsId = new IdType(value);
+				if (isNotBlank(value)) {
+					haveValue = true;
+					try {
+						ResourcePersistentId pid = myIdHelperService.resolveResourcePersistentIds(theRequestPartitionId, theResourceName, valueAsId.getIdPart());
+						orPids.add(pid);
+					} catch (ResourceNotFoundException e) {
+						// This is not an error in a search, it just results in no matches
+						ourLog.debug("Resource ID {} was requested but does not exist", valueAsId.getIdPart());
+					}
+				}
+
+				if (next instanceof TokenParam) {
+					if (((TokenParam) next).getModifier() == TokenParamModifier.NOT) {
+						defaultOperation = SearchFilterParser.CompareOperation.ne;
+					}
+				}
+
+			}
+			if (haveValue) {
+				if (allOrPids == null) {
+					allOrPids = orPids;
+				} else {
+					allOrPids.retainAll(orPids);
+				}
+
+			}
+		}
+
+		if (allOrPids != null && allOrPids.isEmpty()) {
+
+			setMatchNothing();
+
+		} else if (allOrPids != null) {
+
+			SearchFilterParser.CompareOperation operation = defaultIfNull(theOperation, defaultOperation);
+			assert operation == SearchFilterParser.CompareOperation.eq || operation == SearchFilterParser.CompareOperation.ne;
+
+			List<Long> resourceIds = ResourcePersistentId.toLongList(allOrPids);
+			if (theSourceJoinColumn == null) {
+				BaseJoiningPredicateBuilder queryRootTable = super.getOrCreateQueryRootTable();
+				switch (operation) {
+					default:
+					case eq:
+						return queryRootTable.createPredicateResourceIds(false, resourceIds);
+					case ne:
+						return queryRootTable.createPredicateResourceIds(true, resourceIds);
+				}
+			} else {
+				return QueryStack.toEqualToOrInPredicate(theSourceJoinColumn, generatePlaceholders(resourceIds), operation == SearchFilterParser.CompareOperation.ne);
+			}
+
+		}
+
+		return null;
+	}
+
+
+}

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

@@ -0,0 +1,614 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
+import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.interceptor.api.HookParams;
+import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
+import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IDao;
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.index.IdHelperService;
+import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderReference;
+import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
+import ca.uhn.fhir.jpa.search.builder.QueryStack;
+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.jpa.searchparam.registry.ISearchParamRegistry;
+import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
+import ca.uhn.fhir.rest.param.CompositeParam;
+import ca.uhn.fhir.rest.param.DateParam;
+import ca.uhn.fhir.rest.param.NumberParam;
+import ca.uhn.fhir.rest.param.QuantityParam;
+import ca.uhn.fhir.rest.param.ReferenceParam;
+import ca.uhn.fhir.rest.param.SpecialParam;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import com.google.common.collect.Lists;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.ComboCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toAndPredicate;
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toEqualToOrInPredicate;
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toOrPredicate;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
+
+public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ResourceLinkPredicateBuilder.class);
+	private final DbColumn myColumnSrcType;
+	private final DbColumn myColumnSrcPath;
+	private final DbColumn myColumnTargetResourceId;
+	private final DbColumn myColumnTargetResourceUrl;
+	private final DbColumn myColumnSrcResourceId;
+	private final DbColumn myColumnTargetResourceType;
+	private final QueryStack myQueryStack;
+	private final boolean myReversed;
+
+	@Autowired
+	private DaoConfig myDaoConfig;
+	@Autowired
+	private IInterceptorBroadcaster myInterceptorBroadcaster;
+	@Autowired
+	private ISearchParamRegistry mySearchParamRegistry;
+	@Autowired
+	private IdHelperService myIdHelperService;
+	@Autowired
+	private DaoRegistry myDaoRegistry;
+	@Autowired
+	private MatchUrlService myMatchUrlService;
+
+	/**
+	 * Constructor
+	 */
+	public ResourceLinkPredicateBuilder(QueryStack theQueryStack, SearchQueryBuilder theSearchSqlBuilder, boolean theReversed) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_RES_LINK"));
+		myColumnSrcResourceId = getTable().addColumn("SRC_RESOURCE_ID");
+		myColumnSrcType = getTable().addColumn("SOURCE_RESOURCE_TYPE");
+		myColumnSrcPath = getTable().addColumn("SRC_PATH");
+		myColumnTargetResourceId = getTable().addColumn("TARGET_RESOURCE_ID");
+		myColumnTargetResourceUrl = getTable().addColumn("TARGET_RESOURCE_URL");
+		myColumnTargetResourceType = getTable().addColumn("TARGET_RESOURCE_TYPE");
+
+		myReversed = theReversed;
+		myQueryStack = theQueryStack;
+	}
+
+	public DbColumn getColumnSourcePath() {
+		return myColumnSrcPath;
+	}
+
+	public DbColumn getColumnTargetResourceId() {
+		return myColumnTargetResourceId;
+	}
+
+	public DbColumn getColumnSrcResourceId() {
+		return myColumnSrcResourceId;
+	}
+
+	public DbColumn getColumnTargetResourceType() {
+		return myColumnTargetResourceType;
+	}
+
+	@Override
+	public DbColumn getResourceIdColumn() {
+		if (myReversed) {
+			return myColumnTargetResourceId;
+		} else {
+			return myColumnSrcResourceId;
+		}
+	}
+
+	public Condition createPredicate(RequestDetails theRequest, String theResourceType, String theParamName, List<? extends IQueryParameterType> theReferenceOrParamList, SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
+
+		List<IIdType> targetIds = new ArrayList<>();
+		List<String> targetQualifiedUrls = new ArrayList<>();
+
+		for (int orIdx = 0; orIdx < theReferenceOrParamList.size(); orIdx++) {
+			IQueryParameterType nextOr = theReferenceOrParamList.get(orIdx);
+
+			if (nextOr instanceof ReferenceParam) {
+				ReferenceParam ref = (ReferenceParam) nextOr;
+
+				if (isBlank(ref.getChain())) {
+
+					/*
+					 * Handle non-chained search, e.g. Patient?organization=Organization/123
+					 */
+
+					IIdType dt = new IdDt(ref.getBaseUrl(), ref.getResourceType(), ref.getIdPart(), null);
+
+					if (dt.hasBaseUrl()) {
+						if (myDaoConfig.getTreatBaseUrlsAsLocal().contains(dt.getBaseUrl())) {
+							dt = dt.toUnqualified();
+							targetIds.add(dt);
+						} else {
+							targetQualifiedUrls.add(dt.getValue());
+						}
+					} else {
+						targetIds.add(dt);
+					}
+
+				} else {
+
+					/*
+					 * Handle chained search, e.g. Patient?organization.name=Kwik-e-mart
+					 */
+
+					return addPredicateReferenceWithChain(theResourceType, theParamName, theReferenceOrParamList, ref, theRequest, theRequestPartitionId);
+
+				}
+
+			} else {
+				throw new IllegalArgumentException("Invalid token type (expecting ReferenceParam): " + nextOr.getClass());
+			}
+
+		}
+
+		for (IIdType next : targetIds) {
+			if (!next.hasResourceType()) {
+				warnAboutPerformanceOnUnqualifiedResources(theParamName, theRequest, null);
+			}
+		}
+
+		List<String> pathsToMatch = createResourceLinkPaths(theResourceType, theParamName);
+		boolean inverse;
+		if ((theOperation == null) || (theOperation == SearchFilterParser.CompareOperation.eq)) {
+			inverse = false;
+		} else {
+			inverse = true;
+		}
+
+		List<ResourcePersistentId> targetPids = myIdHelperService.resolveResourcePersistentIdsWithCache(theRequestPartitionId, targetIds);
+		List<Long> targetPidList = ResourcePersistentId.toLongList(targetPids);
+
+		if (targetPidList.isEmpty() && targetQualifiedUrls.isEmpty()) {
+			setMatchNothing();
+			return null;
+		} else {
+			Condition retVal = createPredicateReference(inverse, pathsToMatch, targetPidList, targetQualifiedUrls);
+			return combineWithRequestPartitionIdPredicate(getRequestPartitionId(), retVal);
+		}
+
+	}
+
+	private Condition createPredicateReference(boolean theInverse, List<String> thePathsToMatch, List<Long> theTargetPidList, List<String> theTargetQualifiedUrls) {
+
+		Condition targetPidCondition = null;
+		if (!theTargetPidList.isEmpty()) {
+			List<String> placeholders = generatePlaceholders(theTargetPidList);
+			targetPidCondition = toEqualToOrInPredicate(myColumnTargetResourceId, placeholders, theInverse);
+		}
+
+		Condition targetUrlsCondition = null;
+		if (!theTargetQualifiedUrls.isEmpty()) {
+			List<String> placeholders = generatePlaceholders(theTargetQualifiedUrls);
+			targetUrlsCondition = toEqualToOrInPredicate(myColumnTargetResourceUrl, placeholders, theInverse);
+		}
+
+		Condition joinedCondition;
+		if (targetPidCondition != null && targetUrlsCondition != null) {
+			joinedCondition = ComboCondition.or(targetPidCondition, targetUrlsCondition);
+		} else if (targetPidCondition != null) {
+			joinedCondition = targetPidCondition;
+		} else {
+			joinedCondition = targetUrlsCondition;
+		}
+
+		Condition pathPredicate = createPredicateSourcePaths(thePathsToMatch);
+		joinedCondition = ComboCondition.and(pathPredicate, joinedCondition);
+
+		return joinedCondition;
+	}
+
+	@Nonnull
+	private Condition createPredicateSourcePaths(List<String> thePathsToMatch) {
+		return toEqualToOrInPredicate(myColumnSrcPath, generatePlaceholders(thePathsToMatch));
+	}
+
+	public Condition createPredicateSourcePaths(String theResourceName, String theParamName) {
+		List<String> pathsToMatch = createResourceLinkPaths(theResourceName, theParamName);
+		return createPredicateSourcePaths(pathsToMatch);
+	}
+
+
+	private void warnAboutPerformanceOnUnqualifiedResources(String theParamName, RequestDetails theRequest, @Nullable List<String> theCandidateTargetTypes) {
+		StringBuilder builder = new StringBuilder();
+		builder.append("This search uses an unqualified resource(a parameter in a chain without a resource type). ");
+		builder.append("This is less efficient than using a qualified type. ");
+		if (theCandidateTargetTypes != null) {
+			builder.append("[" + theParamName + "] resolves to [" + theCandidateTargetTypes.stream().collect(Collectors.joining(",")) + "].");
+			builder.append("If you know what you're looking for, try qualifying it using the form ");
+			builder.append(theCandidateTargetTypes.stream().map(cls -> "[" + cls + ":" + theParamName + "]").collect(Collectors.joining(" or ")));
+		} else {
+			builder.append("If you know what you're looking for, try qualifying it using the form: '");
+			builder.append(theParamName).append(":[resourceType]");
+			builder.append("'");
+		}
+		String message = builder
+			.toString();
+		StorageProcessingMessage msg = new StorageProcessingMessage()
+			.setMessage(message);
+		HookParams params = new HookParams()
+			.add(RequestDetails.class, theRequest)
+			.addIfMatchesType(ServletRequestDetails.class, theRequest)
+			.add(StorageProcessingMessage.class, msg);
+		JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.JPA_PERFTRACE_WARNING, params);
+	}
+
+
+	/**
+	 * This is for handling queries like the following: /Observation?device.identifier=urn:system|foo in which we use a chain
+	 * on the device.
+	 */
+	private Condition addPredicateReferenceWithChain(String theResourceName, String theParamName, List<? extends IQueryParameterType> theList, ReferenceParam theReferenceParam, RequestDetails theRequest, RequestPartitionId theRequestPartitionId) {
+
+		/*
+		 * Which resource types can the given chained parameter actually link to? This might be a list
+		 * where the chain is unqualified, as in: Observation?subject.identifier=(...)
+		 * since subject can link to several possible target types.
+		 *
+		 * If the user has qualified the chain, as in: Observation?subject:Patient.identifier=(...)
+		 * this is just a simple 1-entry list.
+		 */
+		final List<String> resourceTypes = determineCandidateResourceTypesForChain(theResourceName, theParamName, theReferenceParam);
+
+		/*
+		 * Handle chain on _type
+		 */
+		if (Constants.PARAM_TYPE.equals(theReferenceParam.getChain())) {
+
+			List<String> pathsToMatch = createResourceLinkPaths(theResourceName, theParamName);
+			Condition typeCondition = createPredicateSourcePaths(pathsToMatch);
+
+			String typeValue = theReferenceParam.getValue();
+
+			try {
+				getFhirContext().getResourceDefinition(typeValue).getImplementingClass();
+			} catch (DataFormatException e) {
+				throw newInvalidResourceTypeException(typeValue);
+			}
+			if (!resourceTypes.contains(typeValue)) {
+				throw newInvalidTargetTypeForChainException(theResourceName, theParamName, typeValue);
+			}
+
+			Condition condition = BinaryCondition.equalTo(myColumnTargetResourceType, generatePlaceholder(theReferenceParam.getValue()));
+
+			return toAndPredicate(typeCondition, condition);
+		}
+
+		boolean foundChainMatch = false;
+		List<String> candidateTargetTypes = new ArrayList<>();
+		List<Condition> orPredicates = new ArrayList<>();
+		QueryStack childQueryFactory = myQueryStack.newChildQueryFactoryWithFullBuilderReuse();
+		for (String nextType : resourceTypes) {
+			String chain = theReferenceParam.getChain();
+
+			String remainingChain = null;
+			int chainDotIndex = chain.indexOf('.');
+			if (chainDotIndex != -1) {
+				remainingChain = chain.substring(chainDotIndex + 1);
+				chain = chain.substring(0, chainDotIndex);
+			}
+
+			RuntimeResourceDefinition typeDef = getFhirContext().getResourceDefinition(nextType);
+			String subResourceName = typeDef.getName();
+
+			IDao dao = myDaoRegistry.getResourceDao(nextType);
+			if (dao == null) {
+				ourLog.debug("Don't have a DAO for type {}", nextType);
+				continue;
+			}
+
+			int qualifierIndex = chain.indexOf(':');
+			String qualifier = null;
+			if (qualifierIndex != -1) {
+				qualifier = chain.substring(qualifierIndex);
+				chain = chain.substring(0, qualifierIndex);
+			}
+
+			boolean isMeta = ResourceMetaParams.RESOURCE_META_PARAMS.containsKey(chain);
+			RuntimeSearchParam param = null;
+			if (!isMeta) {
+				param = mySearchParamRegistry.getSearchParamByName(typeDef, chain);
+				if (param == null) {
+					ourLog.debug("Type {} doesn't have search param {}", nextType, param);
+					continue;
+				}
+			}
+
+			ArrayList<IQueryParameterType> orValues = Lists.newArrayList();
+
+			for (IQueryParameterType next : theList) {
+				String nextValue = next.getValueAsQueryToken(getFhirContext());
+				IQueryParameterType chainValue = mapReferenceChainToRawParamType(remainingChain, param, theParamName, qualifier, nextType, chain, isMeta, nextValue);
+				if (chainValue == null) {
+					continue;
+				}
+				foundChainMatch = true;
+				orValues.add(chainValue);
+			}
+
+			if (!foundChainMatch) {
+				throw new InvalidRequestException(getFhirContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidParameterChain", theParamName + '.' + theReferenceParam.getChain()));
+			}
+
+			candidateTargetTypes.add(nextType);
+
+			List<Condition> andPredicates = new ArrayList<>();
+
+			List<List<IQueryParameterType>> chainParamValues = Collections.singletonList(orValues);
+			andPredicates.add(childQueryFactory.searchForIdsWithAndOr(myColumnTargetResourceId, subResourceName, chain, chainParamValues, theRequest, theRequestPartitionId));
+
+			orPredicates.add(toAndPredicate(andPredicates));
+
+		}
+
+		if (candidateTargetTypes.isEmpty()) {
+			throw new InvalidRequestException(getFhirContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidParameterChain", theParamName + '.' + theReferenceParam.getChain()));
+		}
+
+		if (candidateTargetTypes.size() > 1) {
+			warnAboutPerformanceOnUnqualifiedResources(theParamName, theRequest, candidateTargetTypes);
+		}
+
+		Condition multiTypeOrPredicate = toOrPredicate(orPredicates);
+		List<String> pathsToMatch = createResourceLinkPaths(theResourceName, theParamName);
+		Condition pathPredicate = createPredicateSourcePaths(pathsToMatch);
+		return toAndPredicate(pathPredicate, multiTypeOrPredicate);
+	}
+
+	@Nonnull
+	private List<String> determineCandidateResourceTypesForChain(String theResourceName, String theParamName, ReferenceParam theReferenceParam) {
+		final List<Class<? extends IBaseResource>> resourceTypes;
+		if (!theReferenceParam.hasResourceType()) {
+
+			RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(theResourceName, theParamName);
+			resourceTypes = new ArrayList<>();
+
+			if (param.hasTargets()) {
+				Set<String> targetTypes = param.getTargets();
+				for (String next : targetTypes) {
+					resourceTypes.add(getFhirContext().getResourceDefinition(next).getImplementingClass());
+				}
+			}
+
+			if (resourceTypes.isEmpty()) {
+				RuntimeResourceDefinition resourceDef = getFhirContext().getResourceDefinition(theResourceName);
+				RuntimeSearchParam searchParamByName = mySearchParamRegistry.getSearchParamByName(resourceDef, theParamName);
+				if (searchParamByName == null) {
+					throw new InternalErrorException("Could not find parameter " + theParamName);
+				}
+				String paramPath = searchParamByName.getPath();
+				if (paramPath.endsWith(".as(Reference)")) {
+					paramPath = paramPath.substring(0, paramPath.length() - ".as(Reference)".length()) + "Reference";
+				}
+
+				if (paramPath.contains(".extension(")) {
+					int startIdx = paramPath.indexOf(".extension(");
+					int endIdx = paramPath.indexOf(')', startIdx);
+					if (startIdx != -1 && endIdx != -1) {
+						paramPath = paramPath.substring(0, startIdx + 10) + paramPath.substring(endIdx + 1);
+					}
+				}
+
+				Class<? extends IBaseResource> resourceType = getFhirContext().getResourceDefinition(theResourceName).getImplementingClass();
+				BaseRuntimeChildDefinition def = getFhirContext().newTerser().getDefinition(resourceType, paramPath);
+				if (def instanceof RuntimeChildChoiceDefinition) {
+					RuntimeChildChoiceDefinition choiceDef = (RuntimeChildChoiceDefinition) def;
+					resourceTypes.addAll(choiceDef.getResourceTypes());
+				} else if (def instanceof RuntimeChildResourceDefinition) {
+					RuntimeChildResourceDefinition resDef = (RuntimeChildResourceDefinition) def;
+					resourceTypes.addAll(resDef.getResourceTypes());
+					if (resourceTypes.size() == 1) {
+						if (resourceTypes.get(0).isInterface()) {
+							throw new InvalidRequestException("Unable to perform search for unqualified chain '" + theParamName + "' as this SearchParameter does not declare any target types. Add a qualifier of the form '" + theParamName + ":[ResourceType]' to perform this search.");
+						}
+					}
+				} else {
+					throw new ConfigurationException("Property " + paramPath + " of type " + getResourceType() + " is not a resource: " + def.getClass());
+				}
+			}
+
+			if (resourceTypes.isEmpty()) {
+				for (BaseRuntimeElementDefinition<?> next : getFhirContext().getElementDefinitions()) {
+					if (next instanceof RuntimeResourceDefinition) {
+						RuntimeResourceDefinition nextResDef = (RuntimeResourceDefinition) next;
+						resourceTypes.add(nextResDef.getImplementingClass());
+					}
+				}
+			}
+
+		} else {
+
+			try {
+				RuntimeResourceDefinition resDef = getFhirContext().getResourceDefinition(theReferenceParam.getResourceType());
+				resourceTypes = new ArrayList<>(1);
+				resourceTypes.add(resDef.getImplementingClass());
+			} catch (DataFormatException e) {
+				throw newInvalidResourceTypeException(theReferenceParam.getResourceType());
+			}
+
+		}
+
+		return resourceTypes
+			.stream()
+			.map(t -> getFhirContext().getResourceType(t))
+			.collect(Collectors.toList());
+	}
+
+	public List<String> createResourceLinkPaths(String theResourceName, String theParamName) {
+		RuntimeResourceDefinition resourceDef = getFhirContext().getResourceDefinition(theResourceName);
+		RuntimeSearchParam param = mySearchParamRegistry.getSearchParamByName(resourceDef, theParamName);
+		List<String> path = param.getPathsSplit();
+
+		/*
+		 * SearchParameters can declare paths on multiple resource
+		 * types. Here we only want the ones that actually apply.
+		 */
+		path = new ArrayList<>(path);
+
+		ListIterator<String> iter = path.listIterator();
+		while (iter.hasNext()) {
+			String nextPath = trim(iter.next());
+			if (!nextPath.contains(theResourceName + ".")) {
+				iter.remove();
+			}
+		}
+
+		return path;
+	}
+
+
+	private IQueryParameterType mapReferenceChainToRawParamType(String remainingChain, RuntimeSearchParam param, String theParamName, String qualifier, String nextType, String chain, boolean isMeta, String resourceId) {
+		IQueryParameterType chainValue;
+		if (remainingChain != null) {
+			if (param == null || param.getParamType() != RestSearchParameterTypeEnum.REFERENCE) {
+				ourLog.debug("Type {} parameter {} is not a reference, can not chain {}", nextType, chain, remainingChain);
+				return null;
+			}
+
+			chainValue = new ReferenceParam();
+			chainValue.setValueAsQueryToken(getFhirContext(), theParamName, qualifier, resourceId);
+			((ReferenceParam) chainValue).setChain(remainingChain);
+		} else if (isMeta) {
+			IQueryParameterType type = myMatchUrlService.newInstanceType(chain);
+			type.setValueAsQueryToken(getFhirContext(), theParamName, qualifier, resourceId);
+			chainValue = type;
+		} else {
+			chainValue = toParameterType(param, qualifier, resourceId);
+		}
+
+		return chainValue;
+	}
+
+	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 REFERENCE:
+				qp = new ReferenceParam();
+				break;
+			case SPECIAL:
+				if ("Location.position".equals(theParam.getPath())) {
+					qp = new SpecialParam();
+					break;
+				}
+				throw new InternalErrorException("Don't know how to convert param type: " + theParam.getParamType());
+			case URI:
+			case HAS:
+			default:
+				throw new InternalErrorException("Don't know how to convert param type: " + theParam.getParamType());
+		}
+		return qp;
+	}
+
+
+	@Nonnull
+	private InvalidRequestException newInvalidTargetTypeForChainException(String theResourceName, String theParamName, String theTypeValue) {
+		String searchParamName = theResourceName + ":" + theParamName;
+		String msg = getFhirContext().getLocalizer().getMessage(PredicateBuilderReference.class, "invalidTargetTypeForChain", theTypeValue, searchParamName);
+		return new InvalidRequestException(msg);
+	}
+
+	private IQueryParameterType toParameterType(RuntimeSearchParam theParam, String theQualifier, String theValueAsQueryToken) {
+		IQueryParameterType qp = toParameterType(theParam);
+
+		qp.setValueAsQueryToken(getFhirContext(), theParam.getName(), theQualifier, theValueAsQueryToken);
+		return qp;
+	}
+
+	@Nonnull
+	private InvalidRequestException newInvalidResourceTypeException(String theResourceType) {
+		String msg = getFhirContext().getLocalizer().getMessageSanitized(PredicateBuilderReference.class, "invalidResourceType", theResourceType);
+		throw new InvalidRequestException(msg);
+	}
+
+	@Nonnull
+	public Condition createEverythingPredicate(String theResourceName, Long theTargetPid) {
+		if (theTargetPid != null) {
+			return BinaryCondition.equalTo(myColumnTargetResourceId, generatePlaceholder(theTargetPid));
+		} else {
+			return BinaryCondition.equalTo(myColumnTargetResourceType, generatePlaceholder(theResourceName));
+		}
+	}
+}

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

@@ -0,0 +1,86 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.NotCondition;
+import com.healthmarketscience.sqlbuilder.UnaryCondition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+
+import java.util.Set;
+
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toAndPredicate;
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toEqualToOrInPredicate;
+
+public class ResourceTablePredicateBuilder extends BaseJoiningPredicateBuilder {
+	private final DbColumn myColumnResId;
+	private final DbColumn myColumnResDeletedAt;
+	private final DbColumn myColumnResType;
+	private final DbColumn myColumnLastUpdated;
+	private final DbColumn myColumnLanguage;
+
+	/**
+	 * Constructor
+	 */
+	public ResourceTablePredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_RESOURCE"));
+		myColumnResId = getTable().addColumn("RES_ID");
+		myColumnResType = getTable().addColumn("RES_TYPE");
+		myColumnResDeletedAt = getTable().addColumn("RES_DELETED_AT");
+		myColumnLastUpdated = getTable().addColumn("RES_UPDATED");
+		myColumnLanguage = getTable().addColumn("RES_LANGUAGE");
+	}
+
+
+	@Override
+	public DbColumn getResourceIdColumn() {
+		return myColumnResId;
+	}
+
+	public Condition createResourceTypeAndNonDeletedPredicates() {
+		BinaryCondition typePredicate = null;
+		if (getResourceType() != null) {
+			typePredicate = BinaryCondition.equalTo(myColumnResType, generatePlaceholder(getResourceType()));
+		}
+		return toAndPredicate(
+			typePredicate,
+			UnaryCondition.isNull(myColumnResDeletedAt)
+		);
+	}
+
+	public DbColumn getLastUpdatedColumn() {
+		return myColumnLastUpdated;
+	}
+
+	public Condition createLanguagePredicate(Set<String> theValues, boolean theNegated) {
+		Condition condition = toEqualToOrInPredicate(myColumnLanguage, generatePlaceholders(theValues));
+		if (theNegated) {
+			condition = new NotCondition(condition);
+		}
+		return condition;
+	}
+
+	public DbColumn getColumnLastUpdated() {
+		return myColumnLastUpdated;
+	}
+}

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

@@ -0,0 +1,61 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.springframework.beans.factory.annotation.Autowired;
+
+public class SearchParamPresentPredicateBuilder extends BaseJoiningPredicateBuilder {
+
+	private final DbColumn myColumnResourceId;
+	private final DbColumn myColumnHashPresence;
+
+	@Autowired
+	private PartitionSettings myPartitionSettings;
+
+	/**
+	 * Constructor
+	 */
+	public SearchParamPresentPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_RES_PARAM_PRESENT"));
+		myColumnResourceId = getTable().addColumn("RES_ID");
+		myColumnHashPresence = getTable().addColumn("HASH_PRESENCE");
+	}
+
+	@Override
+	public DbColumn getResourceIdColumn() {
+		return myColumnResourceId;
+	}
+
+
+	public Condition createPredicateParamMissingForReference(String theResourceName, String theParamName, boolean theMissing, RequestPartitionId theRequestPartitionId) {
+		Long hash = SearchParamPresent.calculateHashPresence(myPartitionSettings, theRequestPartitionId, theResourceName, theParamName, !theMissing);
+		BinaryCondition predicate = BinaryCondition.equalTo(myColumnHashPresence, generatePlaceholder(hash));
+		return combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
+	}
+
+}

