Implementing add/remove subset for all impls

INCATools · Mar 9, 2024 · 56431ae · 56431ae
1 parent 68566f2
commit 56431ae
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Showing 4 changed files with 43 additions and 1 deletion.
diff --git a/src/oaklib/implementations/pronto/pronto_implementation.py b/src/oaklib/implementations/pronto/pronto_implementation.py
@@ -896,6 +896,12 @@ def apply_patch(
             # rather than forcing all synonyms to be related.
             scope = str(patch.qualifier.value).upper() if patch.qualifier else "RELATED"
             t.add_synonym(description=patch.new_value, scope=scope)
+        elif isinstance(patch, kgcl.AddNodeToSubset):
+            t = self._entity(patch.about_node, strict=True)
+            t.subsets = t.subsets.union({patch.in_subset})
+        elif isinstance(patch, kgcl.RemoveNodeFromSubset):
+            t = self._entity(patch.about_node, strict=True)
+            t.subsets = t.subsets.difference({patch.in_subset})
         elif isinstance(patch, kgcl.EdgeCreation):
             self.add_relationship(patch.subject, patch.predicate, patch.object)
         elif isinstance(patch, kgcl.EdgeDeletion):

diff --git a/src/oaklib/implementations/simpleobo/simple_obo_implementation.py b/src/oaklib/implementations/simpleobo/simple_obo_implementation.py
@@ -859,6 +859,10 @@ def apply_patch(
             t = self._stanza(patch.about_node, strict=True)
             t.add_tag_value(TAG_SUBSET, patch.in_subset)
             modified_entities.append(patch.about_node)
+        elif isinstance(patch, kgcl.RemoveNodeFromSubset):
+            t = self._stanza(patch.about_node, strict=True)
+            t.remove_simple_tag_value(TAG_SUBSET, patch.in_subset)
+            modified_entities.append(patch.about_node)
         elif isinstance(patch, kgcl.NewTextDefinition):
             t = self._stanza(patch.about_node, strict=True)
             t.add_quoted_tag_value(TAG_DEFINITION, patch.new_value.strip("'"), xrefs=[])

diff --git a/src/oaklib/implementations/sqldb/sql_implementation.py b/src/oaklib/implementations/sqldb/sql_implementation.py
@@ -2279,7 +2279,28 @@ def apply_patch(
                         )
                     )
                 )
-
+            elif isinstance(patch, kgcl.AddNodeToSubset):
+                # TODO: implement deterministic subset mapping
+                pfx = about.split(":")[0].lower()
+                subset_curie = f"obo:{pfx}#{patch.in_subset}"
+                self._execute(
+                    insert(Statements).values(
+                        subject=about, predicate=IN_SUBSET, object=subset_curie
+                    )
+                )
+            elif isinstance(patch, kgcl.RemoveNodeFromSubset):
+                # TODO: implement deterministic subset mapping
+                pfx = about.split(":")[0].lower()
+                subset_curie = f"obo:{pfx}#{patch.in_subset}"
+                self._execute(
+                    delete(Statements).where(
+                        and_(
+                            Statements.subject == about,
+                            Statements.predicate == IN_SUBSET,
+                            Statements.object == subset_curie,
+                        )
+                    )
+                )
             elif isinstance(patch, kgcl.NodeObsoletion):
                 self.check_node_exists(about)
                 self._set_predicate_value(

diff --git a/tests/test_implementations/__init__.py b/tests/test_implementations/__init__.py
@@ -1206,6 +1206,17 @@ def test_patcher(
                 ),
                 None,
             ),
+            (
+                kgcl.RemoveNodeFromSubset(
+                    id=generate_change_id(), about_node=NUCLEAR_ENVELOPE, in_subset="goslim_generic"
+                ),
+                False,
+                lambda oi: test.assertNotIn(
+                    NUCLEAR_ENVELOPE,
+                    oi.subset_members("goslim_generic"),
+                ),
+                None,
+            ),
             (
                 kgcl.RemoveSynonym(
                     id=generate_change_id(),