Add inline tag mode (#2748)

* Start work on tag mode 3

* Add changelog

* Test fix

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

@@ -225,14 +225,23 @@ public class FhirContext {
 
 	}
 
+	/**
+	 * @since 5.5.0
+	 */
 	public static FhirContext forDstu3Cached() {
 		return forCached(FhirVersionEnum.DSTU3);
 	}
 
+	/**
+	 * @since 5.5.0
+	 */
 	public static FhirContext forR4Cached() {
 		return forCached(FhirVersionEnum.R4);
 	}
 
+	/**
+	 * @since 5.5.0
+	 */
 	public static FhirContext forR5Cached() {
 		return forCached(FhirVersionEnum.R5);
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Interceptor.java

@@ -27,7 +27,8 @@ import java.lang.annotation.RetentionPolicy;
 import java.lang.annotation.Target;
 
 /**
- * This annotation declares a bean as a subscription interceptor
+ * This annotation declares a bean as a subscription interceptor. This interceptor
+ * is not mandatory for interceptor classes, but is added as a marker by convention.
  */
 @Retention(RetentionPolicy.RUNTIME)
 @Target(ElementType.TYPE)

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/interceptor/TagTrimmingInterceptor.java

@@ -0,0 +1,33 @@
+package ca.uhn.hapi.fhir.docs.interceptor;
+
+import ca.uhn.fhir.interceptor.api.Hook;
+import ca.uhn.fhir.interceptor.api.Interceptor;
+import ca.uhn.fhir.interceptor.api.Pointcut;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+// START SNIPPET: TagTrimmingInterceptor
+/**
+ * This is a simple interceptor for the JPA server that trims all tags, profiles, and security labels from
+ * resources before they are saved.
+ */
+@Interceptor
+public class TagTrimmingInterceptor {
+
+	/** Handle creates */
+	@Hook(Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED)
+	public void insert(IBaseResource theResource) {
+		theResource.getMeta().getTag().clear();
+		theResource.getMeta().getProfile().clear();
+		theResource.getMeta().getSecurity().clear();
+	}
+
+	/** Handle updates */
+	@Hook(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED)
+	public void update(IBaseResource theOldResource, IBaseResource theResource) {
+		theResource.getMeta().getTag().clear();
+		theResource.getMeta().getProfile().clear();
+		theResource.getMeta().getSecurity().clear();
+	}
+
+}
+// END SNIPPET: TagTrimmingInterceptor

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2748-add-inline-tag-mode.yaml

@@ -0,0 +1,7 @@
+---
+type: add
+issue: 2748
+title: "A new tag storage mode called **Inline Tag Mode** tas been added. In this mode, all tags are stored directly
+  in the serialized resource body in the database, instead of using dedicated tables. This has significant performance
+  advantages when storing resources with many distinct tags (i.e. many tags that are unique to each resource, as opposed
+  to being reused across multiple resources)."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2748-fix-profile-search-sp.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 2748
+title: "The SQL generated for the `_profile` search parameter did not use all of the columns on the tag index table,
+   resulting on poor performance on MySQL. This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/interceptors/server_interceptors.md

@@ -6,3 +6,10 @@ In the case of a Plain Server, HAPI FHIR itself performs the role of the Server
 
 In the case of a JPA Server, HAPI FHIR itself performs both roles. This means that **SERVER_xxx** Pointcuts may be intercepted by interceptors on any HAPI FHIR server. However, if you want to intercept **STORAGE_xxx** Pointcuts on a plain server, you will need to trigger them yourself.
 