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

@@ -0,0 +1,62 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class SourcePredicateBuilder extends BaseJoiningPredicateBuilder {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(SourcePredicateBuilder.class);
+	private final DbColumn myColumnSourceUri;
+	private final DbColumn myColumnRequestId;
+	private final DbColumn myResourceIdColumn;
+
+	/**
+	 * Constructor
+	 */
+	public SourcePredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_RES_VER_PROV"));
+
+		myResourceIdColumn = getTable().addColumn("RES_PID");
+		myColumnSourceUri = getTable().addColumn("SOURCE_URI");
+		myColumnRequestId = getTable().addColumn("REQUEST_ID");
+	}
+
+
+	@Override
+	public DbColumn getResourceIdColumn() {
+		return myResourceIdColumn;
+	}
+
+	public Condition createPredicateSourceUri(String theSourceUri) {
+		return BinaryCondition.equalTo(myColumnSourceUri, generatePlaceholder(theSourceUri));
+	}
+
+	public Condition createPredicateRequestId(String theRequestId) {
+		return BinaryCondition.equalTo(myColumnRequestId, generatePlaceholder(theRequestId));
+	}
+
+}

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

@@ -0,0 +1,237 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.RuntimeSearchParam;
+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.model.api.IPrimitiveDatatype;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
+import ca.uhn.fhir.util.StringUtil;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.ComboCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.annotation.Nonnull;
+
+public class StringPredicateBuilder extends BaseSearchParamPredicateBuilder {
+
+	private final DbColumn myColumnResId;
+	private final DbColumn myColumnValueExact;
+	private final DbColumn myColumnValueNormalized;
+	private final DbColumn myColumnHashNormPrefix;
+	private final DbColumn myColumnHashIdentity;
+	private final DbColumn myColumnHashExact;
+	@Autowired
+	private DaoConfig myDaoConfig;
+
+	/**
+	 * Constructor
+	 */
+	public StringPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_SPIDX_STRING"));
+		myColumnResId = getTable().addColumn("RES_ID");
+		myColumnValueExact = getTable().addColumn("SP_VALUE_EXACT");
+		myColumnValueNormalized = getTable().addColumn("SP_VALUE_NORMALIZED");
+		myColumnHashNormPrefix = getTable().addColumn("HASH_NORM_PREFIX");
+		myColumnHashIdentity = getTable().addColumn("HASH_IDENTITY");
+		myColumnHashExact = getTable().addColumn("HASH_EXACT");
+	}
+
+	public DbColumn getColumnValueNormalized() {
+		return myColumnValueNormalized;
+	}
+
+	@Override
+	public DbColumn getResourceIdColumn() {
+		return myColumnResId;
+	}
+
+	public Condition createPredicateString(IQueryParameterType theParameter,
+														String theResourceName,
+														RuntimeSearchParam theSearchParam,
+														StringPredicateBuilder theFrom,
+														SearchFilterParser.CompareOperation operation) {
+		String rawSearchTerm;
+		String paramName = theSearchParam.getName();
+		if (theParameter instanceof TokenParam) {
+			TokenParam id = (TokenParam) theParameter;
+			if (!id.isText()) {
+				throw new IllegalStateException("Trying to process a text search on a non-text token parameter");
+			}
+			rawSearchTerm = id.getValue();
+		} else if (theParameter instanceof StringParam) {
+			StringParam id = (StringParam) theParameter;
+			rawSearchTerm = id.getValue();
+			if (id.isContains()) {
+				if (!myDaoConfig.isAllowContainsSearches()) {
+					throw new MethodNotAllowedException(":contains modifier is disabled on this server");
+				}
+			} else {
+				rawSearchTerm = theSearchParam.encode(rawSearchTerm);
+			}
+		} else if (theParameter instanceof IPrimitiveDatatype<?>) {
+			IPrimitiveDatatype<?> id = (IPrimitiveDatatype<?>) theParameter;
+			rawSearchTerm = id.getValueAsString();
+		} else {
+			throw new IllegalArgumentException("Invalid token type: " + theParameter.getClass());
+		}
+
+		if (rawSearchTerm.length() > ResourceIndexedSearchParamString.MAX_LENGTH) {
+			throw new InvalidRequestException("Parameter[" + paramName + "] has length (" + rawSearchTerm.length() + ") that is longer than maximum allowed ("
+				+ ResourceIndexedSearchParamString.MAX_LENGTH + "): " + rawSearchTerm);
+		}
+
+		boolean exactMatch = theParameter instanceof StringParam && ((StringParam) theParameter).isExact();
+		if (exactMatch) {
+			// Exact match
+			return theFrom.createPredicateExact(theResourceName, paramName, rawSearchTerm);
+		} else {
+			// Normalized Match
+			String normalizedString = StringUtil.normalizeStringForSearchIndexing(rawSearchTerm);
+			String likeExpression;
+			if ((theParameter instanceof StringParam) &&
+				(((((StringParam) theParameter).isContains()) &&
+					(myDaoConfig.isAllowContainsSearches())) ||
+					(operation == SearchFilterParser.CompareOperation.co))) {
+				likeExpression = createLeftAndRightMatchLikeExpression(normalizedString);
+			} else if ((operation != SearchFilterParser.CompareOperation.ne) &&
+				(operation != SearchFilterParser.CompareOperation.gt) &&
+				(operation != SearchFilterParser.CompareOperation.lt) &&
+				(operation != SearchFilterParser.CompareOperation.ge) &&
+				(operation != SearchFilterParser.CompareOperation.le)) {
+				if (operation == SearchFilterParser.CompareOperation.ew) {
+					likeExpression = createRightMatchLikeExpression(normalizedString);
+				} else {
+					likeExpression = createLeftMatchLikeExpression(normalizedString);
+				}
+			} else {
+				likeExpression = normalizedString;
+			}
+
+			Condition predicate;
+			if ((operation == null) ||
+				(operation == SearchFilterParser.CompareOperation.sw)) {
+				predicate = theFrom.createPredicateNormalLike(theResourceName, paramName, normalizedString, likeExpression);
+			} else if ((operation == SearchFilterParser.CompareOperation.ew) || (operation == SearchFilterParser.CompareOperation.co)) {
+				predicate = theFrom.createPredicateLikeExpressionOnly(theResourceName, paramName, likeExpression, false);
+			} else if (operation == SearchFilterParser.CompareOperation.eq) {
+				predicate = theFrom.createPredicateNormal(theResourceName, paramName, normalizedString);
+			} else if (operation == SearchFilterParser.CompareOperation.ne) {
+				predicate = theFrom.createPredicateLikeExpressionOnly(theResourceName, paramName, likeExpression, true);
+			} else if (operation == SearchFilterParser.CompareOperation.gt) {
+				predicate = theFrom.createPredicateNormalGreaterThan(theResourceName, paramName, likeExpression);
+			} else if (operation == SearchFilterParser.CompareOperation.ge) {
+				predicate = theFrom.createPredicateNormalGreaterThanOrEqual(theResourceName, paramName, likeExpression);
+			} else if (operation == SearchFilterParser.CompareOperation.lt) {
+				predicate = theFrom.createPredicateNormalLessThan(theResourceName, paramName, likeExpression);
+			} else if (operation == SearchFilterParser.CompareOperation.le) {
+				predicate = theFrom.createPredicateNormalLessThanOrEqual(theResourceName, paramName, likeExpression);
+			} else {
+				throw new IllegalArgumentException("Don't yet know how to handle operation " + operation + " on a string");
+			}
+
+			return predicate;
+		}
+	}
+
+	@Nonnull
+	public Condition createPredicateExact(String theResourceType, String theParamName, String theTheValueExact) {
+		long hash = ResourceIndexedSearchParamString.calculateHashExact(getPartitionSettings(), getRequestPartitionId(), theResourceType, theParamName, theTheValueExact);
+		String placeholderValue = generatePlaceholder(hash);
+		return BinaryCondition.equalTo(myColumnHashExact, placeholderValue);
+	}
+
+	@Nonnull
+	public Condition createPredicateNormalLike(String theResourceType, String theParamName, String theNormalizedString, String theLikeExpression) {
+		Long hash = ResourceIndexedSearchParamString.calculateHashNormalized(getPartitionSettings(), getRequestPartitionId(), getModelConfig(), theResourceType, theParamName, theNormalizedString);
+		Condition hashPredicate = BinaryCondition.equalTo(myColumnHashNormPrefix, generatePlaceholder(hash));
+		Condition valuePredicate = BinaryCondition.like(myColumnValueNormalized, generatePlaceholder(theLikeExpression));
+		return ComboCondition.and(hashPredicate, valuePredicate);
+	}
+
+	@Nonnull
+	public Condition createPredicateNormal(String theResourceType, String theParamName, String theNormalizedString) {
+		Long hash = ResourceIndexedSearchParamString.calculateHashNormalized(getPartitionSettings(), getRequestPartitionId(), getModelConfig(), theResourceType, theParamName, theNormalizedString);
+		Condition hashPredicate = BinaryCondition.equalTo(myColumnHashNormPrefix, generatePlaceholder(hash));
+		Condition valuePredicate = BinaryCondition.equalTo(myColumnValueNormalized, generatePlaceholder(theNormalizedString));
+		return ComboCondition.and(hashPredicate, valuePredicate);
+	}
+
+	private Condition createPredicateNormalGreaterThanOrEqual(String theResourceType, String theParamName, String theNormalizedString) {
+		Condition hashPredicate = createHashIdentityPredicate(theResourceType, theParamName);
+		Condition valuePredicate = BinaryCondition.greaterThanOrEq(myColumnValueNormalized, generatePlaceholder(theNormalizedString));
+		return ComboCondition.and(hashPredicate, valuePredicate);
+	}
+
+	private Condition createPredicateNormalGreaterThan(String theResourceType, String theParamName, String theNormalizedString) {
+		Condition hashPredicate = createHashIdentityPredicate(theResourceType, theParamName);
+		Condition valuePredicate = BinaryCondition.greaterThan(myColumnValueNormalized, generatePlaceholder(theNormalizedString));
+		return ComboCondition.and(hashPredicate, valuePredicate);
+	}
+
+	private Condition createPredicateNormalLessThanOrEqual(String theResourceType, String theParamName, String theNormalizedString) {
+		Condition hashPredicate = createHashIdentityPredicate(theResourceType, theParamName);
+		Condition valuePredicate = BinaryCondition.lessThanOrEq(myColumnValueNormalized, generatePlaceholder(theNormalizedString));
+		return ComboCondition.and(hashPredicate, valuePredicate);
+	}
+
+	private Condition createPredicateNormalLessThan(String theResourceType, String theParamName, String theNormalizedString) {
+		Condition hashPredicate = createHashIdentityPredicate(theResourceType, theParamName);
+		Condition valuePredicate = BinaryCondition.lessThan(myColumnValueNormalized, generatePlaceholder(theNormalizedString));
+		return ComboCondition.and(hashPredicate, valuePredicate);
+	}
+
+	@Nonnull
+	public Condition createPredicateLikeExpressionOnly(String theResourceType, String theParamName, String theLikeExpression, boolean theInverse) {
+		long hashIdentity = ResourceIndexedSearchParamString.calculateHashIdentity(getPartitionSettings(), getRequestPartitionId(), theResourceType, theParamName);
+		BinaryCondition identityPredicate = BinaryCondition.equalTo(myColumnHashIdentity, generatePlaceholder(hashIdentity));
+		BinaryCondition likePredicate;
+		if (theInverse) {
+			likePredicate = BinaryCondition.notLike(myColumnValueNormalized, generatePlaceholder(theLikeExpression));
+		} else {
+			likePredicate = BinaryCondition.like(myColumnValueNormalized, generatePlaceholder(theLikeExpression));
+		}
+		return ComboCondition.and(identityPredicate, likePredicate);
+	}
+
+	public static String createLeftAndRightMatchLikeExpression(String likeExpression) {
+		return "%" + likeExpression.replace("%", "[%]") + "%";
+	}
+
+	public static String createLeftMatchLikeExpression(String likeExpression) {
+		return likeExpression.replace("%", "[%]") + "%";
+	}
+
+	public static String createRightMatchLikeExpression(String likeExpression) {
+		return "%" + likeExpression.replace("%", "[%]");
+	}
+
+
+}

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

@@ -0,0 +1,91 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import com.google.common.collect.Lists;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.ComboCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbTable;
+import org.apache.commons.lang3.tuple.Pair;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.List;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class TagPredicateBuilder extends BaseJoiningPredicateBuilder {
+	private static final Logger ourLog = LoggerFactory.getLogger(TagPredicateBuilder.class);
+
+	private final DbColumn myColumnResId;
+	private final DbTable myTagDefinitionTable;
+	private final DbColumn myTagDefinitionColumnTagId;
+	private final DbColumn myTagDefinitionColumnTagSystem;
+	private final DbColumn myTagDefinitionColumnTagCode;
+	private final DbColumn myColumnTagId;
+	private final DbColumn myTagDefinitionColumnTagType;
+
+	public TagPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_RES_TAG"));
+
+		myColumnResId = getTable().addColumn("RES_ID");
+		myColumnTagId = getTable().addColumn("TAG_ID");
+
+		myTagDefinitionTable = theSearchSqlBuilder.addTable("HFJ_TAG_DEF");
+		myTagDefinitionColumnTagId = myTagDefinitionTable.addColumn("TAG_ID");
+		myTagDefinitionColumnTagSystem = myTagDefinitionTable.addColumn("TAG_SYSTEM");
+		myTagDefinitionColumnTagCode = myTagDefinitionTable.addColumn("TAG_CODE");
+		myTagDefinitionColumnTagType = myTagDefinitionTable.addColumn("TAG_TYPE");
+	}
+
+
+	public Condition createPredicateTag(TagTypeEnum theTagType, List<Pair<String, String>> theTokens, String theParamName, RequestPartitionId theRequestPartitionId) {
+		addJoin(getTable(), myTagDefinitionTable, myColumnTagId, myTagDefinitionColumnTagId);
+		return createPredicateTagList(theTagType, theTokens);
+	}
+
+	private Condition createPredicateTagList(TagTypeEnum theTagType, List<Pair<String, String>> theTokens) {
+		Condition typePredicate = BinaryCondition.equalTo(myTagDefinitionColumnTagType, generatePlaceholder(theTagType.ordinal()));
+
+		List<Condition> orPredicates = Lists.newArrayList();
+		for (Pair<String, String> next : theTokens) {
+			Condition codePredicate = BinaryCondition.equalTo(myTagDefinitionColumnTagCode, generatePlaceholder(next.getRight()));
+			if (isNotBlank(next.getLeft())) {
+				Condition systemPredicate = BinaryCondition.equalTo(myTagDefinitionColumnTagSystem, generatePlaceholder(next.getLeft()));
+				orPredicates.add(ComboCondition.and(typePredicate, systemPredicate, codePredicate));
+			} else {
+				orPredicates.add(ComboCondition.and(typePredicate, codePredicate));
+			}
+		}
+
+		return ComboCondition.or(orPredicates.toArray(new Condition[0]));
+	}
+
+	@Override
+	public DbColumn getResourceIdColumn() {
+		return myColumnResId;
+	}
+}

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

@@ -0,0 +1,321 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+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.sql.SearchQueryBuilder;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.model.base.composite.BaseCodingDt;
+import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
+import ca.uhn.fhir.rest.param.NumberParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.TokenParamModifier;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.FhirVersionIndependentConcept;
+import com.google.common.collect.Sets;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.InCondition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toAndPredicate;
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toOrPredicate;
+import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class TokenPredicateBuilder extends BaseSearchParamPredicateBuilder {
+
+	private final DbColumn myColumnResId;
+	private final DbColumn myColumnHashSystemAndValue;
+	private final DbColumn myColumnHashSystem;
+	private final DbColumn myColumnHashValue;
+	private final DbColumn myColumnSystem;
+	private final DbColumn myColumnValue;
+
+	@Autowired
+	private ITermReadSvc myTerminologySvc;
+
+
+	/**
+	 * Constructor
+	 */
+	public TokenPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_SPIDX_TOKEN"));
+		myColumnResId = getTable().addColumn("RES_ID");
+		myColumnHashSystem = getTable().addColumn("HASH_SYS");
+		myColumnHashSystemAndValue = getTable().addColumn("HASH_SYS_AND_VALUE");
+		myColumnHashValue = getTable().addColumn("HASH_VALUE");
+		myColumnSystem = getTable().addColumn("SP_SYSTEM");
+		myColumnValue = getTable().addColumn("SP_VALUE");
+	}
+
+	@Override
+	public DbColumn getResourceIdColumn() {
+		return myColumnResId;
+	}
+
+	public Condition createPredicateToken(Collection<IQueryParameterType> theParameters,
+													  String theResourceName,
+													  RuntimeSearchParam theSearchParam,
+													  RequestPartitionId theRequestPartitionId) {
+		return createPredicateToken(
+			theParameters,
+			theResourceName,
+			theSearchParam,
+			null,
+			theRequestPartitionId);
+	}
+
+	public Condition createPredicateToken(Collection<IQueryParameterType> theParameters,
+													  String theResourceName,
+													  RuntimeSearchParam theSearchParam,
+													  SearchFilterParser.CompareOperation theOperation,
+													  RequestPartitionId theRequestPartitionId) {
+		final List<FhirVersionIndependentConcept> codes = new ArrayList<>();
+		String paramName = theSearchParam.getName();
+
+		SearchFilterParser.CompareOperation operation = theOperation;
+
+		TokenParamModifier modifier = null;
+		for (IQueryParameterType nextParameter : theParameters) {
+
+			String code;
+			String system;
+			if (nextParameter instanceof TokenParam) {
+				TokenParam id = (TokenParam) nextParameter;
+				system = id.getSystem();
+				code = (id.getValue());
+				modifier = id.getModifier();
+			} else if (nextParameter instanceof BaseIdentifierDt) {
+				BaseIdentifierDt id = (BaseIdentifierDt) nextParameter;
+				system = id.getSystemElement().getValueAsString();
+				code = (id.getValueElement().getValue());
+			} else if (nextParameter instanceof BaseCodingDt) {
+				BaseCodingDt id = (BaseCodingDt) nextParameter;
+				system = id.getSystemElement().getValueAsString();
+				code = (id.getCodeElement().getValue());
+			} else if (nextParameter instanceof NumberParam) {
+				NumberParam number = (NumberParam) nextParameter;
+				system = null;
+				code = number.getValueAsQueryToken(getFhirContext());
+			} else {
+				throw new IllegalArgumentException("Invalid token type: " + nextParameter.getClass());
+			}
+
+			if (system != null && system.length() > ResourceIndexedSearchParamToken.MAX_LENGTH) {
+				throw new InvalidRequestException(
+					"Parameter[" + paramName + "] has system (" + system.length() + ") that is longer than maximum allowed (" + ResourceIndexedSearchParamToken.MAX_LENGTH + "): " + system);
+			}
+
+			if (code != null && code.length() > ResourceIndexedSearchParamToken.MAX_LENGTH) {
+				throw new InvalidRequestException(
+					"Parameter[" + paramName + "] has code (" + code.length() + ") that is longer than maximum allowed (" + ResourceIndexedSearchParamToken.MAX_LENGTH + "): " + code);
+			}
+
+			/*
+			 * Process token modifiers (:in, :below, :above)
+			 */
+
+			if (modifier == TokenParamModifier.IN) {
+				codes.addAll(myTerminologySvc.expandValueSet(null, code));
+			} else if (modifier == TokenParamModifier.ABOVE) {
+				system = determineSystemIfMissing(theSearchParam, code, system);
+				validateHaveSystemAndCodeForToken(paramName, code, system);
+				codes.addAll(myTerminologySvc.findCodesAbove(system, code));
+			} else if (modifier == TokenParamModifier.BELOW) {
+				system = determineSystemIfMissing(theSearchParam, code, system);
+				validateHaveSystemAndCodeForToken(paramName, code, system);
+				codes.addAll(myTerminologySvc.findCodesBelow(system, code));
+			} else {
+				if (modifier == TokenParamModifier.NOT && operation == null) {
+					operation = SearchFilterParser.CompareOperation.ne;
+				}
+				codes.add(new FhirVersionIndependentConcept(system, code));
+			}
+
+		}
+
+		List<FhirVersionIndependentConcept> sortedCodesList = codes
+			.stream()
+			.filter(t -> t.getCode() != null || t.getSystem() != null)
+			.sorted()
+			.distinct()
+			.collect(Collectors.toList());
+
+		if (codes.isEmpty()) {
+			// This will never match anything
+			setMatchNothing();
+			return null;
+		}
+
+
+		Condition predicate;
+		if (operation == SearchFilterParser.CompareOperation.ne) {
+
+			/*
+			 * For a token :not search, we look for index rows that have the right identity (i.e. it's the right resource and
+			 * param name) but not the actual provided token value.
+			 */
+
+			long hashIdentity = BaseResourceIndexedSearchParam.calculateHashIdentity(getPartitionSettings(), theRequestPartitionId, theResourceName, paramName);
+			Condition hashIdentityPredicate = BinaryCondition.equalTo(getColumnHashIdentity(), generatePlaceholder(hashIdentity));
+
+			Condition hashValuePredicate = createPredicateOrList(theResourceName, theSearchParam.getName(), sortedCodesList, false);
+			predicate = toAndPredicate(hashIdentityPredicate, hashValuePredicate);
+
+		} else {
+
+			predicate = createPredicateOrList(theResourceName, theSearchParam.getName(), sortedCodesList, true);
+
+		}
+
+		return predicate;
+	}
+
+	private String determineSystemIfMissing(RuntimeSearchParam theSearchParam, String code, String theSystem) {
+		String retVal = theSystem;
+		if (retVal == null) {
+			if (theSearchParam != null) {
+				Set<String> valueSetUris = Sets.newHashSet();
+				for (String nextPath : theSearchParam.getPathsSplit()) {
+					Class<? extends IBaseResource> type = getFhirContext().getResourceDefinition(getResourceType()).getImplementingClass();
+					BaseRuntimeChildDefinition def = getFhirContext().newTerser().getDefinition(type, nextPath);
+					if (def instanceof BaseRuntimeDeclaredChildDefinition) {
+						String valueSet = ((BaseRuntimeDeclaredChildDefinition) def).getBindingValueSet();
+						if (isNotBlank(valueSet)) {
+							valueSetUris.add(valueSet);
+						}
+					}
+				}
+				if (valueSetUris.size() == 1) {
+					String valueSet = valueSetUris.iterator().next();
+					ValueSetExpansionOptions options = new ValueSetExpansionOptions()
+						.setFailOnMissingCodeSystem(false);
+					List<FhirVersionIndependentConcept> candidateCodes = myTerminologySvc.expandValueSet(options, valueSet);
+					for (FhirVersionIndependentConcept nextCandidate : candidateCodes) {
+						if (nextCandidate.getCode().equals(code)) {
+							retVal = nextCandidate.getSystem();
+							break;
+						}
+					}
+				}
+			}
+		}
+		return retVal;
+	}
+
+	public DbColumn getColumnSystem() {
+		return myColumnSystem;
+	}
+
+	public DbColumn getColumnValue() {
+		return myColumnValue;
+	}
+
+	private void validateHaveSystemAndCodeForToken(String theParamName, String theCode, String theSystem) {
+		String systemDesc = defaultIfBlank(theSystem, "(missing)");
+		String codeDesc = defaultIfBlank(theCode, "(missing)");
+		if (isBlank(theCode)) {
+			String msg = getFhirContext().getLocalizer().getMessage(LegacySearchBuilder.class, "invalidCodeMissingSystem", theParamName, systemDesc, codeDesc);
+			throw new InvalidRequestException(msg);
+		}
+		if (isBlank(theSystem)) {
+			String msg = getFhirContext().getLocalizer().getMessage(LegacySearchBuilder.class, "invalidCodeMissingCode", theParamName, systemDesc, codeDesc);
+			throw new InvalidRequestException(msg);
+		}
+	}
+
+
+	private Condition createPredicateOrList(String theResourceType, String theSearchParamName, List<FhirVersionIndependentConcept> theCodes, boolean theWantEquals) {
+		Condition[] conditions = new Condition[theCodes.size()];
+
+		Long[] hashes = new Long[theCodes.size()];
+		DbColumn[] columns = new DbColumn[theCodes.size()];
+		boolean haveMultipleColumns = false;
+		for (int i = 0; i < conditions.length; i++) {
+
+			FhirVersionIndependentConcept nextToken = theCodes.get(i);
+			long hash;
+			DbColumn column;
+			if (nextToken.getSystem() == null) {
+				hash = ResourceIndexedSearchParamToken.calculateHashValue(getPartitionSettings(), getRequestPartitionId(), theResourceType, theSearchParamName, nextToken.getCode());
+				column = myColumnHashValue;
+			} else if (isBlank(nextToken.getCode())) {
+				hash = ResourceIndexedSearchParamToken.calculateHashSystem(getPartitionSettings(), getRequestPartitionId(), theResourceType, theSearchParamName, nextToken.getSystem());
+				column = myColumnHashSystem;
+			} else {
+				hash = ResourceIndexedSearchParamToken.calculateHashSystemAndValue(getPartitionSettings(), getRequestPartitionId(), theResourceType, theSearchParamName, nextToken.getSystem(), nextToken.getCode());
+				column = myColumnHashSystemAndValue;
+			}
+			hashes[i] = hash;
+			columns[i] = column;
+			if (i > 0 && columns[0] != columns[i]) {
+				haveMultipleColumns = true;
+			}
+		}
+
+		if (!haveMultipleColumns && conditions.length > 1) {
+			List<Long> values = Arrays.asList(hashes);
+			InCondition predicate = new InCondition(columns[0], generatePlaceholders(values));
+			if (!theWantEquals) {
+				predicate.setNegate(true);
+			}
+			return predicate;
+		}
+
+		for (int i = 0; i < conditions.length; i++) {
+			String valuePlaceholder = generatePlaceholder(hashes[i]);
+			if (theWantEquals) {
+				conditions[i] = BinaryCondition.equalTo(columns[i], valuePlaceholder);
+			} else {
+				conditions[i] = BinaryCondition.notEqualTo(columns[i], valuePlaceholder);
+			}
+		}
+		if (conditions.length > 1) {
+			if (theWantEquals) {
+				return toOrPredicate(conditions);
+			} else {
+				return toAndPredicate(conditions);
+			}
+		} else {
+			return conditions[0];
+		}
+	}
+}

