Don't apply last updated to includes

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

@@ -36,6 +36,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * #L%
  */
 
+@SuppressWarnings("UnusedReturnValue")
 public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 
 	private static final long serialVersionUID = 1L;
@@ -208,6 +209,52 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 		return this;
 	}
 
+	/**
+	 * Sets the lower bound using a string that is compliant with
+	 * FHIR dateTime format (ISO-8601).
+	 * <p>
+	 * This lower bound is assumed to have a <code>ge</code>
+	 * (greater than or equals) modifier.
+	 * </p>
+	 */
+	public DateRangeParam setLowerBound(String theLowerBound) {
+		setLowerBound(new DateParam(GREATERTHAN_OR_EQUALS, theLowerBound));
+		return this;
+	}
+
+	/**
+	 * Sets the lower bound to be greaterthan or equal to the given date
+	 */
+	public DateRangeParam setLowerBoundInclusive(Date theLowerBound) {
+		validateAndSet(new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, theLowerBound), myUpperBound);
+		return this;
+	}
+
+	/**
+	 * Sets the upper bound to be greaterthan or equal to the given date
+	 */
+	public DateRangeParam setUpperBoundInclusive(Date theUpperBound) {
+		validateAndSet(myLowerBound, new DateParam(ParamPrefixEnum.LESSTHAN_OR_EQUALS, theUpperBound));
+		return this;
+	}
+
+
+	/**
+	 * Sets the lower bound to be greaterthan to the given date
+	 */
+	public DateRangeParam setLowerBoundExclusive(Date theLowerBound) {
+		validateAndSet(new DateParam(ParamPrefixEnum.GREATERTHAN, theLowerBound), myUpperBound);
+		return this;
+	}
+
+	/**
+	 * Sets the upper bound to be greaterthan to the given date
+	 */
+	public DateRangeParam setUpperBoundExclusive(Date theUpperBound) {
+		validateAndSet(myLowerBound, new DateParam(ParamPrefixEnum.LESSTHAN, theUpperBound));
+		return this;
+	}
+
 	public Date getLowerBoundAsInstant() {
 		if (myLowerBound == null) {
 			return null;
@@ -237,6 +284,19 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 		return myUpperBound;
 	}
 
+	/**
+	 * Sets the upper bound using a string that is compliant with
+	 * FHIR dateTime format (ISO-8601).
+	 * <p>
+	 * This upper bound is assumed to have a <code>le</code>
+	 * (less than or equals) modifier.
+	 * </p>
+	 */
+	public DateRangeParam setUpperBound(String theUpperBound) {
+		setUpperBound(new DateParam(LESSTHAN_OR_EQUALS, theUpperBound));
+		return this;
+	}
+
 	public DateRangeParam setUpperBound(DateParam theUpperBound) {
 		validateAndSet(myLowerBound, theUpperBound);
 		return this;
@@ -298,19 +358,6 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 		return (getLowerBoundAsInstant() == null) && (getUpperBoundAsInstant() == null);
 	}
 
-	/**
-	 * Sets the lower bound using a string that is compliant with
-	 * FHIR dateTime format (ISO-8601).
-	 * <p>
-	 * This lower bound is assumed to have a <code>ge</code>
-	 * (greater than or equals) modifier.
-	 * </p>
-	 */
-	public DateRangeParam setLowerBound(String theLowerBound) {
-		setLowerBound(new DateParam(GREATERTHAN_OR_EQUALS, theLowerBound));
-		return this;
-	}
-
 	/**
 	 * Sets the range from a pair of dates, inclusive on both ends
 	 *
@@ -394,19 +441,6 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 		validateAndSet(lowerBound, upperBound);
 	}
 
