Source code for indra.explanation.model_checker.signed_graph

import logging
from . import ModelChecker
from indra.statements import *


logger = logging.getLogger(__name__)


[docs]class SignedGraphModelChecker(ModelChecker): """Check an signed MultiDiGraph against a set of INDRA statements. Parameters ---------- model : networkx.MultiDiGraph Signed MultiDiGraph to check. statements : Optional[list[indra.statements.Statement]] A list of INDRA Statements to check the model against. do_sampling : bool Whether to use breadth-first search or weighted sampling to generate paths. Default is False (breadth-first search). seed : int Random seed for sampling (optional, default is None). """ def __init__(self, model, statements=None, do_sampling=False, seed=None): super().__init__(model, statements, do_sampling, seed)
[docs] def get_graph(self): if self.graph: return self.graph self.graph = self.signed_edges_to_signed_nodes(self.model) return self.graph
[docs] def process_statement(self, stmt): # Check if this is one of the statement types that we can check if not isinstance(stmt, (Activation, Inhibition, IncreaseAmount, DecreaseAmount, Influence)): logger.info('Statement type %s not handled' % stmt.__class__.__name__) return (None, None, 'STATEMENT_TYPE_NOT_HANDLED') # Get the polarity for the statement if isinstance(stmt, RegulateActivity): target_polarity = 0 if stmt.is_activation else 1 elif isinstance(stmt, RegulateAmount): target_polarity = 1 if isinstance(stmt, DecreaseAmount) else 0 elif isinstance(stmt, Influence): target_polarity = 1 if stmt.overall_polarity() == -1 else 0 subj, obj = stmt.agent_list() if subj is None or (subj.name, 0) not in self.graph.nodes: return (None, None, 'SUBJECT_NOT_FOUND') if obj is None or (obj.name, target_polarity) not in self.graph.nodes: return (None, None, 'OBJECT_NOT_FOUND') return ([(subj.name, 0)], [(obj.name, target_polarity)], None)
[docs] def process_subject(self, subj): return [subj], None