Merge pull request #572 from emmo-repo/406-harmonize-get_descendants-…

…and-get_ancestors

get_ancestors and get_descendants have harmonized arguments.

ontopy/graph.py

@@ -371,7 +371,6 @@ def add_branch(  # pylint: disable=too-many-arguments,too-many-locals
         also included."""
         if leaves is None:
             leaves = ()
-
         classes = self.ontology.get_branch(
             root=root,
             leaves=leaves,
@@ -400,9 +399,17 @@ def add_branch(  # pylint: disable=too-many-arguments,too-many-locals
             nodeattrs=nodeattrs,
             **attrs,
         )
-
+        closest_ancestors = False
+        ancestor_generations = None
+        if include_parents == "closest":
+            closest_ancestors = True
+        elif isinstance(include_parents, int):
+            ancestor_generations = include_parents
         parents = self.ontology.get_ancestors(
-            classes, include=include_parents, strict=True
+            classes,
+            closest=closest_ancestors,
+            generations=ancestor_generations,
+            strict=True,
         )
         if parents:
             for parent in parents:

ontopy/ontology.py

@@ -4,7 +4,7 @@
 If desirable some of these additions may be moved back into owlready2.
 """
 # pylint: disable=too-many-lines,fixme,arguments-differ,protected-access
-from typing import TYPE_CHECKING, Optional, Union, Sequence
+from typing import TYPE_CHECKING, Optional, Union
 import os
 import itertools
 import inspect
@@ -1513,18 +1513,27 @@ def closest_common_ancestor(*classes):
             "A closest common ancestor should always exist !"
         )
 
-    def get_ancestors(self, classes, include="all", strict=True):
+    def get_ancestors(
+        self,
+        classes: "Union[List, ThingClass]",
+        closest: bool = False,
+        generations: int = None,
+        strict: bool = True,
+    ) -> set:
         """Return ancestors of all classes in `classes`.
-        classes to be provided as list
-
-        The values of `include` may be:
-          - None: ignore this argument
-          - "all": Include all ancestors.
-          - "closest": Include all ancestors up to the closest common
-            ancestor of all classes.
-          - int: Include this number of ancestor levels.  Here `include`
-            may be an integer or a string that can be converted to int.
+        Args:
+            classes: class(es) for which ancestors should be returned.
+            generations: Include this number of generations, default is all.
+            closest: If True, return all ancestors up to and including the
+                closest common ancestor. Return all if False.
+            strict: If True returns only real ancestors, i.e. `classes` are
+                are not included in the returned set.
+        Returns:
+            Set of ancestors to `classes`.
         """
+        if not isinstance(classes, Iterable):
+            classes = [classes]
+
         ancestors = set()
         if not classes:
             return ancestors
@@ -1535,22 +1544,24 @@ def addancestors(entity, counter, subject):
                     subject.add(parent)
                     addancestors(parent, counter - 1, subject)
 
-        if isinstance(include, str) and include.isdigit():
-            include = int(include)
+        if closest:
+            if generations is not None:
+                raise ValueError(
+                    "Only one of `generations` or `closest` may be specified."
+                )
 
-        if include == "all":
-            ancestors.update(*(_.ancestors() for _ in classes))
-        elif include == "closest":
-            closest = self.closest_common_ancestor(*classes)
+            closest_ancestor = self.closest_common_ancestor(*classes)
             for cls in classes:
                 ancestors.update(
-                    _ for _ in cls.ancestors() if closest in _.ancestors()
+                    anc
+                    for anc in cls.ancestors()
+                    if closest_ancestor in anc.ancestors()
                 )
-        elif isinstance(include, int):
+        elif isinstance(generations, int):
             for entity in classes:
-                addancestors(entity, int(include), ancestors)
-        elif include not in (None, "None", "none", ""):
-            raise ValueError('include must be "all", "closest" or None')
+                addancestors(entity, generations, ancestors)
+        else:
+            ancestors.update(*(cls.ancestors() for cls in classes))
 
         if strict:
             return ancestors.difference(classes)
@@ -1559,12 +1570,12 @@ def addancestors(entity, counter, subject):
     def get_descendants(
         self,
         classes: "Union[List, ThingClass]",
-        common: bool = False,
         generations: int = None,
+        common: bool = False,
     ) -> set:
         """Return descendants/subclasses of all classes in `classes`.
         Args:
-            classes: to be provided as list.
+            classes: class(es) for which descendants are desired.
             common: whether to only return descendants common to all classes.
             generations: Include this number of generations, default is all.
         Returns:
@@ -1574,7 +1585,7 @@ def get_descendants(
             'generations' defaults to all.
         """
 
-        if not isinstance(classes, Sequence):
+        if not isinstance(classes, Iterable):
             classes = [classes]
 
         descendants = {name: [] for name in classes}

tests/ontopy_tests/test_graph.py

@@ -76,6 +76,21 @@ class hasPartRenamed(owlready2.ObjectProperty):
     graph.add_legend()
     graph.save(tmpdir / "testonto.png")
 