-	/**
-	 * Sets the upper bound using a string that is compliant with
-	 * FHIR dateTime format (ISO-8601).
-	 * <p>
-	 * This upper bound is assumed to have a <code>le</code>
-	 * (less than or equals) modifier.
-	 * </p>
-	 */
-	public DateRangeParam setUpperBound(String theUpperBound) {
-		setUpperBound(new DateParam(LESSTHAN_OR_EQUALS, theUpperBound));
-		return this;
-	}
-
 	@Override
 	public void setValuesAsQueryTokens(FhirContext theContext, String theParamName, List<QualifiedParamList> theParameters)
 		throws InvalidRequestException {
@@ -512,4 +546,5 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 		myLowerBound = lowerBound;
 		myUpperBound = upperBound;
 	}
+
 }

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

@@ -38,7 +38,7 @@ public interface ISearchBuilder {
 	void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation, EntityManager theEntityManager,
 									FhirContext theContext, IDao theDao);
 
-	Set<Long> loadReverseIncludes(IDao theCallingDao, FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode,
+	Set<Long> loadIncludes(IDao theCallingDao, FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode,
 								  DateRangeParam theLastUpdated);
 
 	/**

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

@@ -1712,7 +1712,7 @@ public class SearchBuilder implements ISearchBuilder {
 	 * THIS SHOULD RETURN HASHSET and not just Set because we add to it later (so it can't be Collections.emptySet())
 	 */
 	@Override
-	public HashSet<Long> loadReverseIncludes(IDao theCallingDao, FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes,
+	public HashSet<Long> loadIncludes(IDao theCallingDao, FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes,
 												 boolean theReverseMode, DateRangeParam theLastUpdated) {
 		if (theMatches.size() == 0) {
 			return new HashSet<>();
@@ -1820,9 +1820,11 @@ public class SearchBuilder implements ISearchBuilder {
 				}
 			}
 
+			if (theReverseMode) {
 				if (theLastUpdated != null && (theLastUpdated.getLowerBoundAsInstant() != null || theLastUpdated.getUpperBoundAsInstant() != null)) {
 					pidsToInclude = new HashSet<>(filterResourceIdsByLastUpdated(theEntityManager, theLastUpdated, pidsToInclude));
 				}
+			}
 			for (Long next : pidsToInclude) {
 				if (original.contains(next) == false && allAdded.contains(next) == false) {
 					theMatches.add(next);
@@ -2172,7 +2174,7 @@ public class SearchBuilder implements ISearchBuilder {
 					myCurrentOffset = end;
 					Collection<Long> pidsToScan = myCurrentPids.subList(start, end);
 					Set<Include> includes = Collections.singleton(new Include("*", true));
-					Set<Long> newPids = loadReverseIncludes(myCallingDao, myContext, myEntityManager, pidsToScan, includes, false, myParams.getLastUpdated());
+					Set<Long> newPids = loadIncludes(myCallingDao, myContext, myEntityManager, pidsToScan, includes, false, myParams.getLastUpdated());
 					myCurrentIterator = newPids.iterator();
 				}
 

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

@@ -1,5 +1,13 @@
 package ca.uhn.fhir.jpa.entity;
 
+import ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+
+import javax.persistence.*;
+import javax.validation.constraints.NotNull;
+import java.io.Serializable;
+import java.util.*;
+
 import static org.apache.commons.lang3.StringUtils.left;
 
