from typing import List, Set, Dict, Optional
import networkx as nx
import stringcase
from cachetools import cached
from kgx.config import get_logger
from kgx.utils.kgx_utils import get_toolkit, get_cache, get_curie_lookup_service, generate_edge_key, CORE_NODE_PROPERTIES, CORE_EDGE_PROPERTIES
from kgx.prefix_manager import PrefixManager
ONTOLOGY_PREFIX_MAP: Dict = {}
ONTOLOGY_GRAPH_CACHE: Dict = {}
log = get_logger()
[docs]def get_parents(graph: nx.MultiDiGraph, node: str, relations: List[str] = None) -> List[str]:
"""
Return all direct `parents` of a specified node, filtered by ``relations``.
Parameters
----------
graph: networkx.MultiDiGraph
Graph to traverse
node: str
node identifier
relations: List[str]
list of relations
Returns
-------
List[str]
A list of parent node(s)
"""
parents = []
if node in graph:
out_edges = [x for x in graph.out_edges(node, data=True)]
if relations is None:
parents = [x[1] for x in out_edges]
else:
parents = [x[1] for x in out_edges if x[2]['edge_label'] in relations]
return parents
[docs]def get_ancestors(graph: nx.MultiDiGraph, node: str, relations: List[str] = None) -> List[str]:
"""
Return all `ancestors` of specified node, filtered by ``relations``.
Parameters
----------
graph: networkx.MultiDiGraph
Graph to traverse
node: str
node identifier
relations: List[str]
list of relations
Returns
-------
List[str]
A list of ancestor nodes
"""
seen = []
nextnodes = [node]
while len(nextnodes) > 0:
nn = nextnodes.pop()
if nn not in seen:
seen.append(nn)
nextnodes += get_parents(graph, nn, relations=relations)
seen.remove(node)
return seen
[docs]@cached(get_cache())
def get_category_via_superclass(graph: nx.MultiDiGraph, curie: str, load_ontology: bool = True) -> Set[str]:
"""
Get category for a given CURIE by tracing its superclass, via ``subclass_of`` hierarchy,
and getting the most appropriate category based on the superclass.
Parameters
----------
graph: networkx.MultiDiGraph
Graph to traverse
curie: str
Input CURIE
load_ontology: bool
Determines whether to load ontology, based on CURIE prefix, or to simply
rely on ``subclass_of`` hierarchy from graph
Returns
-------
Set[str]
A set containing one (or more) category for the given CURIE
"""
log.debug("curie: {}".format(curie))
new_categories = []
toolkit = get_toolkit()
if PrefixManager.is_curie(curie):
ancestors = get_ancestors(graph, curie, relations=['subclass_of'])
if len(ancestors) == 0 and load_ontology:
cls = get_curie_lookup_service()
ontology_graph = cls.ontology_graph
new_categories += [x for x in get_category_via_superclass(ontology_graph, curie, False)]
log.debug("Ancestors for CURIE {} via subClassOf: {}".format(curie, ancestors))
seen = []
for anc in ancestors:
mapping = toolkit.get_by_mapping(anc)
seen.append(anc)
if mapping:
# there is direct mapping to BioLink Model
log.debug("Ancestor {} mapped to {}".format(anc, mapping))
seen_labels = [graph.nodes[x]['name'] for x in seen if 'name' in graph.nodes[x]]
new_categories += [x for x in seen_labels]
new_categories += [x for x in toolkit.ancestors(mapping)]
break
return set(new_categories)
[docs]def curie_lookup(curie: str) -> Optional[str]:
"""
Given a CURIE, find its label.
This method first does a lookup in predefined maps. If none found,
it makes use of CurieLookupService to look for the CURIE in a set
of preloaded ontologies.
Parameters
----------
curie: str
A CURIE
Returns
-------
Optional[str]
The label corresponding to the given CURIE
"""
cls = get_curie_lookup_service()
name: Optional[str] = None
prefix = PrefixManager.get_prefix(curie)
if prefix in ['OIO', 'OWL', 'owl', 'OBO', 'rdfs']:
name = stringcase.snakecase(curie.split(':', 1)[1])
elif curie in cls.curie_map:
name = cls.curie_map[curie]
elif curie in cls.ontology_graph:
name = cls.ontology_graph.nodes[curie]['name']
return name
[docs]def remap_node_identifier(graph: nx.MultiDiGraph, category: str, alternative_property: str, prefix=None) -> nx.MultiDiGraph:
"""
Remap a node's 'id' attribute with value from a node's ``alternative_property`` attribute.
