Fix timeout in large $everything operation (#5298)

* Fixes

* Changelog

* Spotless

* Compress data file

* Remove fixme

* Fix imports

* Test fix

* Compile fix

* Apply spotless

* Address review comments

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5298-fix-everything-timeout.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 5298
+title: "Under some circumstances, a large `$everything` operation could enter an infinite loop and eventually timeout with a failure. This has been corrected."

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

@@ -2679,6 +2679,7 @@ public class QueryStack {
 		Condition predicate =
 				table.createEverythingPredicate(theResourceName, theTypeSourceResourceNames, theTargetPids);
 		mySqlBuilder.addPredicate(predicate);
+		mySqlBuilder.getSelect().setIsDistinct(true);
 	}
 
 	public IQueryParameterType newParameterInstance(

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

@@ -2051,7 +2051,7 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
 				}
 
 				if (myNext == null) {
-					// if we got here, it means the current PjaPid has already been processed
+					// if we got here, it means the current JpaPid has already been processed,
 					// and we will decide (here) if we need to fetch related resources recursively
 					if (myFetchIncludesForEverythingOperation) {
 						myIncludesIterator = new IncludesIterator(myPidSet, myRequest);

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

@@ -32,8 +32,6 @@ import org.hibernate.ScrollableResults;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.sql.Connection;
-import java.sql.PreparedStatement;
 import java.util.Arrays;
 import javax.persistence.EntityManager;
 import javax.persistence.FlushModeType;
@@ -48,14 +46,11 @@ public class SearchQueryExecutor implements ISearchQueryExecutor {
 	private static final Object[] EMPTY_OBJECT_ARRAY = new Object[0];
 	private static final Logger ourLog = LoggerFactory.getLogger(SearchQueryExecutor.class);
 	private final GeneratedSql myGeneratedSql;
-	private final Integer myMaxResultsToFetch;
 
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	private EntityManager myEntityManager;
 
 	private boolean myQueryInitialized;
-	private Connection myConnection;
-	private PreparedStatement myStatement;
 	private ScrollableResultsIterator<Number> myResultSet;
 	private Long myNext;
 
@@ -66,7 +61,6 @@ public class SearchQueryExecutor implements ISearchQueryExecutor {
 		Validate.notNull(theGeneratedSql, "theGeneratedSql must not be null");
 		myGeneratedSql = theGeneratedSql;
 		myQueryInitialized = false;
-		myMaxResultsToFetch = theMaxResultsToFetch;
 	}
 
 	/**
@@ -76,7 +70,6 @@ public class SearchQueryExecutor implements ISearchQueryExecutor {
 		assert NO_MORE != null;
 
 		myGeneratedSql = null;
-		myMaxResultsToFetch = null;
 		myNext = NO_MORE;
 	}