More work on perf

.editorconfig

@@ -3,19 +3,30 @@ root = true
 [*]
 end_of_line = lf
 insert_final_newline = true
+tab_width = 3
+indent_size = 3
 
 [*.java]
 charset = utf-8
 indent_style = tab
+tab_width = 3
+indent_size = 3
 
 [*.xml]
 charset = utf-8
 indent_style = tab
+tab_width = 3
+indent_size = 3
 
 [*.json]
 charset = utf-8
 indent_style = tab
+tab_width = 3
+indent_size = 3
 
 [*.vm]
 charset = utf-8
 indent_style = tab
+tab_width = 3
+indent_size = 3
+

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/Include.java

@@ -3,6 +3,8 @@ package ca.uhn.fhir.model.api;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
+import java.io.Serializable;
+
 import org.apache.commons.lang3.builder.ToStringBuilder;
 
 /*
@@ -33,8 +35,10 @@ import org.apache.commons.lang3.builder.ToStringBuilder;
  * upgrading servers.
  * </p>
  */
-public class Include {
+public class Include implements Serializable {
 
+	private static final long serialVersionUID = 1L;
+	
 	private final boolean myImmutable;
 	private boolean myRecurse;
 	private String myValue;

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/TagList.java

@@ -104,9 +104,9 @@ public class TagList implements Set<Tag>, Serializable, IBase {
 	 * Add a new tag instance
 	 * 
 	 * @param theScheme
-	 *           The tag scheme
+	 *           The tag scheme (the system)
 	 * @param theTerm
-	 *           The tag term
+	 *           The tag term (the code)
 	 * @return Returns the newly created tag instance. Note that the tag is added to the list by this method, so you
 	 *         generally do not need to interact directly with the added tag.
 	 */

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

@@ -1235,6 +1235,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		Set<ResourceIndexedSearchParamCoords> coordsParams = null;
 		Set<ResourceLink> links = null;
 
+		Set<String> populatedResourceLinkParameters = null;
 		if (theDeletedTimestampOrNull != null) {
 
 			stringParams = Collections.emptySet();
@@ -1334,7 +1335,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				}
 
 				links = new HashSet<ResourceLink>();
-				Set<String> populatedResourceLinkParameters = extractResourceLinks(theEntity, theResource, links, theUpdateTime);
+				populatedResourceLinkParameters = extractResourceLinks(theEntity, theResource, links, theUpdateTime);
 
 				/*
 				 * If the existing resource already has links and those match links we still want, use them instead of removing them and re adding them
@@ -1374,28 +1375,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				theEntity.setIndexStatus(INDEX_STATUS_INDEXED);
 				populateFullTextFields(theResource, theEntity);
 
-				/*
-				 * Update the "search param present" table which is used for the
-				 * ?foo:missing=true queries
-				 */
-				Map<String, Boolean> presentSearchParams = new HashMap<String, Boolean>();
-				for (String nextKey : populatedResourceLinkParameters) {
-					presentSearchParams.put(nextKey, Boolean.TRUE);
-				}
-				updateSearchParamPresent(presentSearchParams, stringParams);
-				updateSearchParamPresent(presentSearchParams, tokenParams);
-				updateSearchParamPresent(presentSearchParams, numberParams);
-				updateSearchParamPresent(presentSearchParams, quantityParams);
-				updateSearchParamPresent(presentSearchParams, dateParams);
-				updateSearchParamPresent(presentSearchParams, uriParams);
-				updateSearchParamPresent(presentSearchParams, coordsParams);
-				Set<String> activeSearchParamNames = mySearchParamRegistry.getActiveSearchParams(theEntity.getResourceType()).keySet();
-				for (String nextSpName : activeSearchParamNames) {
-					if (!presentSearchParams.containsKey(nextSpName)) {
-						presentSearchParams.put(nextSpName, Boolean.FALSE);
-					}
-				}
-				mySearchParamPresenceSvc.updatePresence(theEntity, presentSearchParams);
 				
 			} else {
 
@@ -1426,6 +1405,31 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			postUpdate(theEntity, (T) theResource);
 		}
 