Parameters
----------
graph: networkx.MultiDiGraph
The graph
category: string
category referring to nodes whose 'id' needs to be remapped
alternative_property: string
property name from which the new value is pulled from
prefix: string
signifies that the value for ``alternative_property`` is a list
and the ``prefix`` indicates which value to pick from the list
Returns
-------
networkx.MultiDiGraph
The modified graph
"""
mapping: Dict = {}
for nid, data in graph.nodes(data=True):
node_data = data.copy()
if 'category' in node_data and category not in node_data['category']:
continue
if alternative_property in node_data:
alternative_values = node_data[alternative_property]
if isinstance(alternative_values, (list, set, tuple)):
if prefix:
for v in alternative_values:
if prefix in v:
# take the first occurring value that contains the given prefix
mapping[nid] = v
break
else:
# no prefix defined; pick the 1st one from list
mapping[nid] = next(iter(alternative_values))
elif isinstance(alternative_values, str):
if prefix:
if alternative_values.startswith(prefix):
mapping[nid] = alternative_values
else:
# no prefix defined
mapping[nid] = alternative_values
else:
log.error(f"Cannot use {alternative_values} from alternative_property {alternative_property}")
nx.set_node_attributes(graph, values=mapping, name='id')
nx.relabel_nodes(graph, mapping, copy=False)
# update 'subject' of all outgoing edges
update_edge_keys = {}
updated_subject_values = {}
updated_object_values = {}
for u, v, k, edge_data in graph.edges(keys=True, data=True):
if u is not edge_data['subject']:
updated_subject_values[(u, v, k)] = u
update_edge_keys[(u, v, k)] = generate_edge_key(u, edge_data['edge_label'], v)
if v is not edge_data['object']:
updated_object_values[(u, v, k)] = v
update_edge_keys[(u, v, k)] = generate_edge_key(u, edge_data['edge_label'], v)
nx.set_edge_attributes(graph, values=updated_subject_values, name='subject')
nx.set_edge_attributes(graph, values=updated_object_values, name='object')
nx.set_edge_attributes(graph, values=update_edge_keys, name='edge_key')
return graph
[docs]def remap_node_property(graph: nx.MultiDiGraph, category: str, old_property: str, new_property: str) -> None:
"""
Remap the value in node ``old_property`` attribute with value
from node ``new_property`` attribute.
Parameters
----------
graph: networkx.MultiDiGraph
The graph
category: string
Category referring to nodes whose property needs to be remapped
old_property: string
old property name whose value needs to be replaced
new_property: string
new property name from which the value is pulled from
"""
mapping = {}
if old_property in CORE_NODE_PROPERTIES:
raise AttributeError(f"node property {old_property} cannot be modified as it is a core property.")
for nid, data in graph.nodes(data=True):
node_data = data.copy()
if category in node_data and category not in node_data['category']:
continue
if new_property in node_data:
mapping[nid] = node_data[new_property]
nx.set_node_attributes(graph, values=mapping, name=old_property)
[docs]def remap_edge_property(graph: nx.MultiDiGraph, edge_label: str, old_property: str, new_property: str) -> None:
"""
Remap the value in an edge ``old_property`` attribute with value
from edge ``new_property`` attribute.
Parameters
----------
graph: networkx.MultiDiGraph
The graph
edge_label: string
edge_label referring to edges whose property needs to be remapped
old_property: string
Old property name whose value needs to be replaced
new_property: string
New property name from which the value is pulled from
"""
mapping = {}
if old_property in CORE_EDGE_PROPERTIES:
raise AttributeError(f"edge property {old_property} cannot be modified as it is a core property.")
for u, v, k, data in graph.edges(data=True, keys=True):
edge_data = data.copy()
if edge_label is not edge_data['edge_label']:
continue
if new_property in edge_data:
mapping[(u, v, k)] = edge_data[new_property]
nx.set_edge_attributes(graph, values=mapping, name=old_property)