Add warm cache module

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

@@ -25,6 +25,8 @@ import ca.uhn.fhir.i18n.HapiLocalizer;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.provider.SubscriptionRetriggeringProvider;
 import ca.uhn.fhir.jpa.search.*;
+import ca.uhn.fhir.jpa.search.warm.CacheWarmingSvcImpl;
+import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.sp.SearchParamPresenceSvcImpl;
 import ca.uhn.fhir.jpa.subscription.email.SubscriptionEmailInterceptor;
@@ -111,6 +113,11 @@ public abstract class BaseConfig implements SchedulingConfigurer {
 
 	public abstract FhirContext fhirContext();
 
+	@Bean
+	public ICacheWarmingSvc cacheWarmingSvc() {
+		return new CacheWarmingSvcImpl();
+	}
+
 	@Bean
 	public HibernateExceptionTranslator hibernateExceptionTranslator() {
 		return new HibernateExceptionTranslator();

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

@@ -511,9 +511,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Override
 	@Transactional(propagation = Propagation.NEVER)
 	public ExpungeOutcome expunge(IIdType theId, ExpungeOptions theExpungeOptions) {
-		BaseHasResource entity = readEntity(theId);
+
+		TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager);
+
+		BaseHasResource entity = txTemplate.execute(t->readEntity(theId));
 		if (theId.hasVersionIdPart()) {
-			BaseHasResource currentVersion = readEntity(theId.toVersionless());
+			BaseHasResource currentVersion;
+			currentVersion = txTemplate.execute(t->readEntity(theId.toVersionless()));
 			if (entity.getVersion() == currentVersion.getVersion()) {
 				throw new PreconditionFailedException("Can not perform version-specific expunge of resource " + theId.toUnqualified().getValue() + " as this is the current version");
 			}

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

@@ -24,9 +24,9 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
-import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.util.SearchParameterUtil;
+import ca.uhn.fhir.util.StopWatch;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -37,6 +37,8 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.ApplicationContextAware;
 import org.springframework.scheduling.annotation.Scheduled;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.PostConstruct;
 import java.util.*;
@@ -58,7 +60,8 @@ public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implemen
 	private DaoConfig myDaoConfig;
 	private volatile long myLastRefresh;
 	private ApplicationContext myApplicationContext;
-
+	@Autowired
+	private PlatformTransactionManager myTxManager;
 	public BaseSearchParamRegistry() {
 		super();
 	}
@@ -197,7 +200,7 @@ public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implemen
 				});
 				for (String nextBase : next.getBase()) {
 					if (!activeParamNamesToUniqueSearchParams.containsKey(nextBase)) {
-						activeParamNamesToUniqueSearchParams.put(nextBase, new HashMap<Set<String>, List<JpaRuntimeSearchParam>>());
+						activeParamNamesToUniqueSearchParams.put(nextBase, new HashMap<>());
 					}
 					if (!activeParamNamesToUniqueSearchParams.get(nextBase).containsKey(paramNames)) {
 						activeParamNamesToUniqueSearchParams.get(nextBase).put(paramNames, new ArrayList<JpaRuntimeSearchParam>());
@@ -242,86 +245,94 @@ public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implemen
 		long refreshInterval = 60 * DateUtils.MILLIS_PER_MINUTE;
 		if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
 			synchronized (this) {
-				if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
+				TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
-					StopWatch sw = new StopWatch();
+				txTemplate.execute(t->{
+					doRefresh(refreshInterval);
+					return null;
+				});
+			}
+		}
+	}
 
-					Map<String, Map<String, RuntimeSearchParam>> searchParams = new HashMap<>();
+	private void doRefresh(long theRefreshInterval) {
-					for (Map.Entry<String, Map<String, RuntimeSearchParam>> nextBuiltInEntry : getBuiltInSearchParams().entrySet()) {
+		if (System.currentTimeMillis() - theRefreshInterval > myLastRefresh) {
-						for (RuntimeSearchParam nextParam : nextBuiltInEntry.getValue().values()) {
+			StopWatch sw = new StopWatch();
-							String nextResourceName = nextBuiltInEntry.getKey();
-							getSearchParamMap(searchParams, nextResourceName).put(nextParam.getName(), nextParam);
-						}
-					}
 