+# Example: Clearing Tags
+
+The following example shows an interceptor that clears all tags, profiles, and security labels from a resource prior to storage in the JPA server.
+
+```java
+{{snippet:classpath:/ca/uhn/hapi/fhir/docs/interceptor/TagTrimmingInterceptor.java|TagTrimmingInterceptor}}
+``` 

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

@@ -2640,7 +2640,14 @@ public class DaoConfig {
 		/**
 		 * A single set of tags is shared by all resource versions
 		 */
-		NON_VERSIONED
+		NON_VERSIONED,
+
+		/**
+		 * Tags are stored directly in the resource body (in the {@link ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable}
+		 * entry for the resource, meaning that they are not indexed separately, and are versioned with the rest
+		 * of the resource.
+		 */
+		INLINE
 
 	}
 }

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

@@ -119,6 +119,7 @@ import org.springframework.transaction.support.TransactionSynchronization;
 import org.springframework.transaction.support.TransactionSynchronizationManager;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import javax.annotation.PostConstruct;
 import javax.persistence.EntityManager;
 import javax.persistence.NoResultException;
@@ -128,6 +129,7 @@ import javax.persistence.TypedQuery;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
 import javax.persistence.criteria.Root;
+import javax.validation.constraints.Null;
 import javax.xml.stream.events.Characters;
 import javax.xml.stream.events.XMLEvent;
 import java.util.ArrayList;
@@ -568,10 +570,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 
 					}
 				}
-				if (hasExtensions) {
+
+				boolean inlineTagMode = getConfig().getTagStorageMode() == DaoConfig.TagStorageModeEnum.INLINE;
+				if (hasExtensions || inlineTagMode) {
+					if (!inlineTagMode) {
 						excludeElements.add(resourceType + ".meta.profile");
 						excludeElements.add(resourceType + ".meta.tag");
 						excludeElements.add(resourceType + ".meta.security");
+					}
 					excludeElements.add(resourceType + ".meta.versionId");
 					excludeElements.add(resourceType + ".meta.lastUpdated");
 					excludeElements.add(resourceType + ".meta.source");
@@ -609,6 +615,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			}
 
 			boolean skipUpdatingTags = myConfig.isMassIngestionMode() && theEntity.isHasTags();
+			skipUpdatingTags |= myConfig.getTagStorageMode() == DaoConfig.TagStorageModeEnum.INLINE;
 
 			if (!skipUpdatingTags) {
 				Set<ResourceTag> allDefs = new HashSet<>();
@@ -695,7 +702,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	}
 
 	@SuppressWarnings("unchecked")
-	private <R extends IBaseResource> R populateResourceMetadataHapi(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IResource res, Long theVersion) {
+	private <R extends IBaseResource> R populateResourceMetadataHapi(Class<R> theResourceType, IBaseResourceEntity theEntity, @Nullable Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IResource res, Long theVersion) {
 		R retVal = (R) res;
 		if (theEntity.getDeleted() != null) {
 			res = (IResource) myContext.getResourceDefinition(theResourceType).newInstance();
@@ -724,12 +731,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		ResourceMetadataKeyEnum.UPDATED.put(res, theEntity.getUpdated());
 		IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
 
-		Collection<? extends BaseTag> tags = theTagList;
+		if (theTagList != null) {
 			if (theEntity.isHasTags()) {
 				TagList tagList = new TagList();
 				List<IBaseCoding> securityLabels = new ArrayList<>();
 				List<IdDt> profiles = new ArrayList<>();
-			for (BaseTag next : tags) {
+				for (BaseTag next : theTagList) {
 					switch (next.getTag().getTagType()) {
 						case PROFILE:
 							profiles.add(new IdDt(next.getTag().getCode()));
@@ -756,13 +763,13 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 					ResourceMetadataKeyEnum.PROFILES.put(res, profiles);
 				}
 			}
-
+		}
 
 		return retVal;
 	}
 
 	@SuppressWarnings("unchecked")
-	private <R extends IBaseResource> R populateResourceMetadataRi(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IAnyResource res, Long theVersion) {
+	private <R extends IBaseResource> R populateResourceMetadataRi(Class<R> theResourceType, IBaseResourceEntity theEntity, @Nullable Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IAnyResource res, Long theVersion) {
 		R retVal = (R) res;
 		if (theEntity.getDeleted() != null) {
 			res = (IAnyResource) myContext.getResourceDefinition(theResourceType).newInstance();
@@ -784,9 +791,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			}
 		}
 