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

@@ -0,0 +1,197 @@
+package ca.uhn.fhir.jpa.search.builder.predicate;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.interceptor.api.HookParams;
+import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
+import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
+import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
+import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
+import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
+import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
+import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.param.UriParam;
+import ca.uhn.fhir.rest.param.UriParamQualifierEnum;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.ComboCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import static ca.uhn.fhir.jpa.search.builder.QueryStack.toEqualToOrInPredicate;
+import static ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder.createLeftAndRightMatchLikeExpression;
+import static ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder.createLeftMatchLikeExpression;
+import static ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder.createRightMatchLikeExpression;
+
+public class UriPredicateBuilder extends BaseSearchParamPredicateBuilder {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(UriPredicateBuilder.class);
+	private final DbColumn myColumnUri;
+	private final DbColumn myColumnHashUri;
+
+	@Autowired
+	private IResourceIndexedSearchParamUriDao myResourceIndexedSearchParamUriDao;
+	@Autowired
+	private IInterceptorBroadcaster myInterceptorBroadcaster;
+
+	/**
+	 * Constructor
+	 */
+	public UriPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_SPIDX_URI"));
+
+		myColumnUri = getTable().addColumn("SP_URI");
+		myColumnHashUri = getTable().addColumn("HASH_URI");
+	}
+
+
+	public Condition addPredicate(List<? extends IQueryParameterType> theUriOrParameterList, String theParamName, SearchFilterParser.CompareOperation theOperation, RequestDetails theRequestDetails) {
+
+		List<Condition> codePredicates = new ArrayList<>();
+		for (IQueryParameterType nextOr : theUriOrParameterList) {
+
+			if (nextOr instanceof UriParam) {
+				UriParam param = (UriParam) nextOr;
+
+				String value = param.getValue();
+				if (value == null) {
+					continue;
+				}
+
+				if (param.getQualifier() == UriParamQualifierEnum.ABOVE) {
+
+					/*
+					 * :above is an inefficient query- It means that the user is supplying a more specific URL (say
+					 * http://example.com/foo/bar/baz) and that we should match on any URLs that are less
+					 * specific but otherwise the same. For example http://example.com and http://example.com/foo would both
+					 * match.
+					 *
+					 * We do this by querying the DB for all candidate URIs and then manually checking each one. This isn't
+					 * very efficient, but this is also probably not a very common type of query to do.
+					 *
+					 * If we ever need to make this more efficient, lucene could certainly be used as an optimization.
+					 */
+					String msg = "Searching for candidate URI:above parameters for Resource["+getResourceType()+"] param["+theParamName+"]";
+					ourLog.info(msg);
+
+					StorageProcessingMessage message = new StorageProcessingMessage();
+					ourLog.warn(msg);
+					message.setMessage(msg);
+					HookParams params = new HookParams()
+						.add(RequestDetails.class, theRequestDetails)
+						.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
+						.add(StorageProcessingMessage.class, message);
+					JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_WARNING, params);
+
+					Collection<String> candidates = myResourceIndexedSearchParamUriDao.findAllByResourceTypeAndParamName(getResourceType(), theParamName);
+					List<String> toFind = new ArrayList<>();
+					for (String next : candidates) {
+						if (value.length() >= next.length()) {
+							if (value.startsWith(next)) {
+								toFind.add(next);
+							}
+						}
+					}
+
+					if (toFind.isEmpty()) {
+						continue;
+					}
+
+					Condition uriPredicate = toEqualToOrInPredicate(myColumnUri, generatePlaceholders(toFind));
+					Condition hashAndUriPredicate = combineWithHashIdentityPredicate(getResourceType(), theParamName, uriPredicate);
+					codePredicates.add(hashAndUriPredicate);
+
+				} else if (param.getQualifier() == UriParamQualifierEnum.BELOW) {
+
+					Condition uriPredicate = BinaryCondition.like(myColumnUri, generatePlaceholder(createLeftMatchLikeExpression(value)));
+					Condition hashAndUriPredicate = combineWithHashIdentityPredicate(getResourceType(), theParamName, uriPredicate);
+					codePredicates.add(hashAndUriPredicate);
+
+				} else {
+
+					Condition uriPredicate = null;
+					if (theOperation == null || theOperation == SearchFilterParser.CompareOperation.eq) {
+						long hashUri = ResourceIndexedSearchParamUri.calculateHashUri(getPartitionSettings(), getRequestPartitionId(), getResourceType(), theParamName, value);
+						Condition hashPredicate = BinaryCondition.equalTo(myColumnHashUri, generatePlaceholder(hashUri));
+						codePredicates.add(hashPredicate);
+					} else if (theOperation == SearchFilterParser.CompareOperation.ne) {
+						uriPredicate = BinaryCondition.notEqualTo(myColumnUri, generatePlaceholder(value));
+					} else if (theOperation == SearchFilterParser.CompareOperation.co) {
+						uriPredicate = BinaryCondition.like(myColumnUri, generatePlaceholder(createLeftAndRightMatchLikeExpression(value)));
+					} else if (theOperation == SearchFilterParser.CompareOperation.gt) {
+						uriPredicate = BinaryCondition.greaterThan(myColumnUri, generatePlaceholder(value));
+					} else if (theOperation == SearchFilterParser.CompareOperation.lt) {
+						uriPredicate = BinaryCondition.lessThan(myColumnUri, generatePlaceholder(value));
+					} else if (theOperation == SearchFilterParser.CompareOperation.ge) {
+						uriPredicate = BinaryCondition.greaterThanOrEq(myColumnUri, generatePlaceholder(value));
+					} else if (theOperation == SearchFilterParser.CompareOperation.le) {
+						uriPredicate = BinaryCondition.lessThanOrEq(myColumnUri, generatePlaceholder(value));
+					} else if (theOperation == SearchFilterParser.CompareOperation.sw) {
+						uriPredicate = BinaryCondition.like(myColumnUri, generatePlaceholder(createLeftMatchLikeExpression(value)));
+					} else if (theOperation == SearchFilterParser.CompareOperation.ew) {
+						uriPredicate = BinaryCondition.like(myColumnUri, generatePlaceholder(createRightMatchLikeExpression(value)));
+					} else {
+						throw new IllegalArgumentException(String.format("Unsupported operator specified in _filter clause, %s",
+							theOperation.toString()));
+					}
+
+					if (uriPredicate != null) {
+						long hashIdentity = BaseResourceIndexedSearchParam.calculateHashIdentity(getPartitionSettings(), getRequestPartitionId(), getResourceType(), theParamName);
+						BinaryCondition hashIdentityPredicate = BinaryCondition.equalTo(getColumnHashIdentity(), generatePlaceholder(hashIdentity));
+						codePredicates.add(ComboCondition.and(hashIdentityPredicate, uriPredicate));
+					}
+				}
+
+			} else {
+				throw new IllegalArgumentException("Invalid URI type: " + nextOr.getClass());
+			}
+
+		}
+
+		/*
+		 * If we haven't found any of the requested URIs in the candidates, then the whole query should match nothing
+		 */
+		if (codePredicates.isEmpty()) {
+			setMatchNothing();
+			return null;
+		}
+
+		ComboCondition orPredicate = ComboCondition.or(codePredicates.toArray(new Condition[0]));
+		Condition outerPredicate = combineWithHashIdentityPredicate(getResourceType(), theParamName, orPredicate);
+		return outerPredicate;
+
+	}
+
+	public DbColumn getColumnValue() {
+		return myColumnUri;
+	}
+}

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

@@ -0,0 +1,56 @@
+package ca.uhn.fhir.jpa.search.builder.sql;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import java.util.List;
+import java.util.regex.Pattern;
+
+/**
+ * Represents the SQL generated by this query
+ */
+public class GeneratedSql {
+	public static final Pattern INLINE_EQ_PATTERN = Pattern.compile("=\\s*['0-9]");
+	public static final Pattern INLINE_IN_PATTERN = Pattern.compile("(in|IN)\\s*\\(\\s*['0-9]");
+	private final String mySql;
+	private final List<Object> myBindVariables;
+	private final boolean myMatchNothing;
+
+	public GeneratedSql(boolean theMatchNothing, String theSql, List<Object> theBindVariables) {
+		assert INLINE_EQ_PATTERN.matcher(theSql).find() == false : "Non-bound SQL parameter found: " + theSql;
+		assert INLINE_IN_PATTERN.matcher(theSql).find() == false : "Non-bound SQL parameter found: " + theSql;
+
+		myMatchNothing = theMatchNothing;
+		mySql = theSql;
+		myBindVariables = theBindVariables;
+	}
+
+	public boolean isMatchNothing() {
+		return myMatchNothing;
+	}
+
+	public List<Object> getBindVariables() {
+		return myBindVariables;
+	}
+
+	public String getSql() {
+		return mySql;
+	}
+}

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

@@ -0,0 +1,515 @@
+package ca.uhn.fhir.jpa.search.builder.sql;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.config.HibernateDialectProvider;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.search.builder.QueryStack;
+import ca.uhn.fhir.jpa.search.builder.predicate.BaseJoiningPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.CompositeUniqueSearchParameterPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.CoordsPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.DatePredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ForcedIdPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.NumberPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.QuantityPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ResourceIdPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ResourceLinkPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ResourceTablePredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.SearchParamPresentPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.SourcePredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.TagPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.UriPredicateBuilder;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.ParamPrefixEnum;
+import com.healthmarketscience.sqlbuilder.BinaryCondition;
+import com.healthmarketscience.sqlbuilder.ComboCondition;
+import com.healthmarketscience.sqlbuilder.Condition;
+import com.healthmarketscience.sqlbuilder.FunctionCall;
+import com.healthmarketscience.sqlbuilder.InCondition;
+import com.healthmarketscience.sqlbuilder.OrderObject;
+import com.healthmarketscience.sqlbuilder.SelectQuery;
+import com.healthmarketscience.sqlbuilder.dbspec.Join;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbJoin;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbSchema;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbSpec;
+import com.healthmarketscience.sqlbuilder.dbspec.basic.DbTable;
+import org.apache.commons.lang3.Validate;
+import org.hibernate.dialect.Dialect;
+import org.hibernate.dialect.pagination.LimitHandler;
+import org.hibernate.engine.spi.RowSelection;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.UUID;
+import java.util.stream.Collectors;
+
+import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
+
+public class SearchQueryBuilder {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(SearchQueryBuilder.class);
+	private final String myBindVariableSubstitutionBase;
+	private final ArrayList<Object> myBindVariableValues;
+	private final DbSpec mySpec;
+	private final DbSchema mySchema;
+	private final SelectQuery mySelect;
+	private final PartitionSettings myPartitionSettings;
+	private final RequestPartitionId myRequestPartitionId;
+	private final String myResourceType;
+	private final ModelConfig myModelConfig;
+	private final FhirContext myFhirContext;
+	private final SqlObjectFactory mySqlBuilderFactory;
+	private final boolean myCountQuery;
+	private final Dialect myDialect;
+	private boolean myMatchNothing;
+	private ResourceTablePredicateBuilder myResourceTableRoot;
+	private boolean myHaveAtLeastOnePredicate;
+	private BaseJoiningPredicateBuilder myFirstPredicateBuilder;
+
+	/**
+	 * Constructor
+	 */
+	public SearchQueryBuilder(FhirContext theFhirContext, ModelConfig theModelConfig, PartitionSettings thePartitionSettings, RequestPartitionId theRequestPartitionId, String theResourceType, SqlObjectFactory theSqlBuilderFactory, HibernateDialectProvider theDialectProvider, boolean theCountQuery) {
+		this(theFhirContext, theModelConfig, thePartitionSettings, theRequestPartitionId, theResourceType, theSqlBuilderFactory, UUID.randomUUID().toString() + "-", theDialectProvider.getDialect(), theCountQuery, new ArrayList<>());
+	}
+
+	/**
+	 * Constructor for child SQL Builders
+	 */
+	private SearchQueryBuilder(FhirContext theFhirContext, ModelConfig theModelConfig, PartitionSettings thePartitionSettings, RequestPartitionId theRequestPartitionId, String theResourceType, SqlObjectFactory theSqlBuilderFactory, String theBindVariableSubstitutionBase, Dialect theDialect, boolean theCountQuery, ArrayList<Object> theBindVariableValues) {
+		myFhirContext = theFhirContext;
+		myModelConfig = theModelConfig;
+		myPartitionSettings = thePartitionSettings;
+		myRequestPartitionId = theRequestPartitionId;
+		myResourceType = theResourceType;
+		mySqlBuilderFactory = theSqlBuilderFactory;
+		myCountQuery = theCountQuery;
+		myDialect = theDialect;
+
+		mySpec = new DbSpec();
+		mySchema = mySpec.addDefaultSchema();
+		mySelect = new SelectQuery();
+
+		myBindVariableSubstitutionBase = theBindVariableSubstitutionBase;
+		myBindVariableValues = theBindVariableValues;
+	}
+
+	public FhirContext getFhirContext() {
+		return myFhirContext;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a Composite Unique search parameter
+	 */
+	public CompositeUniqueSearchParameterPredicateBuilder addCompositeUniquePredicateBuilder() {
+		CompositeUniqueSearchParameterPredicateBuilder retVal = mySqlBuilderFactory.newCompositeUniqueSearchParameterPredicateBuilder(this);
+		addTable(retVal, null);
+		return retVal;
+	}
+
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a COORDS search parameter
+	 */
+	public CoordsPredicateBuilder addCoordsPredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		CoordsPredicateBuilder retVal = mySqlBuilderFactory.coordsPredicateBuilder(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a DATE search parameter
+	 */
+	public DatePredicateBuilder addDatePredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		DatePredicateBuilder retVal = mySqlBuilderFactory.dateIndexTable(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder for selecting a forced ID. This is only intended for use with sorts so it can not
+	 * be the root query.
+	 */
+	public ForcedIdPredicateBuilder addForcedIdPredicateBuilder(@Nonnull DbColumn theSourceJoinColumn) {
+		Validate.isTrue(theSourceJoinColumn != null);
+
+		ForcedIdPredicateBuilder retVal = mySqlBuilderFactory.newForcedIdPredicateBuilder(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a NUMBER search parameter
+	 */
+	public NumberPredicateBuilder addNumberPredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		NumberPredicateBuilder retVal = mySqlBuilderFactory.numberIndexTable(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a QUANTITY search parameter
+	 */
+	public ResourceTablePredicateBuilder addResourceTablePredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		ResourceTablePredicateBuilder retVal = mySqlBuilderFactory.resourceTable(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a QUANTITY search parameter
+	 */
+	public QuantityPredicateBuilder addQuantityPredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		QuantityPredicateBuilder retVal = mySqlBuilderFactory.quantityIndexTable(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a <code>_source</code> search parameter
+	 */
+	public SourcePredicateBuilder addSourcePredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		SourcePredicateBuilder retVal = mySqlBuilderFactory.newSourcePredicateBuilder(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a REFERENCE search parameter
+	 */
+	public ResourceLinkPredicateBuilder addReferencePredicateBuilder(QueryStack theQueryStack, @Nullable DbColumn theSourceJoinColumn) {
+		ResourceLinkPredicateBuilder retVal = mySqlBuilderFactory.referenceIndexTable(theQueryStack, this, false);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a reosource link where the
+	 * source and target are reversed. This is used for _has queries.
+	 */
+	public ResourceLinkPredicateBuilder addReferencePredicateBuilderReversed(QueryStack theQueryStack, DbColumn theSourceJoinColumn) {
+		ResourceLinkPredicateBuilder retVal = mySqlBuilderFactory.referenceIndexTable(theQueryStack, this, true);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a STRING search parameter
+	 */
+	public StringPredicateBuilder addStringPredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		StringPredicateBuilder retVal = mySqlBuilderFactory.stringIndexTable(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a <code>_tag</code> search parameter
+	 */
+	public TagPredicateBuilder addTagPredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		TagPredicateBuilder retVal = mySqlBuilderFactory.newTagPredicateBuilder(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a TOKEN search parameter
+	 */
+	public TokenPredicateBuilder addTokenPredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		TokenPredicateBuilder retVal = mySqlBuilderFactory.tokenIndexTable(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a <code>:missing</code> search parameter
+	 */
+	public SearchParamPresentPredicateBuilder addSearchParamPresentPredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		SearchParamPresentPredicateBuilder retVal = mySqlBuilderFactory.searchParamPresentPredicateBuilder(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for selecting on a URI search parameter
+	 */
+	public UriPredicateBuilder addUriPredicateBuilder(@Nullable DbColumn theSourceJoinColumn) {
+		UriPredicateBuilder retVal = mySqlBuilderFactory.uriIndexTable(this);
+		addTable(retVal, theSourceJoinColumn);
+		return retVal;
+	}
+
+
+	public ResourceIdPredicateBuilder newResourceIdBuilder() {
+		return mySqlBuilderFactory.resourceId(this);
+	}
+
+
+	/**
+	 * Add and return a predicate builder (or a root query if no root query exists yet) for an arbitrary table
+	 */
+	private void addTable(BaseJoiningPredicateBuilder thePredicateBuilder, @Nullable DbColumn theSourceJoinColumn) {
+		if (theSourceJoinColumn != null) {
+			DbTable fromTable = theSourceJoinColumn.getTable();
+			DbTable toTable = thePredicateBuilder.getTable();
+			DbColumn toColumn = thePredicateBuilder.getResourceIdColumn();
+			addJoin(fromTable, toTable, theSourceJoinColumn, toColumn);
+		} else {
+			if (myFirstPredicateBuilder == null) {
+				ResourceTablePredicateBuilder root;
+				if (thePredicateBuilder instanceof ResourceTablePredicateBuilder) {
+					root = (ResourceTablePredicateBuilder) thePredicateBuilder;
+				} else {
+					root = mySqlBuilderFactory.resourceTable(this);
+				}
+
+				if (myCountQuery) {
+					mySelect.addCustomColumns(FunctionCall.count().setIsDistinct(true).addColumnParams(root.getResourceIdColumn()));
+				} else {
+					mySelect.addColumns(root.getResourceIdColumn());
+				}
+				mySelect.addFromTable(root.getTable());
+				myFirstPredicateBuilder = root;
+
+				if (thePredicateBuilder instanceof ResourceTablePredicateBuilder) {
+					return;
+				}
+			}
+
+			DbTable fromTable = myFirstPredicateBuilder.getTable();
+			DbTable toTable = thePredicateBuilder.getTable();
+			DbColumn fromColumn = myFirstPredicateBuilder.getResourceIdColumn();
+			DbColumn toColumn = thePredicateBuilder.getResourceIdColumn();
+			addJoin(fromTable, toTable, fromColumn, toColumn);
+
+		}
+	}
+
+	public void addJoin(DbTable theFromTable, DbTable theToTable, DbColumn theFromColumn, DbColumn theToColumn) {
+		Join join = new DbJoin(mySpec, theFromTable, theToTable, new DbColumn[]{theFromColumn}, new DbColumn[]{theToColumn});
+		mySelect.addJoins(SelectQuery.JoinType.LEFT_OUTER, join);
+	}
+
+	/**
+	 * Generate and return the SQL generated by this builder
+	 */
+	public GeneratedSql generate(@Nullable Integer theOffset, @Nullable Integer theMaxResultsToFetch) {
+
+		getOrCreateFirstPredicateBuilder();
+
+		mySelect.validate();
+		String sql = mySelect.toString();
+
+		List<Object> bindVariables = new ArrayList<>();
+		while (true) {
+
+			int idx = sql.indexOf(myBindVariableSubstitutionBase);
+			if (idx == -1) {
+				break;
+			}
+
+			int endIdx = sql.indexOf("'", idx + myBindVariableSubstitutionBase.length());
+			String substitutionIndexString = sql.substring(idx + myBindVariableSubstitutionBase.length(), endIdx);
+			int substitutionIndex = Integer.parseInt(substitutionIndexString);
+			bindVariables.add(myBindVariableValues.get(substitutionIndex));
+
+			sql = sql.substring(0, idx - 1) + "?" + sql.substring(endIdx + 1);
+		}
+
+		Integer maxResultsToFetch = theMaxResultsToFetch;
+		Integer offset = theOffset;
+		if (offset != null && offset == 0) {
+			offset = null;
+		}
+		if (maxResultsToFetch != null || offset != null) {
+
+			maxResultsToFetch = defaultIfNull(maxResultsToFetch, 10000);
+
+			sql = "SELECT " +
+				myFirstPredicateBuilder.getResourceIdColumn().getColumnNameSQL() +
+				" FROM ( " + sql + " ) " +
+				" AS " + myFirstPredicateBuilder.getResourceIdColumn().getColumnNameSQL();
+
+			LimitHandler limitHandler = myDialect.getLimitHandler();
+			RowSelection selection = new RowSelection();
+			selection.setFirstRow(offset);
+			selection.setMaxRows(maxResultsToFetch);
+			sql = limitHandler.processSql(sql, selection);
+
+			if (limitHandler.supportsLimit()) {
+				bindVariables.add(maxResultsToFetch);
+			}
+			if (limitHandler.supportsLimitOffset() && offset != null) {
+				bindVariables.add(offset);
+			}
+
+		}
+
+		return new GeneratedSql(myMatchNothing, sql, bindVariables);
+	}
+
+	/**
+	 * If at least one predicate builder already exists, return the last one added to the chain. If none has been selected, create a builder on HFJ_RESOURCE, add it and return it.
+	 */
+	public BaseJoiningPredicateBuilder getOrCreateFirstPredicateBuilder() {
+		if (myFirstPredicateBuilder == null) {
+			getOrCreateResourceTablePredicateBuilder();
+		}
+		return myFirstPredicateBuilder;
+	}
+
+	public ResourceTablePredicateBuilder getOrCreateResourceTablePredicateBuilder() {
+		if (myResourceTableRoot == null) {
+			ResourceTablePredicateBuilder resourceTable = mySqlBuilderFactory.resourceTable(this);
+			addTable(resourceTable, null);
+			Condition typeAndDeletionPredicate = resourceTable.createResourceTypeAndNonDeletedPredicates();
+			addPredicate(typeAndDeletionPredicate);
+			myResourceTableRoot = resourceTable;
+		}
+		return myResourceTableRoot;
+	}
+
+	/**
+	 * The SQL Builder library has one annoying limitation, which is that it does not use/understand bind variables
+	 * for its generated SQL. So we work around this by replacing our contents with a string in the SQL consisting
+	 * of <code>[random UUID]-[value index]</code> and then
+	 */
+	public String generatePlaceholder(Object theValue) {
+		String placeholder = myBindVariableSubstitutionBase + myBindVariableValues.size();
+		myBindVariableValues.add(theValue);
+		return placeholder;
+	}
+
+	public List<String> generatePlaceholders(Collection<?> theValues) {
+		return theValues
+			.stream()
+			.map(t -> generatePlaceholder(t))
+			.collect(Collectors.toList());
+	}
+
+
+	public void setMatchNothing() {
+		myMatchNothing = true;
+	}
+
+	public DbTable addTable(String theTableName) {
+		return mySchema.addTable(theTableName);
+	}
+
+	public PartitionSettings getPartitionSettings() {
+		return myPartitionSettings;
+	}
+
+	public RequestPartitionId getRequestPartitionId() {
+		return myRequestPartitionId;
+	}
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+	public ModelConfig getModelConfig() {
+		return myModelConfig;
+	}
+
+	public void addPredicate(@Nonnull Condition theCondition) {
+		assert theCondition != null;
+		mySelect.addCondition(theCondition);
+		myHaveAtLeastOnePredicate = true;
+	}
+
+	public ComboCondition addPredicateLastUpdated(DateRangeParam theDateRange) {
+		ResourceTablePredicateBuilder resourceTableRoot = getOrCreateResourceTablePredicateBuilder();
+
+		List<Condition> conditions = new ArrayList<>(2);
+		if (theDateRange.getLowerBoundAsInstant() != null) {
+			BinaryCondition condition = createConditionForValueWithComparator(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, resourceTableRoot.getLastUpdatedColumn(), theDateRange.getLowerBoundAsInstant());
+			conditions.add(condition);
+		}
+
+		if (theDateRange.getUpperBoundAsInstant() != null) {
+			BinaryCondition condition = createConditionForValueWithComparator(ParamPrefixEnum.LESSTHAN_OR_EQUALS, resourceTableRoot.getLastUpdatedColumn(), theDateRange.getUpperBoundAsInstant());
+			conditions.add(condition);
+		}
+
+		return ComboCondition.and(conditions.toArray(new Condition[0]));
+	}
+
+
+	public void addResourceIdsPredicate(List<Long> thePidList) {
+		DbColumn resourceIdColumn = getOrCreateFirstPredicateBuilder().getResourceIdColumn();
+		InCondition predicate = new InCondition(resourceIdColumn, generatePlaceholders(thePidList));
+		addPredicate(predicate);
+	}
+
+
+	public BinaryCondition createConditionForValueWithComparator(ParamPrefixEnum theComparator, DbColumn theColumn, Object theValue) {
+		switch (theComparator) {
+			case LESSTHAN:
+				return BinaryCondition.lessThan(theColumn, generatePlaceholder(theValue));
+			case LESSTHAN_OR_EQUALS:
+				return BinaryCondition.lessThanOrEq(theColumn, generatePlaceholder(theValue));
+			case GREATERTHAN:
+				return BinaryCondition.greaterThan(theColumn, generatePlaceholder(theValue));
+			case GREATERTHAN_OR_EQUALS:
+				return BinaryCondition.greaterThanOrEq(theColumn, generatePlaceholder(theValue));
+			default:
+				throw new IllegalArgumentException();
+		}
+	}
+
+	public SearchQueryBuilder newChildSqlBuilder() {
+		return new SearchQueryBuilder(myFhirContext, myModelConfig, myPartitionSettings, myRequestPartitionId, myResourceType, mySqlBuilderFactory, myBindVariableSubstitutionBase, myDialect, false, myBindVariableValues);
+	}
+
+	public SelectQuery getSelect() {
+		return mySelect;
+	}
+
+	public boolean haveAtLeastOnePredicate() {
+		return myHaveAtLeastOnePredicate;
+	}
+
+	public void addSort(DbColumn theColumnValueNormalized, boolean theAscending) {
+		OrderObject.NullOrder nullOrder = OrderObject.NullOrder.LAST;
+		addSort(theColumnValueNormalized, theAscending, nullOrder);
+	}
+
+	public void addSort(DbColumn theTheColumnValueNormalized, boolean theTheAscending, OrderObject.NullOrder theNullOrder) {
+		OrderObject.Dir direction = theTheAscending ? OrderObject.Dir.ASCENDING : OrderObject.Dir.DESCENDING;
+		OrderObject orderObject = new OrderObject(direction, theTheColumnValueNormalized);
+		orderObject.setNullOrder(theNullOrder);
+		mySelect.addCustomOrderings(orderObject);
+	}
+
+}

