Honor direct flag when retrieving children via additional properties

Author: arteymix

src/ubic/basecode/ontology/jena/JenaUtils.java

@@ -13,6 +13,8 @@
 import java.util.*;
 import java.util.function.Predicate;
 
+import static com.hp.hpl.jena.reasoner.ReasonerRegistry.makeDirect;
+
 public class JenaUtils {
 
     public static Collection<OntClass> getParents( OntModel model, Collection<OntClass> ontClasses, boolean direct, @Nullable Set<Restriction> additionalRestrictions ) {
@@ -80,6 +82,9 @@ public static Collection<OntClass> getChildren( OntModel model, Collection<OntCl
             timer.reset();
             timer.start();
             Property subClassOf = model.getProfile().SUB_CLASS_OF();
+            if ( direct ) {
+                subClassOf = ResourceFactory.createProperty( makeDirect( subClassOf.getURI() ) );
+            }
             Set<Restriction> restrictions = UniqueExtendedIterator.create( additionalRestrictions.iterator() )
                     .filterKeep( new RestrictionWithValuesFromFilter( terms ) )
                     .toSet();

test/ubic/basecode/ontology/OntologyTermTest.java

@@ -272,6 +272,7 @@ public void testGetParentsHasPart() {
     public void testGetChildrenHasPart() {
         OntologyTerm t = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0000955" );
         assertNotNull( t );
+        assertEquals( 76, t.getChildren( true ).size() );
         Collection<OntologyTerm> children = t.getChildren( false );
         assertEquals( 1496, children.size() );
         // via subclass of, insect adult brain