Fix missing direct argument in JenaUtils.getParents()

Author: arteymix

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

@@ -18,17 +18,16 @@ public static Collection<OntClass> getParents( OntModel model, Collection<OntCla
         if ( ontClasses.isEmpty() ) {
             return Collections.emptySet();
         }
-        Collection<OntClass> result = new HashSet<>();
         Iterator<OntClass> it = ontClasses.iterator();
         ExtendedIterator<OntClass> iterator = it.next()
                 .inModel( model )
                 .as( OntClass.class )
-                .listSuperClasses( direct )
-                .filterDrop( new PredicateFilter<>( o -> o.equals( model.getProfile().THING() ) ) );
+                .listSuperClasses( direct );
         while ( it.hasNext() ) {
-            iterator = iterator.andThen( it.next().inModel( model ).as( OntClass.class ).listSuperClasses( true ) );
+            iterator = iterator.andThen( it.next().inModel( model ).as( OntClass.class ).listSuperClasses( direct ) );
         }
 
+        Collection<OntClass> result = new HashSet<>();
         while ( iterator.hasNext() ) {
             OntClass c = iterator.next();
 
@@ -49,6 +48,10 @@ public static Collection<OntClass> getParents( OntModel model, Collection<OntCla
             if ( c.getURI() == null )
                 continue;
 
+            // owl:Thing
+            if ( c.equals( model.getProfile().THING() ) )
+                continue;
+
             result.add( c );
         }
 

test/ubic/basecode/ontology/OntologyTermTest.java

@@ -191,7 +191,7 @@ public void testGetParentsFromMultipleTerms() {
         OntologyTerm brain = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0000955" );
         OntologyTerm liver = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0002107" );
         Collection<OntologyTerm> children = uberon.getParents( Arrays.asList( brain, liver ), false, true );
-        assertEquals( 22, children.size() );
+        assertEquals( 30, children.size() );
         assertFalse( children.contains( uberon.getTerm( OWL2.Nothing.getURI() ) ) );
     }