+		/*
+		 * Update the "search param present" table which is used for the
+		 * ?foo:missing=true queries
+		 */
+		if (thePerformIndexing) {
+			Map<String, Boolean> presentSearchParams = new HashMap<String, Boolean>();
+			for (String nextKey : populatedResourceLinkParameters) {
+				presentSearchParams.put(nextKey, Boolean.TRUE);
+			}
+			updateSearchParamPresent(presentSearchParams, stringParams);
+			updateSearchParamPresent(presentSearchParams, tokenParams);
+			updateSearchParamPresent(presentSearchParams, numberParams);
+			updateSearchParamPresent(presentSearchParams, quantityParams);
+			updateSearchParamPresent(presentSearchParams, dateParams);
+			updateSearchParamPresent(presentSearchParams, uriParams);
+			updateSearchParamPresent(presentSearchParams, coordsParams);
+			Set<String> activeSearchParamNames = mySearchParamRegistry.getActiveSearchParams(theEntity.getResourceType()).keySet();
+			for (String nextSpName : activeSearchParamNames) {
+				if (!presentSearchParams.containsKey(nextSpName)) {
+					presentSearchParams.put(nextSpName, Boolean.FALSE);
+				}
+			}
+			mySearchParamPresenceSvc.updatePresence(theEntity, presentSearchParams);
+		}
+		
 		/*
 		 * Create history entry
 		 */

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

@@ -88,8 +88,6 @@ public class SearchBuilder {
 	private EntityManager myEntityManager;
 	private IForcedIdDao myForcedIdDao;
 	private SearchParameterMap myParams;
-	private Collection<Long> myPids;
-	private PlatformTransactionManager myPlatformTransactionManager;
 	private IResourceIndexedSearchParamUriDao myResourceIndexedSearchParamUriDao;
 	private String myResourceName;
 	private Class<? extends IBaseResource> myResourceType;
@@ -97,16 +95,12 @@ public class SearchBuilder {
 	private Search mySearchEntity;
 	private ISearchResultDao mySearchResultDao;
 	private ISearchParamRegistry mySearchParamRegistry;
-
 	private IHapiTerminologySvc myTerminologySvc;
-
 	private Root<ResourceTable> myResourceTableRoot;
-
 	private ArrayList<Predicate> myPredicates;
-
 	private CriteriaBuilder myBuilder;
-
 	private CriteriaQuery<Tuple> myResourceTableQuery;
+	private PlatformTransactionManager myPlatformTransactionManager;
 
 	public SearchBuilder(FhirContext theFhirContext, EntityManager theEntityManager, PlatformTransactionManager thePlatformTransactionManager, IFulltextSearchSvc theFulltextSearchSvc,
 			ISearchResultDao theSearchResultDao, BaseHapiFhirDao<?> theDao,
@@ -158,8 +152,8 @@ public class SearchBuilder {
 
 	private void addPredicateDate(String theParamName, List<? extends IQueryParameterType> theList) {
 
-		if (Boolean.TRUE.equals(theList.get(0).getMissing())) {
+		if (theList.get(0).getMissing() != null) {
-			addPredicateParamMissing("myParamsDate", theParamName, ResourceIndexedSearchParamDate.class);
+			addPredicateParamMissing(theParamName, theList.get(0).getMissing());
 			return;
 		}
 
@@ -167,10 +161,6 @@ public class SearchBuilder {
 
 		List<Predicate> codePredicates = new ArrayList<Predicate>();
 		for (IQueryParameterType nextOr : theList) {
-			if (addPredicateMissingFalseIfPresent(myBuilder, theParamName, join, codePredicates, nextOr)) {
-				continue;
-			}
-
 			IQueryParameterType params = nextOr;
 			Predicate p = createPredicateDate(myBuilder, join, params);
 			codePredicates.add(p);
@@ -304,40 +294,10 @@ public class SearchBuilder {
 		return;
 	}
 
-	private boolean addPredicateMissingFalseIfPresent(CriteriaBuilder theBuilder, String theParamName, From<?, ? extends BaseResourceIndexedSearchParam> from, List<Predicate> codePredicates,
-			IQueryParameterType nextOr) {
-		boolean missingFalse = false;
-		if (nextOr.getMissing() != null) {
-			if (nextOr.getMissing().booleanValue() == true) {
-				throw new InvalidRequestException(myContext.getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "multipleParamsWithSameNameOneIsMissingTrue", theParamName));
-			}
-			Predicate singleCode = from.get("myId").isNotNull();
-			Predicate name = theBuilder.equal(from.get("myParamName"), theParamName);
-			codePredicates.add(theBuilder.and(name, singleCode));
-			missingFalse = true;
-		}
-		return missingFalse;
-	}
-
-	private boolean addPredicateMissingFalseIfPresentForResourceLink(CriteriaBuilder theBuilder, String theParamName, From<?,? extends ResourceLink> from, List<Predicate> codePredicates,
-			IQueryParameterType nextOr) {
-		boolean missingFalse = false;
-		if (nextOr.getMissing() != null) {
-			if (nextOr.getMissing().booleanValue() == true) {
-				throw new InvalidRequestException(myContext.getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "multipleParamsWithSameNameOneIsMissingTrue", theParamName));
-			}
-			Predicate singleCode = from.get("mySourceResource").isNotNull();
-			Predicate name = createResourceLinkPathPredicate(theParamName, from);
-			codePredicates.add(theBuilder.and(name, singleCode));
-			missingFalse = true;
-		}
-		return missingFalse;
-	}
-
 	private void addPredicateNumber(String theParamName, List<? extends IQueryParameterType> theList) {
 