-					SearchParameterMap params = new SearchParameterMap();
+			Map<String, Map<String, RuntimeSearchParam>> searchParams = new HashMap<>();
-					params.setLoadSynchronousUpTo(MAX_MANAGED_PARAM_COUNT);
+			for (Map.Entry<String, Map<String, RuntimeSearchParam>> nextBuiltInEntry : getBuiltInSearchParams().entrySet()) {
-
+				for (RuntimeSearchParam nextParam : nextBuiltInEntry.getValue().values()) {
-					IBundleProvider allSearchParamsBp = getSearchParameterDao().search(params);
+					String nextResourceName = nextBuiltInEntry.getKey();
-					int size = allSearchParamsBp.size();
+					getSearchParamMap(searchParams, nextResourceName).put(nextParam.getName(), nextParam);
-
-					// Just in case..
-					if (size >= MAX_MANAGED_PARAM_COUNT) {
-						ourLog.warn("Unable to support >" + MAX_MANAGED_PARAM_COUNT + " search params!");
-						size = MAX_MANAGED_PARAM_COUNT;
-					}
-
-					List<IBaseResource> allSearchParams = allSearchParamsBp.getResources(0, size);
-					for (IBaseResource nextResource : allSearchParams) {
-						SP nextSp = (SP) nextResource;
-						if (nextSp == null) {
-							continue;
-						}
-
-						RuntimeSearchParam runtimeSp = toRuntimeSp(nextSp);
-						if (runtimeSp == null) {
-							continue;
-						}
-
-						for (String nextBaseName : SearchParameterUtil.getBaseAsStrings(myCtx, nextSp)) {
-							if (isBlank(nextBaseName)) {
-								continue;
-							}
-
-							Map<String, RuntimeSearchParam> searchParamMap = getSearchParamMap(searchParams, nextBaseName);
-							String name = runtimeSp.getName();
-							if (myDaoConfig.isDefaultSearchParamsCanBeOverridden() || !searchParamMap.containsKey(name)) {
-								searchParamMap.put(name, runtimeSp);
-							}
-
-						}
-					}
-
-					Map<String, Map<String, RuntimeSearchParam>> activeSearchParams = new HashMap<>();
-					for (Map.Entry<String, Map<String, RuntimeSearchParam>> nextEntry : searchParams.entrySet()) {
-						for (RuntimeSearchParam nextSp : nextEntry.getValue().values()) {
-							String nextName = nextSp.getName();
-							if (nextSp.getStatus() != RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE) {
-								nextSp = null;
-							}
-
-							if (!activeSearchParams.containsKey(nextEntry.getKey())) {
-								activeSearchParams.put(nextEntry.getKey(), new HashMap<>());
-							}
-							if (activeSearchParams.containsKey(nextEntry.getKey())) {
-								ourLog.debug("Replacing existing/built in search param {}:{} with new one", nextEntry.getKey(), nextName);
-							}
-
-							if (nextSp != null) {
-								activeSearchParams.get(nextEntry.getKey()).put(nextName, nextSp);
-							} else {
-								activeSearchParams.get(nextEntry.getKey()).remove(nextName);
-							}
-						}
-					}
-
-					myActiveSearchParams = activeSearchParams;
-
-					populateActiveSearchParams(activeSearchParams);
-
-					myLastRefresh = System.currentTimeMillis();
-					ourLog.info("Refreshed search parameter cache in {}ms", sw.getMillis());
 				}
 			}
+
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronousUpTo(MAX_MANAGED_PARAM_COUNT);
+
+			IBundleProvider allSearchParamsBp = getSearchParameterDao().search(params);
+			int size = allSearchParamsBp.size();
+
+			// Just in case..
+			if (size >= MAX_MANAGED_PARAM_COUNT) {
+				ourLog.warn("Unable to support >" + MAX_MANAGED_PARAM_COUNT + " search params!");
+				size = MAX_MANAGED_PARAM_COUNT;
+			}
+
+			List<IBaseResource> allSearchParams = allSearchParamsBp.getResources(0, size);
+			for (IBaseResource nextResource : allSearchParams) {
+				SP nextSp = (SP) nextResource;
+				if (nextSp == null) {
+					continue;
+				}
+
+				RuntimeSearchParam runtimeSp = toRuntimeSp(nextSp);
+				if (runtimeSp == null) {
+					continue;
+				}
+
+				for (String nextBaseName : SearchParameterUtil.getBaseAsStrings(myCtx, nextSp)) {
+					if (isBlank(nextBaseName)) {
+						continue;
+					}
+
+					Map<String, RuntimeSearchParam> searchParamMap = getSearchParamMap(searchParams, nextBaseName);
+					String name = runtimeSp.getName();
+					if (myDaoConfig.isDefaultSearchParamsCanBeOverridden() || !searchParamMap.containsKey(name)) {
+						searchParamMap.put(name, runtimeSp);
+					}
+
+				}
+			}
+
+			Map<String, Map<String, RuntimeSearchParam>> activeSearchParams = new HashMap<>();
+			for (Map.Entry<String, Map<String, RuntimeSearchParam>> nextEntry : searchParams.entrySet()) {
+				for (RuntimeSearchParam nextSp : nextEntry.getValue().values()) {
+					String nextName = nextSp.getName();
+					if (nextSp.getStatus() != RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE) {
+						nextSp = null;
+					}
+
+					if (!activeSearchParams.containsKey(nextEntry.getKey())) {
+						activeSearchParams.put(nextEntry.getKey(), new HashMap<>());
+					}
+					if (activeSearchParams.containsKey(nextEntry.getKey())) {
+						ourLog.debug("Replacing existing/built in search param {}:{} with new one", nextEntry.getKey(), nextName);
+					}
+
+					if (nextSp != null) {
+						activeSearchParams.get(nextEntry.getKey()).put(nextName, nextSp);
+					} else {
+						activeSearchParams.get(nextEntry.getKey()).remove(nextName);
+					}
+				}
+			}
+
+			myActiveSearchParams = activeSearchParams;
+
+			populateActiveSearchParams(activeSearchParams);
+
+			myLastRefresh = System.currentTimeMillis();
+			ourLog.info("Refreshed search parameter cache in {}ms", sw.getMillis());
 		}
 	}
 