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

@@ -0,0 +1,147 @@
+package ca.uhn.fhir.jpa.search.builder.sql;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.util.IoUtil;
+import org.apache.commons.lang3.Validate;
+import org.hibernate.ScrollMode;
+import org.hibernate.ScrollableResults;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.transaction.support.TransactionSynchronizationManager;
+
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
+import javax.persistence.PersistenceContextType;
+import javax.persistence.Query;
+import java.io.Closeable;
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.util.Iterator;
+
+public class SearchQueryExecutor implements Iterator<Long>, Closeable {
+
+	private static final Long NO_MORE = -1L;
+	private static final SearchQueryExecutor NO_VALUE_EXECUTOR = new SearchQueryExecutor();
+	private static final Object[] EMPTY_OBJECT_ARRAY = new Object[0];
+	private static final Logger ourLog = LoggerFactory.getLogger(SearchQueryExecutor.class);
+	private final GeneratedSql myGeneratedSql;
+	private final Integer myMaxResultsToFetch;
+
+	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
+	private EntityManager myEntityManager;
+	private boolean myQueryInitialized;
+	private Connection myConnection;
+	private PreparedStatement myStatement;
+	private ScrollableResultsIterator<Number> myResultSet;
+	private Long myNext;
+
+	/**
+	 * Constructor
+	 */
+	public SearchQueryExecutor(GeneratedSql theGeneratedSql, Integer theMaxResultsToFetch) {
+		Validate.notNull(theGeneratedSql, "theGeneratedSql must not be null");
+		myGeneratedSql = theGeneratedSql;
+		myQueryInitialized = false;
+		myMaxResultsToFetch = theMaxResultsToFetch;
+	}
+
+	/**
+	 * Internal constructor for empty executor
+	 */
+	private SearchQueryExecutor() {
+		assert NO_MORE != null;
+
+		myGeneratedSql = null;
+		myMaxResultsToFetch = null;
+		myNext = NO_MORE;
+	}
+
+	@Override
+	public void close() {
+		IoUtil.closeQuietly(myResultSet);
+	}
+
+	@Override
+	public boolean hasNext() {
+		fetchNext();
+		return !NO_MORE.equals(myNext);
+	}
+
+	@Override
+	public Long next() {
+		fetchNext();
+		Validate.isTrue(hasNext(), "Can not call next() right now, no data remains");
+		Long next = myNext;
+		myNext = null;
+		return next;
+	}
+
+	private void fetchNext() {
+		if (myNext == null) {
+			String sql = myGeneratedSql.getSql();
+			Object[] args = myGeneratedSql.getBindVariables().toArray(EMPTY_OBJECT_ARRAY);
+
+			try {
+				if (!myQueryInitialized) {
+
+					/*
+					 * Note that we use the spring managed connection, and the expectation is that a transaction that
+					 * is managed by Spring has been started before this method is called.
+					 */
+					assert TransactionSynchronizationManager.isSynchronizationActive();
+
+					Query nativeQuery = myEntityManager.createNativeQuery(sql);
+					org.hibernate.query.Query<?> hibernateQuery = (org.hibernate.query.Query<?>) nativeQuery;
+					for (int i = 1; i <= args.length; i++) {
+						hibernateQuery.setParameter(i, args[i - 1]);
+					}
+
+					ourLog.trace("About to execute SQL: {}", sql);
+
+					ScrollableResults scrollableResults = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
+					myResultSet = new ScrollableResultsIterator<>(scrollableResults);
+					myQueryInitialized = true;
+
+				}
+
+				if (myResultSet == null || !myResultSet.hasNext()) {
+					myNext = NO_MORE;
+				} else {
+					Number next = myResultSet.next();
+					myNext = next.longValue();
+				}
+
+			} catch (Exception e) {
+				ourLog.error("Failed to create or execute SQL query", e);
+				close();
+				throw new InternalErrorException(e);
+			}
+		}
+	}
+
+	public static SearchQueryExecutor emptyExecutor() {
+		return NO_VALUE_EXECUTOR;
+	}
+}
+

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

@@ -0,0 +1,110 @@
+package ca.uhn.fhir.jpa.search.builder.sql;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2020 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.search.builder.QueryStack;
+import ca.uhn.fhir.jpa.search.builder.predicate.CompositeUniqueSearchParameterPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.CoordsPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.DatePredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ForcedIdPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.NumberPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.QuantityPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ResourceIdPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ResourceLinkPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.ResourceTablePredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.SearchParamPresentPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.SourcePredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.TagPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder;
+import ca.uhn.fhir.jpa.search.builder.predicate.UriPredicateBuilder;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
+
+public class SqlObjectFactory {
+
+	@Autowired
+	private ApplicationContext myApplicationContext;
+
+	public CompositeUniqueSearchParameterPredicateBuilder newCompositeUniqueSearchParameterPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(CompositeUniqueSearchParameterPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public CoordsPredicateBuilder coordsPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(CoordsPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public DatePredicateBuilder dateIndexTable(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(DatePredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public ForcedIdPredicateBuilder newForcedIdPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(ForcedIdPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public NumberPredicateBuilder numberIndexTable(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(NumberPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public QuantityPredicateBuilder quantityIndexTable(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(QuantityPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public ResourceLinkPredicateBuilder referenceIndexTable(QueryStack theQueryStack, SearchQueryBuilder theSearchSqlBuilder, boolean theReversed) {
+		return myApplicationContext.getBean(ResourceLinkPredicateBuilder.class, theQueryStack, theSearchSqlBuilder, theReversed);
+	}
+
+	public ResourceTablePredicateBuilder resourceTable(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(ResourceTablePredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public ResourceIdPredicateBuilder resourceId(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(ResourceIdPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public SearchParamPresentPredicateBuilder searchParamPresentPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(SearchParamPresentPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public StringPredicateBuilder stringIndexTable(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(StringPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public TokenPredicateBuilder tokenIndexTable(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(TokenPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public UriPredicateBuilder uriIndexTable(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(UriPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public TagPredicateBuilder newTagPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(TagPredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public SourcePredicateBuilder newSourcePredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
+		return myApplicationContext.getBean(SourcePredicateBuilder.class, theSearchSqlBuilder);
+	}
+
+	public SearchQueryExecutor newSearchQueryExecutor(GeneratedSql theGeneratedSql, Integer theMaxResultsToFetch) {
+		return myApplicationContext.getBean(SearchQueryExecutor.class, theGeneratedSql, theMaxResultsToFetch);
+	}
+}

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

@@ -20,7 +20,8 @@ package ca.uhn.fhir.jpa.util;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
+import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
 
 import java.util.List;
 import java.util.function.Consumer;

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

@@ -26,6 +26,7 @@ import org.hibernate.engine.jdbc.internal.BasicFormatterImpl;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.regex.Pattern;
 
 import static org.apache.commons.lang3.StringUtils.trim;
 

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

@@ -21,13 +21,13 @@ import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
 @ExtendWith(MockitoExtension.class)
-public class SearchBuilderTest {
+public class LegacySearchBuilderTest {
 
 
 	@Test
 	public void testIncludeIterator() {
 		BaseHapiFhirDao<?> mockDao = mock(BaseHapiFhirDao.class);
-		SearchBuilder searchBuilder = new SearchBuilder(mockDao, null, null);
+		LegacySearchBuilder searchBuilder = new LegacySearchBuilder(mockDao, null, null);
 		searchBuilder.setDaoConfigForUnitTest(new DaoConfig());
 		searchBuilder.setParamsForUnitTest(new SearchParameterMap());
 		EntityManager mockEntityManager = mock(EntityManager.class);
@@ -46,7 +46,7 @@ public class SearchBuilderTest {
 		resultList.add(link);
 		when(mockQuery.getResultList()).thenReturn(resultList);
 
-		SearchBuilder.IncludesIterator includesIterator = searchBuilder.new IncludesIterator(pidSet, null);
+		LegacySearchBuilder.IncludesIterator includesIterator = searchBuilder.new IncludesIterator(pidSet, null);
 		// hasNext() should return false if the pid added was already on our list going in.
 		assertFalse(includesIterator.hasNext());
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchCustomSearchParamTest.java

@@ -493,14 +493,16 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 		assertThat(foundResources, contains(p2id.getValue()));
 
 		// Search by chain
-		map = new SearchParameterMap();
+		myCaptureQueriesListener.clear();
+		map = new SearchParameterMap().setLoadSynchronous(true);
 		map.add("sibling", new ReferenceParam("name", "P1"));
 		results = myPatientDao.search(map);
 		foundResources = toUnqualifiedVersionlessIdValues(results);
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 		assertThat(foundResources, contains(p2id.getValue()));
 
 		// Search by two level chain
-		map = new SearchParameterMap();
+		map = new SearchParameterMap().setLoadSynchronous(true);
 		map.add("patient", new ReferenceParam("sibling.name", "P1"));
 		results = myAppointmentDao.search(map);
 		foundResources = toUnqualifiedVersionlessIdValues(results);
@@ -1031,7 +1033,7 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 	}
 
@@ -1068,7 +1070,7 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 
 		// Try with normal gender SP

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchFtTest.java

@@ -11,7 +11,6 @@ import javax.servlet.http.HttpServletRequest;
 
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.springframework.transaction.TransactionStatus;
@@ -24,7 +23,6 @@ import ca.uhn.fhir.model.primitive.Base64BinaryDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.param.*;
-import ca.uhn.fhir.util.TestUtil;
 
 public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 
@@ -360,7 +358,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.patientTypeEverything(request, null, null, null, null, param, null, null, mySrd));
-		assertThat(actual, containsInAnyOrder(ptId1, obsId1, obsId4, devId1));
+		assertThat(actual, containsInAnyOrder(ptId2, ptId1, obsId1, obsId4, devId1));
 
 		/*
 		 * Make one previous match no longer match

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

@@ -37,7 +37,6 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java

@@ -69,14 +69,12 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.RandomStringUtils;
 import org.hamcrest.Matchers;
 import org.hamcrest.core.StringContains;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
@@ -1600,7 +1598,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 			found = toList(myPatientDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Patient.SP_BIRTHDATE + "AAAA", new DateParam(ParamPrefixEnum.GREATERTHAN, "2000-01-01"))));
 			assertEquals(0, found.size());
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
+			assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 
 	}
@@ -1629,13 +1627,13 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 		myObservationDao.create(obs, mySrd);
 
-		List<Observation> found = toList(myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add("value-quantity", new QuantityDt(111))));
+		List<Observation> found = toList(myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add("value-quantity", new QuantityParam(111))));
 		assertEquals(1, found.size());
 
-		found = toList(myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add("value-quantity", new QuantityDt(112))));
+		found = toList(myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add("value-quantity", new QuantityParam(112))));
 		assertEquals(0, found.size());
 
-		found = toList(myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add("value-quantity", new QuantityDt(212))));
+		found = toList(myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add("value-quantity", new QuantityParam(212))));
 		assertEquals(0, found.size());
 
 	}
@@ -1665,7 +1663,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		// found = ourPatientDao.search(Patient.SP_GENDER, new IdentifierDt(null, "F"));
 		// assertEquals(0, found.size());
 
-		SearchParameterMap map = new SearchParameterMap();
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
 		map.add(Patient.SP_IDENTIFIER, new IdentifierDt("urn:system", "001testPersistSearchParams"));
 		map.add(Patient.SP_GENDER, new IdentifierDt("urn:some:wrong:system", AdministrativeGenderEnum.MALE.getCode()));
 		found = toList(myPatientDao.search(map));
@@ -2112,14 +2110,14 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		pm.setSort(new SortSpec(Patient.SP_BIRTHDATE));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		assertThat(actual, contains(id4, id1, id2, id3));
+		assertThat(actual, contains(id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testtestSortByDate"));
 		pm.setSort(new SortSpec(Patient.SP_BIRTHDATE).setOrder(SortOrderEnum.ASC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		assertThat(actual, contains(id4, id1, id2, id3));
+		assertThat(actual, contains(id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testtestSortByDate"));
@@ -2164,21 +2162,21 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		pm.setSort(new SortSpec(BaseResource.SP_RES_ID));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(5, actual.size());
-		assertThat(actual, contains(id1, id2, id3, id4, idMethodName));
+		assertThat(actual, contains(idMethodName, id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", methodName));
 		pm.setSort(new SortSpec(BaseResource.SP_RES_ID).setOrder(SortOrderEnum.ASC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(5, actual.size());
-		assertThat(actual, contains(id1, id2, id3, id4, idMethodName));
+		assertThat(actual, contains(idMethodName, id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", methodName));
 		pm.setSort(new SortSpec(BaseResource.SP_RES_ID).setOrder(SortOrderEnum.DESC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(5, actual.size());
-		assertThat(actual, contains(idMethodName, id4, id3, id2, id1));
+		assertThat(actual, contains(id4, id3, id2, id1, idMethodName));
 	}
 
 	@Test
@@ -2404,14 +2402,14 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		pm.setSort(new SortSpec(Patient.SP_FAMILY));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		assertThat(actual, contains(id4, id1, id2, id3));
+		assertThat(actual, contains(id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", string));
 		pm.setSort(new SortSpec(Patient.SP_FAMILY).setOrder(SortOrderEnum.ASC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		assertThat(actual, contains(id4, id1, id2, id3));
+		assertThat(actual, contains(id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", string));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2Test.java

@@ -49,6 +49,7 @@ import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Collectors;
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.*;
@@ -429,7 +430,14 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerbEnum.POST).setIfNoneExist("Patient?identifier=urn%3Asystem%7C" + methodName);
 
 		try {
+			myCaptureQueriesListener.clear();
 			mySystemDao.transaction(mySrd, request);
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+
+			runInTransaction(()->{
+				ourLog.info("Tokens:\n * {}", myResourceIndexedSearchParamTokenDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+			});
+
 			fail();
 		} catch (InvalidRequestException e) {
 			assertEquals(e.getMessage(), "Unable to process Transaction - Request would cause multiple resources to match URL: \"Patient?identifier=urn%3Asystem%7CtestTransactionCreateWithDuplicateMatchUrl01\". Does transaction request contain duplicates?");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java

@@ -1015,7 +1015,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 	}
 
@@ -1053,7 +1053,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 
 		// Try with normal gender SP

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchFtTest.java

@@ -457,7 +457,7 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
 		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, param, null, null, mockSrd()));
-		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, obsId4, devId1)));
+		assertThat(actual, containsInAnyOrder(toValues(ptId1, ptId2, obsId1, obsId4, devId1)));
 
 		/*
 		 * Make one previous match no longer match

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java

@@ -92,7 +92,6 @@ import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
@@ -109,6 +108,7 @@ import java.util.Date;
 import java.util.List;
 import java.util.Set;
 import java.util.TreeSet;
+import java.util.stream.Collectors;
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
@@ -1424,9 +1424,11 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 			assertThat(patients, hasItems(id1a, id1b, id2));
 		}
 		{
-			SearchParameterMap params = new SearchParameterMap();
+			SearchParameterMap params = SearchParameterMap.newSynchronous();
 			params.setLastUpdated(new DateRangeParam(beforeR2, null));
+			myCaptureQueriesListener.clear();
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 			assertThat(patients, hasItems(id2));
 			assertThat(patients, not(hasItems(id1a, id1b)));
 		}
@@ -3287,7 +3289,9 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 			TokenParam param = new TokenParam();
 			param.setMissing(false);
 			params.add(Observation.SP_CODE, param);
+			myCaptureQueriesListener.clear();
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 			assertThat(patients, not(containsInRelativeOrder(missing)));
 			assertThat(patients, containsInRelativeOrder(notMissing));
 		}
@@ -3458,7 +3462,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 		map = new SearchParameterMap();
 		map.setSort(new SortSpec("_id", SortOrderEnum.ASC));
 		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(ids, contains(id1, id2, "Patient/AA", "Patient/AB"));
+		assertThat(ids, contains("Patient/AA", "Patient/AB", id1, id2));
 
 	}
 
@@ -3614,7 +3618,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 		map = new SearchParameterMap();
 		map.setSort(new SortSpec(Patient.SP_FAMILY, SortOrderEnum.ASC).setChain(new SortSpec(Patient.SP_GIVEN, SortOrderEnum.ASC)));
 		ids = toUnqualifiedVersionlessIds(myPatientDao.search(map));
-		assertThat(ids.toString(), ids, contains(pid1, pid2, pid3, pid4, pid5));
+		assertThat(ids.toString(), ids, contains(pid2, pid4, pid5, pid3, pid1));
 		assertEquals(5, ids.size());
 
 	}
@@ -3670,7 +3674,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 		map.setSort(new SortSpec("gender").setChain(new SortSpec("family", SortOrderEnum.ASC).setChain(new SortSpec("given", SortOrderEnum.ASC))));
 		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
 		ourLog.info("IDS: {}", ids);
-		assertThat(ids.toString(), ids, contains("Patient/CA", "Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB"));
+		assertThat(ids.toString(), ids, contains("Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB", "Patient/CA"));
 
 		map = new SearchParameterMap();
 		map.add(Patient.SP_ACTIVE, new TokenParam(null, "true"));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -30,7 +30,6 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.util.TestUtil;
 import com.google.common.collect.Lists;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.RandomStringUtils;
@@ -81,7 +80,6 @@ import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
@@ -2025,7 +2023,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 			found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_BIRTHDATE + "AAAA", new DateParam(ParamPrefixEnum.GREATERTHAN, "2000-01-01")).setLoadSynchronous(true)));
 			assertEquals(0, found.size());
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
+			assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 	}
 
@@ -2600,14 +2598,14 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		pm.setSort(new SortSpec(Patient.SP_BIRTHDATE));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		assertThat(actual, contains(id4, id1, id2, id3));
+		assertThat(actual, contains(id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testtestSortByDate"));
 		pm.setSort(new SortSpec(Patient.SP_BIRTHDATE).setOrder(SortOrderEnum.ASC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		assertThat(actual, contains(id4, id1, id2, id3));
+		assertThat(actual, contains(id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testtestSortByDate"));
@@ -2652,21 +2650,21 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		pm.setSort(new SortSpec(IAnyResource.SP_RES_ID));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(5, actual.size());
-		assertThat(actual.toString(), actual, contains(id1, id2, id3, id4, idMethodName));
+		assertThat(actual.toString(), actual, contains(idMethodName, id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", methodName));
 		pm.setSort(new SortSpec(IAnyResource.SP_RES_ID).setOrder(SortOrderEnum.ASC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(5, actual.size());
-		assertThat(actual.toString(), actual, contains(id1, id2, id3, id4, idMethodName));
+		assertThat(actual.toString(), actual, contains(idMethodName, id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", methodName));
 		pm.setSort(new SortSpec(IAnyResource.SP_RES_ID).setOrder(SortOrderEnum.DESC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(5, actual.size());
-		assertThat(actual.toString(), actual, contains(idMethodName, id4, id3, id2, id1));
+		assertThat(actual.toString(), actual, contains(id4, id3, id2, id1, idMethodName));
 	}
 
 	@Test
@@ -2891,14 +2889,14 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		pm.setSort(new SortSpec(Patient.SP_FAMILY));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		assertThat(actual, contains(id4, id1, id2, id3));
+		assertThat(actual, contains(id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", string));
 		pm.setSort(new SortSpec(Patient.SP_FAMILY).setOrder(SortOrderEnum.ASC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		assertThat(actual, contains(id4, id1, id2, id3));
+		assertThat(actual, contains(id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", string));

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.jpa.dao.predicate;
 
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.util.CoordCalculator;
 import ca.uhn.fhir.jpa.util.CoordCalculatorTest;
 import ca.uhn.fhir.jpa.util.SearchBox;
@@ -27,13 +27,13 @@ import static org.mockito.Mockito.when;
 @ExtendWith(MockitoExtension.class)
 public class PredicateBuilderCoordsTest {
 	PredicateBuilderCoords myPredicateBuilderCoords;
-	private SearchBuilder mySearchBuilder;
+	private LegacySearchBuilder mySearchBuilder;
 	private CriteriaBuilder myBuilder;
 	private From myFrom;
 
 	@BeforeEach
 	public void before() {
-		mySearchBuilder = mock(SearchBuilder.class);
+		mySearchBuilder = mock(LegacySearchBuilder.class);
 		myBuilder = mock(CriteriaBuilder.class);
 		myFrom = mock(From.class);
 		myPredicateBuilderCoords = new PredicateBuilderCoords(mySearchBuilder);

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

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.jpa.dao.predicate;
 
-import ca.uhn.fhir.jpa.dao.SearchBuilderTest;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilderTest;
 import ca.uhn.fhir.rest.param.ParamPrefixEnum;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
@@ -14,7 +14,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.hamcrest.MatcherAssert.assertThat;
 
 public class SearchFuzzUtilTest {
-	private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilderTest.class);
+	private static final Logger ourLog = LoggerFactory.getLogger(LegacySearchBuilderTest.class);
 
 	@Test
 	public void testCalculateMultiplierEqualNoDecimal() {

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTagDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedCompositeStringUniqueDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamCoordsDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamDateDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamQuantityDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamStringDao;
@@ -72,6 +73,7 @@ import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
+import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.parser.StrictErrorHandler;
 import ca.uhn.fhir.rest.api.Constants;
@@ -204,6 +206,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 	@Autowired
 	protected IResourceIndexedSearchParamTokenDao myResourceIndexedSearchParamTokenDao;
 	@Autowired
+	protected IResourceIndexedSearchParamCoordsDao myResourceIndexedSearchParamCoordsDao;
+	@Autowired
 	protected IResourceIndexedSearchParamQuantityDao myResourceIndexedSearchParamQuantityDao;
 	@Autowired
 	protected IResourceIndexedSearchParamDateDao myResourceIndexedSearchParamDateDao;
@@ -458,6 +462,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 	private IdHelperService myIdHelperService;
 	@Autowired
 	protected IBatchJobSubmitter myBatchJobSubmitter;
+	@Autowired
+	protected ValidationSettings myValidationSettings;
 
 	@AfterEach()
 	public void afterCleanupDao() {
@@ -532,6 +538,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 		myDaoConfig.setHardTagListLimit(1000);
 		myDaoConfig.setIncludeLimit(2000);
 		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
+		myValidationSettings.setLocalReferenceValidationDefaultPolicy(new ValidationSettings().getLocalReferenceValidationDefaultPolicy());
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4FilterTest.java

@@ -1,8 +1,8 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.dao.data.IResourceProvenanceDao;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.jpa.util.TestUtil;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.StringParam;
@@ -15,21 +15,29 @@ import org.hl7.fhir.r4.model.DecimalType;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.RiskAssessment;
 import org.hl7.fhir.r4.model.ValueSet;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 
 import java.util.List;
+import java.util.stream.Collectors;
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hamcrest.Matchers.empty;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.fail;
 
 @SuppressWarnings({"Duplicates"})
 public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 
+	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4FilterTest.class);
+	@Autowired
+	private IResourceProvenanceDao myResourceProvenanceDao;
+
 	@AfterEach
 	public void after() {
 		myDaoConfig.setFilterParameterEnabled(new DaoConfig().isFilterParameterEnabled());
@@ -103,7 +111,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("name eq smi"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
@@ -162,6 +170,38 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testSourceComparatorEq() {
+		myDaoConfig.setStoreMetaSourceInformation(DaoConfig.StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID);
+
+		Patient p = new Patient();
+		p.getMeta().setSource("http://source");
+		p.addName().setFamily("Smith").addGiven("John");
+		p.setActive(true);
+		String ptId = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
+
+		p = new Patient();
+		p.addName().setFamily("Smith").addGiven("John2");
+		p.setActive(true);
+		myPatientDao.create(p).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map;
+		List<String> found;
+
+		runInTransaction(() -> {
+			ourLog.info("Provenance:\n * {}", myResourceProvenanceDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
+		});
+
+		map = new SearchParameterMap();
+		map.setLoadSynchronous(true);
+		map.add(Constants.PARAM_FILTER, new StringParam("_source eq http://source"));
+		myCaptureQueriesListener.clear();
+		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertThat(found, containsInAnyOrder(ptId));
+
+	}
+
 	@Test
 	public void testFilterDisabled() {
 		myDaoConfig.setFilterParameterEnabled(false);
@@ -176,6 +216,9 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		}
 	}
 
+	/**
+	 * Use the Encounter DAO to find things that would match a Patient
+	 */
 	@Test
 	public void testRetrieveDifferentTypeEq() {
 
@@ -190,24 +233,29 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
-		map.add(Constants.PARAM_FILTER, new StringParam(String.format("status eq active or _id eq %s",
+		map.add(Constants.PARAM_FILTER, new StringParam(String.format("status eq active or _id eq %s", idVal)));
-			idVal)));
+		myCaptureQueriesListener.clear();
 		found = toUnqualifiedVersionlessIdValues(myEncounterDao.search(map));
-		assertThat(found, Matchers.empty());
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertThat(found, empty());
 
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
-		map.add(Constants.PARAM_FILTER, new StringParam(String.format("_id eq %s",
+		map.add(Constants.PARAM_FILTER, new StringParam(String.format("status eq inactive or _id eq %s", idVal)));
-			idVal)));
 		found = toUnqualifiedVersionlessIdValues(myEncounterDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
-		map.add(Constants.PARAM_FILTER, new StringParam(String.format("_id eq %s",
+		map.add(Constants.PARAM_FILTER, new StringParam(String.format("status eq inactive or _id eq Patient/FOO")));
-			idVal)));
+		found = toUnqualifiedVersionlessIdValues(myEncounterDao.search(map));
-		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		assertThat(found, empty());
-		assertThat(found, containsInAnyOrder(id1));
+
+		map = new SearchParameterMap();
+		map.setLoadSynchronous(true);
+		map.add(Constants.PARAM_FILTER, new StringParam(String.format("_id eq %s", idVal)));
+		found = toUnqualifiedVersionlessIdValues(myEncounterDao.search(map));
+		assertThat(found, empty());
 
 	}
 
@@ -272,9 +320,10 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 
 		CarePlan cp = new CarePlan();
 		cp.getSubject().setReference(ptId.getValue());
-		String cpId = myCarePlanDao.create(cp).getId().toUnqualifiedVersionless().getValue();
+		myCarePlanDao.create(cp).getId().toUnqualifiedVersionless().getValue();
 
 		cp = new CarePlan();
+		cp.getSubject().setReference(ptId2.getValue());
 		cp.addActivity().getDetail().addPerformer().setReference(ptId2.getValue());
 		String cpId2 = myCarePlanDao.create(cp).getId().toUnqualifiedVersionless().getValue();
 
