Merge pull request #979 from ontodev/976-fix

Handle subclass of cycles in related object selections

CHANGELOG.md

@@ -6,8 +6,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+
+### Changed
 - Sort [`report`] violations by rule name within level [#955]
 
+### Fixed
+- Fix subClassOf cycles in related object selection [#979]
+
 ## [1.8.3] - 2021-12-16
 
 ### Changed
@@ -294,6 +299,7 @@ First official release of ROBOT!
 [`template`]: http://robot.obolibrary.org/template
 [`validate`]: http://robot.obolibrary.org/validate
 
+[#979]: https://github.com/ontodev/robot/pull/979
 [#955]: https://github.com/ontodev/robot/pull/955
 [#953]: https://github.com/ontodev/robot/pull/953
 [#951]: https://github.com/ontodev/robot/pull/951

robot-core/src/main/java/org/obolibrary/robot/RelatedObjectsHelper.java

@@ -2032,6 +2032,10 @@ private static void selectClassAncestors(
     for (OWLClassExpression classExpression : EntitySearcher.getSuperClasses(cls, ontology)) {
       if (!classExpression.isAnonymous()) {
         OWLClass superClass = classExpression.asOWLClass();
+        if (ancestors.contains(superClass)) {
+          // Subclass of/equivalent class can cause a loop - see #976
+          continue;
+        }
         ancestors.add(superClass);
         if (!superClass.isTopEntity()) {
           selectClassAncestors(ontology, superClass, ancestors);
@@ -2055,6 +2059,10 @@ private static void selectClassDescendants(
     for (OWLClassExpression classExpression : EntitySearcher.getSubClasses(cls, ontology)) {
       if (!classExpression.isAnonymous()) {
         OWLClass subClass = classExpression.asOWLClass();
+        if (descendants.contains(subClass)) {
+          // Subclass of/equivalent class can cause a loop - see #976
+          continue;
+        }
         descendants.add(subClass);
         if (!EntitySearcher.getSubClasses(subClass, ontology).isEmpty()) {
           selectClassDescendants(ontology, subClass, descendants);

robot-core/src/test/java/org/obolibrary/robot/RelatedObjectsHelperTest.java

@@ -4,6 +4,8 @@
 
 import com.google.common.collect.Sets;
 import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.Set;
 import org.junit.Test;
@@ -151,6 +153,29 @@ public void testGetAnnotationByRegex() throws Exception {
     assertTrue(annotations.contains(annotation2));
   }
 
+  /**
+   * Test selecting ancestors and descendants with a subClassOf cycle.
+   *
+   * @throws Exception on any problem
+   */
+  @Test
+  public void testSelectCycle() throws Exception {
+    IOHelper ioHelper = new IOHelper();
+    OWLOntology patoRole = loadOntology("/pato_role.owl");
+
+    // Use BFO role as our starting object - then get all ancestors and descendants
+    Set<OWLObject> objects =
+        new HashSet<>(
+            Collections.singletonList(
+                df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/BFO_0000023"))));
+    Set<OWLObject> relatedObjects =
+        RelatedObjectsHelper.select(
+            patoRole, ioHelper, objects, Arrays.asList("ancestors", "descendants"));
+
+    // Check that the select returned all classes in this ontology (all descendants of role)
+    assert relatedObjects.size() == patoRole.getClassesInSignature().size();
+  }
+
   /** @throws Exception */
   private OWLOntology getOntology() throws Exception {
     OWLOntology ontology = manager.createOntology();