def get_value_type_for_slot(self,
slot_name,
formatted: bool = False) -> str:
"""
Get the value type for a given slot.
Parameters
----------
slot_name: str
The name or alias of a slot in the Biolink Model
formatted: bool
Whether to format element names as CURIEs
Returns
-------
str
The slot type
"""
element_type = None
element = self.get_element(slot_name)
if element:
types = self.get_all_types()
if element.range in types:
et = element.range
else:
et = 'uriorcurie'
if formatted:
element_type = format_element(self.generator.obj_for(et))
else:
element_type = et
return element_type
def get_parent(self, name: str, formatted: bool = False) -> Optional[str]:
"""
Gets the name of the parent.
Parameters
----------
name: str
The name of an element in the Biolink Model
formatted: bool
Whether to format element names as CURIEs
Returns
-------
Optional[str]
The name of the given elements parent
"""
parent = None
element = self.get_element(name)
if element:
p = element.is_a if isinstance(element, Definition) else None
if p and formatted:
parent = format_element(element)
else:
parent = p
return parent
def _format_all_elements(self,
elements: List[str],
formatted: bool = False) -> List[str]:
"""
Format all the elements in a given list.
Parameters
----------
elements: str
A list of elements
formatted: bool
Whether to format element names as CURIEs
Returns
-------
List[str]
The formatted list of elements
"""
if formatted:
formatted_elements = [
format_element(self.generator.obj_for(x)) for x in elements
]
else:
formatted_elements = elements
return formatted_elements
def get_element_by_mapping(
self,
identifier: str,
most_specific: bool = False,
formatted: bool = False,
mixin: bool = True,
) -> Optional[str]:
"""
Get a Biolink Model element by mapping.
This method return the common ancestor of the set of elements referenced by uriorcurie.
Parameters
----------
identifier: str
The identifier as an IRI or CURIE
most_specific: bool
Whether or not to get the first available mapping in the order of specificity
or to get all mappings of varying specificity
formatted: bool
Whether to format element names as CURIEs
mixin: bool
If True, then that means we want to find mixin ancestors as well as is_a ancestors
Returns
-------
Optional[str]
The Biolink element (or the common ancestor) corresponding to the given URI/CURIE
"""
if most_specific:
mappings = self._get_element_by_mapping(identifier)
else:
mappings = self.get_all_elements_by_mapping(identifier)
if mappings:
ancestors: List[List[str]] = []
for m in mappings:
ancestors.append(
[x for x in self.get_ancestors(m, mixin)[::-1] if x in mappings]
)
logger.debug(ancestors)
without_empty_lists = list(filter(None, ancestors))
common_ancestors = reduce(
lambda s, l: s.intersection(set(l)), without_empty_lists[1:], set(without_empty_lists[0])
)
logger.debug("common_ancestors")
logger.debug(common_ancestors)
for a in without_empty_lists[0]:
logger.debug("ancestors[0]")
logger.debug(a)
if a in common_ancestors:
if formatted:
element = format_element(self.generator.obj_for(a))
else:
element = a
return element
def get_element_by_mapping(self,
identifier: str,
most_specific: bool = False,
formatted: bool = False) -> Optional[str]:
"""
Get a Biolink Model element by mapping.
This method return the common ancestor of the set of elements referenced by uriorcurie.
Parameters
----------
identifier: str
The identifier as an IRI or CURIE
most_specific: bool
Whether or not to get the first available mapping in the order of specificity
or to get all mappings of varying specificity
formatted: bool
Whether to format element names as CURIEs
Returns
-------
Optional[str]
The Biolink element (or the common ancestor) corresponding to the given URI/CURIE
"""
if most_specific:
mappings = self._get_element_by_mapping(identifier)
else:
mappings = self.get_all_elements_by_mapping(identifier)
if mappings:
ancestors: List[List[str]] = []
for m in mappings:
ancestors.append(
[x for x in self.get_ancestors(m)[::-1] if x in mappings])
common_ancestors = reduce(lambda s, l: s.intersection(set(l)),
ancestors[1:], set(ancestors[0]))
for a in ancestors[0]:
if a in common_ancestors:
if formatted:
element = format_element(self.generator.obj_for(a))
else:
element = a
return element
def test_format_element(query, toolkit):
n = format_element(toolkit.get_element(query[0]))
assert n == query[1]