 /*
@@ -22,104 +30,86 @@ import static org.apache.commons.lang3.StringUtils.left;
  * #L%
  */
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.Set;
-
-import javax.persistence.*;
-import javax.validation.constraints.NotNull;
-
-import org.hibernate.annotations.Fetch;
-
-import ca.uhn.fhir.model.api.Include;
-import ca.uhn.fhir.rest.param.DateRangeParam;
-
 @Entity
-@Table(name = "HFJ_SEARCH", uniqueConstraints= {
+@Table(name = "HFJ_SEARCH", uniqueConstraints = {
-	@UniqueConstraint(name="IDX_SEARCH_UUID", columnNames="SEARCH_UUID")
+	@UniqueConstraint(name = "IDX_SEARCH_UUID", columnNames = "SEARCH_UUID")
-}, indexes= {
+}, indexes = {
-	@Index(name="IDX_SEARCH_LASTRETURNED", columnList="SEARCH_LAST_RETURNED"),
+	@Index(name = "IDX_SEARCH_LASTRETURNED", columnList = "SEARCH_LAST_RETURNED"),
-	@Index(name="IDX_SEARCH_RESTYPE_HASHS", columnList="RESOURCE_TYPE,SEARCH_QUERY_STRING_HASH,CREATED")
+	@Index(name = "IDX_SEARCH_RESTYPE_HASHS", columnList = "RESOURCE_TYPE,SEARCH_QUERY_STRING_HASH,CREATED")
 })
 public class Search implements Serializable {
 
+	private static final int MAX_SEARCH_QUERY_STRING = 10000;
+	private static final int UUID_COLUMN_LENGTH = 36;
 	private static final int FAILURE_MESSAGE_LENGTH = 500;
-
 	private static final long serialVersionUID = 1L;
-	public static final int MAX_SEARCH_QUERY_STRING = 10000;
-	public static final int UUID_COLUMN_LENGTH = 36;
-
 	@Temporal(TemporalType.TIMESTAMP)
-	@Column(name="CREATED", nullable=false, updatable=false)
+	@Column(name = "CREATED", nullable = false, updatable = false)
 	private Date myCreated;
 
-	@Column(name="FAILURE_CODE", nullable=true)
+	@Column(name = "FAILURE_CODE", nullable = true)
 	private Integer myFailureCode;
 
-	@Column(name="FAILURE_MESSAGE", length=FAILURE_MESSAGE_LENGTH, nullable=true)
+	@Column(name = "FAILURE_MESSAGE", length = FAILURE_MESSAGE_LENGTH, nullable = true)
 	private String myFailureMessage;
 
 	@Id
-	@GeneratedValue(strategy = GenerationType.AUTO, generator="SEQ_SEARCH")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_SEARCH")
-	@SequenceGenerator(name="SEQ_SEARCH", sequenceName="SEQ_SEARCH")
+	@SequenceGenerator(name = "SEQ_SEARCH", sequenceName = "SEQ_SEARCH")
 	@Column(name = "PID")
 	private Long myId;
 
-	@OneToMany(mappedBy="mySearch")
+	@OneToMany(mappedBy = "mySearch")
 	private Collection<SearchInclude> myIncludes;
 
 	@Temporal(TemporalType.TIMESTAMP)
-	@Column(name="LAST_UPDATED_HIGH", nullable=true, insertable=true, updatable=false)
+	@Column(name = "LAST_UPDATED_HIGH", nullable = true, insertable = true, updatable = false)
 	private Date myLastUpdatedHigh;
 
 	@Temporal(TemporalType.TIMESTAMP)
-	@Column(name="LAST_UPDATED_LOW", nullable=true, insertable=true, updatable=false)
+	@Column(name = "LAST_UPDATED_LOW", nullable = true, insertable = true, updatable = false)
 	private Date myLastUpdatedLow;
 
-	@Column(name="NUM_FOUND", nullable=false)
+	@Column(name = "NUM_FOUND", nullable = false)
 	private int myNumFound;
 
-	@Column(name="PREFERRED_PAGE_SIZE", nullable=true)
+	@Column(name = "PREFERRED_PAGE_SIZE", nullable = true)
 	private Integer myPreferredPageSize;
 
-	@Column(name="RESOURCE_ID", nullable=true)
+	@Column(name = "RESOURCE_ID", nullable = true)
 	private Long myResourceId;
 
-	@Column(name="RESOURCE_TYPE", length=200, nullable=true)
+	@Column(name = "RESOURCE_TYPE", length = 200, nullable = true)
 	private String myResourceType;
 