-		res.getMeta().getTag().clear();
-		res.getMeta().getProfile().clear();
-		res.getMeta().getSecurity().clear();
 		res.getMeta().setLastUpdated(null);
 		res.getMeta().setVersionId(null);
 
@@ -796,6 +800,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		res.getMeta().setLastUpdated(theEntity.getUpdatedDate());
 		IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
 
+		if (theTagList != null) {
+			res.getMeta().getTag().clear();
+			res.getMeta().getProfile().clear();
+			res.getMeta().getSecurity().clear();
 			for (BaseTag next : theTagList) {
 				switch (next.getTag().getTagType()) {
 					case PROFILE:
@@ -815,6 +823,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 						break;
 				}
 			}
+		}
 
 		return retVal;
 	}
@@ -913,6 +922,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		// 1. get resource, it's encoding and the tags if any
 		byte[] resourceBytes;
 		ResourceEncodingEnum resourceEncoding;
+		@Nullable
 		Collection<? extends BaseTag> tagList = Collections.emptyList();
 		long version;
 		String provenanceSourceUri = null;
@@ -922,14 +932,20 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			ResourceHistoryTable history = (ResourceHistoryTable) theEntity;
 			resourceBytes = history.getResource();
 			resourceEncoding = history.getEncoding();
-			if (getConfig().getTagStorageMode() == DaoConfig.TagStorageModeEnum.VERSIONED) {
+			switch (getConfig().getTagStorageMode()) {
+				case VERSIONED:
+				default:
 					if (history.isHasTags()) {
 						tagList = history.getTags();
 					}
-			} else {
+					break;
+				case NON_VERSIONED:
 					if (history.getResourceTable().isHasTags()) {
 						tagList = history.getResourceTable().getTags();
 					}
+					break;
+				case INLINE:
+					tagList = null;
 			}
 			version = history.getVersion();
 			if (history.getProvenance() != null) {
@@ -952,11 +968,19 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			}
 			resourceBytes = history.getResource();
 			resourceEncoding = history.getEncoding();
+			switch (getConfig().getTagStorageMode()) {
+				case VERSIONED:
+				case NON_VERSIONED:
 					if (resource.isHasTags()) {
 						tagList = resource.getTags();
 					} else {
 						tagList = Collections.emptyList();
 					}
+					break;
+				case INLINE:
+					tagList = null;
+					break;
+			}
 			version = history.getVersion();
 			if (history.getProvenance() != null) {
 				provenanceRequestId = history.getProvenance().getRequestId();
@@ -970,10 +994,19 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			version = view.getVersion();
 			provenanceRequestId = view.getProvenanceRequestId();
 			provenanceSourceUri = view.getProvenanceSourceUri();
-			if (theTagList == null)
+			switch (getConfig().getTagStorageMode()) {
-				tagList = new HashSet<>();
+				case VERSIONED:
-			else
+				case NON_VERSIONED:
+					if (theTagList != null) {
 						tagList = theTagList;
+					} else {
+						tagList = Collections.emptyList();
+					}
+					break;
+				case INLINE:
+					tagList = null;
+					break;
+			}
 		} else {
 			// something wrong
 			return null;
@@ -984,6 +1017,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 
 		// 3. Use the appropriate custom type if one is specified in the context
 		Class<R> resourceType = theResourceType;
+		if (tagList != null) {
 			if (myContext.hasDefaultTypeForProfile()) {
 				for (BaseTag nextTag : tagList) {
 					if (nextTag.getTag().getTagType() == TagTypeEnum.PROFILE) {
@@ -999,6 +1033,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 					}
 				}
 			}
+		}
 
 		// 4. parse the text to FHIR
 		R retVal;