@@ -284,23 +333,43 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("subject ne " + ptId.getValue()));
+		myCaptureQueriesListener.clear();
 		found = toUnqualifiedVersionlessIdValues(myCarePlanDao.search(map));
-		assertThat(found, containsInAnyOrder(cpId2));
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
-
-		map = new SearchParameterMap();
-		map.setLoadSynchronous(true);
-		map.add(Constants.PARAM_FILTER, new StringParam("subject ne " + ptId.getIdPart()));
-		found = toUnqualifiedVersionlessIdValues(myCarePlanDao.search(map));
 		assertThat(found, containsInAnyOrder(cpId2));
 
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("(subject ne " + ptId.getIdPart() + ") and (performer ne " + ptId2.getValue() + ")"));
 		found = toUnqualifiedVersionlessIdValues(myCarePlanDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
+
+	@Test
+	public void testLanguageComparatorEq() {
+
+		Patient p = new Patient();
+		p.setLanguage("en");
+		p.addName().setFamily("Smith").addGiven("John");
+		p.setBirthDateElement(new DateType("1955-01-01"));
+		p.setActive(true);
+		String id1 = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
+
+		SearchParameterMap map;
+		List<String> found;
+
+		map = new SearchParameterMap();
+		map.setLoadSynchronous(true);
+		map.add(Constants.PARAM_FILTER, new StringParam("_language eq en"));
+		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		assertThat(found, containsInAnyOrder(id1));
+
+	}
+
+
+
 	@Test
 	public void testStringComparatorCo() {
 
@@ -369,7 +438,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("name sw mi"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
@@ -405,7 +474,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("name ew it"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
@@ -447,7 +516,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("given gt john"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
@@ -483,7 +552,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("given lt frank"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
@@ -506,7 +575,9 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("family ge jones"));
+		myCaptureQueriesListener.clear();
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 		assertThat(found, containsInAnyOrder(id1, id2));
 
 		map = new SearchParameterMap();
@@ -525,7 +596,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("given ge jon"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
@@ -561,7 +632,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("family le jackson"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
@@ -601,7 +672,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("birthdate ne 1955-01-01"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
@@ -633,7 +704,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("birthdate gt 1955-01-01"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
@@ -659,7 +730,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("birthdate lt 1955-01-01"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
@@ -691,7 +762,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("birthdate ge 1955-01-02"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
@@ -717,7 +788,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("birthdate le 1954-12-31"));
 		found = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
@@ -764,7 +835,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("probability eq 0.1"));
 		found = toUnqualifiedVersionlessIdValues(myRiskAssessmentDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
@@ -840,7 +911,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("probability gt 0.3"));
 		found = toUnqualifiedVersionlessIdValues(myRiskAssessmentDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
@@ -875,7 +946,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		map.add(Constants.PARAM_FILTER, new StringParam("probability lt 0.25"));
 		found = toUnqualifiedVersionlessIdValues(myRiskAssessmentDao.search(map));
-		assertThat(found, Matchers.empty());
+		assertThat(found, empty());
 
 	}
 
@@ -961,17 +1032,17 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		IIdType vsId2 = myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
 
 		IBundleProvider result;
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url eq http://hl7.org/foo/baz")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url eq http://hl7.org/foo/bar")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId2));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url eq http://hl7.org/foo/bar/bar")));
-		assertThat(toUnqualifiedVersionlessIds(result), Matchers.empty());
+		assertThat(toUnqualifiedVersionlessIds(result), empty());
 
 	}
 
@@ -987,17 +1058,17 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		IIdType vsId2 = myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
 
 		IBundleProvider result;
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url ne http://hl7.org/foo/baz")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId2));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url ne http://hl7.org/foo/bar")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url ne http://hl7.org/foo/baz and url ne http://hl7.org/foo/bar")));
-		assertThat(toUnqualifiedVersionlessIds(result), Matchers.empty());
+		assertThat(toUnqualifiedVersionlessIds(result), empty());
 
 	}
 
@@ -1013,17 +1084,17 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		IIdType vsId2 = myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
 
 		IBundleProvider result;
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url co http://hl7.org/foo")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1, vsId2));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url co baz")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url co http://hl7.org/foo/bat")));
-		assertThat(toUnqualifiedVersionlessIds(result), Matchers.empty());
+		assertThat(toUnqualifiedVersionlessIds(result), empty());
 
 	}
 
@@ -1039,17 +1110,17 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		IIdType vsId2 = myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
 
 		IBundleProvider result;
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url gt http://hl7.org/foo")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1, vsId2));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url gt http://hl7.org/foo/bar")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url gt http://hl7.org/foo/baza")));
-		assertThat(toUnqualifiedVersionlessIds(result), Matchers.empty());
+		assertThat(toUnqualifiedVersionlessIds(result), empty());
 
 	}
 
@@ -1065,15 +1136,15 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		IIdType vsId2 = myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
 
 		IBundleProvider result;
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url lt http://hl7.org/foo")));
-		assertThat(toUnqualifiedVersionlessIds(result), Matchers.empty());
+		assertThat(toUnqualifiedVersionlessIds(result), empty());
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url lt http://hl7.org/foo/baz")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId2));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url lt http://hl7.org/foo/bara")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId2));
 
@@ -1091,13 +1162,13 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		IIdType vsId2 = myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
 
 		IBundleProvider result;
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url ge http://hl7.org/foo/bar")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1, vsId2));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url ge http://hl7.org/foo/baza")));
-		assertThat(toUnqualifiedVersionlessIds(result), Matchers.empty());
+		assertThat(toUnqualifiedVersionlessIds(result), empty());
 
 	}
 
@@ -1113,15 +1184,15 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		IIdType vsId2 = myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
 
 		IBundleProvider result;
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url le http://hl7.org/foo/baz")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1, vsId2));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url le http://hl7.org/foo/bar")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId2));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url lt http://hl7.org/foo/baza")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1, vsId2));
 
@@ -1139,13 +1210,13 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		IIdType vsId2 = myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
 
 		IBundleProvider result;
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url sw http://hl7.org")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1, vsId2));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url sw hl7.org/foo/bar")));
-		assertThat(toUnqualifiedVersionlessIds(result), Matchers.empty());
+		assertThat(toUnqualifiedVersionlessIds(result), empty());
 
 	}
 
@@ -1161,15 +1232,27 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
 		IIdType vsId2 = myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
 
 		IBundleProvider result;
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url ew baz")));
 		assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(vsId1));
 
-		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Constants.PARAM_FILTER,
+		result = myValueSetDao.search(SearchParameterMap.newSynchronous().add(Constants.PARAM_FILTER,
 			new StringParam("url ew ba")));
-		assertThat(toUnqualifiedVersionlessIds(result), Matchers.empty());
+		assertThat(toUnqualifiedVersionlessIds(result), empty());
 
 	}
 
+	@Test
+	public void testUnknownSearchParam() {
+		SearchParameterMap map = new SearchParameterMap();
+		map.setLoadSynchronous(true);
+		map.add(Constants.PARAM_FILTER, new StringParam("foo eq smith"));
+		try {
+			myPatientDao.search(map);
+		} catch (InvalidRequestException e) {
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
+		}
+	}
+
 
 }

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

@@ -535,7 +535,8 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
 		assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
 
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(1, StringUtils.countMatches(myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true).toLowerCase(), "join"));
+		String sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true).toLowerCase();
+		assertEquals(2, StringUtils.countMatches(sql, "join"), sql);
 	}
 
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java

@@ -70,11 +70,13 @@ import org.springframework.transaction.support.TransactionTemplate;
 
 import java.util.List;
 
+import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.hasItems;
 import static org.hamcrest.Matchers.not;
 import static org.hamcrest.Matchers.startsWith;
@@ -807,27 +809,45 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 		SearchParameterMap map;
 		IBundleProvider results;
 		List<String> foundResources;
+		String sql;
 
 		// Search by ref
-		map = new SearchParameterMap();
+		map = SearchParameterMap.newSynchronous();
 		map.add("sibling", new ReferenceParam(p1id.getValue()));
+		myCaptureQueriesListener.clear();
 		results = myPatientDao.search(map);
 		foundResources = toUnqualifiedVersionlessIdValues(results);
 		assertThat(foundResources, contains(p2id.getValue()));
+		sql = myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertThat(sql, countMatches(sql, "JOIN"), equalTo(1));
+		assertThat(sql, countMatches(sql, "t0.SRC_PATH = 'Patient.extension('http://acme.org/sibling')'"), equalTo(1));
+		assertThat(sql, countMatches(sql, "t0.TARGET_RESOURCE_ID = '"), equalTo(1));
 
 		// Search by chain
-		map = new SearchParameterMap();
+		map = SearchParameterMap.newSynchronous();
 		map.add("sibling", new ReferenceParam("name", "P1"));
+		myCaptureQueriesListener.clear();
 		results = myPatientDao.search(map);
 		foundResources = toUnqualifiedVersionlessIdValues(results);
 		assertThat(foundResources, contains(p2id.getValue()));
+		sql = myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertThat(sql, countMatches(sql, "JOIN"), equalTo(2));
+		assertThat(sql, countMatches(sql, "SRC_PATH = 'Patient.extension('http://acme.org/sibling')'"), equalTo(1));
+		assertThat(sql, countMatches(sql, "HASH_NORM_PREFIX = '"), equalTo(39));
+		assertThat(sql, countMatches(sql, "SP_VALUE_NORMALIZED LIKE "), equalTo(39));
 
 		// Search by two level chain
-		map = new SearchParameterMap();
+		map = SearchParameterMap.newSynchronous();
 		map.add("patient", new ReferenceParam("sibling.name", "P1"));
+		myCaptureQueriesListener.clear();
 		results = myAppointmentDao.search(map);
 		foundResources = toUnqualifiedVersionlessIdValues(results);
 		assertThat(foundResources, containsInAnyOrder(appid.getValue()));
+		sql = myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertThat(sql, countMatches(sql, "JOIN"), equalTo(3));
+		assertThat(sql, countMatches(sql, "SRC_PATH = 'Appointment.participant.actor.where(resolve() is Patient)'"), equalTo(1));
+		assertThat(sql, countMatches(sql, "SRC_PATH = 'Patient.extension('http://acme.org/sibling')'"), equalTo(1));
+		assertThat(sql, countMatches(sql, "SP_VALUE_NORMALIZED LIKE 'P1%'"), equalTo(39));
 
 	}
 
@@ -1426,7 +1446,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 	}
 
@@ -1464,7 +1484,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 			myPatientDao.search(map).size();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
+			assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 
 		// Try with normal gender SP

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchFtTest.java

@@ -451,7 +451,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
 		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, param, null, null, mockSrd()));
-		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, obsId4, devId1)));
+		assertThat(actual, containsInAnyOrder(toValues(ptId1, ptId2, obsId1, obsId4, devId1)));
 
 		/*
 		 * Make one previous match no longer match

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNAsyncIT.java

@@ -1,9 +1,9 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
 import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.entity.Search;
+import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.TokenParam;
@@ -66,7 +66,7 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
 	@Test
 	public void testLastNChunking() {
 
-		runInTransaction(()->{
+		runInTransaction(() -> {
 			for (Search search : mySearchDao.findAll()) {
 				mySearchDao.updateDeleted(search.getId(), true);
 			}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
+import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.TokenParam;
@@ -64,25 +65,25 @@ public class FhirResourceDaoR4SearchLastNIT extends BaseR4SearchLastN {
 		assertEquals(4, queries.size());
 
 		// The first and third chunked queries should have a full complement of PIDs
-		StringBuilder firstQueryPattern = new StringBuilder(".*RES_ID in \\('[0-9]+'");
+		StringBuilder firstQueryPattern = new StringBuilder(".*RES_ID IN \\('[0-9]+'");
 		for (int pidIndex = 1; pidIndex < 50; pidIndex++) {
-			firstQueryPattern.append(" , '[0-9]+'");
+			firstQueryPattern.append(",'[0-9]+'");
 		}
 		firstQueryPattern.append("\\).*");
-		assertThat(queries.get(0), matchesPattern(firstQueryPattern.toString()));
+		assertThat(queries.get(0).toUpperCase().replaceAll(" , ", ","), matchesPattern(firstQueryPattern.toString()));
-		assertThat(queries.get(2), matchesPattern(firstQueryPattern.toString()));
+		assertThat(queries.get(2).toUpperCase().replaceAll(" , ", ","), matchesPattern(firstQueryPattern.toString()));
 
 		// the second and fourth chunked queries should be padded with "-1".
-		StringBuilder secondQueryPattern = new StringBuilder(".*RES_ID in \\('[0-9]+'");
+		StringBuilder secondQueryPattern = new StringBuilder(".*RES_ID IN \\('[0-9]+'");
 		for (int pidIndex = 1; pidIndex < 25; pidIndex++) {
-			secondQueryPattern.append(" , '[0-9]+'");
+			secondQueryPattern.append(",'[0-9]+'");
 		}
 		for (int pidIndex = 0; pidIndex < 25; pidIndex++) {
-			secondQueryPattern.append(" , '-1'");
+			secondQueryPattern.append(",'-1'");
 		}
 		secondQueryPattern.append("\\).*");
-		assertThat(queries.get(1), matchesPattern(secondQueryPattern.toString()));
+		assertThat(queries.get(1).toUpperCase().replaceAll(" , ", ","), matchesPattern(secondQueryPattern.toString()));
-		assertThat(queries.get(3), matchesPattern(secondQueryPattern.toString()));
+		assertThat(queries.get(3).toUpperCase().replaceAll(" , ", ","), matchesPattern(secondQueryPattern.toString()));
 
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchMissingTest.java

@@ -17,6 +17,7 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.util.List;
+import java.util.stream.Collectors;
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.*;
@@ -31,11 +32,24 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testIndexMissingFieldsDisabledDontAllowInSearch() {
+	public void testIndexMissingFieldsDisabledDontAllowInSearch_NonReference() {
 		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
 
 		SearchParameterMap params = new SearchParameterMap();
-		params.add("foo", new StringParam().setMissing(true));
+		params.add(Patient.SP_ACTIVE, new StringParam().setMissing(true));
+		try {
+			myPatientDao.search(params);
+		} catch (MethodNotAllowedException e) {
+			assertEquals(":missing modifier is disabled on this server", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testIndexMissingFieldsDisabledDontAllowInSearch_Reference() {
+		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
+
+		SearchParameterMap params = new SearchParameterMap();
+		params.add(Patient.SP_ORGANIZATION, new StringParam().setMissing(true));
 		try {
 			myPatientDao.search(params);
 		} catch (MethodNotAllowedException e) {
@@ -162,6 +176,39 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 		}
 	}
 
+	@Test
+	public void testSearchWithMissingCoords() {
+		String locId = myLocationDao.create(new Location(), mySrd).getId().toUnqualifiedVersionless().getValue();
+		String locId2 = myLocationDao.create(new Location().setPosition(new Location.LocationPositionComponent(new DecimalType(10), new DecimalType(10))), mySrd).getId().toUnqualifiedVersionless().getValue();
+
+		runInTransaction(()->{
+			ourLog.info("Coords:\n * {}", myResourceIndexedSearchParamCoordsDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+		});
+
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			TokenParam param = new TokenParam();
+			param.setMissing(true);
+			params.add(Location.SP_NEAR, param);
+			myCaptureQueriesListener.clear();
+			List<String> patients = toUnqualifiedVersionlessIdValues(myLocationDao.search(params));
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+			assertThat(patients, containsInRelativeOrder(locId));
+			assertThat(patients, not(containsInRelativeOrder(locId2)));
+		}
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			TokenParam param = new TokenParam();
+			param.setMissing(false);
+			params.add(Location.SP_NEAR, param);
+			List<String> patients = toUnqualifiedVersionlessIdValues(myLocationDao.search(params));
+			assertThat(patients, containsInRelativeOrder(locId2));
+			assertThat(patients, not(containsInRelativeOrder(locId)));
+		}
+	}
+
 	@Test
 	public void testSearchWithMissingDate2() {
 		MedicationRequest mr1 = new MedicationRequest();

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

@@ -121,7 +121,6 @@ import org.hl7.fhir.r4.model.Substance;
 import org.hl7.fhir.r4.model.Task;
 import org.hl7.fhir.r4.model.Timing;
 import org.hl7.fhir.r4.model.ValueSet;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
@@ -148,6 +147,7 @@ import java.util.TreeSet;
 import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.rest.api.Constants.PARAM_TYPE;
+import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
@@ -206,7 +206,9 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			SearchParameterMap map = new SearchParameterMap();
 			map.setLoadSynchronous(true);
 			map.add(StructureDefinition.SP_VALUESET, new ReferenceParam("http://foo2"));
+			myCaptureQueriesListener.clear();
 			List<String> ids = toUnqualifiedVersionlessIdValues(myStructureDefinitionDao.search(map));
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 			assertThat(ids, empty());
 		}
 	}
@@ -415,8 +417,8 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		myCaptureQueriesListener.clear();
 		results = myEncounterDao.search(map);
 		searchSql = myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
-		assertEquals(0, StringUtils.countMatches(searchSql, "RES_DELETED_AT"));
+		assertEquals(0, countMatches(searchSql, "RES_DELETED_AT"));
-		assertEquals(0, StringUtils.countMatches(searchSql, "RES_TYPE"));
+		assertEquals(0, countMatches(searchSql, "RES_TYPE"));
 		ids = toUnqualifiedVersionlessIdValues(results);
 		assertThat(ids, hasItems(enc1Id, enc2Id));
 
@@ -478,9 +480,11 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
 		map.add(Encounter.SP_SUBJECT, new ReferenceParam("subject", "Patient").setChain(PARAM_TYPE));
+		myCaptureQueriesListener.clear();
 		results = myEncounterDao.search(map);
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 		ids = toUnqualifiedVersionlessIdValues(results);
-		assertThat(ids, contains(enc1Id));
+		assertThat(ids.toString(), ids, contains(enc1Id));
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
 
 		map = new SearchParameterMap();
@@ -540,8 +544,8 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		map.add(DiagnosticReport.SP_PERFORMER, new ReferenceParam("CareTeam").setChain(PARAM_TYPE));
 		results = myDiagnosticReportDao.search(map);
 		ids = toUnqualifiedVersionlessIdValues(results);
-		assertThat(ids.toString(), ids, contains(drId1.getValue()));
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+		assertThat(ids.toString(), ids, contains(drId1.getValue()));
 
 	}
 
@@ -558,10 +562,18 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		ma.setMedication(new Reference(medId));
 		IIdType moId = myMedicationAdministrationDao.create(ma).getId().toUnqualified();
 
-		SearchParameterMap map = new SearchParameterMap();
+		runInTransaction(() -> {
+			ourLog.info("Resource Links:\n * {}", myResourceLinkDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
+			ourLog.info("Token indexes:\n * {}", myResourceIndexedSearchParamTokenDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
+		});
+
+		SearchParameterMap map =  SearchParameterMap.newSynchronous();
 		map.add(MedicationAdministration.SP_MEDICATION, new ReferenceAndListParam().addAnd(new ReferenceOrListParam().add(new ReferenceParam("code", "04823543"))));
+
+		myCaptureQueriesListener.clear();
 		IBundleProvider results = myMedicationAdministrationDao.search(map);
 		List<String> ids = toUnqualifiedIdValues(results);
+		myCaptureQueriesListener.logSelectQueries();
 
 		assertThat(ids, contains(moId.getValue()));
 	}
@@ -739,23 +751,41 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		pat.getManagingOrganization().setReferenceElement(orgId);
 		IIdType patId = myPatientDao.create(pat, mySrd).getId().toUnqualifiedVersionless();
 
-		Patient pat2 = new Patient();
-		pat2.addAddress().addLine(methodName + "2");
-		pat2.getManagingOrganization().setReferenceElement(orgId);
-		IIdType patId2 = myPatientDao.create(pat2, mySrd).getId().toUnqualifiedVersionless();
-
 		MedicationRequest mo = new MedicationRequest();
 		mo.getSubject().setReferenceElement(patId);
 		mo.setMedication(new Reference(medId));
 		IIdType moId = myMedicationRequestDao.create(mo, mySrd).getId().toUnqualifiedVersionless();
 
-		HttpServletRequest request = mock(HttpServletRequest.class);
+		// Nothing links to this one
-		IBundleProvider resp = myPatientDao.patientTypeEverything(request, null, null, null, null, null, null, null, mySrd);
+		Patient pat2 = new Patient();
-		assertThat(toUnqualifiedVersionlessIds(resp), containsInAnyOrder(orgId, medId, patId, moId, patId2));
+		pat2.addAddress().addLine(methodName + "2");
+		pat2.getManagingOrganization().setReferenceElement(orgId);
+		IIdType patId2 = myPatientDao.create(pat2, mySrd).getId().toUnqualifiedVersionless();
 
+		runInTransaction(()->{
+			ourLog.info("Links:\n * {}", myResourceLinkDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+		});
+
+		// All patient IDs
+		HttpServletRequest request = mock(HttpServletRequest.class);
+		myCaptureQueriesListener.clear();
+		myCaptureQueriesListener.setCaptureQueryStackTrace(true);
+		IBundleProvider resp = myPatientDao.patientTypeEverything(request, null, null, null, null, null, null, null, mySrd);
+		List<IIdType> actual = toUnqualifiedVersionlessIds(resp);
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+		assertThat(actual, containsInAnyOrder(orgId, medId, patId, moId, patId2));
+		assertEquals(5, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
+
+		// Specific patient ID with linked stuff
 		request = mock(HttpServletRequest.class);
 		resp = myPatientDao.patientInstanceEverything(request, patId, null, null, null, null, null, null, null, mySrd);
 		assertThat(toUnqualifiedVersionlessIds(resp), containsInAnyOrder(orgId, medId, patId, moId));
+
+		// Specific patient ID with no linked stuff
+		request = mock(HttpServletRequest.class);
+		resp = myPatientDao.patientInstanceEverything(request, patId2, null, null, null, null, null, null, null, mySrd);
+		assertThat(toUnqualifiedVersionlessIds(resp), containsInAnyOrder(patId2, orgId));
+
 	}
 
 	/**
@@ -921,7 +951,9 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		SearchParameterMap params = new SearchParameterMap();
 		params.setLoadSynchronous(true);
 		params.add("_has", new HasParam("Observation", "subject", "identifier", "urn:system|FOO"));
+		myCaptureQueriesListener.clear();
 		assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(pid0.getValue()));
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 
 		// No targets exist
 		params = new SearchParameterMap();
@@ -1385,6 +1417,37 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	}
 
+
+	@Test
+	public void testSearchByIdParamInverse() {
+		String id1;
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
+			id1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
+		}
+		String id2;
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
+			id2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
+		}
+
+		SearchParameterMap params;
+
+		// inverse
+		params = SearchParameterMap.newSynchronous();
+		params.add("_id", new TokenParam(id1).setModifier(TokenParamModifier.NOT));
+		assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(id2));
+
+		// Non-inverse
+		params = SearchParameterMap.newSynchronous();
+		params.add("_id", new TokenParam(id1));
+		assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(id1));
+
+	}
+
+
 	@Test
 	public void testSearchByIdParam_QueryIsMinimal() {
 		// With only an _id parameter
@@ -1398,11 +1461,11 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			assertEquals(1, selectQueries.size());
 
 			String sqlQuery = selectQueries.get(0).getSql(true, true).toLowerCase();
-			ourLog.debug("SQL Query:\n{}", sqlQuery);
+			ourLog.info("SQL Query:\n{}", sqlQuery);
-			assertEquals(1, StringUtils.countMatches(sqlQuery, "resourceta0_.res_id in"));
+			assertEquals(1, countMatches(sqlQuery, "res_id = '123'"), sqlQuery);
-			assertEquals(0, StringUtils.countMatches(sqlQuery, "join"));
+			assertEquals(0, countMatches(sqlQuery, "join"), sqlQuery);
-			assertEquals(1, StringUtils.countMatches(sqlQuery, "resourceta0_.res_type='diagnosticreport'"));
+			assertEquals(1, countMatches(sqlQuery, "res_type = 'diagnosticreport'"), sqlQuery);
-			assertEquals(1, StringUtils.countMatches(sqlQuery, "resourceta0_.res_deleted_at is null"));
+			assertEquals(1, countMatches(sqlQuery, "res_deleted_at is null"), sqlQuery);
 		}
 		// With an _id parameter and a standard search param
 		{
@@ -1417,11 +1480,11 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 			String sqlQuery = selectQueries.get(0).getSql(true, true).toLowerCase();
 			ourLog.info("SQL Query:\n{}", sqlQuery);
-			assertEquals(1, StringUtils.countMatches(sqlQuery, "resourceta0_.res_id in"));
+			assertEquals(1, countMatches(sqlQuery, "res_id = '123'"), sqlQuery);
-			assertEquals(1, StringUtils.countMatches(sqlQuery, "join"));
+			assertEquals(1, countMatches(sqlQuery, "join"), sqlQuery);
-			assertEquals(1, StringUtils.countMatches(sqlQuery, "hash_sys_and_value"));
+			assertEquals(1, countMatches(sqlQuery, "hash_sys_and_value"), sqlQuery);
-			assertEquals(0, StringUtils.countMatches(sqlQuery, "diagnosticreport"));
+			assertEquals(1, countMatches(sqlQuery, "res_type = 'diagnosticreport"), sqlQuery); // could be 0
-			assertEquals(0, StringUtils.countMatches(sqlQuery, "res_deleted_at"));
+			assertEquals(1, countMatches(sqlQuery, "res_deleted_at"), sqlQuery); // could be 0
 		}
 	}
 
@@ -1438,10 +1501,10 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 		String sqlQuery = selectQueries.get(0).getSql(true, true).toLowerCase();
 		ourLog.info("SQL Query:\n{}", sqlQuery);
-		assertEquals(1, StringUtils.countMatches(sqlQuery, "resourceta0_.res_id in"));
+		assertEquals(1, countMatches(sqlQuery, "res_id = '123'"), sqlQuery);
-		assertEquals(0, StringUtils.countMatches(sqlQuery, "join"));
+		assertEquals(0, countMatches(sqlQuery, "join"), sqlQuery);
-		assertEquals(1, StringUtils.countMatches(sqlQuery, "resourceta0_.res_type='diagnosticreport'"));
+		assertEquals(1, countMatches(sqlQuery, "res_type = 'diagnosticreport'"), sqlQuery);
-		assertEquals(1, StringUtils.countMatches(sqlQuery, "resourceta0_.res_deleted_at is null"));
+		assertEquals(1, countMatches(sqlQuery, "res_deleted_at is null"), sqlQuery);
 	}
 
 	@Test
@@ -1526,10 +1589,14 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 		// With lastupdated
 