-	@OneToMany(mappedBy="mySearch")
+	@OneToMany(mappedBy = "mySearch")
 	private Collection<SearchResult> myResults;
 
 	@NotNull
 	@Temporal(TemporalType.TIMESTAMP)
-	@Column(name="SEARCH_LAST_RETURNED", nullable=false, updatable=false)
+	@Column(name = "SEARCH_LAST_RETURNED", nullable = false, updatable = false)
 	private Date mySearchLastReturned;
 
 	@Lob()
-	@Basic(fetch=FetchType.LAZY)
+	@Basic(fetch = FetchType.LAZY)
-	@Column(name="SEARCH_QUERY_STRING", nullable=true, updatable=false, length = MAX_SEARCH_QUERY_STRING)
+	@Column(name = "SEARCH_QUERY_STRING", nullable = true, updatable = false, length = MAX_SEARCH_QUERY_STRING)
 	private String mySearchQueryString;
 
-	@Column(name="SEARCH_QUERY_STRING_HASH", nullable=true, updatable=false)
+	@Column(name = "SEARCH_QUERY_STRING_HASH", nullable = true, updatable = false)
 	private Integer mySearchQueryStringHash;
 
 	@Enumerated(EnumType.ORDINAL)
-	@Column(name="SEARCH_TYPE", nullable=false)
+	@Column(name = "SEARCH_TYPE", nullable = false)
 	private SearchTypeEnum mySearchType;
 
 	@Enumerated(EnumType.STRING)
-	@Column(name="SEARCH_STATUS", nullable=false, length=10)
+	@Column(name = "SEARCH_STATUS", nullable = false, length = 10)
 	private SearchStatusEnum myStatus;
 
-	@Column(name="TOTAL_COUNT", nullable=true)
+	@Column(name = "TOTAL_COUNT", nullable = true)
 	private Integer myTotalCount;
 
-	@Column(name="SEARCH_UUID", length= UUID_COLUMN_LENGTH, nullable=false, updatable=false)
+	@Column(name = "SEARCH_UUID", length = UUID_COLUMN_LENGTH, nullable = false, updatable = false)
 	private String myUuid;
 
 	/**
@@ -133,21 +123,33 @@ public class Search implements Serializable {
 		return myCreated;
 	}
 
+	public void setCreated(Date theCreated) {
+		myCreated = theCreated;
+	}
+
 	public Integer getFailureCode() {
 		return myFailureCode;
 	}
 
+	public void setFailureCode(Integer theFailureCode) {
+		myFailureCode = theFailureCode;
+	}
+
 	public String getFailureMessage() {
 		return myFailureMessage;
 	}
 
+	public void setFailureMessage(String theFailureMessage) {
+		myFailureMessage = left(theFailureMessage, FAILURE_MESSAGE_LENGTH);
+	}
+
 	public Long getId() {
 		return myId;
 	}
 
 	public Collection<SearchInclude> getIncludes() {
 		if (myIncludes == null) {
-			myIncludes = new ArrayList<SearchInclude>();
+			myIncludes = new ArrayList<>();
 		}
 		return myIncludes;
 	}
@@ -160,6 +162,16 @@ public class Search implements Serializable {
 		}
 	}
 
+	public void setLastUpdated(DateRangeParam theLastUpdated) {
+		if (theLastUpdated == null) {
+			myLastUpdatedLow = null;
+			myLastUpdatedHigh = null;
+		} else {
+			myLastUpdatedLow = theLastUpdated.getLowerBoundAsInstant();
+			myLastUpdatedHigh = theLastUpdated.getUpperBoundAsInstant();
+		}
+	}
+
 	public Date getLastUpdatedHigh() {
 		return myLastUpdatedHigh;
 	}
@@ -172,90 +184,46 @@ public class Search implements Serializable {
 		return myNumFound;
 	}
 