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao;
 
 import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
+import ca.uhn.fhir.jpa.search.warm.WarmCacheEntry;
 import ca.uhn.fhir.jpa.util.JpaConstants;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import com.google.common.collect.Sets;
@@ -153,6 +154,7 @@ public class DaoConfig {
 	private Set<String> myBundleTypesAllowedForStorage;
 	private boolean myValidateSearchParameterExpressionsOnSave = true;
 	private List<Integer> myPreFetchThresholds = Arrays.asList(500, 2000, -1);
+	private List<WarmCacheEntry> myWarmCacheEntries = new ArrayList<>();
 
 	/**
 	 * Constructor
@@ -171,6 +173,22 @@ public class DaoConfig {
 		}
 	}
 
+	/**
+	 * Returns a set of searches that should be kept "warm", meaning that
+	 * searches will periodically be performed in the background to
+	 * keep results ready for this search
+	 */
+	public List<WarmCacheEntry> getWarmCacheEntries() {
+		if (myWarmCacheEntries == null) {
+			myWarmCacheEntries = new ArrayList<>();
+		}
+		return myWarmCacheEntries;
+	}
+
+	public void setWarmCacheEntries(List<WarmCacheEntry> theWarmCacheEntries) {
+		myWarmCacheEntries = theWarmCacheEntries;
+	}
+
 	/**
 	 * If set to <code>true</code> (default is false), the reindexing of search parameters
 	 * using a query on the HFJ_RESOURCE.SP_INDEX_STATUS column will be disabled completely.

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

@@ -1359,6 +1359,8 @@ public class SearchBuilder implements ISearchBuilder {
 	}
 
 	private TypedQuery<Long> createQuery(SortSpec sort, Integer theMaximumResults, boolean theCount) {
+		myPredicates = new ArrayList<>();
+
 		CriteriaQuery<Long> outerQuery;
 		/*
 		 * Sort
@@ -1369,30 +1371,48 @@ public class SearchBuilder implements ISearchBuilder {
 		if (sort != null) {
 			assert !theCount;
 
+//			outerQuery = myBuilder.createQuery(Long.class);
+//			Root<ResourceTable> outerQueryFrom = outerQuery.from(ResourceTable.class);
+//
+//			List<Order> orders = Lists.newArrayList();
+//			List<Predicate> predicates = Lists.newArrayList();
+//
+//			createSort(myBuilder, outerQueryFrom, sort, orders, predicates);
+//			if (orders.size() > 0) {
+//				outerQuery.orderBy(orders);
+//			}
+//
+//			Subquery<Long> subQ = outerQuery.subquery(Long.class);
+//			Root<ResourceTable> subQfrom = subQ.from(ResourceTable.class);
+//
+//			myResourceTableQuery = subQ;
+//			myResourceTableRoot = subQfrom;
+//
+//			Expression<Long> selectExpr = subQfrom.get("myId").as(Long.class);
+//			subQ.select(selectExpr);
+//
+//			predicates.add(0, myBuilder.in(outerQueryFrom.get("myId").as(Long.class)).value(subQ));
+//
+//			outerQuery.multiselect(outerQueryFrom.get("myId").as(Long.class));
+//			outerQuery.where(predicates.toArray(new Predicate[0]));
+
 			outerQuery = myBuilder.createQuery(Long.class);
-			Root<ResourceTable> outerQueryFrom = outerQuery.from(ResourceTable.class);
+			myResourceTableQuery = outerQuery;
+			myResourceTableRoot = myResourceTableQuery.from(ResourceTable.class);
+			if (theCount) {
+				outerQuery.multiselect(myBuilder.countDistinct(myResourceTableRoot));
+			} else {
+				outerQuery.multiselect(myResourceTableRoot.get("myId").as(Long.class));
+			}
 
 			List<Order> orders = Lists.newArrayList();
-			List<Predicate> predicates = Lists.newArrayList();
+			List<Predicate> predicates = myPredicates; // Lists.newArrayList();
 
-			createSort(myBuilder, outerQueryFrom, sort, orders, predicates);
+			createSort(myBuilder, myResourceTableRoot, sort, orders, predicates);
 			if (orders.size() > 0) {
 				outerQuery.orderBy(orders);
 			}
 
-			Subquery<Long> subQ = outerQuery.subquery(Long.class);
-			Root<ResourceTable> subQfrom = subQ.from(ResourceTable.class);
-
-			myResourceTableQuery = subQ;
-			myResourceTableRoot = subQfrom;
-
-			Expression<Long> selectExpr = subQfrom.get("myId").as(Long.class);
-			subQ.select(selectExpr);
-
-			predicates.add(0, myBuilder.in(outerQueryFrom.get("myId").as(Long.class)).value(subQ));
-
-			outerQuery.multiselect(outerQueryFrom.get("myId").as(Long.class));
-			outerQuery.where(predicates.toArray(new Predicate[0]));
 