-		params = new SearchParameterMap();
+		params = SearchParameterMap.newSynchronous();
 		params.add("_id", new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam(id2.getIdPart())));
 		params.setLastUpdated(new DateRangeParam(new Date(betweenTime), null));
-		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id2));
+
+		myCaptureQueriesListener.clear();
+		IBundleProvider search = myPatientDao.search(params);
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertThat(toUnqualifiedVersionlessIds(search).toString(), toUnqualifiedVersionlessIds(search), containsInAnyOrder(id2));
 
 	}
 
@@ -1706,7 +1773,9 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 150, "http://bar", "code1");
 			CompositeParam<TokenParam, QuantityParam> val = new CompositeParam<>(v0, v1);
 			SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true).add(param, val);
+			myCaptureQueriesListener.clear();
 			IBundleProvider result = myObservationDao.search(map);
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 			assertThat("Got: " + toUnqualifiedVersionlessIdValues(result), toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id2.getValue()));
 		}
 		{
@@ -2171,6 +2240,8 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		}
 
 		SearchParameterMap params;
+		List result;
+
 		params = new SearchParameterMap();
 		params.setLoadSynchronous(true);
 		params.add("_id", new StringParam("TEST"));
@@ -2179,7 +2250,10 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		params = new SearchParameterMap();
 		params.setLoadSynchronous(true);
 		params.add("_language", new StringParam("TEST"));
-		assertEquals(1, toList(myPatientDao.search(params)).size());
+		myCaptureQueriesListener.clear();
+		result = toList(myPatientDao.search(params));
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertEquals(1, result.size());
 
 		params = new SearchParameterMap();
 		params.setLoadSynchronous(true);
@@ -2249,7 +2323,9 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			params.setLoadSynchronous(true);
 
 			params.add(IAnyResource.SP_RES_LANGUAGE, new StringParam("en_CA"));
+			myCaptureQueriesListener.clear();
 			List<IBaseResource> patients = toList(myPatientDao.search(params));
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 			assertEquals(1, patients.size());
 			assertEquals(id1.toUnqualifiedVersionless(), patients.get(0).getIdElement().toUnqualifiedVersionless());
 		}
@@ -2668,7 +2744,9 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		e2.addPrediction().setProbability(new DecimalType(4));
 		IIdType id2 = myRiskAssessmentDao.create(e2, mySrd).getId();
 		{
+			myCaptureQueriesListener.clear();
 			IBundleProvider found = myRiskAssessmentDao.search(new SearchParameterMap().setLoadSynchronous(true).add(RiskAssessment.SP_PROBABILITY, new NumberParam(">2")));
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread();
 			assertEquals(2, found.size().intValue());
 			assertThat(toUnqualifiedVersionlessIds(found), containsInAnyOrder(id1.toUnqualifiedVersionless(), id2.toUnqualifiedVersionless()));
 		}
@@ -3037,8 +3115,10 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		List<IIdType> result;
 		SearchParameterMap params;
 
+		myCaptureQueriesListener.clear();
 		result = toUnqualifiedVersionlessIds(myObservationDao
 			.search(new SearchParameterMap().setLoadSynchronous(true).add(Observation.SP_SUBJECT, new ReferenceParam(Patient.SP_NAME, "testSearchResourceLinkWithChainWithMultipleTypesXX"))));
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 		assertThat(result, containsInAnyOrder(obsId01));
 		assertEquals(1, result.size());
 
@@ -3148,24 +3228,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	}
 
-	@Test
-	public void testSearchStringParamWithLike() {
-		SearchParameterMap map = new SearchParameterMap();
-		map.add(Patient.SP_FAMILY, new StringOrListParam().addOr(new StringParam("AAA")).addOr(new StringParam("BBB")));
-		map.setLoadSynchronous(true);
-		myPatientDao.search(map);
-
-		List<String> queries = myCaptureQueriesListener
-			.getCapturedQueries()
-			.stream()
-			.map(t -> t.getSql(true, true))
-			.filter(t -> t.contains("select"))
-			.collect(Collectors.toList());
-
-		ourLog.info("Queries:\n  " + queries.stream().collect(Collectors.joining("\n  ")));
-	}
-
-
 	@Test
 	public void testSearchTokenListLike() {
 
@@ -3193,8 +3255,8 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			.collect(Collectors.toList());
 		String resultingQueryNotFormatted = queries.get(0);
 
-		assertEquals(1, StringUtils.countMatches(resultingQueryNotFormatted, "HASH_VALUE"), resultingQueryNotFormatted);
+		assertEquals(1, countMatches(resultingQueryNotFormatted, "HASH_VALUE"), resultingQueryNotFormatted);
-		assertThat(resultingQueryNotFormatted, containsString("HASH_VALUE in ('3140583648400062149' , '4929264259256651518')"));
+		assertThat(resultingQueryNotFormatted, containsString("HASH_VALUE IN ('3140583648400062149','4929264259256651518')"));
 
 		// Ensure that the search actually worked
 		assertEquals(2, search.size().intValue());
@@ -3229,8 +3291,8 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			.collect(Collectors.toList());
 		String resultingQueryNotFormatted = queries.get(0);
 
-		assertEquals(1, StringUtils.countMatches(resultingQueryNotFormatted, "HASH_VALUE"), resultingQueryNotFormatted);
+		assertEquals(2, countMatches(resultingQueryNotFormatted, "HASH_VALUE"), resultingQueryNotFormatted);
-		assertThat(resultingQueryNotFormatted, containsString("HASH_VALUE in ('3140583648400062149' , '4929264259256651518')"));
+		assertEquals(1, countMatches(resultingQueryNotFormatted, "HASH_SYS"), resultingQueryNotFormatted);
 
 		// Ensure that the search actually worked
 		assertEquals(3, search.size().intValue());
@@ -3394,8 +3456,10 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		String id2 = myPatientDao.create(p2).getId().toUnqualifiedVersionless().getValue();
 
 		{
+			myCaptureQueriesListener.clear();
 			IBundleProvider found = myPatientDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Patient.SP_FAMILY, new StringParam("AAA")));
-			assertThat(toUnqualifiedVersionlessIdValues(found), containsInAnyOrder(id1));
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+			assertThat(toUnqualifiedVersionlessIdValues(found).toString(), toUnqualifiedVersionlessIdValues(found), containsInAnyOrder(id1));
 			assertEquals(1, found.size().intValue());
 		}
 		{
@@ -3443,8 +3507,8 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			.collect(Collectors.toList());
 
 		String searchQuery = queries.get(0);
-		assertEquals(3, StringUtils.countMatches(searchQuery.toUpperCase(), "HFJ_SPIDX_TOKEN"), searchQuery);
+		assertEquals(3, countMatches(searchQuery.toUpperCase(), "HFJ_SPIDX_TOKEN"), searchQuery);
-		assertEquals(4, StringUtils.countMatches(searchQuery.toUpperCase(), "LEFT OUTER JOIN"), searchQuery);
+		assertEquals(5, countMatches(searchQuery.toUpperCase(), "LEFT OUTER JOIN"), searchQuery);
 	}
 
 
@@ -3468,9 +3532,9 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			.collect(Collectors.toList());
 
 		String searchQuery = queries.get(0);
-		assertEquals(1, StringUtils.countMatches(searchQuery.toUpperCase(), "HFJ_SPIDX_TOKEN"), searchQuery);
+		assertEquals(1, countMatches(searchQuery.toUpperCase(), "HFJ_SPIDX_TOKEN"), searchQuery);
-		assertEquals(1, StringUtils.countMatches(searchQuery.toUpperCase(), "LEFT OUTER JOIN"), searchQuery);
+		assertEquals(2, countMatches(searchQuery.toUpperCase(), "LEFT OUTER JOIN"), searchQuery);
-		assertEquals(2, StringUtils.countMatches(searchQuery.toUpperCase(), "AND RESOURCETA0_.RES_UPDATED"), searchQuery);
+		assertEquals(2, countMatches(searchQuery.toUpperCase(), "RES_UPDATED"), searchQuery);
 	}
 
 	@Disabled
@@ -3665,20 +3729,33 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		myPatientDao.create(patient, mySrd);
 
 		patient = new Patient();
-		patient.addIdentifier().setSystem("urn:system2").setValue("testSearchTokenParam002");
+		patient.addIdentifier().setSystem("urn:system2").setValue("testSearchTokenParam003");
 		patient.addName().setFamily("Tester").addGiven("testSearchTokenParam2");
 		myPatientDao.create(patient, mySrd);
 
+		patient = new Patient();
+		patient.addIdentifier().setSystem("urn:system2").setValue("testSearchTokenParam004");
+		patient.addName().setFamily("Tester").addGiven("testSearchTokenParam2");
+		myPatientDao.create(patient, mySrd);
+
+		runInTransaction(()->{
+			ourLog.info("Token indexes:\n * {}", myResourceIndexedSearchParamTokenDao.findAll().stream().filter(t->t.getParamName().equals("identifier")).map(t->t.toString()).collect(Collectors.joining("\n * ")));
+		});
+
 		{
-			SearchParameterMap map = new SearchParameterMap();
+			SearchParameterMap map = SearchParameterMap.newSynchronous();
 			map.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", null));
+			myCaptureQueriesListener.clear();
 			IBundleProvider retrieved = myPatientDao.search(map);
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 			assertEquals(2, retrieved.size().intValue());
 		}
 		{
-			SearchParameterMap map = new SearchParameterMap();
+			SearchParameterMap map = SearchParameterMap.newSynchronous();
 			map.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", ""));
+			myCaptureQueriesListener.clear();
 			IBundleProvider retrieved = myPatientDao.search(map);
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 			assertEquals(2, retrieved.size().intValue());
 		}
 	}
@@ -3704,20 +3781,69 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			female = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
 		}
 
+		runInTransaction(()->{
+			ourLog.info("Tokens:\n * {}", myResourceIndexedSearchParamTokenDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+		});
+
 		List<String> patients;
 		SearchParameterMap params;
 
+		// Yes match - one value
 		params = new SearchParameterMap();
 		params.add(Patient.SP_GENDER, new TokenParam(null, "male"));
 		params.setLoadSynchronous(true);
 		patients = toUnqualifiedVersionlessIdValues(myPatientDao.search(params));
 		assertThat(patients, contains(male));
 
+		// Yes match - two values
+		params = new SearchParameterMap();
+		params.add(Patient.SP_GENDER, new TokenOrListParam()
+			.addOr(new TokenParam(null, "male"))
+			.addOr(new TokenParam(null, "blah"))
+		);
+		params.setLoadSynchronous(true);
+		patients = toUnqualifiedVersionlessIdValues(myPatientDao.search(params));
+		assertThat(patients, contains(male));
+
+		// Yes match - two values with different specificities
+		params = new SearchParameterMap();
+		params.add(Patient.SP_GENDER, new TokenOrListParam()
+			.addOr(new TokenParam(null, "male"))
+			.addOr(new TokenParam("http://help-im-a-bug", "blah"))
+		);
+		params.setLoadSynchronous(true);
+		patients = toUnqualifiedVersionlessIdValues(myPatientDao.search(params));
+		assertThat(patients, contains(male));
+
+		// No match - one value
 		params = new SearchParameterMap();
 		params.add(Patient.SP_GENDER, new TokenParam(null, "male").setModifier(TokenParamModifier.NOT));
 		params.setLoadSynchronous(true);
+		myCaptureQueriesListener.clear();
+		patients = toUnqualifiedVersionlessIdValues(myPatientDao.search(params));
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertThat(patients, contains(female));
+
+		// No match - two values
+		params = new SearchParameterMap();
+		params.add(Patient.SP_GENDER, new TokenOrListParam()
+			.addOr(new TokenParam(null, "male").setModifier(TokenParamModifier.NOT))
+			.addOr(new TokenParam(null, "blah").setModifier(TokenParamModifier.NOT))
+		);
+		params.setLoadSynchronous(true);
 		patients = toUnqualifiedVersionlessIdValues(myPatientDao.search(params));
 		assertThat(patients, contains(female));
+
+		// No match - two values with different specificities
+		params = new SearchParameterMap();
+		params.add(Patient.SP_GENDER, new TokenOrListParam()
+			.addOr(new TokenParam(null, "male").setModifier(TokenParamModifier.NOT))
+			.addOr(new TokenParam("http://help-im-a-bug", "blah").setModifier(TokenParamModifier.NOT))
+		);
+		params.setLoadSynchronous(true);
+		patients = toUnqualifiedVersionlessIdValues(myPatientDao.search(params));
+		assertThat(patients, contains(female));
+
 	}
 
 	@Test
@@ -3823,8 +3949,16 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		map.setLoadSynchronous(true);
 		param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, null);
 		map.add(Observation.SP_VALUE_QUANTITY, param);
+		myCaptureQueriesListener.clear();
 		found = myObservationDao.search(map);
-		assertThat(toUnqualifiedVersionlessIdValues(found), contains(id1));
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertThat(toUnqualifiedVersionlessIdValues(found).toString(), toUnqualifiedVersionlessIdValues(found), contains(id1));
+
+		String searchQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+		assertEquals(1, countMatches(searchQuery.toLowerCase(), "join"), searchQuery);
+		assertEquals(0, countMatches(searchQuery.toLowerCase(), "partition"), searchQuery);
+		assertEquals(1, countMatches(searchQuery.toLowerCase(), "hash_identity"), searchQuery);
+		assertEquals(1, countMatches(searchQuery.toLowerCase(), "sp_value"), searchQuery);
 
 		map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
@@ -4107,9 +4241,9 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			assertThat(patients.toString(), patients, contains(obsId1));
 			String searchQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search query:\n{}", searchQuery);
-			assertEquals(1, StringUtils.countMatches(searchQuery.toLowerCase(), "join"), searchQuery);
+			assertEquals(1, countMatches(searchQuery.toLowerCase(), "join"), searchQuery);
-			assertEquals(1, StringUtils.countMatches(searchQuery.toLowerCase(), "hash_identity"), searchQuery);
+			assertEquals(1, countMatches(searchQuery.toLowerCase(), "t0.sp_value_low_date_ordinal >= '20200605'"), searchQuery);
-			assertEquals(2, StringUtils.countMatches(searchQuery.toLowerCase(), "sp_value_low"), searchQuery);
+			assertEquals(1, countMatches(searchQuery.toLowerCase(), "t0.sp_value_low_date_ordinal <= '20200606'"), searchQuery);
 		}
 
 		// Two AND instances of 1 SP and 1 instance of another
@@ -4125,9 +4259,10 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			assertThat(patients.toString(), patients, contains(obsId1));
 			String searchQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search query:\n{}", searchQuery);
-			assertEquals(2, StringUtils.countMatches(searchQuery.toLowerCase(), "join"), searchQuery);
+			assertEquals(0, countMatches(searchQuery.toLowerCase(), "partition"), searchQuery);
-			assertEquals(2, StringUtils.countMatches(searchQuery.toLowerCase(), "hash_identity"), searchQuery);
+			assertEquals(2, countMatches(searchQuery.toLowerCase(), "join"), searchQuery);
-			assertEquals(4, StringUtils.countMatches(searchQuery.toLowerCase(), "sp_value_low"), searchQuery);
+			assertEquals(2, countMatches(searchQuery.toLowerCase(), "hash_identity"), searchQuery);
+			assertEquals(4, countMatches(searchQuery.toLowerCase(), "sp_value_low"), searchQuery);
 		}
 
 		// Period search
@@ -4140,9 +4275,9 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			assertThat(patients.toString(), patients, containsInAnyOrder(obsId3, obsId4));
 			String searchQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search query:\n{}", searchQuery);
-			assertEquals(1, StringUtils.countMatches(searchQuery.toLowerCase(), "join"), searchQuery);
+			assertEquals(1, countMatches(searchQuery.toLowerCase(), "join"), searchQuery);
-			assertEquals(1, StringUtils.countMatches(searchQuery.toLowerCase(), "hash_identity"), searchQuery);
+			assertEquals(1, countMatches(searchQuery.toLowerCase(), "hash_identity"), searchQuery);
-			assertEquals(1, StringUtils.countMatches(searchQuery.toLowerCase(), "sp_value_low"), searchQuery);
+			assertEquals(1, countMatches(searchQuery.toLowerCase(), "sp_value_low"), searchQuery);
 		}
 
 	}
@@ -4160,9 +4295,13 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 		SearchParameterMap map = new SearchParameterMap();
 		map.setLoadSynchronous(true);
+		myCaptureQueriesListener.clear();
 		IBundleProvider values = myPatientDao.search(map);
 		assertEquals(null, values.size());
 		assertEquals(5, values.getResources(0, 1000).size());
+
+		String sql = myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertEquals(1, countMatches(sql, "limit '5'"), sql);
 	}
 
 	@Test
@@ -4627,6 +4766,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params));
 			assertThat(patients, containsInAnyOrder(tag2id));
 		}
+
 		// TODO: get multiple/AND working
 		{
 			// And tags
@@ -4675,9 +4815,11 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 		{
 			// One tag
-			SearchParameterMap params = new SearchParameterMap();
+			SearchParameterMap params = SearchParameterMap.newSynchronous();
 			params.add("_tag", new TokenParam("urn:taglist", methodName + "1a").setModifier(TokenParamModifier.NOT));
+			myCaptureQueriesListener.clear();
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params));
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 			assertThat(patients, containsInAnyOrder(tag2id));
 			assertThat(patients, not(containsInAnyOrder(tag1id)));
 		}
@@ -5116,12 +5258,14 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		// Matches
 		Encounter e1 = new Encounter();
 		e1.setPeriod(new Period().setStartElement(new DateTimeType("2020-09-14T12:00:00Z")).setEndElement(new DateTimeType("2020-09-14T12:00:00Z")));
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e1));
 		String e1Id = myEncounterDao.create(e1).getId().toUnqualifiedVersionless().getValue();
 		Communication c1 = new Communication();
 		c1.getEncounter().setReference(e1Id);
-		myCommunicationDao.create(c1);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(c1));
+		String c1Id = myCommunicationDao.create(c1).getId().toUnqualifiedVersionless().getValue();
 
-		// Doesn't match
+		// Doesn't match (wrong date)
 		Encounter e2 = new Encounter();
 		e2.setPeriod(new Period().setStartElement(new DateTimeType("2020-02-14T12:00:00Z")).setEndElement(new DateTimeType("2020-02-14T12:00:00Z")));
 		String e2Id = myEncounterDao.create(e2).getId().toUnqualifiedVersionless().getValue();
@@ -5129,12 +5273,36 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		c2.getEncounter().setReference(e2Id);
 		myCommunicationDao.create(c2);
 
-		SearchParameterMap map = SearchParameterMap.newSynchronous();
+		// Doesn't match (wrong field - Encounter.location.period is also indexed in the "location-period" SP)
+		Encounter e3 = new Encounter();
+		e3.addLocation().setPeriod(new Period().setStartElement(new DateTimeType("2020-09-14T12:00:00Z")).setEndElement(new DateTimeType("2020-09-14T12:00:00Z")));
+		String e3Id = myEncounterDao.create(e3).getId().toUnqualifiedVersionless().getValue();
+		Communication c3 = new Communication();
+		c3.getEncounter().setReference(e3Id);
+		myCommunicationDao.create(c3);
+
+		runInTransaction(()->{
+			ourLog.info("Links:\n * {}", myResourceLinkDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+			ourLog.info("Dates:\n * {}", myResourceIndexedSearchParamDateDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+		});
+
+		SearchParameterMap map;
+
+		map = SearchParameterMap.newSynchronous();
 		map.add(Communication.SP_ENCOUNTER, new ReferenceParam("ge2020-09-14").setChain("date"));
 		map.add(Communication.SP_ENCOUNTER, new ReferenceParam("le2020-09-15").setChain("date"));
 
+		myCaptureQueriesListener.clear();
 		IBundleProvider outcome = myCommunicationDao.search(map);
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+
+		assertThat(toUnqualifiedVersionlessIdValues(outcome).toString(), toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder(c1Id));
 		assertEquals(1, outcome.sizeOrThrowNpe());
+
+		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+		assertEquals(4, countMatches(searchSql, "JOIN"));
+		assertEquals(1, countMatches(searchSql, "SELECT"));
+
 	}
 
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoHashesTest.java

@@ -93,7 +93,6 @@ import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
 import org.hl7.fhir.r4.model.Substance;
 import org.hl7.fhir.r4.model.Task;
 import org.hl7.fhir.r4.model.ValueSet;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
@@ -501,8 +500,9 @@ public class FhirResourceDaoR4SearchNoHashesTest extends BaseJpaR4Test {
 			.collect(Collectors.toList());
 		String resultingQueryNotFormatted = queries.get(0);
 
-		assertEquals(1, StringUtils.countMatches(resultingQueryNotFormatted, "SP_VALUE"), resultingQueryNotFormatted);
+		assertEquals(0, StringUtils.countMatches(resultingQueryNotFormatted, "SP_VALUE"), resultingQueryNotFormatted);
-		assertThat(resultingQueryNotFormatted, containsString("SP_VALUE in ('BAR' , 'FOO')"));
+		assertEquals(1, StringUtils.countMatches(resultingQueryNotFormatted, "HASH_VALUE"), resultingQueryNotFormatted);
+		assertThat(resultingQueryNotFormatted, containsString("HASH_VALUE IN ('3140583648400062149','4929264259256651518')"));
 
 		// Ensure that the search actually worked
 		assertEquals(2, search.size().intValue());
@@ -2362,36 +2362,38 @@ public class FhirResourceDaoR4SearchNoHashesTest extends BaseJpaR4Test {
 		patient.addName().setFamily("Tester").addGiven("testSearchTokenParam1");
 		patient.addCommunication().getLanguage().setText("testSearchTokenParamComText").addCoding().setCode("testSearchTokenParamCode").setSystem("testSearchTokenParamSystem")
 			.setDisplay("testSearchTokenParamDisplay");
-		myPatientDao.create(patient, mySrd);
+		String id1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
 
 		patient = new Patient();
 		patient.addIdentifier().setSystem("urn:system").setValue("testSearchTokenParam002");
 		patient.addName().setFamily("Tester").addGiven("testSearchTokenParam2");
-		myPatientDao.create(patient, mySrd);
+		String id2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
 
 		patient = new Patient();
 		patient.addIdentifier().setSystem("urn:system").setValue(null);
 		patient.addName().setFamily("Tester").addGiven("testSearchTokenParam2");
-		myPatientDao.create(patient, mySrd);
+		String id3 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
 
 		patient = new Patient();
 		patient.addIdentifier().setSystem("urn:system2").setValue("testSearchTokenParam002");
 		patient.addName().setFamily("Tester").addGiven("testSearchTokenParam2");
-		myPatientDao.create(patient, mySrd);
+		String id4 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
 
 		{
-			// Match system="urn:system" and value = *
+			SearchParameterMap map = SearchParameterMap.newSynchronous();
-			SearchParameterMap map = new SearchParameterMap();
 			map.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", null));
-			IBundleProvider retrieved = myPatientDao.search(map);
+			myCaptureQueriesListener.clear();
-			assertEquals(2, retrieved.size().intValue());
+			List<String> values = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+			assertThat(values, containsInAnyOrder(id1, id2));
 		}
 		{
-			// Match system="urn:system" and value = ""
+			SearchParameterMap map = SearchParameterMap.newSynchronous();
-			SearchParameterMap map = new SearchParameterMap();
 			map.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", ""));
-			IBundleProvider retrieved = myPatientDao.search(map);
+			myCaptureQueriesListener.clear();
-			assertEquals(2, retrieved.size().intValue());
+			List<String> values = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+			assertThat(values, containsInAnyOrder(id1, id2));
 		}
 	}
 

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
@@ -8,6 +9,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
 import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
+import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
 import ca.uhn.fhir.rest.api.SortSpec;
@@ -18,13 +20,15 @@ import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.DateTimeType;
+import org.hl7.fhir.r4.model.Enumerations;
+import org.hl7.fhir.r4.model.Organization;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Reference;
 import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.springframework.aop.framework.AopProxyUtils;
@@ -41,8 +45,15 @@ import java.util.stream.Collectors;
 import static org.apache.commons.lang3.StringUtils.leftPad;
 import static org.awaitility.Awaitility.await;
 import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.containsString;
-import static org.junit.jupiter.api.Assertions.*;
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.matchesPattern;
+import static org.hamcrest.Matchers.not;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
 
 
 public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
@@ -53,6 +64,8 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 	private ISearchDao mySearchEntityDao;
 	@Autowired
 	private ISearchResultDao mySearchResultDao;
+	@Autowired
+	private MatchUrlService myMatchUrlService;
 
 	@BeforeEach
 	public void before() {
@@ -123,8 +136,22 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		String uuid;
 		List<String> ids;
 
-		// Search with count only
+		// Search with count only (synchronous)
-		params = new SearchParameterMap();
+		params = new SearchParameterMap().setLoadSynchronous(true);
+		params.add(Patient.SP_NAME, new StringParam("FAM"));
+		params.setSummaryMode((SummaryEnum.COUNT));
+		myCaptureQueriesListener.clear();
+		results = myPatientDao.search(params);
+		String sql = myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertThat(sql, containsString("COUNT(DISTINCT "));
+		uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
+		assertEquals(201, results.size().intValue());
+		ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
+		assertThat(ids, empty());
+
+		// Search with count only (non-synchronous)
+		params = new SearchParameterMap().setLoadSynchronous(false);
 		params.add(Patient.SP_NAME, new StringParam("FAM"));
 		params.setSummaryMode((SummaryEnum.COUNT));
 		results = myPatientDao.search(params);
@@ -744,13 +771,28 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 
 		String resultingQueryNotFormatted = queries.get(0);
 		assertEquals(1, StringUtils.countMatches(resultingQueryNotFormatted, "Patient.managingOrganization"), resultingQueryNotFormatted);
-		assertThat(resultingQueryNotFormatted, containsString("TARGET_RESOURCE_ID in ('" + ids.get(0) + "' , '" + ids.get(1) + "' , '" + ids.get(2) + "' , '" + ids.get(3) + "' , '" + ids.get(4) + "')"));
+		assertThat(resultingQueryNotFormatted, containsString("TARGET_RESOURCE_ID IN ('" + ids.get(0) + "','" + ids.get(1) + "','" + ids.get(2) + "','" + ids.get(3) + "','" + ids.get(4) + "')"));
 
 		// Ensure that the search actually worked
 		assertEquals(5, search.size().intValue());
 
 	}
 
+	@Test
+	public void testChainedSearchUsesJoinNotSubselect() {
+		myCaptureQueriesListener.clear();
+
+		RuntimeResourceDefinition resourceDef = myFhirCtx.getResourceDefinition("Observation");
+		SearchParameterMap params = myMatchUrlService.translateMatchUrl("/Observation?subject:patient.identifier=urn:oid:ZOOP.MRN.OID|1234", resourceDef, null);
+		params.setLoadSynchronous(true);
+		myObservationDao.search(params);
+		myCaptureQueriesListener.logSelectQueries();
+
+		String selectQuery = myCaptureQueriesListener.getSelectQueries().get(0).getSql(true, true);
+		ourLog.info(selectQuery);
+		assertEquals(2, StringUtils.countMatches(selectQuery, "JOIN"));
+		assertEquals(1, StringUtils.countMatches(selectQuery, "SELECT"));
+	}
 