-	public Integer getPreferredPageSize() {
-		return myPreferredPageSize;
-	}
-
-	public Long getResourceId() {
-		return myResourceId;
-	}
-
-	public String getResourceType() {
-		return myResourceType;
-	}
-
-	public Date getSearchLastReturned() {
-		return mySearchLastReturned;
-	}
-	
-	public String getSearchQueryString() {
-		return mySearchQueryString;
-	}
-
-	public SearchTypeEnum getSearchType() {
-		return mySearchType;
-	}
-
-	public SearchStatusEnum getStatus() {
-		return myStatus;
-	}
-
-	public Integer getTotalCount() {
-		return myTotalCount;
-	}
-
-	public String getUuid() {
-		return myUuid;
-	}
-
-	public void setCreated(Date theCreated) {
-		myCreated = theCreated;
-	}
-
-
-	public void setFailureCode(Integer theFailureCode) {
-		myFailureCode = theFailureCode;
-	}
-
-	public void setFailureMessage(String theFailureMessage) {
-		myFailureMessage = left(theFailureMessage, FAILURE_MESSAGE_LENGTH);
-	}
-
-	public void setLastUpdated(Date theLowerBound, Date theUpperBound) {
-		myLastUpdatedLow = theLowerBound;
-		myLastUpdatedHigh = theUpperBound;
-	}
-	public void setLastUpdated(DateRangeParam theLastUpdated) {
-		if (theLastUpdated == null) {
-			myLastUpdatedLow = null;
-			myLastUpdatedHigh = null;
-		} else {
-			myLastUpdatedLow = theLastUpdated.getLowerBoundAsInstant();
-			myLastUpdatedHigh = theLastUpdated.getUpperBoundAsInstant();
-		}
-	}
-	
 	public void setNumFound(int theNumFound) {
 		myNumFound = theNumFound;
 	}
 
+	public Integer getPreferredPageSize() {
+		return myPreferredPageSize;
+	}
+
 	public void setPreferredPageSize(Integer thePreferredPageSize) {
 		myPreferredPageSize = thePreferredPageSize;
 	}
 
+	public Long getResourceId() {
+		return myResourceId;
+	}
+
 	public void setResourceId(Long theResourceId) {
 		myResourceId = theResourceId;
 	}
 
+	public String getResourceType() {
+		return myResourceType;
+	}
 
 	public void setResourceType(String theResourceType) {
 		myResourceType = theResourceType;
 	}
 
+	public Date getSearchLastReturned() {
+		return mySearchLastReturned;
+	}
+
 	public void setSearchLastReturned(Date theDate) {
 		mySearchLastReturned = theDate;
 	}
 
+	public String getSearchQueryString() {
+		return mySearchQueryString;
+	}
+
 	public void setSearchQueryString(String theSearchQueryString) {
 		if (theSearchQueryString != null && theSearchQueryString.length() > MAX_SEARCH_QUERY_STRING) {
 			mySearchQueryString = null;
@@ -264,26 +232,47 @@ public class Search implements Serializable {
 		}
 	}
 
-	public void setSearchQueryStringHash(Integer theSearchQueryStringHash) {
+	public SearchTypeEnum getSearchType() {
-		mySearchQueryStringHash = theSearchQueryStringHash;
+		return mySearchType;
 	}
 
 	public void setSearchType(SearchTypeEnum theSearchType) {
 		mySearchType = theSearchType;
 	}
 
+	public SearchStatusEnum getStatus() {
+		return myStatus;
+	}
+
 	public void setStatus(SearchStatusEnum theStatus) {
 		myStatus = theStatus;
 	}
 
+	public Integer getTotalCount() {
+		return myTotalCount;
+	}
+
 	public void setTotalCount(Integer theTotalCount) {
 		myTotalCount = theTotalCount;
 	}
 
+	public String getUuid() {
+		return myUuid;
+	}
+
 	public void setUuid(String theUuid) {
 		myUuid = theUuid;
 	}
 