-		if (Boolean.TRUE.equals(theList.get(0).getMissing())) {
+		if (theList.get(0).getMissing() != null) {
-			addPredicateParamMissing("myParamsNumber", theParamName, ResourceIndexedSearchParamNumber.class);
+			addPredicateParamMissing(theParamName, theList.get(0).getMissing());
 			return;
 		}
 
@@ -347,10 +307,6 @@ public class SearchBuilder {
 		for (IQueryParameterType nextOr : theList) {
 			IQueryParameterType params = nextOr;
 
-			if (addPredicateMissingFalseIfPresent(myBuilder, theParamName, join, codePredicates, nextOr)) {
-				continue;
-			}
-
 			if (params instanceof NumberParam) {
 				NumberParam param = (NumberParam) params;
 
@@ -376,62 +332,18 @@ public class SearchBuilder {
 		myPredicates.add(myBuilder.or(toArray(codePredicates)));
 	}
 
-	private void addPredicateParamMissing(String joinName, String theParamName, Class<? extends BaseResourceIndexedSearchParam> theParamTable) {
+	private void addPredicateParamMissing(String theParamName, boolean theMissing) {
-		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
+		Join<ResourceTable, SearchParamPresent> paramPresentJoin = myResourceTableRoot.join("mySearchParamPresents", JoinType.LEFT);
-		CriteriaQuery<Long> cq = builder.createQuery(Long.class);
+		Join<SearchParamPresent, SearchParam> paramJoin = paramPresentJoin.join("mySearchParam", JoinType.LEFT);
-		Root<ResourceTable> from = cq.from(ResourceTable.class);
-		cq.select(from.get("myId").as(Long.class));
 
-		Subquery<Long> subQ = cq.subquery(Long.class);
+		myPredicates.add(myBuilder.equal(paramJoin.get("myResourceName"), myResourceName));
-		Root<? extends BaseResourceIndexedSearchParam> subQfrom = subQ.from(theParamTable);
+		myPredicates.add(myBuilder.equal(paramJoin.get("myParamName"), theParamName));
-		subQ.select(subQfrom.get("myResourcePid").as(Long.class));
+		myPredicates.add(myBuilder.equal(paramPresentJoin.get("myPresent"), !theMissing));
-		Predicate subQname = builder.equal(subQfrom.get("myParamName"), theParamName);
-		Predicate subQtype = builder.equal(subQfrom.get("myResourceType"), myResourceName);
-		subQ.where(builder.and(subQtype, subQname));
-
-		List<Predicate> predicates = new ArrayList<Predicate>();
-		predicates.add(builder.not(builder.in(from.get("myId")).value(subQ)));
-		predicates.add(builder.equal(from.get("myResourceType"), myResourceName));
-		predicates.add(builder.isNull(from.get("myDeleted")));
-		createPredicateResourceId(builder, cq, predicates, from.get("myId").as(Long.class));
-
-		cq.where(builder.and(toArray(predicates)));
-
-		ourLog.info("Adding :missing qualifier for parameter '{}'", theParamName);
-
-		TypedQuery<Long> q = myEntityManager.createQuery(cq);
-		doSetPids(q.getResultList());
-	}
-
-	private void addPredicateParamMissingResourceLink(String joinName, String theParamName) {
-		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
-		CriteriaQuery<Long> cq = builder.createQuery(Long.class);
-		Root<ResourceTable> from = cq.from(ResourceTable.class);
-		cq.select(from.get("myId").as(Long.class));
-
-		Subquery<Long> subQ = cq.subquery(Long.class);
-		Root<ResourceLink> subQfrom = subQ.from(ResourceLink.class);
-		subQ.select(subQfrom.get("mySourceResourcePid").as(Long.class));
-
-		// subQ.where(builder.equal(subQfrom.get("myParamName"), theParamName));
-		Predicate path = createResourceLinkPathPredicate(theParamName, subQfrom);
-		subQ.where(path);
-
-		List<Predicate> predicates = new ArrayList<Predicate>();
-		createPredicateResourceId(builder, cq, predicates, from.get("myId").as(Long.class));
-		predicates.add(builder.not(builder.in(from.get("myId")).value(subQ)));
-		predicates.add(builder.equal(from.get("myResourceType"), myResourceName));
-
-		cq.where(builder.and(toArray(predicates)));
-
-		TypedQuery<Long> q = myEntityManager.createQuery(cq);
-		List<Long> resultList = q.getResultList();
-		doSetPids(new HashSet<Long>(resultList));
 	}
 
 	private void addPredicateQuantity(String theParamName, List<? extends IQueryParameterType> theList) {
-		if (Boolean.TRUE.equals(theList.get(0).getMissing())) {
+		if (theList.get(0).getMissing() != null) {
-			addPredicateParamMissing("myParamsQuantity", theParamName, ResourceIndexedSearchParamQuantity.class);
+			addPredicateParamMissing(theParamName, theList.get(0).getMissing());
 			return;
 		}
 