 	@AfterEach
 	public void afterResetDao() {
@@ -1128,7 +1170,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		// The search itself
 		resultingQueryNotFormatted = queries.get(1);
 		assertEquals(1, StringUtils.countMatches(resultingQueryNotFormatted, "Patient.managingOrganization"), resultingQueryNotFormatted);
-		assertThat(resultingQueryNotFormatted, matchesPattern(".*TARGET_RESOURCE_ID in \\('[0-9]+' , '[0-9]+' , '[0-9]+' , '[0-9]+' , '[0-9]+'\\).*"));
+		assertThat(resultingQueryNotFormatted, matchesPattern(".*TARGET_RESOURCE_ID IN \\('[0-9]+','[0-9]+','[0-9]+','[0-9]+','[0-9]+'\\).*"));
 
 		// Ensure that the search actually worked
 		assertEquals(5, search.size().intValue());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SortTest.java

@@ -90,12 +90,12 @@ public class FhirResourceDaoR4SortTest extends BaseJpaR4Test {
 		map = new SearchParameterMap();
 		map.setSort(new SortSpec("_id", SortOrderEnum.ASC));
 		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(ids, contains(id1, id2, "Patient/AA", "Patient/AB"));
+		assertThat(ids, contains("Patient/AA", "Patient/AB", id1, id2));
 
 		map = new SearchParameterMap();
 		map.setSort(new SortSpec("_id", SortOrderEnum.DESC));
 		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
-		assertThat(ids, contains("Patient/AB", "Patient/AA", id2, id1));
+		assertThat(ids, contains(id2, id1, "Patient/AB", "Patient/AA"));
 	}
 
 	@Test
@@ -258,7 +258,7 @@ public class FhirResourceDaoR4SortTest extends BaseJpaR4Test {
 		map.setSort(new SortSpec(Patient.SP_FAMILY, SortOrderEnum.ASC).setChain(new SortSpec(Patient.SP_GIVEN, SortOrderEnum.ASC)));
 		ids = toUnqualifiedVersionlessIds(myPatientDao.search(map));
 		ourLog.info("** Got IDs: {}", ids);
-		assertThat(ids, contains(pid1, pid2, pid3, pid4, pid5));
+		assertThat(ids.toString(), ids, contains(pid2, pid4, pid5, pid3, pid1));
 		assertEquals(5, ids.size());
 
 	}
@@ -316,7 +316,7 @@ public class FhirResourceDaoR4SortTest extends BaseJpaR4Test {
 		map.setSort(new SortSpec("gender").setChain(new SortSpec("family", SortOrderEnum.ASC).setChain(new SortSpec("given", SortOrderEnum.ASC))));
 		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
 		ourLog.info("IDS: {}", ids);
-		assertThat(ids, contains("Patient/CA", "Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB"));
+		assertThat(ids, contains("Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB", "Patient/CA"));
 
 		map = new SearchParameterMap();
 		map.add(Patient.SP_ACTIVE, new TokenParam(null, "true"));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -98,7 +98,6 @@ import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.r4.model.Timing;
 import org.hl7.fhir.r4.model.UriType;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
@@ -122,12 +121,14 @@ import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 
+import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.greaterThan;
 import static org.hamcrest.Matchers.hasItem;
 import static org.hamcrest.Matchers.hasSize;
@@ -2385,7 +2386,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 			found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_BIRTHDATE + "AAAA", new DateParam(ParamPrefixEnum.GREATERTHAN, "2000-01-01")).setLoadSynchronous(true)));
 			assertEquals(0, found.size());
 		} catch (InvalidRequestException e) {
-			assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, active, address, address-city, address-country, address-postalcode, address-state, address-use, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
+			assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
 		}
 	}
 
@@ -3029,16 +3030,14 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		pm.setSort(new SortSpec(Patient.SP_BIRTHDATE));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		// Nulls first for H2
+		assertThat(actual, contains(id1, id2, id3, id4));
-		assertThat(actual, contains(id4, id1, id2, id3));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testtestSortByDate"));
 		pm.setSort(new SortSpec(Patient.SP_BIRTHDATE).setOrder(SortOrderEnum.ASC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		// Nulls first for H2
+		assertThat(actual, contains(id1, id2, id3, id4));
-		assertThat(actual, contains(id4, id1, id2, id3));
 
 		pm = new SearchParameterMap();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testtestSortByDate"));
@@ -3046,7 +3045,6 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
 		assertThat(actual, contains(id3, id2, id1, id4));
-//		assertThat(actual, contains(id4, id3, id2, id1));
 
 	}
 
@@ -3084,6 +3082,20 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		assertThat(actual, contains(toValues(id3, id2, id1)));
 	}
 
+	@Test
+	public void testSortByInvalidParameter() {
+
+		SearchParameterMap pm = SearchParameterMap.newSynchronous();
+		pm.setSort(new SortSpec("hello", SortOrderEnum.DESC));
+		try {
+			myObservationDao.search(pm);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Unknown _sort parameter value \"hello\" for resource type \"Observation\" (Note: sort parameters values must use a valid Search Parameter). Valid values for this search are: [_id, _language, _lastUpdated, based-on, category, code, code-value-concept, code-value-date, code-value-quantity, code-value-string, combo-code, combo-code-value-concept, combo-code-value-quantity, combo-data-absent-reason, combo-value-concept, combo-value-quantity, component-code, component-code-value-concept, component-code-value-quantity, component-data-absent-reason, component-value-concept, component-value-quantity, data-absent-reason, date, derived-from, device, encounter, focus, has-member, identifier, method, part-of, patient, performer, specimen, status, subject, value-concept, value-date, value-quantity, value-string]", e.getMessage());
+		}
+	}
+
+
 	@Test
 	public void testSortById() {
 		String methodName = "testSortBTyId";
@@ -3097,15 +3109,21 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		IIdType id2 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
 
 		p = new Patient();
-		p.setId(methodName);
+		p.setId(methodName+"1");
 		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IIdType idMethodName = myPatientDao.update(p, mySrd).getId().toUnqualifiedVersionless();
+		IIdType idMethodName1 = myPatientDao.update(p, mySrd).getId().toUnqualifiedVersionless();
-		assertEquals(methodName, idMethodName.getIdPart());
+		assertEquals(methodName+"1", idMethodName1.getIdPart());
 
 		p = new Patient();
 		p.addIdentifier().setSystem("urn:system").setValue(methodName);
 		IIdType id3 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
 
+		p = new Patient();
+		p.setId(methodName+"2");
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IIdType idMethodName2 = myPatientDao.update(p, mySrd).getId().toUnqualifiedVersionless();
+		assertEquals(methodName+"2", idMethodName2.getIdPart());
+
 		p = new Patient();
 		p.addIdentifier().setSystem("urn:system").setValue(methodName);
 		IIdType id4 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
@@ -3113,26 +3131,26 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		SearchParameterMap pm;
 		List<IIdType> actual;
 
-		pm = new SearchParameterMap();
+		pm = SearchParameterMap.newSynchronous();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", methodName));
 		pm.setSort(new SortSpec(IAnyResource.SP_RES_ID));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertEquals(5, actual.size());
+		assertEquals(6, actual.size());
-		assertThat(actual, contains(id1, id2, id3, id4, idMethodName));
+		assertThat(actual, contains(idMethodName1, idMethodName2, id1, id2, id3, id4));
 
-		pm = new SearchParameterMap();
+		pm = SearchParameterMap.newSynchronous();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", methodName));
 		pm.setSort(new SortSpec(IAnyResource.SP_RES_ID).setOrder(SortOrderEnum.ASC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertEquals(5, actual.size());
+		assertEquals(6, actual.size());
-		assertThat(actual, contains(id1, id2, id3, id4, idMethodName));
+		assertThat(actual, contains(idMethodName1, idMethodName2, id1, id2, id3, id4));
 
-		pm = new SearchParameterMap();
+		pm = SearchParameterMap.newSynchronous();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", methodName));
 		pm.setSort(new SortSpec(IAnyResource.SP_RES_ID).setOrder(SortOrderEnum.DESC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertEquals(5, actual.size());
+		assertEquals(6, actual.size());
-		assertThat(actual, contains(idMethodName, id4, id3, id2, id1));
+		assertThat(actual, contains(id4, id3, id2, id1, idMethodName2, idMethodName1));
 	}
 
 	@Test
@@ -3140,6 +3158,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		String methodName = "testSortByLastUpdated";
 
 		Patient p = new Patient();
+		p.setActive(true);
 		p.addIdentifier().setSystem("urn:system1").setValue(methodName);
 		p.addName().setFamily(methodName);
 		IIdType id1 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
@@ -3147,6 +3166,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		TestUtil.sleepOneClick();
 
 		p = new Patient();
+		p.setActive(true);
 		p.addIdentifier().setSystem("urn:system2").setValue(methodName);
 		p.addName().setFamily(methodName);
 		IIdType id2 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
@@ -3154,6 +3174,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		TestUtil.sleepOneClick();
 
 		p = new Patient();
+		p.setActive(true);
 		p.addIdentifier().setSystem("urn:system3").setValue(methodName);
 		p.addName().setFamily(methodName);
 		IIdType id3 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
@@ -3161,6 +3182,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		TestUtil.sleepOneClick();
 
 		p = new Patient();
+		p.setActive(true);
 		p.addIdentifier().setSystem("urn:system4").setValue(methodName);
 		p.addName().setFamily(methodName);
 		IIdType id4 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
@@ -3168,22 +3190,30 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		SearchParameterMap pm;
 		List<IIdType> actual;
 
-		pm = new SearchParameterMap();
+		// With no search parameter
+		pm = SearchParameterMap.newSynchronous();
 		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertThat(actual, contains(id1, id2, id3, id4));
 
-		pm = new SearchParameterMap();
+		// With a search parameter
+		pm = SearchParameterMap.newSynchronous();
+		pm.add(Patient.SP_ACTIVE, new TokenParam("true"));
+		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
+		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
+		assertThat(actual, contains(id1, id2, id3, id4));
+
+		pm = SearchParameterMap.newSynchronous();
 		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.ASC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertThat(actual, contains(id1, id2, id3, id4));
 
-		pm = new SearchParameterMap();
+		pm = SearchParameterMap.newSynchronous();
 		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertThat(actual, contains(id4, id3, id2, id1));
 
-		pm = new SearchParameterMap();
+		pm = SearchParameterMap.newSynchronous();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam(null, methodName));
 		pm.setSort(new SortSpec(Patient.SP_NAME).setChain(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC)));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
@@ -3224,7 +3254,6 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	@Disabled
 	public void testSortByQuantity() {
 		Observation res;
 
@@ -3246,13 +3275,13 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		SearchParameterMap pm = new SearchParameterMap();
 		pm.setSort(new SortSpec(Observation.SP_VALUE_QUANTITY));
-		List<IIdType> actual = toUnqualifiedVersionlessIds(myConceptMapDao.search(pm));
+		List<IIdType> actual = toUnqualifiedVersionlessIds(myObservationDao.search(pm));
 		assertEquals(4, actual.size());
 		assertThat(actual, contains(id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
 		pm.setSort(new SortSpec(Observation.SP_VALUE_QUANTITY, SortOrderEnum.ASC));
-		actual = toUnqualifiedVersionlessIds(myConceptMapDao.search(pm));
+		actual = toUnqualifiedVersionlessIds(myObservationDao.search(pm));
 		assertEquals(4, actual.size());
 		assertThat(actual, contains(id1, id2, id3, id4));
 
@@ -3353,27 +3382,30 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		SearchParameterMap pm;
 		List<IIdType> actual;
 
-		pm = new SearchParameterMap();
+		myCaptureQueriesListener.clear();
+		pm = SearchParameterMap.newSynchronous();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", string));
 		pm.setSort(new SortSpec(Patient.SP_FAMILY));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		assertThat(actual, contains(id4, id1, id2, id3));
+		assertThat(actual, contains(id1, id2, id3, id4));
+		String sql = myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+		assertThat(sql, countMatches(sql, "JOIN"), equalTo(2));
+		assertThat(sql, countMatches(sql, "ORDER BY"), equalTo(1));
 
-		pm = new SearchParameterMap();
+		pm = SearchParameterMap.newSynchronous();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", string));
 		pm.setSort(new SortSpec(Patient.SP_FAMILY).setOrder(SortOrderEnum.ASC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
-		assertThat(actual, contains(id4, id1, id2, id3));
+		assertThat(actual, contains(id1, id2, id3, id4));
 
-		pm = new SearchParameterMap();
+		pm = SearchParameterMap.newSynchronous();
 		pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", string));
 		pm.setSort(new SortSpec(Patient.SP_FAMILY).setOrder(SortOrderEnum.DESC));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
 		assertEquals(4, actual.size());
 		assertThat(actual, contains(id3, id2, id1, id4));
-//		assertThat(actual, contains(id4, id3, id2, id1));
 	}
 
 	/**
@@ -3492,32 +3524,31 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	@Disabled
 	public void testSortByUri() {
 		ConceptMap res = new ConceptMap();
-		res.addGroup().setSource("http://foo2");
+		res.setUrl("http://foo2");
 		IIdType id2 = myConceptMapDao.create(res, mySrd).getId().toUnqualifiedVersionless();
 
 		res = new ConceptMap();
-		res.addGroup().setSource("http://foo1");
+		res.setUrl("http://foo1");
 		IIdType id1 = myConceptMapDao.create(res, mySrd).getId().toUnqualifiedVersionless();
 
 		res = new ConceptMap();
-		res.addGroup().setSource("http://bar3");
+		res.setUrl("http://foo3");
 		IIdType id3 = myConceptMapDao.create(res, mySrd).getId().toUnqualifiedVersionless();
 
 		res = new ConceptMap();
-		res.addGroup().setSource("http://bar4");
+		res.setUrl("http://foo4");
 		IIdType id4 = myConceptMapDao.create(res, mySrd).getId().toUnqualifiedVersionless();
 
 		SearchParameterMap pm = new SearchParameterMap();
-		pm.setSort(new SortSpec(ConceptMap.SP_SOURCE));
+		pm.setSort(new SortSpec(ConceptMap.SP_URL));
 		List<IIdType> actual = toUnqualifiedVersionlessIds(myConceptMapDao.search(pm));
 		assertEquals(4, actual.size());
 		assertThat(actual, contains(id1, id2, id3, id4));
 
 		pm = new SearchParameterMap();
-		pm.setSort(new SortSpec(Encounter.SP_LENGTH, SortOrderEnum.DESC));
+		pm.setSort(new SortSpec(ConceptMap.SP_URL, SortOrderEnum.DESC));
 		actual = toUnqualifiedVersionlessIds(myConceptMapDao.search(pm));
 		assertEquals(4, actual.size());
 		assertThat(actual, contains(id4, id3, id2, id1));
@@ -3534,13 +3565,13 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		SearchParameterMap map;
 
-		map = new SearchParameterMap();
+		map = SearchParameterMap.newSynchronous();
 		map.add(IAnyResource.SP_RES_ID, new StringParam(id1.getIdPart()));
 		map.setLastUpdated(new DateRangeParam("2001", "2003"));
 		map.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
 		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), empty());
 
-		map = new SearchParameterMap();
+		map = SearchParameterMap.newSynchronous();
 		map.add(IAnyResource.SP_RES_ID, new StringParam(id1.getIdPart()));
 		map.setLastUpdated(new DateRangeParam("2001", "2003"));
 		map.setSort(new SortSpec(Patient.SP_NAME));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java

@@ -442,8 +442,8 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		myCaptureQueriesListener.logFirstSelectQueryForCurrentThread();
 		unformattedSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
 		assertThat(unformattedSql, stringContainsInOrder(
-			"IDX_STRING='Patient?identifier=urn%7C111'",
+			"IDX_STRING = 'Patient?identifier=urn%7C111'",
-			"HASH_SYS_AND_VALUE in ('-3122824860083758210')"
+			"HASH_SYS_AND_VALUE = '-3122824860083758210'"
 		));
 		assertThat(unformattedSql, not(containsString(("RES_DELETED_AT"))));
 		assertThat(unformattedSql, not(containsString(("RES_TYPE"))));
@@ -461,7 +461,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		myCaptureQueriesListener.logFirstSelectQueryForCurrentThread();
 		assertThat(toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder(id1));
 		unformattedSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
-		assertThat(unformattedSql, containsString("HASH_SYS_AND_VALUE in ('4101160957635429999' , '-3122824860083758210')"));
+		assertThat(unformattedSql, containsString("HASH_SYS_AND_VALUE IN ('4101160957635429999','-3122824860083758210')"));
 		assertThat(unformattedSql, not(containsString(("IDX_STRING"))));
 		assertThat(unformattedSql, not(containsString(("RES_DELETED_AT"))));
 		assertThat(unformattedSql, not(containsString(("RES_TYPE"))));
@@ -579,8 +579,8 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		assertThat(toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder(srId));
 		unformattedSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
 		assertThat(unformattedSql, stringContainsInOrder(
-			"IDX_STRING='ServiceRequest?identifier=sys%7C111&patient=Patient%2F" + ptId.getIdPart() + "&performer=Practitioner%2F" + practId.getIdPart() + "'",
+			"IDX_STRING = 'ServiceRequest?identifier=sys%7C111&patient=Patient%2F" + ptId.getIdPart() + "&performer=Practitioner%2F" + practId.getIdPart() + "'",
-			"HASH_SYS_AND_VALUE in ('6795110643554413877')"
+			"HASH_SYS_AND_VALUE = '6795110643554413877'"
 		));
 		assertThat(unformattedSql, not(containsString(("RES_DELETED_AT"))));
 		assertThat(unformattedSql, not(containsString(("RES_TYPE"))));
@@ -601,8 +601,8 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		assertThat(toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder(srId));
 		unformattedSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
 		assertThat(unformattedSql, stringContainsInOrder(
-			"SRC_PATH in ('ServiceRequest.subject.where(resolve() is Patient)')",
+			"SRC_PATH = 'ServiceRequest.subject.where(resolve() is Patient)'",
-			"SRC_PATH in ('ServiceRequest.performer')"
+			"SRC_PATH = 'ServiceRequest.performer'"
 		));
 		assertThat(unformattedSql, not(containsString(("RES_DELETED_AT"))));
 		assertThat(unformattedSql, not(containsString(("RES_TYPE"))));

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

@@ -439,6 +439,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		myGroupDao.update(group);
 
 		Patient patient = new Patient();
+		patient.getText().setStatus(Narrative.NarrativeStatus.GENERATED).setDivAsString("<div>Hello</div>");
 		patient.setId("DEF");
 		patient.setActive(true);
 		myPatientDao.update(patient);
@@ -450,7 +451,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 		Observation obs = new Observation();
 		obs.getMeta().addProfile("http://example.com/fhir/StructureDefinition/vitalsigns-2");
-		obs.getText().setDivAsString("<div>Hello</div>");
+		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED).setDivAsString("<div>Hello</div>");
 		obs.getCategoryFirstRep().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs");
 		obs.addPerformer(new Reference("Practitioner/P"));
 		obs.setEffective(DateTimeType.now());
@@ -459,9 +460,11 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 		obs.getCode().getCodingFirstRep().setSystem("http://loinc.org").setCode("123-4").setDisplay("Display 3");
 
+		OperationOutcome oo;
+
 		// Non-existent target
 		obs.setSubject(new Reference("Group/123"));
-		OperationOutcome oo = validateAndReturnOutcome(obs);
+		oo = validateAndReturnOutcome(obs);
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
 		assertEquals("Unable to resolve resource 'Group/123'", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
 
@@ -523,9 +526,11 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 		obs.getCode().getCodingFirstRep().setSystem("http://loinc.org").setCode("123-4").setDisplay("Display 3");
 
+		OperationOutcome oo;
+
 		// Non-existent target
 		obs.setSubject(new Reference("Group/123"));
-		OperationOutcome oo = validateAndReturnOutcome(obs);
+		oo = validateAndReturnOutcome(obs);
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
 		assertEquals("Unable to resolve resource 'Group/123'", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
 

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

@@ -28,6 +28,9 @@ import ca.uhn.fhir.rest.param.DateAndListParam;
 import ca.uhn.fhir.rest.param.DateOrListParam;
 import ca.uhn.fhir.rest.param.DateParam;
 import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.HasAndListParam;
+import ca.uhn.fhir.rest.param.HasOrListParam;
+import ca.uhn.fhir.rest.param.HasParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
@@ -50,6 +53,8 @@ import org.hl7.fhir.r4.model.IdType;
 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.PractitionerRole;
 import org.hl7.fhir.r4.model.SearchParameter;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
@@ -645,7 +650,6 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 	}
 
 
-
 	@Test
 	public void testCreateInTransaction_ServerId_WithPartition() {
 		createUniqueCompositeSp();
@@ -769,7 +773,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 			assertEquals(myPartitionDate, resourceTable.getPartitionId().getPartitionDate());
 
 			// HFJ_SPIDX_TOKEN
-			ourLog.info("Tokens:\n * {}", myResourceIndexedSearchParamTokenDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+			ourLog.info("Tokens:\n * {}", myResourceIndexedSearchParamTokenDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
 			assertEquals(3, myResourceIndexedSearchParamTokenDao.countForResourceId(patientId));
 		});
 
@@ -790,7 +794,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 			assertEquals(myPartitionDate, resourceTable.getPartitionId().getPartitionDate());
 
 			// HFJ_SPIDX_TOKEN
-			ourLog.info("Tokens:\n * {}", myResourceIndexedSearchParamTokenDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+			ourLog.info("Tokens:\n * {}", myResourceIndexedSearchParamTokenDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
 			assertEquals(3, myResourceIndexedSearchParamTokenDao.countForResourceId(patientId));
 
 			// HFJ_RES_VER
@@ -1031,7 +1035,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
 			assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING='true'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING = 'true'"));
 		}
 
 		// :missing=false
@@ -1048,7 +1052,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
 			assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING='false'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING = 'false'"));
 		}
 	}
 
@@ -1072,8 +1076,8 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "myparamsto1_.PARTITION_ID='1'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "t0.PARTITION_ID = '1'"), searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING='true'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING = 'true'"), searchSql);
 		}
 
 		// :missing=false
@@ -1089,8 +1093,8 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "myparamsst1_.PARTITION_ID='1'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "t0.PARTITION_ID = '1'"));
-			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING='false'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING = 'false'"));
 		}
 	}
 
@@ -1113,8 +1117,8 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID is null"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID IS NULL"));
-			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING='true'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING = 'true'"));
 		}
 
 		// :missing=false
@@ -1130,8 +1134,8 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID is null"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID IS NULL"));
-			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING='false'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "SP_MISSING = 'false'"));
 		}
 	}
 
@@ -1158,7 +1162,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 			ourLog.info("Search SQL:\n{}", searchSql);
 			assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"));
 			assertEquals(1, StringUtils.countMatches(searchSql, "HFJ_RES_PARAM_PRESENT"));
-			assertEquals(1, StringUtils.countMatches(searchSql, "HASH_PRESENCE='1919227773735728687'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "HASH_PRESENCE = '1919227773735728687'"));
 		}
 	}
 
@@ -1183,10 +1187,10 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "mysearchpa1_.PARTITION_ID='1'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "t0.PARTITION_ID = '1'"), searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "HFJ_RES_PARAM_PRESENT"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "HFJ_RES_PARAM_PRESENT"), searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "HASH_PRESENCE='-3438137196820602023'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "HASH_PRESENCE = '-3438137196820602023'"), searchSql);
 		}
 	}
 
@@ -1211,10 +1215,10 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "mysearchpa1_.PARTITION_ID='1'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "t0.PARTITION_ID = '1'"), searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "HFJ_RES_PARAM_PRESENT"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "HFJ_RES_PARAM_PRESENT"), searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "HASH_PRESENCE='1919227773735728687'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "HASH_PRESENCE = '1919227773735728687'"), searchSql);
 		}
 	}
 
@@ -1237,10 +1241,10 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "mysearchpa1_.PARTITION_ID is null"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "t0.PARTITION_ID IS NULL"), searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "HFJ_RES_PARAM_PRESENT"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "HFJ_RES_PARAM_PRESENT"), searchSql);
-			assertEquals(1, StringUtils.countMatches(searchSql, "HASH_PRESENCE='1919227773735728687'"));
+			assertEquals(1, StringUtils.countMatches(searchSql, "HASH_PRESENCE = '1919227773735728687'"), searchSql);
 		}
 	}
 
@@ -1390,8 +1394,8 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "SP_VALUE_LOW"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "SP_VALUE_LOW"), searchSql);
 
 		// Date OR param
 
@@ -1521,6 +1525,45 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 	}
 
+	@Test
+	public void testSearch_HasParam_SearchOnePartition() {
+		addReadPartition(1);
+		addCreatePartition(1, null);
+		Organization org = new Organization();
+		org.setId("ORG");
+		org.setName("ORG");
+		myOrganizationDao.update(org);
+
+		addReadPartition(1);
+		addCreatePartition(1, null);
+		Practitioner practitioner = new Practitioner();
+		practitioner.setId("PRACT");
+		practitioner.addName().setFamily("PRACT");
+		myPractitionerDao.update(practitioner);
+
+		addReadPartition(1);
+		addCreatePartition(1, null);
+		PractitionerRole role = new PractitionerRole();
+		role.setId("ROLE");
+		role.getPractitioner().setReference("Practitioner/PRACT");
+		role.getOrganization().setReference("Organization/ORG");
+		myPractitionerRoleDao.update(role);
+
+		addReadPartition(1);
+		SearchParameterMap params = SearchParameterMap.newSynchronous();
+		HasAndListParam value = new HasAndListParam();
+		value.addAnd(new HasOrListParam().addOr(new HasParam("PractitionerRole", "practitioner", "_id", "ROLE")));
+		params.add("_has", value);
+		myCaptureQueriesListener.clear();
+		IBundleProvider outcome = myPractitionerDao.search(params);
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(1);
+		assertEquals(1, outcome.getResources(0, 1).size());
+
+		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+		ourLog.info("Search SQL:\n{}", searchSql);
+		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
+	}
+
 
 	@Test
 	public void testSearch_StringParam_SearchAllPartitions() {
@@ -1684,7 +1727,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
 		assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM='http://system'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM = 'http://system'"));
 