+	public void setLastUpdated(Date theLowerBound, Date theUpperBound) {
+		myLastUpdatedLow = theLowerBound;
+		myLastUpdatedHigh = theUpperBound;
+	}
+
+	public void setSearchQueryStringHash(Integer theSearchQueryStringHash) {
+		mySearchQueryStringHash = theSearchQueryStringHash;
+	}
+
 	private Set<Include> toIncList(boolean theWantReverse) {
 		HashSet<Include> retVal = new HashSet<Include>();
 		for (SearchInclude next : getIncludes()) {
@@ -302,4 +291,7 @@ public class Search implements Serializable {
 		return toIncList(true);
 	}
 
+	public void addInclude(SearchInclude theInclude) {
+		getIncludes().add(theInclude);
+	}
 }

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

@@ -32,6 +32,7 @@ import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@@ -134,13 +135,8 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		final List<Long> pidsSubList = mySearchCoordinatorSvc.getResources(myUuid, theFromIndex, theToIndex);
 
 		TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
-		template.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
+		template.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
-		return template.execute(new TransactionCallback<List<IBaseResource>>() {
+		return template.execute(theStatus -> toResourceList(sb, pidsSubList));
-			@Override
-			public List<IBaseResource> doInTransaction(TransactionStatus theStatus) {
-				return toResourceList(sb, pidsSubList);
-			}
-		});
 	}
 
 	private void ensureDependenciesInjected() {
@@ -273,8 +269,8 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 	List<IBaseResource> toResourceList(ISearchBuilder sb, List<Long> pidsSubList) {
 		Set<Long> includedPids = new HashSet<>();
 		if (mySearchEntity.getSearchType() == SearchTypeEnum.SEARCH) {
-			includedPids.addAll(sb.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated()));
+			includedPids.addAll(sb.loadIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated()));
-			includedPids.addAll(sb.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated()));
+			includedPids.addAll(sb.loadIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated()));
 		}
 
 		// Execute the query and make sure we return distinct results

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

@@ -258,8 +258,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 					 * individually for pages as we return them to clients
 					 */
 					final Set<Long> includedPids = new HashSet<Long>();
-					includedPids.addAll(sb.loadReverseIncludes(theCallingDao, myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated()));
+					includedPids.addAll(sb.loadIncludes(theCallingDao, myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated()));
-					includedPids.addAll(sb.loadReverseIncludes(theCallingDao, myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated()));
+					includedPids.addAll(sb.loadIncludes(theCallingDao, myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated()));
 
 					List<IBaseResource> resources = new ArrayList<IBaseResource>();
 					sb.loadResourcesByPid(pids, resources, includedPids, false, myEntityManager, myContext, theCallingDao);
@@ -336,10 +336,10 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		search.setSearchQueryStringHash(queryString.hashCode());
 
 		for (Include next : theParams.getIncludes()) {
-			search.getIncludes().add(new SearchInclude(search, next.getValue(), false, next.isRecurse()));
+			search.addInclude(new SearchInclude(search, next.getValue(), false, next.isRecurse()));
 		}
 		for (Include next : theParams.getRevIncludes()) {
-			search.getIncludes().add(new SearchInclude(search, next.getValue(), true, next.isRecurse()));
+			search.addInclude(new SearchInclude(search, next.getValue(), true, next.isRecurse()));
 		}
 
 		SearchTask task = new SearchTask(search, theCallingDao, theParams, theResourceType, searchUuid);

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

@@ -47,7 +47,7 @@ import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
 import static org.mockito.Mockito.mock;
 
-@SuppressWarnings("unchecked")
+@SuppressWarnings({"unchecked", "Duplicates"})
 public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4SearchNoFtTest.class);
 
@@ -145,6 +145,59 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		assertThat(ids, empty());
 	}
 