 		} else {
 
@@ -1407,8 +1427,6 @@ public class SearchBuilder implements ISearchBuilder {
 
 		}
 
-		myPredicates = new ArrayList<>();
-
 		if (myParams.getEverythingMode() != null) {
 			Join<ResourceTable, ResourceLink> join = myResourceTableRoot.join("myResourceLinks", JoinType.LEFT);
 
@@ -1590,7 +1608,8 @@ public class SearchBuilder implements ISearchBuilder {
 			if (param.getParamType() == RestSearchParameterTypeEnum.REFERENCE) {
 				thePredicates.add(join.get("mySourcePath").as(String.class).in(param.getPathsSplit()));
 			} else {
-				Predicate joinParam1 = theBuilder.equal(join.get("myParamName"), theSort.getParamName());
+				Long hashIdentity = BaseResourceIndexedSearchParam.calculateHashIdentity(myResourceName, theSort.getParamName());
+				Predicate joinParam1 = theBuilder.equal(join.get("myHashIdentity"), hashIdentity);
 				thePredicates.add(joinParam1);
 			}
 		} else {
@@ -1940,11 +1959,11 @@ public class SearchBuilder implements ISearchBuilder {
 			return;
 		}
 
-		if (theParamName.equals(BaseResource.SP_RES_ID)) {
+		if (theParamName.equals(IAnyResource.SP_RES_ID)) {
 
 			addPredicateResourceId(theAndOrParams);
 
-		} else if (theParamName.equals(BaseResource.SP_RES_LANGUAGE)) {
+		} else if (theParamName.equals(IAnyResource.SP_RES_LANGUAGE)) {
 
 			addPredicateLanguage(theAndOrParams);
 

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

@@ -44,6 +44,10 @@ import static org.apache.commons.lang3.StringUtils.left;
 	 * do not reuse these names:
 	 * IDX_SP_STRING
 	 */
+
+	// This one us used only for sorting
+	@Index(name = "IDX_SP_STRING_HASH_IDENT", columnList = "HASH_IDENTITY"),
+
 	@Index(name = "IDX_SP_STRING_HASH_NRM", columnList = "HASH_NORM_PREFIX,SP_VALUE_NORMALIZED"),
 	@Index(name = "IDX_SP_STRING_HASH_EXCT", columnList = "HASH_EXACT"),
 
@@ -130,6 +134,11 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 	 */
 	@Column(name = "HASH_NORM_PREFIX", nullable = true)
 	private Long myHashNormalizedPrefix;
+	/**
+	 * @since 3.6.0 - At some point this should be made not-null
+	 */
+	@Column(name = "HASH_IDENTITY", nullable = true)
+	private Long myHashIdentity;
 	/**
 	 * @since 3.4.0 - At some point this should be made not-null
 	 */
@@ -137,12 +146,10 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 	private Long myHashExact;
 	@Transient
 	private transient DaoConfig myDaoConfig;
-
 	public ResourceIndexedSearchParamString() {
 		super();
 	}
 
-
 	public ResourceIndexedSearchParamString(DaoConfig theDaoConfig, String theName, String theValueNormalized, String theValueExact) {
 		setDaoConfig(theDaoConfig);
 		setParamName(theName);
@@ -150,6 +157,10 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 		setValueExact(theValueExact);
 	}
 
+	public void setHashIdentity(Long theHashIdentity) {
+		myHashIdentity = theHashIdentity;
+	}
+
 	@PrePersist
 	public void calculateHashes() {
 		if (myHashNormalizedPrefix == null && myDaoConfig != null) {
@@ -159,6 +170,7 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 			String valueExact = getValueExact();
 			setHashNormalizedPrefix(calculateHashNormalized(myDaoConfig, resourceType, paramName, valueNormalized));
 			setHashExact(calculateHashExact(resourceType, paramName, valueExact));
+			setHashIdentity(calculateHashIdentity(resourceType, paramName));
 		}
 	}
 

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

@@ -5,8 +5,6 @@ import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import org.apache.commons.lang3.SerializationUtils;
 import org.hibernate.annotations.OptimisticLock;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import javax.persistence.*;
 import javax.validation.constraints.NotNull;
@@ -150,13 +148,6 @@ public class Search implements Serializable {
 		myFailureMessage = left(theFailureMessage, FAILURE_MESSAGE_LENGTH);
 	}
 
-	// FIXME: remove this
-	private static final Logger ourLog = LoggerFactory.getLogger(Search.class);
-	@PrePersist
-	public void prePersist() {
-		ourLog.info("*** SAVING WITH VERSION {} TOTAL {}", myVersion, myTotalCount);
-	}
-
 	public Long getId() {
 		return myId;
 	}

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

@@ -166,8 +166,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 						return false;
 					}
 
-					// FIXME: remove
+					ourLog.trace("Retrieved search with version {} and total {}", mySearchEntity.getVersion(), mySearchEntity.getTotalCount());
-					ourLog.info("** Retrieved search with version {} and total {}", mySearchEntity.getVersion(), mySearchEntity.getTotalCount());
 
 					// Load the includes now so that they are available outside of this transaction
 					mySearchEntity.getIncludes().size();