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

@@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.search.builder;
  */
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
@@ -1079,13 +1078,24 @@ public class QueryStack {
 			case Constants.PARAM_TAG:
 			case Constants.PARAM_PROFILE:
 			case Constants.PARAM_SECURITY:
+				if (myDaoConfig.getTagStorageMode() == DaoConfig.TagStorageModeEnum.INLINE) {
+					return createPredicateSearchParameter(theSourceJoinColumn, theResourceName, theParamName, theAndOrParams, theRequest, theRequestPartitionId, theSearchContainedMode);
+				} else {
 					return createPredicateTag(theSourceJoinColumn, theAndOrParams, theParamName, theRequestPartitionId);
+				}
 
 			case Constants.PARAM_SOURCE:
 				return createPredicateSourceForAndList(theSourceJoinColumn, theAndOrParams);
 
 			default:
+				return createPredicateSearchParameter(theSourceJoinColumn, theResourceName, theParamName, theAndOrParams, theRequest, theRequestPartitionId, theSearchContainedMode);
 
+		}
+
+	}
+
+	@Nullable
+	private Condition createPredicateSearchParameter(@Nullable DbColumn theSourceJoinColumn, String theResourceName, String theParamName, List<List<IQueryParameterType>> theAndOrParams, RequestDetails theRequest, RequestPartitionId theRequestPartitionId, SearchContainedModeEnum theSearchContainedMode) {
 		List<Condition> andPredicates = new ArrayList<>();
 		RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(theResourceName, theParamName);
 		if (nextParamDef != null) {
@@ -1201,9 +1211,6 @@ public class QueryStack {
 		}
 
 		return toAndPredicate(andPredicates);
-
-		}
-
 	}
 
 	public void addPredicateCompositeUnique(String theIndexString, RequestPartitionId theRequestPartitionId) {

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

@@ -21,24 +21,23 @@ package ca.uhn.fhir.jpa.search.builder.predicate;
  */
 
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 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.UnaryCondition;
 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;
@@ -72,11 +71,20 @@ public class TagPredicateBuilder extends BaseJoiningPredicateBuilder {
 
 		List<Condition> orPredicates = Lists.newArrayList();
 		for (Pair<String, String> next : theTokens) {
-			Condition codePredicate = BinaryCondition.equalTo(myTagDefinitionColumnTagCode, generatePlaceholder(next.getRight()));
+			String system = next.getLeft();
-			if (isNotBlank(next.getLeft())) {
+			String code = next.getRight();
-				Condition systemPredicate = BinaryCondition.equalTo(myTagDefinitionColumnTagSystem, generatePlaceholder(next.getLeft()));
+
+			if (theTagType == TagTypeEnum.PROFILE) {
+				system = BaseHapiFhirDao.NS_JPA_PROFILE;
+			}
+
+			Condition codePredicate = BinaryCondition.equalTo(myTagDefinitionColumnTagCode, generatePlaceholder(code));
+			if (isNotBlank(system)) {
+				Condition systemPredicate = BinaryCondition.equalTo(myTagDefinitionColumnTagSystem, generatePlaceholder(system));
 				orPredicates.add(ComboCondition.and(typePredicate, systemPredicate, codePredicate));
 			} else {
+				// Note: We don't have an index for this combo, which means that this may not perform
+				// well on MySQL (and maybe others) without an added index
 				orPredicates.add(ComboCondition.and(typePredicate, codePredicate));
 			}
 		}

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

@@ -2298,7 +2298,11 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 		{
 			SearchParameterMap params = new SearchParameterMap();
 			params.add("_profile", new UriParam("http://" + methodName));
+
+			logAllTokenIndexes();
+			myCaptureQueriesListener.clear();
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params));
+			myCaptureQueriesListener.logSelectQueries();
 			assertThat(patients, containsInAnyOrder(tag2id));
 		}
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchSqlTest.java

@@ -1,15 +1,35 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
+import org.hamcrest.Matchers;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.SearchParameter;
+import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
+import java.util.UUID;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsString;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class FhirResourceDaoR4SearchSqlTest extends BaseJpaR4Test {
 