+	/**
+	 * See #1053
+	 */
+	@Test
+	public void testLastUpdateShouldntApplyToIncludes() {
+		SearchParameterMap map;
+		List<String> ids;
+
+		Date beforeAll = new Date();
+		ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast(100);
+
+		Organization org = new Organization();
+		org.setName("O1");
+		org.setId("O1");
+		myOrganizationDao.update(org);
+		ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast(100);
+
+		Date beforePatient = new Date();
+		ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast(100);
+
+		Patient p = new Patient();
+		p.setId("P1");
+		p.setActive(true);
+		p.setManagingOrganization(new Reference("Organization/O1"));
+		myPatientDao.update(p);
+
+		ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast(100);
+		Date afterAll = new Date();
+
+		// Search with between date (should still return Organization even though
+		// it was created before that date, since it's an include)
+		map = new SearchParameterMap();
+		map.setLastUpdated(new DateRangeParam().setLowerBoundInclusive(beforePatient));
+		map.addInclude(Patient.INCLUDE_ORGANIZATION);
+		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		assertThat(ids, contains("Patient/P1", "Organization/O1"));
+
+		// Search before everything
+		map = new SearchParameterMap();
+		map.setLastUpdated(new DateRangeParam().setLowerBoundInclusive(beforeAll));
+		map.addInclude(Patient.INCLUDE_ORGANIZATION);
+		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		assertThat(ids, contains("Patient/P1", "Organization/O1"));
+
+		// Search after everything
+		map = new SearchParameterMap();
+		map.setLastUpdated(new DateRangeParam().setLowerBoundInclusive(afterAll));
+		map.addInclude(Patient.INCLUDE_ORGANIZATION);
+		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		assertThat(ids, empty());
+
+	}
+
 	@Test
 	public void testEverythingTimings() {
 		String methodName = "testEverythingTimings";

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/param/DateRangeParamTest.java

@@ -1,31 +1,5 @@
 package ca.uhn.fhir.rest.param;
 
-import static ca.uhn.fhir.rest.param.ParamPrefixEnum.APPROXIMATE;
-import static ca.uhn.fhir.rest.param.ParamPrefixEnum.EQUAL;
-import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN;
-import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN_OR_EQUALS;
-import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN;
-import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN_OR_EQUALS;
-import static ca.uhn.fhir.rest.param.ParamPrefixEnum.NOT_EQUAL;
-import static com.google.common.collect.Lists.newArrayList;
-import static java.lang.System.currentTimeMillis;
-import static java.util.concurrent.TimeUnit.SECONDS;
-import static org.hamcrest.core.Is.is;
-import static org.hamcrest.core.IsEqual.equalTo;
-import static org.hamcrest.core.IsNot.not;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertThat;
-
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.*;
-import java.util.concurrent.TimeUnit;
-
-import com.google.common.testing.EqualsTester;
-import org.junit.AfterClass;
-import org.junit.Test;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import ca.uhn.fhir.model.primitive.DateTimeDt;
@@ -33,18 +7,57 @@ import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.api.QualifiedParamList;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.TestUtil;
+import com.google.common.testing.EqualsTester;
+import org.junit.AfterClass;
+import org.junit.Test;
+
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.TimeZone;
+
+import static ca.uhn.fhir.rest.param.ParamPrefixEnum.*;
+import static java.lang.System.currentTimeMillis;
+import static java.util.concurrent.TimeUnit.SECONDS;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 
 public class DateRangeParamTest {
 