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

@@ -46,9 +46,7 @@ import org.apache.commons.lang3.exception.ExceptionUtils;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.domain.Page;
+import org.springframework.data.domain.*;
-import org.springframework.data.domain.PageRequest;
-import org.springframework.data.domain.Pageable;
 import org.springframework.scheduling.concurrent.CustomizableThreadFactory;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
@@ -363,7 +361,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		PersistedJpaSearchFirstPageBundleProvider retVal = new PersistedJpaSearchFirstPageBundleProvider(search, theCallingDao, task, sb, myManagedTxManager);
 		populateBundleProvider(retVal);
 
-		ourLog.info("Search initial phase completed in {}ms", w.getMillis());
+		ourLog.debug("Search initial phase completed in {}ms", w.getMillis());
 		return retVal;
 
 	}
@@ -675,25 +673,21 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 		private void doSaveSearch() {
 
-			// FIXME: remove
+			Search newSearch;
-			Integer totalCount = mySearch.getTotalCount();
-			TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronization() {
-				@Override
-				public void afterCommit() {
-					ourLog.info("Have flushed save with total {}", totalCount);
-				}
-			});
-			ourLog.info("** Saving search version {} count {}", mySearch.getVersion(), totalCount);
-
 			if (mySearch.getId() == null) {
-				mySearch = mySearchDao.saveAndFlush(mySearch);
+				newSearch = mySearchDao.save(mySearch);
 				for (SearchInclude next : mySearch.getIncludes()) {
 					mySearchIncludeDao.save(next);
 				}
 			} else {
-				mySearch = mySearchDao.saveAndFlush(mySearch);
+				newSearch = mySearchDao.save(mySearch);
 			}
 
+			// mySearchDao.save is not supposed to return null, but in unit tests
+			// it can if the mock search dao isn't set up to handle that
+			if (newSearch != null) {
+				mySearch = newSearch;
+			}
 		}
 
 		/**
@@ -712,14 +706,13 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			boolean wantCount = myParams.getSummaryMode().contains(SummaryEnum.COUNT);
 			boolean wantOnlyCount = wantCount && myParams.getSummaryMode().size() == 1;
 			if (wantCount) {
-				ourLog.info("** performing count");
+				ourLog.trace("Performing count");
 				ISearchBuilder sb = newSearchBuilder();
 				Iterator<Long> countIterator = sb.createCountQuery(myParams, mySearch.getUuid());
 				Long count = countIterator.next();
-				ourLog.info("** got count {}", count);
+				ourLog.trace("Got count {}", count);
 
 				TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
-//				txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 				txTemplate.execute(new TransactionCallbackWithoutResult() {
 					@Override
 					protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
@@ -728,6 +721,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 							mySearch.setStatus(SearchStatusEnum.FINISHED);
 						}
 						doSaveSearch();
+						mySearchDao.flush();
 					}
 				});
 				if (wantOnlyCount) {
@@ -735,7 +729,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				}
 			}
 
-			ourLog.info("** done count");
+			ourLog.trace("Done count");
 			ISearchBuilder sb = newSearchBuilder();
 
 			/*
@@ -957,13 +951,33 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 		int pageIndex = theFromIndex / pageSize;
 
-		Pageable page = new PageRequest(pageIndex, pageSize) {
+		Pageable page = new AbstractPageRequest(pageIndex, pageSize) {
 			private static final long serialVersionUID = 1L;
 
 			@Override
 			public long getOffset() {
 				return theFromIndex;
 			}
+
+			@Override
+			public Sort getSort() {
+				return Sort.unsorted();
+			}
+
+			@Override
+			public Pageable next() {
+				return null;
+			}
+
+			@Override
+			public Pageable previous() {
+				return null;
+			}
+
+			@Override
+			public Pageable first() {
+				return null;
+			}
 		};
 
 		return page;