+	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4SearchSqlTest.class);
+
+	@AfterEach
+	public void after() {
+		myDaoConfig.setTagStorageMode(DaoConfig.DEFAULT_TAG_STORAGE_MODE);
+	}
+
 	/**
 	 * One regular search params - Doesn't need HFJ_RESOURCE as root
 	 */
@@ -43,5 +63,68 @@ public class FhirResourceDaoR4SearchSqlTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testSearchByProfile_VersionedMode() {
+
+		// Put a tag in so we can search for it
+		String code = "http://" + UUID.randomUUID();
+		Patient p = new Patient();
+		p.getMeta().addProfile(code);
+		IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+		myMemoryCacheService.invalidateAllCaches();
+
+		// Search
+		myCaptureQueriesListener.clear();
+		SearchParameterMap map = SearchParameterMap.newSynchronous()
+			.add(Constants.PARAM_PROFILE, new TokenParam(code));
+		IBundleProvider outcome = myPatientDao.search(map);
+		assertEquals(3, myCaptureQueriesListener.countSelectQueries());
+		// Query 1 - Find resources: Make sure we search for tag type+system+code always
+		String sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(false, false);
+		assertEquals("SELECT t0.RES_ID FROM HFJ_RESOURCE t0 LEFT OUTER JOIN HFJ_RES_TAG t1 ON (t0.RES_ID = t1.RES_ID) LEFT OUTER JOIN HFJ_TAG_DEF t2 ON (t1.TAG_ID = t2.TAG_ID) WHERE (((t0.RES_TYPE = ?) AND (t0.RES_DELETED_AT IS NULL)) AND ((t2.TAG_TYPE = ?) AND (t2.TAG_SYSTEM = ?) AND (t2.TAG_CODE = ?)))", sql);
+		// Query 2 - Load resourece contents
+		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(false, false);
+		assertThat(sql, containsString("where resourcese0_.RES_ID in (?)"));
+		// Query 3 - Load tags and defintions
+		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2).getSql(false, false);
+		assertThat(sql, containsString("from HFJ_RES_TAG resourceta0_ inner join HFJ_TAG_DEF"));
+
+		assertThat(toUnqualifiedVersionlessIds(outcome), Matchers.contains(id));
+
+	}
+
+	@Test
+	public void testSearchByProfile_InlineMode() {
+		myDaoConfig.setTagStorageMode(DaoConfig.TagStorageModeEnum.INLINE);
+
+		SearchParameter searchParameter = FhirResourceDaoR4TagsTest.createSearchParamForInlineResourceProfile();
+		ourLog.info("SearchParam:\n{}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
+		mySearchParameterDao.update(searchParameter, mySrd);
+		mySearchParamRegistry.forceRefresh();
+
+		// Put a tag in so we can search for it
+		String code = "http://" + UUID.randomUUID();
+		Patient p = new Patient();
+		p.getMeta().addProfile(code);
+		IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+		myMemoryCacheService.invalidateAllCaches();
+
+		// Search
+		myCaptureQueriesListener.clear();
+		SearchParameterMap map = SearchParameterMap.newSynchronous()
+			.add(Constants.PARAM_PROFILE, new TokenParam(code));
+		IBundleProvider outcome = myPatientDao.search(map);
+		assertEquals(2, myCaptureQueriesListener.countSelectQueries());
+		// Query 1 - Find resources: Just a standard token search in this mode
+		String sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(false, false);
+		assertEquals("SELECT t0.RES_ID FROM HFJ_SPIDX_TOKEN t0 WHERE (t0.HASH_VALUE = ?)", sql);
+		// Query 2 - Load resourece contents
+		sql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(false, false);
+		assertThat(sql, containsString("where resourcese0_.RES_ID in (?)"));
+
+		assertThat(toUnqualifiedVersionlessIds(outcome), Matchers.contains(id));
+
+	}
+
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TagsTest.java

@@ -1,10 +1,15 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.TokenParam;
+import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.SearchParameter;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.Test;
 