 		// And with another param
 
@@ -1694,15 +1737,15 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		map.add(Constants.PARAM_TAG, new TokenParam("http://system", "code2").setModifier(TokenParamModifier.NOT));
 		map.add(Patient.SP_IDENTIFIER, new TokenParam("http://foo", "bar"));
 		map.setLoadSynchronous(true);
-		 results = myPatientDao.search(map);
+		results = myPatientDao.search(map);
-		 ids = toUnqualifiedVersionlessIds(results);
+		ids = toUnqualifiedVersionlessIds(results);
 		assertThat(ids, Matchers.contains(patientIdNull, patientId1));
 
-		 searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+		searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
-		assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"));
+		assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM='http://system'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM = 'http://system'"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "myparamsto1_.HASH_SYS_AND_VALUE in"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "t1.HASH_SYS_AND_VALUE ="), searchSql);
 
 
 	}
@@ -1725,8 +1768,8 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
 		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID is null"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID IS NULL"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM='http://system'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM = 'http://system'"));
 
 		assertThat(ids.toString(), ids, Matchers.contains(patientIdNull));
 	}
@@ -1753,7 +1796,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
 		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM='http://system'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM = 'http://system'"));
 	}
 
 	@Test
@@ -1775,7 +1818,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
 		assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM='http://system'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM = 'http://system'"));
 	}
 
 	@Test
@@ -1790,16 +1833,18 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		SearchParameterMap map = new SearchParameterMap();
 		map.add(Constants.PARAM_TAG, new TokenParam("http://system", "code"));
 		map.setLoadSynchronous(true);
+		myCaptureQueriesListener.clear();
 		IBundleProvider results = myPatientDao.search(map);
 		List<IIdType> ids = toUnqualifiedVersionlessIds(results);
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 		assertThat(ids, Matchers.contains(patientId1));
 
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
 
-		// If this ever got optimized down to 1 that would be OK too
+		assertEquals(2, StringUtils.countMatches(searchSql, "JOIN"));
-		assertEquals(2, StringUtils.countMatches(searchSql, "PARTITION_ID"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM='http://system'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM = 'http://system'"));
 	}
 
 	@Test
@@ -1824,7 +1869,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
 		assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM='http://system'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM = 'http://system'"));
 	}
 
 	@Test
@@ -1849,7 +1894,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
 		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM='http://system'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM = 'http://system'"));
 	}
 
 	@Test
@@ -1872,7 +1917,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
 		assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "IDX_STRING='Patient?birthdate=2020-01-01'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "IDX_STRING = 'Patient?birthdate=2020-01-01'"));
 	}
 
 
@@ -1895,7 +1940,7 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
 		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "IDX_STRING='Patient?birthdate=2020-01-01'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "IDX_STRING = 'Patient?birthdate=2020-01-01'"));
 
 		// Same query, different partition
 		addReadPartition(2);
@@ -1929,10 +1974,10 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
 		ourLog.info("Search SQL:\n{}", searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.PARTITION_ID='1'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "t0.PARTITION_ID = '1'"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.SRC_PATH in ('Observation.subject')"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "t0.SRC_PATH = 'Observation.subject'"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.TARGET_RESOURCE_ID='" + patientId.getIdPartAsLong() + "'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "t0.TARGET_RESOURCE_ID = '" + patientId.getIdPartAsLong() + "'"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
 
 		// Same query, different partition
 		addReadPartition(2);
@@ -1962,14 +2007,13 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		map.setLoadSynchronous(true);
 		IBundleProvider results = myObservationDao.search(map);
 		List<IIdType> ids = toUnqualifiedVersionlessIds(results);
-		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
 		assertThat(ids, Matchers.contains(observationId));
 
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
 		ourLog.info("Search SQL:\n{}", searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.PARTITION_ID is null"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "t0.PARTITION_ID IS NULL"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.SRC_PATH in ('Observation.subject')"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "t0.SRC_PATH = 'Observation.subject'"));
-		assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.TARGET_RESOURCE_ID='" + patientId.getIdPartAsLong() + "'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "t0.TARGET_RESOURCE_ID = '" + patientId.getIdPartAsLong() + "'"));
 		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
 
 		// Same query, different partition
@@ -2004,9 +2048,9 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "forcedid0_.PARTITION_ID='1' "));
+		assertEquals(1, StringUtils.countMatches(searchSql, "forcedid0_.PARTITION_ID='1'"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "and forcedid0_.RESOURCE_TYPE='Patient'"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "and forcedid0_.RESOURCE_TYPE='Patient'"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
 
 		// Same query, different partition
 		addReadPartition(2);
@@ -2040,9 +2084,9 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
 		ourLog.info("Search SQL:\n{}", searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "forcedid0_.PARTITION_ID is null"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "forcedid0_.PARTITION_ID is null"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "forcedid0_.RESOURCE_TYPE='Patient' "));
+		assertEquals(1, StringUtils.countMatches(searchSql, "forcedid0_.RESOURCE_TYPE='Patient'"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
+		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
 
 		// Same query, different partition
 		addReadPartition(2);
@@ -2090,24 +2134,26 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		assertEquals(4, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
 
 		// Resolve resource
-		String sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
-		ourLog.info("SQL:{}", sql);
+		ourLog.info("SQL:{}", searchSql);
-		assertEquals(0, countMatches(sql, "PARTITION_ID="));
+		assertEquals(0, countMatches(searchSql, "PARTITION_ID="), searchSql);
 
 		// Fetch history resource
-		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
+		searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
-		ourLog.info("SQL:{}", sql);
+		ourLog.info("SQL:{}", searchSql);
-		assertEquals(0, countMatches(sql, "PARTITION_ID"));
+		assertEquals(0, countMatches(searchSql, "PARTITION_ID"), searchSql);
 
 		// Fetch history resource
-		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2).getSql(true, true);
+		searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2).getSql(true, true);
-		ourLog.info("SQL:{}", sql);
+		ourLog.info("SQL:{}", searchSql);
-		assertEquals(0, countMatches(sql, "PARTITION_IDAA"));
+		assertEquals(0, countMatches(searchSql, "PARTITION_ID="), searchSql.replace(" ", "").toUpperCase());
+		assertEquals(0, countMatches(searchSql, "PARTITION_IDIN"), searchSql.replace(" ", "").toUpperCase());
 
 		// Fetch history resource
-		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(3).getSql(true, true);
+		searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(3).getSql(true, true);
-		ourLog.info("SQL:{}", sql);
+		ourLog.info("SQL:{}", searchSql);
-		assertEquals(0, countMatches(sql, "PARTITION_IDAA"));
+		assertEquals(0, countMatches(searchSql, "PARTITION_ID="), searchSql.replace(" ", "").toUpperCase());
+		assertEquals(0, countMatches(searchSql, "PARTITION_IDIN"), searchSql.replace(" ", "").toUpperCase());
 	}
 
 	@Test
@@ -2158,17 +2204,17 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		// Fetch history resource
 		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
 		ourLog.info("SQL:{}", sql);
-		assertEquals(0, countMatches(sql, "PARTITION_ID"));
+		assertEquals(0, countMatches(sql, "PARTITION_ID="));
 
 		// Fetch history resource
 		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2).getSql(true, true);
 		ourLog.info("SQL:{}", sql);
-		assertEquals(0, countMatches(sql, "PARTITION_IDAA"));
+		assertEquals(0, countMatches(sql, "PARTITION_ID="));
 
 		// Fetch history resource
 		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(3).getSql(true, true);
 		ourLog.info("SQL:{}", sql);
-		assertEquals(0, countMatches(sql, "PARTITION_IDAA"));
+		assertEquals(0, countMatches(sql, "PARTITION_ID="));
 	}
 
 	@Test
@@ -2221,20 +2267,21 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		assertEquals(3, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
 
 		// Count
-		String sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
-		ourLog.info("SQL:{}", sql);
+		ourLog.info("SQL:{}", searchSql);
-		assertEquals(1, countMatches(sql, "count("));
+		assertEquals(1, countMatches(searchSql, "count("));
-		assertEquals(1, countMatches(sql, "PARTITION_ID='1'"));
+		assertEquals(1, countMatches(searchSql, "PARTITION_ID='1'"));
 
 		// Fetch history
-		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
+		searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
-		ourLog.info("SQL:{}", sql);
+		ourLog.info("SQL:{}", searchSql);
-		assertEquals(1, countMatches(sql, "PARTITION_ID='1'"));
+		assertEquals(1, countMatches(searchSql, "PARTITION_ID='1'"));
 
 		// Fetch history resource
-		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2).getSql(true, true);
+		searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2).getSql(true, true);
-		ourLog.info("SQL:{}", sql);
+		ourLog.info("SQL:{}", searchSql);
-		assertEquals(0, countMatches(sql, "PARTITION_IDAA"));
+		assertEquals(0, countMatches(searchSql, "PARTITION_ID="), searchSql.replace(" ", "").toUpperCase());
+		assertEquals(0, countMatches(searchSql, "PARTITION_IDIN"), searchSql.replace(" ", "").toUpperCase());
 	}
 
 	@Test
@@ -2257,19 +2304,20 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		assertEquals(3, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
 
 		// Count
-		String sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
-		ourLog.info("SQL:{}", sql);
+		ourLog.info("SQL:{}", searchSql);
-		assertEquals(1, countMatches(sql, "PARTITION_ID is null"));
+		assertEquals(1, countMatches(searchSql, "PARTITION_ID is null"), searchSql);
 
 		// Fetch history
-		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
+		searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
-		ourLog.info("SQL:{}", sql);
+		ourLog.info("SQL:{}", searchSql);
-		assertEquals(1, countMatches(sql, "PARTITION_ID is null"));
+		assertEquals(1, countMatches(searchSql, "PARTITION_ID is null"), searchSql);
 
 		// Fetch history resource
-		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2).getSql(true, true);
+		searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2).getSql(true, true);
-		ourLog.info("SQL:{}", sql);
+		ourLog.info("SQL:{}", searchSql);
-		assertEquals(0, countMatches(sql, "PARTITION_IDzzz"));
+		assertEquals(0, countMatches(searchSql, "PARTITION_ID="), searchSql.replace(" ", "").toUpperCase());
+		assertEquals(0, countMatches(searchSql, "PARTITION_IDIN"), searchSql.replace(" ", "").toUpperCase());
 	}
 
 	@Test
@@ -2341,18 +2389,18 @@ public class PartitioningSqlR4Test extends BaseJpaR4SystemTest {
 		assertEquals(3, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
 
 		// Resolve resource
-		String sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+		String sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true).toUpperCase();
-		assertEquals(1, countMatches(sql, "PARTITION_ID is null"));
+		assertEquals(1, countMatches(sql, "PARTITION_ID IS NULL"));
 		assertEquals(1, countMatches(sql, "PARTITION_ID"));
 
 		// Fetch history resource
-		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
+		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true).toUpperCase();
-		assertEquals(1, countMatches(sql, "PARTITION_ID is null"));
+		assertEquals(1, countMatches(sql, "PARTITION_ID IS NULL"));
 
 		// Resolve forced IDs
-		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2).getSql(true, true);
+		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2).getSql(true, true).toUpperCase();
-		assertEquals(1, countMatches(sql, "forcedid0_.RESOURCE_PID in"), sql);
+		assertEquals(1, countMatches(sql, "FORCEDID0_.RESOURCE_PID IN"), sql);
-		assertEquals(0, countMatches(sql, "PARTITION_ID is null"), sql);
+		assertEquals(0, countMatches(sql, "PARTITION_ID IS NULL"), sql);
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchWithInterceptorR4Test.java

@@ -68,7 +68,7 @@ public class SearchWithInterceptorR4Test extends BaseJpaR4Test {
 			String query = list.get(0).getSql(true, false);
 			ourLog.info("Query: {}", query);
 
-			assertThat(query, containsString("HASH_SYS_AND_VALUE in ('3788488238034018567')"));
+			assertThat(query, containsString("HASH_SYS_AND_VALUE = '3788488238034018567'"));
 
 		} finally {
 			myInterceptorRegistry.unregisterInterceptor(interceptor);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5SearchNoFtTest.java

@@ -18,6 +18,7 @@ import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Test;
 
 import java.util.Date;
+import java.util.stream.Collectors;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
@@ -95,11 +96,17 @@ public class FhirResourceDaoR5SearchNoFtTest extends BaseJpaR5Test {
 		role.getOrganization().setReference("Organization/ORG");
 		myPractitionerRoleDao.update(role);
 
-		SearchParameterMap params = new SearchParameterMap();
+		runInTransaction(()->{
+			ourLog.info("Links:\n * {}", myResourceLinkDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
+		});
+
+		SearchParameterMap params = SearchParameterMap.newSynchronous();
 		HasAndListParam value = new HasAndListParam();
 		value.addAnd(new HasOrListParam().addOr(new HasParam("PractitionerRole", "practitioner", "_id", "ROLE")));
 		params.add("_has", value);
+		myCaptureQueriesListener.clear();
 		IBundleProvider outcome = myPractitionerDao.search(params);
+		myCaptureQueriesListener.logSelectQueriesForCurrentThread(1);
 		assertEquals(1, outcome.getResources(0, 1).size());
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/HookInterceptorR4Test.java

@@ -32,6 +32,7 @@ public class HookInterceptorR4Test extends BaseResourceProviderR4Test {
 	@Autowired
 	IdHelperService myIdHelperService;
 
+	@Override
 	@BeforeEach
 	public void before() throws Exception {
 		super.before();
@@ -39,6 +40,7 @@ public class HookInterceptorR4Test extends BaseResourceProviderR4Test {
 		myDaoConfig.setExpungeEnabled(true);
 	}
 
+	@Override
 	@AfterEach
 	public void after() throws Exception {
 		myDaoConfig.setExpungeEnabled(new DaoConfig().isExpungeEnabled());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInterceptorR4Test.java

@@ -49,9 +49,16 @@ import static org.apache.commons.lang3.time.DateUtils.MILLIS_PER_SECOND;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.startsWith;
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.atLeast;
+import static org.mockito.Mockito.eq;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.reset;
+import static org.mockito.Mockito.timeout;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
 
 public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Test {
 
@@ -95,11 +102,11 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 
 		Bundle results = myClient.search().forResource(Patient.class).returnBundle(Bundle.class).execute();
 
-		verify(interceptor, times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_FIRST_RESULT_LOADED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10000).times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_FIRST_RESULT_LOADED), myParamsCaptor.capture());
-		verify(interceptor, times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_SELECT_COMPLETE), myParamsCaptor.capture());
+		verify(interceptor, timeout(10000).times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_SELECT_COMPLETE), myParamsCaptor.capture());
-		verify(interceptor, times(0)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_COMPLETE), myParamsCaptor.capture());
+		verify(interceptor, timeout(10000).times(0)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_COMPLETE), myParamsCaptor.capture());
-		verify(interceptor, times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_PASS_COMPLETE), myParamsCaptor.capture());
+		verify(interceptor, timeout(10000).times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_PASS_COMPLETE), myParamsCaptor.capture());
-		verify(interceptor, times(0)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_FAILED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10000).times(0)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_FAILED), myParamsCaptor.capture());
 
 		SearchRuntimeDetails details = myParamsCaptor.getAllValues().get(0).get(SearchRuntimeDetails.class);
 		assertEquals(SearchStatusEnum.PASSCMPLET, details.getSearchStatus());
@@ -108,11 +115,11 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 		reset(interceptor);
 		results = myClient.loadPage().next(results).execute();
 		assertNotNull(results);
-		verify(interceptor, times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_FIRST_RESULT_LOADED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10000).times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_FIRST_RESULT_LOADED), myParamsCaptor.capture());
-		verify(interceptor, times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_SELECT_COMPLETE), myParamsCaptor.capture());
+		verify(interceptor, timeout(10000).times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_SELECT_COMPLETE), myParamsCaptor.capture());
-		verify(interceptor, times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_COMPLETE), myParamsCaptor.capture());
+		verify(interceptor, timeout(10000).times(1)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_COMPLETE), myParamsCaptor.capture());
-		verify(interceptor, times(0)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_PASS_COMPLETE), myParamsCaptor.capture());
+		verify(interceptor, timeout(10000).times(0)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_PASS_COMPLETE), myParamsCaptor.capture());
-		verify(interceptor, times(0)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_FAILED), myParamsCaptor.capture());
+		verify(interceptor, timeout(10000).times(0)).invoke(eq(Pointcut.JPA_PERFTRACE_SEARCH_FAILED), myParamsCaptor.capture());
 
 	}
 
@@ -327,26 +334,6 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 		}
 	}
 
-	public class ReflexInterceptor extends ServerOperationInterceptorAdapter {
-		@Override
-		public void resourceCreated(RequestDetails theRequest, IBaseResource theResource) {
-			if (theResource instanceof Patient) {
-				((ServletRequestDetails) theRequest).getServletRequest().setAttribute("CREATED_PATIENT", theResource);
-			}
-		}
-
-		@Override
-		public void processingCompletedNormally(ServletRequestDetails theRequestDetails) {
-			Patient createdPatient = (Patient) theRequestDetails.getServletRequest().getAttribute("CREATED_PATIENT");
-			if (createdPatient != null) {
-				Observation observation = new Observation();
-				observation.setSubject(new Reference(createdPatient.getId()));
-
-				myClient.create().resource(observation).execute();
-			}
-		}
-	}
-
 	@Test
 	public void testInterceptorExpandsSearch() {
 
@@ -421,6 +408,25 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 
 	}
 
+	public class ReflexInterceptor extends ServerOperationInterceptorAdapter {
+		@Override
+		public void resourceCreated(RequestDetails theRequest, IBaseResource theResource) {
+			if (theResource instanceof Patient) {
+				((ServletRequestDetails) theRequest).getServletRequest().setAttribute("CREATED_PATIENT", theResource);
+			}
+		}
+
+		@Override
+		public void processingCompletedNormally(ServletRequestDetails theRequestDetails) {
+			Patient createdPatient = (Patient) theRequestDetails.getServletRequest().getAttribute("CREATED_PATIENT");
+			if (createdPatient != null) {
+				Observation observation = new Observation();
+				observation.setSubject(new Reference(createdPatient.getId()));
+
+				myClient.create().resource(observation).execute();
+			}
+		}
+	}
 
 	public static void verifyDaoInterceptor(IServerInterceptor theDaoInterceptor) {
 		ArgumentCaptor<ActionRequestDetails> ardCaptor;

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

@@ -2050,13 +2050,21 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		c.getSubject().setReferenceElement(pId);
 		IIdType cId = myClient.create().resource(c).execute().getId().toUnqualifiedVersionless();
 
+		ourLog.info("Resource IDs:\n * {}\n * {}\n * {}", oId, pId, cId);
+		runInTransaction(() -> {
+			ourLog.info("Resource Links:\n * {}", myResourceLinkDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
+			ourLog.info("Resources:\n * {}", myResourceTableDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
+		});
+
 		Thread.sleep(10);
 		long time3 = System.currentTimeMillis();
 
 		// %3E=> %3C=<
 
+		myCaptureQueriesListener.clear();
 		HttpGet get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantType(new Date(time1)).getValueAsString());
 		CloseableHttpResponse response = ourHttpClient.execute(get);
+		myCaptureQueriesListener.logSelectQueries();
 		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			String output = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
@@ -2918,6 +2926,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 	}
 
+	@Disabled
 	@Test
 	public void testPagingOverEverythingSetWithNoPagingProvider() {
 		ourRestServer.setPagingProvider(null);
@@ -2956,7 +2965,9 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		assertEquals(null, response.getTotalElement().getValue());
 		assertThat(response.getLink("next").getUrl(), not(emptyString()));
 
+		myCaptureQueriesListener.clear();
 		response = myClient.fetchResourceFromUrl(Bundle.class, response.getLink("next").getUrl());
+		myCaptureQueriesListener.logSelectQueries();
 
 		assertEquals(1, response.getEntry().size());
 		assertEquals(21, response.getTotalElement().getValue().intValue());
@@ -4494,6 +4505,19 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		} catch (InvalidRequestException e) {
 			assertThat(e.getMessage(), containsString("Unable to handle number prefix \"eb\" for value: eb100"));
 		}
+
+		try {
+			myClient
+				.search()
+				.forResource(MolecularSequence.class)
+				.where(MolecularSequence.VARIANT_END.withPrefix(ParamPrefixEnum.STARTS_AFTER).number(100))
+				.prettyPrint()
+				.returnBundle(Bundle.class)
+				.execute();
+			fail();
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("Unable to handle number prefix \"sa\" for value: sa100"));
+		}
 	}
 
 	@Test()

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5Test.java

@@ -233,11 +233,14 @@ public class ResourceProviderR5Test extends BaseResourceProviderR5Test {
 		observation.setEffective(new DateTimeType("1965-08-10"));
 		myObservationDao.create(observation).getId().toUnqualified();
 
+		myCaptureQueriesListener.clear();
 		Bundle output = myClient
 			.search()
 			.byUrl("Observation?_count=0")
 			.returnBundle(Bundle.class)
 			.execute();
+		ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
+		myCaptureQueriesListener.logSelectQueries();
 
 		assertEquals(2, output.getTotal());
 		assertEquals(0, output.getEntry().size());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/PagingMultinodeProviderDstu3Test.java

@@ -121,10 +121,12 @@ public class PagingMultinodeProviderDstu3Test extends BaseResourceProviderDstu3T
 		assertThat(found.getLink().stream().filter(l -> l.getRelation().equals("next")).map(l -> l.getUrl()).findAny()
 			.orElseThrow(() -> new IllegalStateException("No next page link")).contains("_offset=10"), is(true));
 
+		myCaptureQueriesListener.clear();
 		found = ourClient
 			.loadPage()
 			.next(found)
 			.execute();
+		myCaptureQueriesListener.logSelectQueries();
 		assertThat(toUnqualifiedVersionlessIdValues(found), contains("Patient/A010", "Patient/A011", "Patient/A012", "Patient/A013", "Patient/A014", "Patient/A015", "Patient/A016", "Patient/A017", "Patient/A018", "Patient/A019"));
 
 		found = ourClient

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

@@ -10,7 +10,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.config.dstu3.BaseDstu3Config;
 import ca.uhn.fhir.jpa.dao.IResultIterator;
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
 import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
@@ -94,7 +94,7 @@ public class SearchCoordinatorSvcImplTest {
 	private EntityManager myEntityManager;
 	private int myExpectedNumberOfSearchBuildersCreated = 2;
 	@Mock
-	private SearchBuilder mySearchBuilder;
+	private LegacySearchBuilder mySearchBuilder;
 	@Mock
 	private ISearchCacheSvc mySearchCacheSvc;
 	@Mock

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/builder/sql/GeneratedSqlTest.java

@@ -0,0 +1,20 @@
+package ca.uhn.fhir.jpa.search.builder.sql;
+
+import org.junit.jupiter.api.Test;
+
+import java.util.Collections;
+
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+public class GeneratedSqlTest {
+
+	@Test
+	public void testBlockInlineNonBoundParameters() {
+		assertThrows(AssertionError.class, () -> new GeneratedSql(false, "SELECT * FROM FOO WHERE t = '123'", Collections.emptyList()));
+		assertThrows(AssertionError.class, () -> new GeneratedSql(false, "SELECT * FROM FOO WHERE t='123'", Collections.emptyList()));
+		assertThrows(AssertionError.class, () -> new GeneratedSql(false, "SELECT * FROM FOO WHERE t in ('123')", Collections.emptyList()));
+		assertThrows(AssertionError.class, () -> new GeneratedSql(false, "SELECT * FROM FOO WHERE t IN ('123')", Collections.emptyList()));
+		assertThrows(AssertionError.class, () -> new GeneratedSql(false, "SELECT * FROM FOO WHERE t IN('123')", Collections.emptyList()));
+	}
+
+}

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

@@ -21,8 +21,20 @@ package ca.uhn.fhir.jpa.model.entity;
  */
 
 import ca.uhn.fhir.rest.api.Constants;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
 
-import javax.persistence.*;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.ForeignKey;
+import javax.persistence.Id;
+import javax.persistence.Index;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.MapsId;
+import javax.persistence.OneToOne;
+import javax.persistence.Table;
 
 @Table(name = "HFJ_RES_VER_PROV", indexes = {
 	@Index(name = "IDX_RESVERPROV_SOURCEURI", columnList = "SOURCE_URI"),
@@ -55,6 +67,15 @@ public class ResourceHistoryProvenanceEntity extends BasePartitionable {
 		super();
 	}
 
+	@Override
+	public String toString() {
+		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+		b.append("resourceId", myResourceTable.getId());
+		b.append("sourceUri", mySourceUri);
+		b.append("requestId", myRequestId);
+		return b.toString();
+	}
+
 	public void setResourceTable(ResourceTable theResourceTable) {
 		myResourceTable = theResourceTable;
 	}

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

@@ -169,8 +169,12 @@ public class ResourceIndexedSearchParamCoords extends BaseResourceIndexedSearchP
 		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
 		b.append("paramName", getParamName());
 		b.append("resourceId", getResourcePid());
-		b.append("lat", getLatitude());
+		if (isMissing()) {
-		b.append("lon", getLongitude());
+			b.append("missing", isMissing());
+		} else {
+			b.append("lat", getLatitude());
+			b.append("lon", getLongitude());
+		}
 		return b.build();
 	}
 

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

@@ -257,6 +257,8 @@ public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchPar
 		b.append("resourceId", getResourcePid());
 		b.append("valueLow", new InstantDt(getValueLow()));
 		b.append("valueHigh", new InstantDt(getValueHigh()));
+		b.append("ordLow", myValueLowDateOrdinal);
+		b.append("ordHigh", myValueHighDateOrdinal);
 		b.append("hashIdentity", myHashIdentity);
 		b.append("missing", isMissing());
 		return b.build();

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

@@ -246,9 +246,15 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
 		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
 		b.append("resourceType", getResourceType());
 		b.append("paramName", getParamName());
-		b.append("system", getSystem());
+		if (isMissing()) {
-		b.append("value", getValue());
+			b.append("missing", true);
+		} else {
+			b.append("system", getSystem());
+			b.append("value", getValue());
+		}
 		b.append("hashIdentity", myHashIdentity);
+		b.append("hashSystem", myHashSystem);
+		b.append("hashValue", myHashValue);
 		return b.build();
 	}
 

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

@@ -36,11 +36,13 @@ import javax.persistence.Id;
 import javax.persistence.Index;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
 import javax.persistence.Transient;
+import java.util.Collection;
 import java.util.Date;
 
 @Entity
@@ -90,6 +92,7 @@ public class ResourceLink extends BaseResourceIndex {
 	@Column(name = "SP_UPDATED", nullable = true) // TODO: make this false after HAPI 2.3
 	@Temporal(TemporalType.TIMESTAMP)
 	private Date myUpdated;
+
 	@Transient
 	private transient String myTargetResourceId;