@@ -439,9 +351,6 @@ public class SearchBuilder {
 
 		List<Predicate> codePredicates = new ArrayList<Predicate>();
 		for (IQueryParameterType nextOr : theList) {
-			if (addPredicateMissingFalseIfPresent(myBuilder, theParamName, join, codePredicates, nextOr)) {
-				continue;
-			}
 
 			Predicate singleCode = createPredicateQuantity(myBuilder, join, nextOr);
 			codePredicates.add(singleCode);
@@ -453,8 +362,8 @@ public class SearchBuilder {
 	private void addPredicateReference(String theParamName, List<? extends IQueryParameterType> theList) {
 		assert theParamName.contains(".") == false;
 
-		if (Boolean.TRUE.equals(theList.get(0).getMissing())) {
+		if (theList.get(0).getMissing() != null) {
-			addPredicateParamMissingResourceLink("myResourceLinks", theParamName);
+			addPredicateParamMissing(theParamName, theList.get(0).getMissing());
 			return;
 		}
 
@@ -465,10 +374,6 @@ public class SearchBuilder {
 		for (IQueryParameterType nextOr : theList) {
 			IQueryParameterType params = nextOr;
 
-			if (addPredicateMissingFalseIfPresentForResourceLink(myBuilder, theParamName, join, codePredicates, nextOr)) {
-				continue;
-			}
-
 			if (params instanceof ReferenceParam) {
 				ReferenceParam ref = (ReferenceParam) params;
 
@@ -585,34 +490,34 @@ public class SearchBuilder {
 						}
 
 						foundChainMatch = true;
-//						Set<Long> pids = dao.searchForIds(chain, chainValue);
+						// Set<Long> pids = dao.searchForIds(chain, chainValue);
 
 						Subquery<Long> subQ = myResourceTableQuery.subquery(Long.class);
 						Root<ResourceTable> subQfrom = subQ.from(ResourceTable.class);
 						subQ.select(subQfrom.get("myId").as(Long.class));
-						
+
 						List<List<? extends IQueryParameterType>> andOrParams = new ArrayList<List<? extends IQueryParameterType>>();
 						andOrParams.add(Collections.singletonList(chainValue));
 
 						/*
 						 * We're doing a chain call, so push the current query root
 						 * and predicate list down and put new ones at the top of the
-						 * stack and run a subuery 
+						 * stack and run a subuery
 						 */
 						Root<ResourceTable> stackRoot = myResourceTableRoot;
 						ArrayList<Predicate> stackPredicates = myPredicates;
 						myResourceTableRoot = subQfrom;
 						myPredicates = new ArrayList<Predicate>();
-						
+
 						searchForIdsWithAndOr(chain, andOrParams);
 						subQ.where(toArray(myPredicates));
-						
+
 						/*
 						 * Pop the old query root and predicate list back
 						 */
 						myResourceTableRoot = stackRoot;
 						myPredicates = stackPredicates;
-						
+
 						Predicate eq = join.get("myTargetResourcePid").in(subQ);
 						codePredicates.add(eq);
 
@@ -633,20 +538,16 @@ public class SearchBuilder {
 	}
 
 	private void addPredicateString(String theParamName, List<? extends IQueryParameterType> theList) {
-		if (Boolean.TRUE.equals(theList.get(0).getMissing())) {
+		if (theList.get(0).getMissing() != null) {
-			addPredicateParamMissing("myParamsString", theParamName, ResourceIndexedSearchParamString.class);
+			addPredicateParamMissing(theParamName, theList.get(0).getMissing());
 			return;
 		}
 
 		Join<ResourceTable, ResourceIndexedSearchParamString> join = myResourceTableRoot.join("myParamsString", JoinType.LEFT);
-		
+
 		List<Predicate> codePredicates = new ArrayList<Predicate>();
 		for (IQueryParameterType nextOr : theList) {
 			IQueryParameterType theParameter = nextOr;
-			if (addPredicateMissingFalseIfPresent(myBuilder, theParamName, join, codePredicates, nextOr)) {
-				continue;
-			}
-
 			Predicate singleCode = createPredicateString(theParameter, theParamName, myBuilder, join);
 			codePredicates.add(singleCode);
 		}
@@ -775,7 +676,7 @@ public class SearchBuilder {
 
