rename edge to mapping (#775)

* rename edge to mapping * Update differ_interface.py * Added MappingReplacement and RemoveMapping * MappingPredicateChange * formatted * Added mapping change * simpleobo + mapping change implemented * Edited expected changes * replace hard-coding to vars --------- Co-authored-by: Chris Mungall <[email protected]> Co-authored-by: Harshad Hegde <[email protected]> Co-authored-by: Harshad <[email protected]>
INCATools · Jun 20, 2024 · 2baba34 · 2baba34
1 parent 8b25588
commit 2baba34
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Showing 6 changed files with 216 additions and 88 deletions.
diff --git a/src/oaklib/implementations/simpleobo/simple_obo_implementation.py b/src/oaklib/implementations/simpleobo/simple_obo_implementation.py
@@ -907,14 +907,14 @@ def _tv_dict(stanza: Stanza) -> Dict[str, List[str]]:
             elif tag == TAG_SUBSET:
                 if node_is_deleted:
                     continue
-                subsets1 = stanza1.simple_values(TAG_SUBSET)
-                subsets2 = stanza2.simple_values(TAG_SUBSET)
-                for subset in subsets1:
-                    if subset not in subsets2:
-                        yield kgcl.RemoveNodeFromSubset(id=_id(), about_node=t1id, in_subset=subset)
-                for subset in subsets2:
-                    if subset not in subsets1:
-                        yield kgcl.AddNodeToSubset(id=_id(), about_node=t2id, in_subset=subset)
+                xrefs1 = stanza1.simple_values(TAG_SUBSET)
+                xrefs2 = stanza2.simple_values(TAG_SUBSET)
+                for xref in xrefs1:
+                    if xref not in xrefs2:
+                        yield kgcl.RemoveNodeFromSubset(id=_id(), about_node=t1id, in_subset=xref)
+                for xref in xrefs2:
+                    if xref not in xrefs1:
+                        yield kgcl.AddNodeToSubset(id=_id(), about_node=t2id, in_subset=xref)
             elif tag == TAG_IS_A:
                 isas1 = stanza1.simple_values(TAG_IS_A)
                 isas2 = stanza2.simple_values(TAG_IS_A)
@@ -950,6 +950,21 @@ def _tv_dict(stanza: Stanza) -> Dict[str, List[str]]:
                         yield kgcl.NewSynonym(
                             id=_id(), about_node=t2id, new_value=syn[0], predicate=pred
                         )
+            elif tag == TAG_XREF:
+                if node_is_deleted:
+                    continue
+                xrefs1 = stanza1.simple_values(TAG_XREF)
+                xrefs2 = stanza2.simple_values(TAG_XREF)
+                for xref in xrefs1:
+                    if xref not in xrefs2:
+                        yield kgcl.RemoveMapping(
+                            id=_id(), about_node=t1id, object=xref, predicate=HAS_DBXREF
+                        )
+                for xref in xrefs2:
+                    if xref not in xrefs1:
+                        yield kgcl.MappingCreation(
+                            id=_id(), subject=t2id, object=xref, predicate=HAS_DBXREF
+                        )
 
     def different_from(self, entity: CURIE, other_ontology: DifferInterface) -> bool:
         t1 = self._stanza(entity, strict=False)

diff --git a/src/oaklib/interfaces/differ_interface.py b/src/oaklib/interfaces/differ_interface.py
@@ -11,9 +11,10 @@
     Change,
     ClassCreation,
     Edge,
-    EdgeChange,
-    EdgeCreation,
     EdgeDeletion,
+    MappingCreation,
+    # MappingReplacement,
+    MappingPredicateChange,
     NewSynonym,
     NewTextDefinition,
     NodeCreation,
@@ -26,6 +27,7 @@
     NodeTextDefinitionChange,
     NodeUnobsoletion,
     PredicateChange,
+    RemoveMapping,
     RemoveNodeFromSubset,
     RemoveSynonym,
     RemoveTextDefinition,
@@ -275,34 +277,35 @@ def diff(
             if mappings_added_set:
                 for mapping in mappings_added_set:
                     predicate, xref = mapping
-                    edge_created = EdgeCreation(
+                    mapping_created = MappingCreation(
                         id=_gen_id(),
                         subject=entity,
                         predicate=predicate,
                         object=xref,
                     )
-                    yield edge_created
+                    yield mapping_created
             if mappings_removed_set:
                 for mapping in mappings_removed_set:
                     predicate, xref = mapping
-                    deleted_edge = EdgeDeletion(
+                    deleted_mapping = RemoveMapping(
                         id=_gen_id(),
-                        subject=entity,
+                        about_node=entity,
                         predicate=predicate,
                         object=xref,
                     )
-                    yield deleted_edge
+                    yield deleted_mapping
             if mapping_changed_set:
                 for changes in mapping_changed_set:
                     object, new_predicate, old_predicate = changes
-                    edge_change = EdgeChange(
+                    mapping_change = MappingPredicateChange(
                         id=_gen_id(),
-                        about_edge=Edge(subject=entity, predicate=old_predicate, object=object),
+                        about_node=entity,
+                        object=object,
                         old_value=old_predicate,
                         new_value=new_predicate,
                     )
 
-                    yield edge_change
+                    yield mapping_change
 
             # ! Subset changes
             self_subsets = set(self.terms_subsets([entity]))