@@ -142,6 +147,175 @@ public class FhirResourceDaoR4TagsTest extends BaseJpaR4Test {
 	}
 
 
+	@Test
+	public void testInlineTags_StoreAndRetrieve() {
+		myDaoConfig.setTagStorageMode(DaoConfig.TagStorageModeEnum.INLINE);
+
+		// Store a first version
+		Patient patient = new Patient();
+		patient.setId("Patient/A");
+		patient.getMeta().addProfile("http://profile1");
+		patient.getMeta().addTag("http://tag1", "vtag1", "dtag1");
+		patient.getMeta().addSecurity("http://sec1", "vsec1", "dsec1");
+		patient.setActive(true);
+		myPatientDao.update(patient, mySrd);
+
+		runInTransaction(()->{
+			assertEquals(0, myResourceTagDao.count());
+			assertEquals(0, myResourceHistoryTagDao.count());
+			assertEquals(0, myTagDefinitionDao.count());
+		});
+
+		// Read it back
+		patient = myPatientDao.read(new IdType("Patient/A/_history/1"), mySrd);
+		assertThat(toProfiles(patient).toString(), toProfiles(patient), contains("http://profile1"));
+		assertThat(toTags(patient).toString(), toTags(patient), contains("http://tag1|vtag1|dtag1"));
+		assertThat(toSecurityLabels(patient).toString(), toSecurityLabels(patient), contains("http://sec1|vsec1|dsec1"));
+
+		// Store a second version
+		patient = new Patient();
+		patient.setId("Patient/A");
+		patient.getMeta().addProfile("http://profile2");
+		patient.getMeta().addTag("http://tag2", "vtag2", "dtag2");
+		patient.getMeta().addSecurity("http://sec2", "vsec2", "dsec2");
+		patient.setActive(true);
+		myPatientDao.update(patient, mySrd);
+
+		runInTransaction(()->{
+			assertEquals(0, myResourceTagDao.count());
+			assertEquals(0, myResourceHistoryTagDao.count());
+			assertEquals(0, myTagDefinitionDao.count());
+		});
+
+		// First version should have only the initial tags
+		patient = myPatientDao.read(new IdType("Patient/A/_history/1"), mySrd);
+		assertThat(toProfiles(patient).toString(), toProfiles(patient), contains("http://profile1"));
+		assertThat(toTags(patient).toString(), toTags(patient), contains("http://tag1|vtag1|dtag1"));
+		assertThat(toSecurityLabels(patient).toString(), toSecurityLabels(patient), contains("http://sec1|vsec1|dsec1"));
+
+		// Second version should have the new set of tags
+		// TODO: We could copy these forward like we do for non-inline mode. Perhaps in the future.
+		patient = myPatientDao.read(new IdType("Patient/A/_history/2"), mySrd);
+		assertThat(toProfiles(patient).toString(), toProfiles(patient), contains("http://profile2"));
+		assertThat(toTags(patient).toString(), toTags(patient), containsInAnyOrder("http://tag2|vtag2|dtag2"));
+		assertThat(toSecurityLabels(patient).toString(), toSecurityLabels(patient), containsInAnyOrder("http://sec2|vsec2|dsec2"));
+
+	}
+
+
+	@Test
+	public void testInlineTags_Search_Tag() {
+		myDaoConfig.setTagStorageMode(DaoConfig.TagStorageModeEnum.INLINE);
+
+		SearchParameter searchParameter = createResourceTagSearchParameter();
+		ourLog.info("SearchParam:\n{}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
+		mySearchParameterDao.update(searchParameter, mySrd);
+		mySearchParamRegistry.forceRefresh();
+
+		createPatientsForInlineSearchTests();
+
+		logAllTokenIndexes();
+
+		// Perform a search
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
+		map.add("_tag", new TokenParam("http://tag1", "vtag1"));
+		IBundleProvider outcome = myPatientDao.search(map, mySrd);
+		assertThat(toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder("Patient/A", "Patient/B"));
+
+		validatePatientSearchResultsForInlineTags(outcome);
+	}
+
+	@Test
+	public void testInlineTags_Search_Profile() {
+		myDaoConfig.setTagStorageMode(DaoConfig.TagStorageModeEnum.INLINE);
+
+		SearchParameter searchParameter = createSearchParamForInlineResourceProfile();
+		ourLog.info("SearchParam:\n{}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