 			Join<ResourceTable, ResourceTag> tagJoin = myResourceTableRoot.join("myTags", JoinType.LEFT);
 			From<ResourceTag, TagDefinition> defJoin = tagJoin.join("myTag");
-			
+
 			List<Predicate> orPredicates = createPredicateTagList(defJoin, myBuilder, tagType, tokens);
 			myPredicates.add(myBuilder.or(toArray(orPredicates)));
 
@@ -785,8 +686,8 @@ public class SearchBuilder {
 
 	private void addPredicateToken(String theParamName, List<? extends IQueryParameterType> theList) {
 
-		if (Boolean.TRUE.equals(theList.get(0).getMissing())) {
+		if (theList.get(0).getMissing() != null) {
-			addPredicateParamMissing("myParamsToken", theParamName, ResourceIndexedSearchParamToken.class);
+			addPredicateParamMissing(theParamName, theList.get(0).getMissing());
 			return;
 		}
 
@@ -794,9 +695,6 @@ public class SearchBuilder {
 
 		List<Predicate> codePredicates = new ArrayList<Predicate>();
 		for (IQueryParameterType nextOr : theList) {
-			if (addPredicateMissingFalseIfPresent(myBuilder, theParamName, join, codePredicates, nextOr)) {
-				continue;
-			}
 
 			if (nextOr instanceof TokenParam) {
 				TokenParam id = (TokenParam) nextOr;
@@ -822,8 +720,8 @@ public class SearchBuilder {
 	}
 
 	private void addPredicateUri(String theParamName, List<? extends IQueryParameterType> theList) {
-		if (Boolean.TRUE.equals(theList.get(0).getMissing())) {
+		if (theList.get(0).getMissing() != null) {
-			addPredicateParamMissing("myParamsUri", theParamName, ResourceIndexedSearchParamUri.class);
+			addPredicateParamMissing(theParamName, theList.get(0).getMissing());
 			return;
 		}
 
@@ -833,10 +731,6 @@ public class SearchBuilder {
 		for (IQueryParameterType nextOr : theList) {
 			IQueryParameterType params = nextOr;
 
-			if (addPredicateMissingFalseIfPresent(myBuilder, theParamName, join, codePredicates, nextOr)) {
-				continue;
-			}
-
 			if (params instanceof UriParam) {
 				UriParam param = (UriParam) params;
 
@@ -1265,7 +1159,7 @@ public class SearchBuilder {
 		return singleCode;
 	}
 
-	private Predicate createResourceLinkPathPredicate(String theParamName, From<?,? extends ResourceLink> from) {
+	private Predicate createResourceLinkPathPredicate(String theParamName, From<?, ? extends ResourceLink> from) {
 		return createResourceLinkPathPredicate(myCallingDao, myContext, theParamName, from, myResourceType);
 	}
 
@@ -1368,10 +1262,6 @@ public class SearchBuilder {
 			thePredicates.add(theBuilder.equal(stringJoin.get("myParamName"), theSort.getParamName()));
 		}
 
-		// Predicate p = theBuilder.equal(stringJoin.get("myParamName"), theSort.getParamName());
-		// Predicate pn = theBuilder.isNull(stringJoin.get("myParamName"));
-		// thePredicates.add(theBuilder.or(p, pn));
-
 		for (String next : sortAttrName) {
 			if (theSort.getOrder() == null || theSort.getOrder() == SortOrderEnum.ASC) {
 				theOrders.add(theBuilder.asc(stringJoin.get(next)));
@@ -1565,30 +1455,30 @@ public class SearchBuilder {
 		mySearchEntity.setSearchType(myParams.getEverythingMode() != null ? SearchTypeEnum.EVERYTHING : SearchTypeEnum.SEARCH);
 		mySearchEntity.setLastUpdated(myParams.getLastUpdated());
 		mySearchEntity.setResourceType(myResourceName);
-		
+
 		for (Include next : myParams.getIncludes()) {
 			mySearchEntity.getIncludes().add(new SearchInclude(mySearchEntity, next.getValue(), false, next.isRecurse()));
 		}
 		for (Include next : myParams.getRevIncludes()) {
 			mySearchEntity.getIncludes().add(new SearchInclude(mySearchEntity, next.getValue(), true, next.isRecurse()));
 		}
-		
+
 		List<Long> firstPage = loadSearchPage(theParams, 0, 999);
 		mySearchEntity.setTotalCount(firstPage.size());
-		
+
 		myEntityManager.persist(mySearchEntity);
 		for (SearchInclude next : mySearchEntity.getIncludes()) {
 			myEntityManager.persist(next);
 		}
-		
+
 		IBundleProvider retVal = doReturnProvider();
-		
+
 		ourLog.info("Search initial phase completed in {}ms", w);
 		return retVal;
 	}
 