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

@@ -0,0 +1,96 @@
+package ca.uhn.fhir.jpa.search.warm;
+
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.jpa.dao.*;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.scheduling.annotation.Scheduled;
+
+import javax.annotation.PostConstruct;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+public class CacheWarmingSvcImpl implements ICacheWarmingSvc {
+
+	@Autowired
+	private DaoConfig myDaoConfig;
+	private Map<WarmCacheEntry, Long> myCacheEntryToNextRefresh = new LinkedHashMap<>();
+	@Autowired
+	private FhirContext myCtx;
+	@Autowired
+	private DaoRegistry myDaoRegistry;
+
+	@Override
+	@Scheduled(fixedDelay = 1000)
+	public synchronized void performWarmingPass() {
+
+		for (WarmCacheEntry nextCacheEntry : new ArrayList<>(myCacheEntryToNextRefresh.keySet())) {
+
+			long nextRefresh = myCacheEntryToNextRefresh.get(nextCacheEntry);
+			if (nextRefresh < System.currentTimeMillis()) {
+
+				// Perform the search
+				refreshNow(nextCacheEntry);
+
+				// Set the next time to warm this search
+				nextRefresh = nextCacheEntry.getPeriodMillis() + System.currentTimeMillis();
+				myCacheEntryToNextRefresh.put(nextCacheEntry, nextRefresh);
+
+			}
+
+		}
+
+	}
+
+	private void refreshNow(WarmCacheEntry theCacheEntry) {
+		String nextUrl = theCacheEntry.getUrl();
+
+		RuntimeResourceDefinition resourceDef = parseWarmUrlResourceType(nextUrl);
+		IFhirResourceDao<?> callingDao = myDaoRegistry.getResourceDao(resourceDef.getName());
+		String queryPart = parseWarmUrlParamPart(nextUrl);
+		SearchParameterMap responseCriteriaUrl = BaseHapiFhirDao.translateMatchUrl(callingDao, myCtx, queryPart, resourceDef);
+
+		callingDao.search(responseCriteriaUrl);
+	}
+
+	private String parseWarmUrlParamPart(String theNextUrl) {
+		int paramIndex = theNextUrl.indexOf('?');
+		if (paramIndex == -1) {
+			throw new ConfigurationException("Invalid warm cache URL (must have ? character)");
+		}
+		return theNextUrl.substring(paramIndex);
+	}
+
+	private RuntimeResourceDefinition parseWarmUrlResourceType(String theNextUrl) {
+		int paramIndex = theNextUrl.indexOf('?');
+		String resourceName = theNextUrl.substring(0, paramIndex);
+		if (resourceName.contains("/")) {
+			resourceName = resourceName.substring(resourceName.lastIndexOf('/') + 1);
+		}
+		RuntimeResourceDefinition resourceDef = myCtx.getResourceDefinition(resourceName);
+		return resourceDef;
+	}
+
+	@PostConstruct
+	public void start() {
+		initCacheMap();
+	}
+
+	public synchronized void initCacheMap() {
+
+		myCacheEntryToNextRefresh.clear();
+		List<WarmCacheEntry> warmCacheEntries = myDaoConfig.getWarmCacheEntries();
+		for (WarmCacheEntry next : warmCacheEntries) {
+
+			// Validate
+			parseWarmUrlParamPart(next.getUrl());
+			parseWarmUrlResourceType(next.getUrl());
+
+			myCacheEntryToNextRefresh.put(next, 0L);
+		}
+		
+	}
+}

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

@@ -0,0 +1,8 @@
+package ca.uhn.fhir.jpa.search.warm;
+
+import org.springframework.scheduling.annotation.Scheduled;
+
+public interface ICacheWarmingSvc {
+	@Scheduled(fixedDelay = 1000)
+	void performWarmingPass();
+}

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

@@ -0,0 +1,61 @@
+package ca.uhn.fhir.jpa.search.warm;
+
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+
+/**
+ * Denotes a search that should be performed in the background
+ * periodically in order to keep a fresh copy in the query cache.
+ * This improves performance for searches by keeping a copy
+ * loaded in the background.
+ */
+public class WarmCacheEntry {
+
+	private long myPeriodMillis;
+	private String myUrl;
+
+	@Override
+	public boolean equals(Object theO) {
+		if (this == theO) {
+			return true;
+		}
+
+		if (theO == null || getClass() != theO.getClass()) {
+			return false;
+		}
+
+		WarmCacheEntry that = (WarmCacheEntry) theO;
+
+		return new EqualsBuilder()
+			.append(myPeriodMillis, that.myPeriodMillis)
+			.append(myUrl, that.myUrl)
+			.isEquals();
+	}
+
+	@Override
+	public int hashCode() {
+		return new HashCodeBuilder(17, 37)
+			.append(myPeriodMillis)
+			.append(myUrl)
+			.toHashCode();
+	}
+
+	public long getPeriodMillis() {
+		return myPeriodMillis;
+	}
+
+	public WarmCacheEntry setPeriodMillis(long thePeriodMillis) {
+		myPeriodMillis = thePeriodMillis;
+		return this;
+	}
+
+	public String getUrl() {
+		return myUrl;
+	}
+
+	public WarmCacheEntry setUrl(String theUrl) {
+		myUrl = theUrl;
+		return this;
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java

@@ -6,9 +6,6 @@ import ca.uhn.fhir.validation.ResultSeverityEnum;
 import net.ttddyy.dsproxy.listener.ThreadQueryCountHolder;
 import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
 import org.apache.commons.dbcp2.BasicDataSource;
-import org.hibernate.cfg.AvailableSettings;
-import org.hibernate.query.criteria.LiteralHandlingMode;
-import org.hibernate.resource.jdbc.spi.PhysicalConnectionHandlingMode;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Lazy;

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

@@ -11,6 +11,7 @@ import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
+import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
@@ -51,7 +52,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.util.Map;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.fail;
 import static org.mockito.Mockito.mock;
 
 @RunWith(SpringJUnit4ClassRunner.class)
@@ -260,6 +261,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Autowired
 	protected ITermConceptMapGroupElementTargetDao myTermConceptMapGroupElementTargetDao;
 	@Autowired
+	protected ICacheWarmingSvc myCacheWarmingSvc;
+	@Autowired
 	private JpaValidationSupportChainR4 myJpaValidationSupportChainR4;
 
 	@After()

