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 <cjm@berkeleybop.org>
Co-authored-by: Harshad Hegde <hegdehb@gmail.com>
Co-authored-by: Harshad <hrshdhgd@users.noreply.github.com>

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)

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]))