def get_element(self, name: str) -> Optional[Element]:
"""
Gets an element that is identified by the given name, either as its name
or as one of its aliases.
Parameters
----------
name: str
The name or alias of an element in the Biolink Model
Returns
-------
Element
The element identified by the given name
"""
parsed_name = parse_name(name)
logger.debug(parsed_name)
element = self.generator.obj_for(parsed_name)
if element is None and name in self.generator.aliases:
logger.debug("in aliases")
logger.debug(self.generator.aliases)
element = self.get_element(self.generator.aliases[name])
if element is None and "_" in name:
logger.debug("has a _")
element = self.get_element(name.replace("_", " "))
return element
def get_element(self, name: str) -> Optional[Element]:
"""
Gets an element that is identified by the given name, either as its name
or as one of its aliases.
Parameters
----------
name: str
The name or alias of an element in the Biolink Model
Returns
-------
Element
The element identified by the given name
"""
parsed_name = parse_name(name)
element = self.generator.obj_for(parsed_name)
if element is None:
if name in self.generator.aliases:
element = self.get_element(self.generator.aliases[name])
if element is None:
if '_' in name:
element = self.get_element(name.replace('_', ' '))
if not element:
logging.warning(f"{name} is not a valid Biolink Model element")
return element
def in_subset(self, name: str, subset: str) -> bool:
"""
Determines whether the given name is in a given subset
in the Biolink Model.
Parameters
----------
name: str
The name or alias of an element in the Biolink Model.
subset: str
The name of the subset
Returns
-------
bool
That the named element is part of a given subset in Biolink Model
"""
parsed_name = parse_name(name)
element = self.generator.obj_for(parsed_name)
return subset in element.in_subset
def test_parse_name(query):
n = parse_name(query[0])
assert n == query[1]