 	public List<Long> loadSearchPage(SearchParameterMap theParams, int theFromIndex, int theToIndex) {
-		
+
 		if (myFulltextSearchSvc == null) {
 			if (theParams.containsKey(Constants.PARAM_TEXT)) {
 				throw new InvalidRequestException("Fulltext search is not enabled on this service, can not process parameter: " + Constants.PARAM_TEXT);
@@ -1613,28 +1503,28 @@ public class SearchBuilder {
 		myPredicates = new ArrayList<Predicate>();
 		myPredicates.add(myBuilder.equal(myResourceTableRoot.get("myResourceType"), myResourceName));
 		myPredicates.add(myBuilder.isNull(myResourceTableRoot.get("myDeleted")));
-		
+
 		DateRangeParam lu = theParams.getLastUpdated();
 		List<Predicate> lastUpdatedPredicates = createLastUpdatedPredicates(lu, myBuilder, myResourceTableRoot);
 		myPredicates.addAll(lastUpdatedPredicates);
-		
+
 		searchForIdsWithAndOr(theParams);
-		
+
 		myResourceTableQuery.where(myBuilder.and(SearchBuilder.toArray(myPredicates)));
 
 		myResourceTableQuery.multiselect(myResourceTableRoot.get("myId").as(Long.class));
 		TypedQuery<Tuple> query = myEntityManager.createQuery(myResourceTableQuery);
 		query.setFirstResult(theFromIndex);
 		query.setMaxResults(theToIndex - theFromIndex);
-		
+
 		List<Long> pids = new ArrayList<Long>();
 		for (Tuple next : query.getResultList()) {
 			pids.add(next.get(0, Long.class));
 		}
 
-		return pids;		
+		return pids;
 	}
-	
+
 	public IBundleProvider loadPage(SearchParameterMap theParams, int theFromIndex, int theToIndex) {
 		StopWatch sw = new StopWatch();
 		DateRangeParam lu = theParams.getLastUpdated();
@@ -1702,9 +1592,8 @@ public class SearchBuilder {
 				}
 			}
 
-			
 			if (!theParams.isEmpty()) {
-//				searchForIdsWithAndOr(theParams, lu);
+				// searchForIdsWithAndOr(theParams, lu);
 			}
 
 		}
@@ -1729,7 +1618,7 @@ public class SearchBuilder {
 		return doReturnProvider();
 
 	}
-	
+
 	private void searchForIdsWithAndOr(SearchParameterMap theParams) {
 		SearchParameterMap params = theParams;
 		if (params == null) {
@@ -1810,7 +1699,7 @@ public class SearchBuilder {
 						addPredicateUri(nextParamName, nextAnd);
 					}
 					break;
-				case HAS: 
+				case HAS:
 					// should not happen
 					break;
 				}
@@ -1834,21 +1723,20 @@ public class SearchBuilder {
 								orPids.add(entity.getId());
 							}
 						} catch (ResourceNotFoundException e) {
-							/* 
+							/*
 							 * This isn't an error, just means no result found
 							 * that matches the ID the client provided
 							 */
 						}
 					}
 				}
-				
-				if (orPids.size() > 0) {
-					Predicate nextPredicate = myResourceTableRoot.get("myId").as(Long.class).in(orPids);
-					myPredicates.add(nextPredicate);
-				}
-				
 			}
-			
+
+			if (orPids.size() > 0) {
+				Predicate nextPredicate = myResourceTableRoot.get("myId").as(Long.class).in(orPids);
+				myPredicates.add(nextPredicate);
+			}
+
 		}
 	}
 
@@ -1942,7 +1830,7 @@ public class SearchBuilder {
 		return likeExpression.replace("%", "[%]") + "%";
 	}
 
-	private static Predicate createResourceLinkPathPredicate(IDao theCallingDao, FhirContext theContext, String theParamName, From<?,? extends ResourceLink> from,
+	private static Predicate createResourceLinkPathPredicate(IDao theCallingDao, FhirContext theContext, String theParamName, From<?, ? extends ResourceLink> from,
 			Class<? extends IBaseResource> resourceType) {
 		RuntimeResourceDefinition resourceDef = theContext.getResourceDefinition(resourceType);
 		RuntimeSearchParam param = theCallingDao.getSearchParamByName(resourceDef, theParamName);

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

@@ -32,7 +32,7 @@ import ca.uhn.fhir.jpa.entity.SearchParamPresent;
 
 public interface ISearchParamPresentDao extends JpaRepository<SearchParamPresent, Long> {
 