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CacheWarmingTest.java

@@ -0,0 +1,112 @@
+package ca.uhn.fhir.jpa.dao.r4;
+
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
+import ca.uhn.fhir.jpa.search.warm.CacheWarmingSvcImpl;
+import ca.uhn.fhir.jpa.search.warm.WarmCacheEntry;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.util.TestUtil;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.ArrayList;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+public class FhirResourceDaoR4CacheWarmingTest extends BaseJpaR4Test {
+	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4CacheWarmingTest.class);
+
+	@After
+	public void afterResetDao() {
+		myDaoConfig.setResourceServerIdStrategy(new DaoConfig().getResourceServerIdStrategy());
+
+		myDaoConfig.setWarmCacheEntries(new ArrayList<>());
+		CacheWarmingSvcImpl cacheWarmingSvc = (CacheWarmingSvcImpl) myCacheWarmingSvc;
+		cacheWarmingSvc.initCacheMap();
+	}
+
+
+	@Test
+	public void testInvalidCacheEntries() {
+		CacheWarmingSvcImpl cacheWarmingSvc = (CacheWarmingSvcImpl) myCacheWarmingSvc;
+
+		myDaoConfig.setWarmCacheEntries(new ArrayList<>());
+		myDaoConfig.getWarmCacheEntries().add(
+			new WarmCacheEntry()
+				.setPeriodMillis(10)
+				.setUrl("BadResource?name=smith")
+		);
+		try {
+			cacheWarmingSvc.initCacheMap();
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("Unknown resource name \"BadResource\" (this name is not known in FHIR version \"R4\")", e.getMessage());
+		}
+
+		myDaoConfig.setWarmCacheEntries(new ArrayList<>());
+		myDaoConfig.getWarmCacheEntries().add(
+			new WarmCacheEntry()
+				.setPeriodMillis(10)
+				.setUrl("foo/Patient")
+		);
+		try {
+			cacheWarmingSvc.initCacheMap();
+			fail();
+		} catch (ConfigurationException e) {
+			assertEquals("Invalid warm cache URL (must have ? character)", e.getMessage());
+		}
+
+
+	}
+
+	@Test
+	public void testKeepCacheWarm() throws InterruptedException {
+		myDaoConfig.setWarmCacheEntries(new ArrayList<>());
+		myDaoConfig.getWarmCacheEntries().add(
+			new WarmCacheEntry()
+				.setPeriodMillis(10)
+				.setUrl("Patient?name=smith")
+		);
+		CacheWarmingSvcImpl cacheWarmingSvc = (CacheWarmingSvcImpl) myCacheWarmingSvc;
+		cacheWarmingSvc.initCacheMap();
+
+		Patient p1 = new Patient();
+		p1.setId("p1");
+		p1.setActive(true);
+		myPatientDao.update(p1);
+
+		Patient p2 = new Patient();
+		p2.setId("p2");
+		p2.setActive(true);
+		p2.addName().setFamily("Smith");
+		myPatientDao.update(p2);
+
+		Thread.sleep(2000);
+
+		SearchParameterMap params = new SearchParameterMap();
+		params.add("name", new StringParam("smith"));
+		IBundleProvider result = myPatientDao.search(params);
+		assertEquals(PersistedJpaBundleProvider.class, result.getClass());
+
+		PersistedJpaBundleProvider resultCasted = (PersistedJpaBundleProvider) result;
+		assertTrue(resultCasted.isCacheHit());
+	}
+
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+}

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

@@ -70,6 +70,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSummaryMode(Sets.newHashSet(SummaryEnum.COUNT));
 		IBundleProvider results = myPatientDao.search(params);
 		String uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		assertEquals(200, results.size().intValue());
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertThat(ids, empty());
@@ -98,6 +99,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSummaryMode(Sets.newHashSet(SummaryEnum.COUNT));
 		IBundleProvider results = myPatientDao.search(params);
 		String uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		assertEquals(201, results.size().intValue());
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertThat(ids, empty());
@@ -109,6 +111,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSummaryMode(Sets.newHashSet(SummaryEnum.COUNT, SummaryEnum.DATA));
 		results = myPatientDao.search(params);
 		uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		assertEquals(201, results.size().intValue());
 		ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertThat(ids, hasSize(10));
@@ -120,6 +123,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSummaryMode(Sets.newHashSet(SummaryEnum.COUNT));
 		results = myPatientDao.search(params);
 		uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		assertEquals(201, results.size().intValue());
 		ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertThat(ids, empty());
@@ -144,12 +148,15 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 
 //		assertEquals(200, myDatabaseBackedPagingProvider.retrieveResultList(uuid).size().intValue());
 		assertEquals(200, results.size().intValue());
+		ourLog.info("** Asking for results");
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 5, true);
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals("Patient/PT00004", ids.get(4));
 
 		ourLog.info("** About to make new query for search with UUID: {}", uuid);
-		assertEquals(200, myDatabaseBackedPagingProvider.retrieveResultList(uuid).size().intValue());
+		IBundleProvider search2 = myDatabaseBackedPagingProvider.retrieveResultList(uuid);
+		Integer search2Size = search2.size();
+		assertEquals(200, search2Size.intValue());
 	}
 