-	private static FhirContext ourCtx = FhirContext.forDstu3();
 	private static final SimpleDateFormat ourFmt;
-
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DateRangeParamTest.class);
+	private static FhirContext ourCtx = FhirContext.forDstu3();
 
 	static {
 		ourFmt = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSSS");
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	private static DateRangeParam create(String theLower, String theUpper) throws InvalidRequestException {
+		DateRangeParam p = new DateRangeParam();
+		List<QualifiedParamList> tokens = new ArrayList<QualifiedParamList>();
+		tokens.add(QualifiedParamList.singleton(null, theLower));
+		if (theUpper != null) {
+			tokens.add(QualifiedParamList.singleton(null, theUpper));
+		}
+		p.setValuesAsQueryTokens(ourCtx, null, tokens);
+		return p;
+	}
+
+	public static Date parse(String theString) throws ParseException {
+		return ourFmt.parse(theString);
+	}
+
+	public static Date parseM1(String theString) throws ParseException {
+		return new Date(ourFmt.parse(theString).getTime() - 1L);
+	}
+
 	private DateRangeParam create(String theString) {
 		return new DateRangeParam(new DateParam(theString));
 	}
@@ -119,6 +132,26 @@ public class DateRangeParamTest {
 		assertEquals(parseM1("2011-01-02 00:00:00.0000"), create("2011-01-01").getUpperBoundAsInstant());
 	}
 
+	@Test
+	public void testSetBoundsWithDatesInclusive() {
+		DateRangeParam range = new DateRangeParam();
+		range.setLowerBoundInclusive(new Date());
+		range.setUpperBoundInclusive(new Date());
+
+		assertEquals(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, range.getLowerBound().getPrefix());
+		assertEquals(ParamPrefixEnum.LESSTHAN_OR_EQUALS, range.getUpperBound().getPrefix());
+	}
+
+	@Test
+	public void testSetBoundsWithDatesExclusive() {
+		DateRangeParam range = new DateRangeParam();
+		range.setLowerBoundExclusive(new Date());
+		range.setUpperBoundExclusive(new Date());
+
+		assertEquals(ParamPrefixEnum.GREATERTHAN, range.getLowerBound().getPrefix());
+		assertEquals(ParamPrefixEnum.LESSTHAN, range.getUpperBound().getPrefix());
+	}
+
 	@Test
 	public void testOrList() {
 		assertNotNull(new DateOrListParam().newInstance());
@@ -195,11 +228,6 @@ public class DateRangeParamTest {
 		assertEquals(parseM1("2014-01-01 00:00:00.0000"), create("gt2011", "le2013").getUpperBoundAsInstant());
 	}
 
-	@AfterClass
-	public static void afterClassClearContext() {
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
 	@Test()
 	public void testEqualsAndHashCode() {
 		Date lowerBound = new Date(currentTimeMillis());
@@ -218,23 +246,4 @@ public class DateRangeParamTest {
 				new DateRangeParam(null, new DateParam(LESSTHAN_OR_EQUALS, upperBound)))
 			.testEquals();
 	}
-
-	private static DateRangeParam create(String theLower, String theUpper) throws InvalidRequestException {
-		DateRangeParam p = new DateRangeParam();
-		List<QualifiedParamList> tokens = new ArrayList<QualifiedParamList>();
-		tokens.add(QualifiedParamList.singleton(null, theLower));
-		if (theUpper != null) {
-			tokens.add(QualifiedParamList.singleton(null, theUpper));
-		}
-		p.setValuesAsQueryTokens(ourCtx, null, tokens);
-		return p;
-	}
-
-	public static Date parse(String theString) throws ParseException {
-		return ourFmt.parse(theString);
-	}
-
-	public static Date parseM1(String theString) throws ParseException {
-		return new Date(ourFmt.parse(theString).getTime() - 1L);
-	}
 }

src/changes/changes.xml

@@ -249,6 +249,11 @@
 				queue (only the ID), which should reduce the memory/disk footprint of the queue
 				when it grows long.
 			</action>
+			<action type="fix" issue="1053">
+				A bug was fixed in JPA server searches: When performing a search with a _lastUpdate 
+				filter, the filter was applied to any _include values, which it should not have been.
+				Thanks to Deepak Garg for reporting!
+			</action>
 		</release>
 		<release version="3.4.0" date="2018-05-28">
 			<action type="add">