-	@Query("SELECT s FROM SearchParamPresent s WHERE s.myResourceTable = :res")
+	@Query("SELECT s FROM SearchParamPresent s WHERE s.myResource = :res")
 	public Collection<SearchParamPresent> findAllForResource(@Param("res") ResourceTable theResource);
 
 }

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

@@ -236,6 +236,9 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	@OneToMany(mappedBy = "myResource", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
 	private Set<ResourceTag> myTags;
 
+	@OneToMany(mappedBy = "myResource", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
+	private Collection<SearchParamPresent> mySearchParamPresents;
+
 	@Column(name = "RES_VER")
 	private long myVersion;
 

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

@@ -11,7 +11,7 @@ public class SearchParam {
 	@Id
 	@SequenceGenerator(name = "SEQ_SEARCHPARM_ID", sequenceName = "SEQ_SEARCHPARM_ID")
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_SEARCHPARM_ID")
-	@Column(name = "RES_ID")
+	@Column(name = "PID")
 	private Long myId;
 
 	@Column(name="PARAM_NAME", length=BaseResourceIndexedSearchParam.MAX_SP_NAME, nullable=false, updatable=false)

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

@@ -25,14 +25,14 @@ public class SearchParamPresent implements Serializable {
 
 	@ManyToOne()
 	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, foreignKey = @ForeignKey(name = "FK_RESPARMPRES_RESID"))
-	private ResourceTable myResourceTable;
+	private ResourceTable myResource;
 
 	@ManyToOne()
 	@JoinColumn(name = "SP_ID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_RESPARMPRES_SPID"))
 	private SearchParam mySearchParam;
 
-	public ResourceTable getResourceTable() {
+	public ResourceTable getResource() {
-		return myResourceTable;
+		return myResource;
 	}
 
 	public SearchParam getSearchParam() {
@@ -47,8 +47,8 @@ public class SearchParamPresent implements Serializable {
 		myPresent = thePresent;
 	}
 
-	public void setResourceTable(ResourceTable theResourceTable) {
+	public void setResource(ResourceTable theResourceTable) {
-		myResourceTable = theResourceTable;
+		myResource = theResourceTable;
 	}
 
 	public void setSearchParam(SearchParam theSearchParam) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sp/SearchParamPresenceSvcImpl.java

@@ -16,23 +16,29 @@ import ca.uhn.fhir.jpa.entity.SearchParamPresent;
 public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamPresenceSvcImpl.class);
-	
+
-	private Map<Pair<String, String>, SearchParam> myResourceTypeToSearchParamToEntity = new ConcurrentHashMap<Pair<String,String>, SearchParam>();
+	private Map<Pair<String, String>, SearchParam> myResourceTypeToSearchParamToEntity = new ConcurrentHashMap<Pair<String, String>, SearchParam>();
-	
+
 	@Autowired
 	private ISearchParamDao mySearchParamDao;
-	
+
 	@Autowired
 	private ISearchParamPresentDao mySearchParamPresentDao;
 
 	@Override
 	public void updatePresence(ResourceTable theResource, Map<String, Boolean> theParamNameToPresence) {
-		
+
 		Map<String, Boolean> presenceMap = new HashMap<String, Boolean>(theParamNameToPresence);
 		List<SearchParamPresent> entitiesToSave = new ArrayList<SearchParamPresent>();
 		List<SearchParamPresent> entitiesToDelete = new ArrayList<SearchParamPresent>();
-		
+
-		Collection<SearchParamPresent> existing = mySearchParamPresentDao.findAllForResource(theResource);
+		Collection<SearchParamPresent> existing;
+//		if (theResource.getId() != null) {
+			existing = mySearchParamPresentDao.findAllForResource(theResource);
+//		} else {
+//			existing = Collections.emptyList();
+//		}
+
 		for (SearchParamPresent nextExistingEntity : existing) {
 			String nextSearchParamName = nextExistingEntity.getSearchParam().getParamName();
 			Boolean existingValue = presenceMap.remove(nextSearchParamName);
@@ -45,12 +51,12 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
 				entitiesToSave.add(nextExistingEntity);
 			}
 		}
-		
+
 		for (Entry<String, Boolean> next : presenceMap.entrySet()) {
-			String resourceType =  theResource.getResourceType();
+			String resourceType = theResource.getResourceType();
 			String paramName = next.getKey();
 			Pair<String, String> key = Pair.of(resourceType, paramName);
-			
+
 			SearchParam searchParam = myResourceTypeToSearchParamToEntity.get(key);
 			if (searchParam == null) {
 				searchParam = mySearchParamDao.findForResource(resourceType, paramName);
@@ -63,19 +69,19 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
 					mySearchParamDao.save(searchParam);
 					// Don't add the newly saved entity to the map in case the save fails
 				}
-				
+
 				SearchParamPresent present = new SearchParamPresent();
-				present.setResourceTable(theResource);
+				present.setResource(theResource);
 				present.setSearchParam(searchParam);
 				present.setPresent(next.getValue());
 				entitiesToSave.add(present);
 			}
-			
+
 			mySearchParamPresentDao.deleteInBatch(entitiesToDelete);
 			mySearchParamPresentDao.save(entitiesToSave);
-		
+
 		}
-		
+
 	}
-	
+
 }

