def test_descendants():
toolkit = Toolkit()
assert 'causes' in toolkit.get_descendants('related to')
assert 'interacts with' in toolkit.get_descendants('related to')
assert 'gene' in toolkit.get_descendants('named thing')
assert 'phenotypic feature' in toolkit.get_descendants('named thing')
assert 'biolink:PhenotypicFeature' in toolkit.get_descendants(
'named thing', formatted=True)
assert 'genomic entity' in toolkit.get_ancestors('genomic entity')
assert 'genomic entity' in toolkit.get_ancestors('genomic entity',
reflexive=True)
assert 'genomic entity' not in toolkit.get_ancestors('genomic entity',
reflexive=False)
assert 'biolink:GenomicEntity' in toolkit.get_ancestors('gene',
formatted=True)
assert 'gross anatomical structure' in toolkit.get_ancestors(
'tissue', reflexive=True)
assert 'molecular activity_has output' not in toolkit.get_descendants(
'molecular activity', reflexive=True)
assert 'molecular activity_has output' not in toolkit.get_descendants(
'has output', reflexive=True)
class WrappedBMT:
"""
Wrapping around some of the BMT Toolkit functions
to provide case conversions to the new format
"""
def __init__(self):
self.bmt = BMToolkit()
self.all_slots = self.bmt.get_all_slots()
self.all_slots_formatted = [
"biolink:" + s.replace(" ", "_") for s in self.all_slots
]
self.prefix = "biolink:"
self.entity_prefix_mapping = {
bmt.util.format(el_name, case="pascal"): id_prefixes
for el_name in self.bmt.get_all_classes()
if (el := self.bmt.get_element(el_name)) is not None
if (id_prefixes := getattr(el, "id_prefixes", []))
}
def new_case_to_old_case(self, s):
"""
Convert new biolink case format (biolink:GeneOrGeneProduct)
to old case format (gene or gene product)
Also works with slots (biolink:related_to -> related to)
"""
s = s.replace(self.prefix, "")
if s in self.all_slots_formatted:
return s.replace("_", " ")
else:
return camel_to_snake(s)
def old_case_to_new_case(self, s):
"""
Convert old case format (gene or gene product)
to new biolink case format (biolink:GeneOrGeneProduct)
Also works with slots (related to -> biolink:related_to)
"""
if s in self.all_slots:
return self.prefix + s.replace(" ", "_")
else:
return self.prefix + snake_to_camel(s)
def get_descendants(self, concept):
"""Wrapped BMT descendants function that does case conversions"""
descendants = self.bmt.get_descendants(concept, formatted=True)
if len(descendants) == 0:
descendants.append(concept)
return descendants
def get_ancestors(self, concept, reflexive=True):
"""Wrapped BMT ancestors function that does case conversions"""
concept_old_format = self.new_case_to_old_case(concept)
ancestors_old_format = self.bmt.get_ancestors(concept_old_format,
reflexive=reflexive)
ancestors = [
self.old_case_to_new_case(a) for a in ancestors_old_format
]
return ancestors
def predicate_is_symmetric(self, predicate):
"""Get whether a given predicate is symmetric"""
predicate_old_format = self.new_case_to_old_case(predicate)
predicate_element = self.bmt.get_element(predicate_old_format)
if not predicate_element:
# Not in the biolink model
return False
return predicate_element.symmetric
def predicate_inverse(self, predicate):
"""Get the inverse of a predicate if it has one"""
predicate_old_format = self.new_case_to_old_case(predicate)
predicate_element = self.bmt.get_element(predicate_old_format)
if not predicate_element:
# Not in the biolink model
return None
if predicate_element.symmetric:
return predicate
predicate_inverse_old_format = predicate_element.inverse
if not predicate_inverse_old_format:
# No inverse
return None
return self.old_case_to_new_case(predicate_inverse_old_format)