+    with pytest.warns() as record:
+        graph2 = OntoGraph(
+            testonto,
+            testonto.TestClass,
+            relations="all",
+            addnodes=True,
+            edgelabels=None,
+        )
+        assert str(record[0].message) == (
+            "Style not defined for relation hasSpecialRelation. "
+            "Resorting to default style."
+        )
+    graph2.add_legend()
+    graph2.save(tmpdir / "testonto2.png")
+
 
 def test_emmo_graphs(emmo: "Ontology", tmpdir: "Path") -> None:
     """Testing OntoGraph on various aspects of EMMO.
@@ -217,8 +232,8 @@ def test_emmo_graphs(emmo: "Ontology", tmpdir: "Path") -> None:
         graph = OntoGraph(emmo)
         graph.add_entities(semiotic, relations="all", edgelabels=False)
         graph.add_legend()
-        graph.save(tmpdir / "measurement.png")
-
+        graph.save(tmpdir / "measurement.png", fmt="graphviz")
+        print("reductionistc")
         # Reductionistic perspective
         graph = OntoGraph(
             emmo,
@@ -236,7 +251,53 @@ def test_emmo_graphs(emmo: "Ontology", tmpdir: "Path") -> None:
             edgelabels=None,
         )
         graph.add_legend()
-        graph.save(tmpdir / "Reductionistic.png", fmt="graphviz")
+        graph.save(tmpdir / "Reductionistic.png")
+
+        # Reductionistic perspective, choose leaf_generations
+        graph = OntoGraph(
+            emmo,
+            emmo.Reductionistic,
+            relations="all",
+            addnodes=False,
+            parents=2,
+            edgelabels=None,
+        )
+        graph.add_branch(
+            emmo.Reductionistic,
+            leaves=[
+                emmo.Quantity,
+                emmo.String,
+                emmo.PrefixedUnit,
+                emmo.SymbolicConstruct,
+                emmo.Matter,
+            ],
+        )
+
+        graph.add_legend()
+        graph.save(tmpdir / "Reductionistic_addbranch.png")
+
+        graph2 = OntoGraph(
+            emmo,
+            emmo.Reductionistic,
+            relations="all",
+            addnodes=False,
+            # parents=2,
+            edgelabels=None,
+        )
+        graph2.add_branch(
+            emmo.Reductionistic,
+            leaves=[
+                emmo.Quantity,
+                emmo.String,
+                emmo.PrefixedUnit,
+                emmo.SymbolicConstruct,
+                emmo.Matter,
+            ],
+            include_parents=2,
+        )
+
+        graph2.add_legend()
+        graph2.save(tmpdir / "Reductionistic_addbranch_2.png")
 
         # View modules
 

tests/test_generation_search.py

@@ -80,3 +80,70 @@ def test_descendants(emmo: "Ontology", repo_dir: "Path") -> None:
     assert onto.get_descendants([onto.Tree, onto.NaturalDye], common=True) == {
         onto.Avocado
     }
+
+
+def test_ancestors(emmo: "Ontology", repo_dir: "Path") -> None:
+    from ontopy import get_ontology
+    from ontopy.utils import LabelDefinitionError
+
+    ontopath = repo_dir / "tests" / "testonto" / "testontology.ttl"
+
+    onto = get_ontology(ontopath).load()
+
+    # Test that default gives all ancestors.
+    assert onto.get_ancestors(onto.NorwaySpruce) == {
+        onto.Spruce,
+        onto.Tree,
+        onto.EvergreenTree,
+        onto.Thing,
+    }
+
+    # Test that asking for 0 generations returns empty set
+    assert onto.get_ancestors(onto.NorwaySpruce, generations=0) == set()
+
+    # Check that number of generations are returned correctly
+    assert onto.get_ancestors(onto.NorwaySpruce, generations=2) == {
+        onto.Spruce,
+        onto.EvergreenTree,
+    }
+
+    assert onto.get_ancestors(onto.NorwaySpruce, generations=1) == {
+        onto.Spruce,
+    }
+    # Check that no error is generated if one of the classes do
+    # not have enough parents for all given generations
+    assert onto.get_ancestors(onto.NorwaySpruce, generations=10) == (
+        onto.get_ancestors(onto.NorwaySpruce)
+    )
+
+    # Check that ancestors of a list is returned correctly
+    assert onto.get_ancestors([onto.NorwaySpruce, onto.Avocado]) == {
+        onto.Tree,
+        onto.EvergreenTree,
+        onto.Spruce,
+        onto.NaturalDye,
+        onto.Thing,
+    }
+    # Check that classes up to closest common ancestor are returned
+
+    assert onto.get_ancestors(
+        [onto.NorwaySpruce, onto.Avocado], closest=True
+    ) == {
+        onto.EvergreenTree,
+        onto.Spruce,
+    }
+
+    with pytest.raises(ValueError):
+        onto.get_ancestors(onto.NorwaySpruce, closest=True, generations=4)
+
+    # Test strict == False
+    assert onto.get_ancestors(
+        [onto.NorwaySpruce, onto.Avocado],
+        closest=True,
+        strict=False,
+    ) == {
+        onto.EvergreenTree,
+        onto.Spruce,
+        onto.NorwaySpruce,
+        onto.Avocado,
+    }