Adding option to traverse breadth or depth first up ancestor hierarchy

Author: cmungall

linkml_runtime/utils/schemaview.py

@@ -3,7 +3,7 @@
 import logging
 from functools import lru_cache
 from copy import copy, deepcopy
-from collections import defaultdict
+from collections import defaultdict, OrderedDict
 from typing import Mapping, Tuple, Type
 from linkml_runtime.utils.namespaces import Namespaces
 from deprecated.classic import deprecated
@@ -30,22 +30,28 @@
 ENUM_NAME = Union[EnumDefinitionName, str]
 
 
-def _closure(f, x, reflexive=True, **kwargs):
+def _closure(f, x, reflexive=True, depth_first=True, **kwargs):
     if reflexive:
         rv = [x]
     else:
         rv = []
     visited = []
     todo = [x]
     while len(todo) > 0:
-        i = todo.pop()
+        if depth_first:
+            i = todo.pop()
+        else:
+            i = todo[0]
+            todo = todo[1:]
         visited.append(i)
         vals = f(i)
         for v in vals:
             if v not in visited:
                 todo.append(v)
-                rv.append(v)
+                if v not in rv:
+                    rv.append(v)
     return rv
+    #return list(OrderedDict.fromkeys(rv))
 
 
 def load_schema_wrap(path: str, **kwargs):
@@ -498,7 +504,8 @@ def slot_children(self, slot_name: SLOT_NAME, imports=True, mixins=True, is_a=Tr
         return [x.name for x in elts if (x.is_a == slot_name and is_a) or (mixins and slot_name in x.mixins)]
 
     @lru_cache()
-    def class_ancestors(self, class_name: CLASS_NAME, imports=True, mixins=True, reflexive=True, is_a=True) -> List[ClassDefinitionName]:
+    def class_ancestors(self, class_name: CLASS_NAME, imports=True, mixins=True, reflexive=True, is_a=True,
+                        depth_first=True) -> List[ClassDefinitionName]:
         """
         Closure of class_parents method
 
@@ -507,9 +514,12 @@ def class_ancestors(self, class_name: CLASS_NAME, imports=True, mixins=True, ref
         :param mixins: include mixins (default is True)
         :param is_a: include is_a parents (default is True)
         :param reflexive: include self in set of ancestors
+        :param depth_first:
         :return: ancestor class names
         """
-        return _closure(lambda x: self.class_parents(x, imports=imports, mixins=mixins, is_a=is_a), class_name, reflexive=reflexive)
+        return _closure(lambda x: self.class_parents(x, imports=imports, mixins=mixins, is_a=is_a),
+                        class_name,
+                        reflexive=reflexive,  depth_first=depth_first)
 
     @lru_cache()
     def slot_ancestors(self, slot_name: SLOT_NAME, imports=True, mixins=True, reflexive=True, is_a=True) -> List[SlotDefinitionName]:
@@ -523,7 +533,9 @@ def slot_ancestors(self, slot_name: SLOT_NAME, imports=True, mixins=True, reflex
         :param reflexive: include self in set of ancestors
         :return: ancestor slot names
         """
-        return _closure(lambda x: self.slot_parents(x, imports=imports, mixins=mixins, is_a=is_a), slot_name, reflexive=reflexive)
+        return _closure(lambda x: self.slot_parents(x, imports=imports, mixins=mixins, is_a=is_a),
+                        slot_name,
+                        reflexive=reflexive)
 
     @lru_cache()
     def class_descendants(self, class_name: CLASS_NAME, imports=True, mixins=True, reflexive=True, is_a=True) -> List[ClassDefinitionName]:

tests/test_utils/test_schemaview.py

@@ -2,6 +2,7 @@
 import unittest
 import logging
 from copy import copy
+from typing import List
 
 from linkml_runtime.linkml_model.meta import SchemaDefinition, ClassDefinition, SlotDefinitionName, SlotDefinition
 from linkml_runtime.loaders.yaml_loader import YAMLLoader
@@ -290,6 +291,37 @@ def test_merge_imports(self):
         all_c2_noi = copy(view.all_classes(imports=False))
         assert len(all_c2_noi) == len(all_c2)
 
+    def test_traversal(self):
+        schema = SchemaDefinition(id='test', name='traversal-test')
+        view = SchemaView(schema)
+        view.add_class(ClassDefinition('Root', mixins=['RootMixin']))
+        view.add_class(ClassDefinition('A', is_a='Root', mixins=['Am1', 'Am2', 'AZ']))
+        view.add_class(ClassDefinition('B', is_a='A', mixins=['Bm1', 'Bm2', 'BY']))
+        view.add_class(ClassDefinition('C', is_a='B', mixins=['Cm1', 'Cm2', 'CX']))
+        view.add_class(ClassDefinition('RootMixin', mixin=True))
+        view.add_class(ClassDefinition('Am1', is_a='RootMixin', mixin=True))
+        view.add_class(ClassDefinition('Am2', is_a='RootMixin', mixin=True))
+        view.add_class(ClassDefinition('Bm1', is_a='Am1', mixin=True))
+        view.add_class(ClassDefinition('Bm2', is_a='Am2', mixin=True))
+        view.add_class(ClassDefinition('Cm1', is_a='Bm1', mixin=True))
+        view.add_class(ClassDefinition('Cm2', is_a='Bm2', mixin=True))
+        view.add_class(ClassDefinition('AZ', is_a='RootMixin', mixin=True))
+        view.add_class(ClassDefinition('BY', is_a='RootMixin', mixin=True))
+        view.add_class(ClassDefinition('CX', is_a='RootMixin', mixin=True))
+        def check(ancs: List, expected: List):
+            #print(ancs)
+            self.assertEqual(ancs, expected)
+        check(view.class_ancestors('C', depth_first=True),
+              ['C', 'Cm1', 'Cm2', 'CX', 'B', 'Bm1', 'Bm2', 'BY', 'A', 'Am1', 'Am2', 'AZ', 'Root', 'RootMixin'])
+        check(view.class_ancestors('C', depth_first=False),
+              ['C', 'Cm1', 'Cm2', 'CX', 'B', 'Bm1', 'Bm2', 'RootMixin', 'BY', 'A', 'Am1', 'Am2', 'AZ', 'Root'])
+        check(view.class_ancestors('C', mixins=False),
+              ['C', 'B', 'A', 'Root'])
+        check(view.class_ancestors('C', is_a=False),
+              ['C', 'Cm1', 'Cm2', 'CX'])
+
+
+
     def test_slot_inheritance(self):
         schema = SchemaDefinition(id='test', name='test')
         view = SchemaView(schema)