runoak diff erroneously names "relationships" --> "mappings" in markdown summary

[matentzn]

The "Relation ship added" section is erroneously called "Mappings added".

Example: obophenotype/human-phenotype-ontology#10446 (comment)

reports/difference_release_base.md: tmp/hp-released.obo $(KGCL_ONTOLOGY)
	runoak -i simpleobo:tmp/hp-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type md

[hrshdhgd]

So there might be some misunderstanding on my part or a bug in code. The table created under Mappings added are derived from the Change object EdgeCreation. This is designed from oaklib's simple_mappings_by_curie() output. So it should be mappings(?) or relationships?

Similarly

• Mappings removed: EdgeDeletion
• Mappings changed: EdgeChange

Code from differ_interface:

ontology-access-kit/src/oaklib/interfaces/differ_interface.py

Lines 269 to 305 in 41c1d95

	# ! Mappings
	self_mappings = set(self.simple_mappings_by_curie(entity))
	other_mappings = set(other_ontology.simple_mappings_by_curie(entity))
	mappings_added_set = other_mappings - self_mappings
	mappings_removed_set = self_mappings - other_mappings
	mapping_changed_set = _find_mapping_changes(self_mappings, other_mappings)
	if mappings_added_set:
	for mapping in mappings_added_set:
	predicate, xref = mapping
	edge_created = EdgeCreation(
	id=_gen_id(),
	subject=entity,
	predicate=predicate,
	object=xref,
	)
	yield edge_created
	if mappings_removed_set:
	for mapping in mappings_removed_set:
	predicate, xref = mapping
	deleted_edge = EdgeDeletion(
	id=_gen_id(),
	subject=entity,
	predicate=predicate,
	object=xref,
	)
	yield deleted_edge
	if mapping_changed_set:
	for changes in mapping_changed_set:
	object, new_predicate, old_predicate = changes
	edge_change = EdgeChange(
	id=_gen_id(),
	about_edge=Edge(subject=entity, predicate=old_predicate, object=object),
	old_value=old_predicate,
	new_value=new_predicate,
	)
	yield edge_change

Code from simpleobo:

ontology-access-kit/src/oaklib/implementations/simpleobo/simple_obo_implementation.py

Lines 900 to 910 in 41c1d95

	elif tag == TAG_RELATIONSHIP:
	rels1 = stanza1.pair_values(TAG_RELATIONSHIP)
	rels2 = stanza2.pair_values(TAG_RELATIONSHIP)
	for p, v in rels1:
	p_curie = self.map_shorthand_to_curie(p)
	if (p, v) not in rels2:
	yield kgcl.EdgeDeletion(id=_id(), subject=t1id, predicate=p_curie, object=v)
	for p, v in rels2:
	p_curie = self.map_shorthand_to_curie(p)
	if (p, v) not in rels1:
	yield kgcl.EdgeCreation(id=_id(), subject=t2id, predicate=p_curie, object=v)

map_shorthand_to_curie() uses simple_mappings_by_curie()

ontology-access-kit/src/oaklib/implementations/simpleobo/simple_obo_implementation.py

Lines 483 to 497 in 41c1d95

	def map_shorthand_to_curie(self, rel_code: PRED_CODE) -> PRED_CURIE:
	"""
	Maps either a true relationship type CURIE or a shorthand packages to a CURIE.
	See `section 5.9 <https://owlcollab.github.io/oboformat/doc/obo-syntax.html#5.9>`_
	:param rel_code:
	:return:
	"""
	for _, x in self.simple_mappings_by_curie(rel_code):
	if x.startswith("BFO:") or x.startswith("RO:"):
	return x
	if ":" not in rel_code and ":" in x:
	return x
	return rel_code

Thoughts @cmungall

[cmungall]

edge is very generic in KGCL, it encompasses relationships and mappings

[cmungall]

OK, I misspoke. edges is KGCL are the same as edges in OAK

this code is not quite right:

            if mappings_added_set:
                for mapping in mappings_added_set:
                    predicate, xref = mapping
                    edge_created = EdgeCreation(
                        id=_gen_id(),
                        subject=entity,
                        predicate=predicate,
                        object=xref,
                    )
                    yield edge_created
            if mappings_removed_set:
                for mapping in mappings_removed_set:
                    predicate, xref = mapping
                    deleted_edge = EdgeDeletion(
                        id=_gen_id(),
                        subject=entity,
                        predicate=predicate,
                        object=xref,
                    )
                    yield deleted_edge
            if mapping_changed_set:
                for changes in mapping_changed_set:
                    object, new_predicate, old_predicate = changes
                    edge_change = EdgeChange(
                        id=_gen_id(),
                        about_edge=Edge(subject=entity, predicate=old_predicate, object=object),
                        old_value=old_predicate,
                        new_value=new_predicate,
                    )

                    yield edge_change

simply change edge_ to mapping_ and Edge* to Mapping* to get the correct KGCL types

[hrshdhgd]

Fixed by #775