+		mySearchParameterDao.update(searchParameter, mySrd);
+		mySearchParamRegistry.forceRefresh();
+
+		createPatientsForInlineSearchTests();
+
+		logAllTokenIndexes();
+
+		// Perform a search
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
+		map.add("_profile", new TokenParam("http://profile1"));
+		IBundleProvider outcome = myPatientDao.search(map, mySrd);
+		assertThat(toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder("Patient/A", "Patient/B"));
+
+		validatePatientSearchResultsForInlineTags(outcome);
+	}
+
+	@Test
+	public void testInlineTags_Search_Security() {
+		myDaoConfig.setTagStorageMode(DaoConfig.TagStorageModeEnum.INLINE);
+
+		SearchParameter searchParameter = new SearchParameter();
+		searchParameter.setId("SearchParameter/resource-security");
+		for (String next : myFhirCtx.getResourceTypes().stream().sorted().collect(Collectors.toList())) {
+			searchParameter.addBase(next);
+		}
+		searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		searchParameter.setType(Enumerations.SearchParamType.TOKEN);
+		searchParameter.setCode("_security");
+		searchParameter.setName("Security");
+		searchParameter.setExpression("meta.security");
+		ourLog.info("SearchParam:\n{}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
+		mySearchParameterDao.update(searchParameter, mySrd);
+		mySearchParamRegistry.forceRefresh();
+
+		createPatientsForInlineSearchTests();
+
+		logAllTokenIndexes();
+
+		// Perform a search
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
+		map.add("_security", new TokenParam("http://sec1", "vsec1"));
+		IBundleProvider outcome = myPatientDao.search(map, mySrd);
+		assertThat(toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder("Patient/A", "Patient/B"));
+
+		validatePatientSearchResultsForInlineTags(outcome);
+	}
+
+	private void validatePatientSearchResultsForInlineTags(IBundleProvider outcome) {
+		Patient patient;
+		patient = (Patient) outcome.getResources(0, 1).get(0);
+		assertThat(toProfiles(patient).toString(), toProfiles(patient), contains("http://profile1"));
+		assertThat(toTags(patient).toString(), toTags(patient), contains("http://tag1|vtag1|dtag1"));
+		assertThat(toSecurityLabels(patient).toString(), toSecurityLabels(patient), contains("http://sec1|vsec1|dsec1"));
+		patient = (Patient) outcome.getResources(1, 2).get(0);
+		assertThat(toProfiles(patient).toString(), toProfiles(patient), contains("http://profile1"));
+		assertThat(toTags(patient).toString(), toTags(patient), contains("http://tag1|vtag1|dtag1"));
+		assertThat(toSecurityLabels(patient).toString(), toSecurityLabels(patient), contains("http://sec1|vsec1|dsec1"));
+	}
+
+	private void createPatientsForInlineSearchTests() {
+		Patient patient = new Patient();
+		patient.setId("Patient/A");
+		patient.getMeta().addProfile("http://profile1");
+		patient.getMeta().addTag("http://tag1", "vtag1", "dtag1");
+		patient.getMeta().addSecurity("http://sec1", "vsec1", "dsec1");
+		patient.setActive(true);
+		myPatientDao.update(patient, mySrd);
+
+		patient = new Patient();
+		patient.setId("Patient/B");
+		patient.getMeta().addProfile("http://profile1");
+		patient.getMeta().addTag("http://tag1", "vtag1", "dtag1");
+		patient.getMeta().addSecurity("http://sec1", "vsec1", "dsec1");
+		patient.setActive(true);
+		myPatientDao.update(patient, mySrd);
+
+		patient = new Patient();
+		patient.setId("Patient/NO");
+		patient.getMeta().addProfile("http://profile99");
+		patient.getMeta().addTag("http://tag99", "vtag99", "dtag99");
+		patient.getMeta().addSecurity("http://sec99", "vsec99", "dsec99");
+		patient.setActive(true);
+		myPatientDao.update(patient, mySrd);
+	}
+
 	private void initializeNonVersioned() {
 		myDaoConfig.setTagStorageMode(DaoConfig.TagStorageModeEnum.NON_VERSIONED);
 