 	@Test
@@ -162,6 +169,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSummaryMode(Sets.newHashSet(SummaryEnum.COUNT, SummaryEnum.DATA));
 		IBundleProvider results = myPatientDao.search(params);
 		String uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		assertEquals(200, results.size().intValue());
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertEquals("Patient/PT00000", ids.get(0));
@@ -176,6 +184,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSummaryMode(Sets.newHashSet(SummaryEnum.COUNT, SummaryEnum.DATA));
 		results = myPatientDao.search(params);
 		uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		assertEquals(200, results.size().intValue());
 		ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertEquals("Patient/PT00000", ids.get(0));
@@ -197,6 +206,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSort(new SortSpec(Patient.SP_NAME));
 		IBundleProvider results = myPatientDao.search(params);
 		String uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 200, true);
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals("Patient/PT00199", ids.get(199));
@@ -250,6 +260,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSort(new SortSpec(Patient.SP_NAME));
 		IBundleProvider results = myPatientDao.search(params);
 		String uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals("Patient/PT00009", ids.get(9));
@@ -375,6 +386,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setCount(50);
 		IBundleProvider results = myPatientDao.search(params);
 		String uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 50, true);
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals("Patient/PT00049", ids.get(49));
@@ -408,6 +420,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSort(new SortSpec(Patient.SP_NAME));
 		IBundleProvider results = myPatientDao.search(params);
 		String uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals("Patient/PT00009", ids.get(9));
@@ -465,6 +478,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSort(new SortSpec(Patient.SP_NAME));
 		final IBundleProvider results = myPatientDao.search(params);
 		String uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals("Patient/PT00009", ids.get(9));
@@ -529,6 +543,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.add(Patient.SP_RES_ID, new TokenParam("PT00000"));
 		IBundleProvider results = myPatientDao.search(params);
 		String uuid = results.getUuid();
+		ourLog.info("** Search returned UUID: {}", uuid);
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals(1, ids.size());

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
+import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.SortOrderEnum;
@@ -206,31 +207,38 @@ public class FhirResourceDaoR4SortTest extends BaseJpaR4Test {
 	@SuppressWarnings("unused")
 	@Test
 	public void testSortOnSparselyPopulatedFields() {
+//		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
+
 		IIdType pid1, pid2, pid3, pid4, pid5, pid6;
 		{
 			Patient p = new Patient();
+			p.setId("pid1");
 			p.setActive(true);
-			pid1 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
+			pid1 = myPatientDao.update(p, mySrd).getId().toUnqualifiedVersionless();
 		}
 		{
 			Patient p = new Patient();
+			p.setId("pid2");
 			p.addName().setFamily("A");
-			pid2 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
+			pid2 = myPatientDao.update(p, mySrd).getId().toUnqualifiedVersionless();
 		}
 		{
 			Patient p = new Patient();
+			p.setId("pid3");
 			p.addName().setFamily("B");
-			pid3 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
+			pid3 = myPatientDao.update(p, mySrd).getId().toUnqualifiedVersionless();
 		}
 		{
 			Patient p = new Patient();
+			p.setId("pid4");
 			p.addName().setFamily("B").addGiven("A");
-			pid4 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
+			pid4 = myPatientDao.update(p, mySrd).getId().toUnqualifiedVersionless();
 		}
 		{
 			Patient p = new Patient();
+			p.setId("pid5");
 			p.addName().setFamily("B").addGiven("B");
-			pid5 = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
+			pid5 = myPatientDao.update(p, mySrd).getId().toUnqualifiedVersionless();
 		}
 
 		SearchParameterMap map;
@@ -239,6 +247,7 @@ public class FhirResourceDaoR4SortTest extends BaseJpaR4Test {
 		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));
+		ourLog.info("** Got IDs: {}", ids);
 		assertThat(ids, contains(pid2, pid4, pid5, pid3, pid1));
 		assertEquals(5, ids.size());
 

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -298,7 +298,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 			"where HFJ_RES_PARAM_PRESENT.HASH_PRESENCE is null";
 		consolidateSearchParamPresenceIndexesTask.addQuery(sql, ArbitrarySqlTask.QueryModeEnum.BATCH_UNTIL_NO_MORE, t -> {
 			Long pid = (Long) t.get("PID");
-			Boolean present = (Boolean) t.get("HASH_PRESENCE");
+			Boolean present = (Boolean) t.get("SP_PRESENT");
 			String resType = (String) t.get("RES_TYPE");
 			String paramName = (String) t.get("PARAM_NAME");
 			Long hash = SearchParamPresent.calculateHashPresence(resType, paramName, present);

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/model/Order.java

@@ -30,12 +30,14 @@ package org.hl7.fhir.instance.model;
 */
 
 // Generated on Wed, Jul 13, 2016 05:32+1000 for FHIR v1.0.2
-import java.util.*;
 
+import ca.uhn.fhir.model.api.annotation.*;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
 
-import ca.uhn.fhir.model.api.annotation.*;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
 /**
  * A request to perform an action.
  */

src/changes/changes.xml

@@ -71,6 +71,11 @@
 				timezones where the date that could apply. This makes the search slightly more
 				inclusive, which errs on the side of caution.
 			</action>
+			<action type="fix">
+				A bug was fixed in the JPA server $expunge operation where a database connection
+				could sometimes be opened and not returned to the pool immediately, leading to
+				pool starvation if the operation was called many times in a row.
+			</action>
 		</release>
 
 		<release version="3.5.0" date="2018-09-17">