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

@@ -30,28 +30,7 @@ import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.entity.ForcedId;
+import ca.uhn.fhir.jpa.entity.*;
-import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
-import ca.uhn.fhir.jpa.entity.ResourceHistoryTag;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
-import ca.uhn.fhir.jpa.entity.ResourceLink;
-import ca.uhn.fhir.jpa.entity.ResourceTable;
-import ca.uhn.fhir.jpa.entity.ResourceTag;
-import ca.uhn.fhir.jpa.entity.SearchInclude;
-import ca.uhn.fhir.jpa.entity.SearchResult;
-import ca.uhn.fhir.jpa.entity.SubscriptionFlaggedResource;
-import ca.uhn.fhir.jpa.entity.SubscriptionTable;
-import ca.uhn.fhir.jpa.entity.TagDefinition;
-import ca.uhn.fhir.jpa.entity.TermCodeSystem;
-import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
-import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
 import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
@@ -225,6 +204,9 @@ public abstract class BaseJpaTest {
 		txTemplate.execute(new TransactionCallback<Void>() {
 			@Override
 			public Void doInTransaction(TransactionStatus theStatus) {
+				entityManager.createQuery("DELETE from " + SearchParamPresent.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + SearchParam.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + SubscriptionFlaggedResource.class.getSimpleName() + " d").executeUpdate();
 				entityManager.createQuery("DELETE from " + SubscriptionFlaggedResource.class.getSimpleName() + " d").executeUpdate();
 				entityManager.createQuery("DELETE from " + ForcedId.class.getSimpleName() + " d").executeUpdate();
 				entityManager.createQuery("DELETE from " + ResourceIndexedSearchParamDate.class.getSimpleName() + " d").executeUpdate();

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

@@ -1747,27 +1747,27 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 		String methodName = "testSearchValueQuantity";
 
 		String id1;
-		{		
+		{
 			Observation o = new Observation();
 			o.getCode().addCoding().setSystem("urn:foo").setCode(methodName + "code");
 			Quantity q = new Quantity().setSystem("urn:bar:" + methodName).setCode(methodName + "units").setValue(100);
 			o.setValue(q);
 			id1 = myObservationDao.create(o, mySrd).getId().toUnqualifiedVersionless().getValue();
 		}
-		
+
 		String id2;
-		{		
+		{
 			Observation o = new Observation();
 			o.getCode().addCoding().setSystem("urn:foo").setCode(methodName + "code");
 			Quantity q = new Quantity().setSystem("urn:bar:" + methodName).setCode(methodName + "units").setValue(5);
 			o.setValue(q);
 			id2 = myObservationDao.create(o, mySrd).getId().toUnqualifiedVersionless().getValue();
 		}
-		
+
 		Map<String, IQueryParameterType> map = new HashMap<String, IQueryParameterType>();
 		IBundleProvider found;
 		QuantityParam param;
-		
+
 		param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, null);
 		map.put(Observation.SP_VALUE_QUANTITY, param);
 		found = myObservationDao.search(map);
@@ -2146,8 +2146,8 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 			param.setMissing(false);
 			params.put(Patient.SP_BIRTHDATE, param);
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, not(containsInRelativeOrder(missing)));
 			assertThat(patients, containsInRelativeOrder(notMissing));
+			assertThat(patients, not(containsInRelativeOrder(missing)));
 		}
 		{
 			Map<String, IQueryParameterType> params = new HashMap<String, IQueryParameterType>();
@@ -2158,6 +2158,14 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 			assertThat(patients, containsInRelativeOrder(missing));
 			assertThat(patients, not(containsInRelativeOrder(notMissing)));
 		}
+		// {
+		// Map<String, IQueryParameterType> params = new HashMap<String, IQueryParameterType>();
+		// DateParam param = new DateParam();
+		// param.setMissing(true);
+		// params.put(Patient.SP_DECEASED, param);
+		// List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+		// assertThat(patients, containsInRelativeOrder(missing, notMissing));
+		// }
 	}
 
 	@Test