@@ -183,9 +357,44 @@ public class FhirResourceDaoR4TagsTest extends BaseJpaR4Test {
 		return patient.getMeta().getTag().stream().map(t -> t.getSystem() + "|" + t.getCode() + "|" + t.getDisplay()).collect(Collectors.toList());
 	}
 
+	@Nonnull
+	private List<String> toSecurityLabels(Patient patient) {
+		return patient.getMeta().getSecurity().stream().map(t -> t.getSystem() + "|" + t.getCode() + "|" + t.getDisplay()).collect(Collectors.toList());
+	}
+
 	@Nonnull
 	private List<String> toProfiles(Patient patient) {
 		return patient.getMeta().getProfile().stream().map(t -> t.getValue()).collect(Collectors.toList());
 	}
 
+	@Nonnull
+	public static SearchParameter createSearchParamForInlineResourceProfile() {
+		SearchParameter searchParameter = new SearchParameter();
+		searchParameter.setId("SearchParameter/resource-profile");
+		for (String next : FhirContext.forR4Cached().getResourceTypes().stream().sorted().collect(Collectors.toList())) {
+			searchParameter.addBase(next);
+		}
+		searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		searchParameter.setType(Enumerations.SearchParamType.TOKEN);
+		searchParameter.setCode("_profile");
+		searchParameter.setName("Profile");
+		searchParameter.setExpression("meta.profile");
+		return searchParameter;
+	}
+
+	@Nonnull
+	public static SearchParameter createResourceTagSearchParameter() {
+		SearchParameter searchParameter = new SearchParameter();
+		searchParameter.setId("SearchParameter/resource-tag");
+		for (String next : FhirContext.forR4Cached().getResourceTypes().stream().sorted().collect(Collectors.toList())) {
+			searchParameter.addBase(next);
+		}
+		searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		searchParameter.setType(Enumerations.SearchParamType.TOKEN);
+		searchParameter.setCode("_tag");
+		searchParameter.setName("Tag");
+		searchParameter.setExpression("meta.tag");
+		return searchParameter;
+	}
+
 }

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

@@ -48,36 +48,32 @@ import java.util.Collection;
 public class TagDefinition implements Serializable {
 
 	private static final long serialVersionUID = 1L;
-
 	@Column(name = "TAG_CODE", length = 200)
 	private String myCode;
-
 	@Column(name = "TAG_DISPLAY", length = 200)
 	private String myDisplay;
-
 	@Id
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_TAGDEF_ID")
 	@SequenceGenerator(name = "SEQ_TAGDEF_ID", sequenceName = "SEQ_TAGDEF_ID")
 	@Column(name = "TAG_ID")
 	private Long myId;
-
 	@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "myTag")
 	private Collection<ResourceTag> myResources;
-
 	@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "myTag")
 	private Collection<ResourceHistoryTag> myResourceVersions;
-
 	@Column(name = "TAG_SYSTEM", length = 200)
 	private String mySystem;
-
 	@Column(name = "TAG_TYPE", nullable = false)
 	@Enumerated(EnumType.ORDINAL)
 	private TagTypeEnum myTagType;
-
 	@Transient
 	private transient Integer myHashCode;
 
+	/**
+	 * Constructor
+	 */
 	public TagDefinition() {
+		super();
 	}
 
 	public TagDefinition(TagTypeEnum theTagType, String theSystem, String theCode, String theDisplay) {