# -*- coding: utf-8 -*-
"""Filter functions for nodes in BEL graphs.
A node predicate is a function that takes two arguments: a :class:`BELGraph` and a node. It returns a boolean
representing whether the node passed the given test.
This module contains a set of default functions for filtering lists of nodes and building node predicates.
A general use for a node predicate is to use the built-in :func:`filter` in code like
:code:`filter(your_node_predicate, graph)`
"""
from typing import Iterable, Set
from .node_predicate_builders import (
function_inclusion_filter_builder,
namespace_inclusion_builder,
)
from .node_predicates import concatenate_node_predicates
from .typing import NodePredicates
from ..graph import BELGraph
from ...dsl import BaseEntity
from ...typing import Strings
__all__ = [
"filter_nodes",
"get_nodes",
"count_passed_node_filter",
"summarize_node_filter",
"get_nodes_by_function",
"get_nodes_by_namespace",
]
[docs]def filter_nodes(graph: BELGraph, node_predicates: NodePredicates) -> Iterable[BaseEntity]:
"""Apply a set of predicates to the nodes iterator of a BEL graph."""
concatenated_predicate = concatenate_node_predicates(node_predicates=node_predicates)
for node in graph:
if concatenated_predicate(graph, node):
yield node
[docs]def get_nodes(graph: BELGraph, node_predicates: NodePredicates) -> Set[BaseEntity]:
"""Get the set of all nodes that pass the predicates."""
return set(filter_nodes(graph, node_predicates=node_predicates))
[docs]def count_passed_node_filter(graph: BELGraph, node_predicates: NodePredicates) -> int:
"""Count how many nodes pass a given set of node predicates."""
return sum(1 for _ in filter_nodes(graph, node_predicates=node_predicates))
[docs]def summarize_node_filter(graph: BELGraph, node_filters: NodePredicates) -> None:
"""Print a summary of the number of nodes passing a given set of filters.
:param graph: A BEL graph
:param node_filters: A node filter or list/tuple of node filters
"""
passed = count_passed_node_filter(graph, node_filters)
print("{}/{} nodes passed".format(passed, graph.number_of_nodes()))
[docs]def get_nodes_by_function(graph: BELGraph, func: Strings) -> Set[BaseEntity]:
"""Get all nodes with the given function(s)."""
return get_nodes(graph, function_inclusion_filter_builder(func))
[docs]def get_nodes_by_namespace(graph, namespaces: Strings) -> Set[BaseEntity]:
"""Get all nodes identified by the given namespace(s)."""
return get_nodes(graph, namespace_inclusion_builder(namespaces))