def test_belgraph_to_signed_graph():
braf_no_act = Agent('BRAF', db_refs={'HGNC': '1097', 'UP': 'P15056'})
mek = Agent('MAP2K1', db_refs={'HGNC': '6840', 'UP': 'Q02750'})
stmt = Activation(braf_no_act, mek)
hsh = stmt.get_hash(refresh=True)
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
pb_seg = pa.belgraph_to_signed_graph(belgraph, propagate_annotations=True)
assert len(pb_seg.edges) == 1
edge = (braf_dsl, map2k1_dsl, 0)
assert edge in pb_seg.edges
edge_dict = pb_seg.edges.get(edge)
assert edge_dict
assert 'stmt_hash' in edge_dict
assert isinstance(edge_dict['stmt_hash'], int)
assert hsh == edge_dict['stmt_hash']
assert 'uuid' in edge_dict
assert isinstance(edge_dict['uuid'], str)
assert stmt.uuid == edge_dict['uuid']
assert 'belief' in edge_dict
assert isinstance(edge_dict['belief'], (float, int))
assert stmt.belief == edge_dict['belief']
def get_graph(self):
"""Convert a PyBELGraph to a graph with signed nodes."""
# This import is done here rather than at the top level to avoid
# making pybel an implicit dependency of the model checker
from indra.assemblers.pybel.assembler import belgraph_to_signed_graph
if self.graph:
return self.graph
signed_edges = belgraph_to_signed_graph(self.model)
self.graph = self.signed_edges_to_signed_nodes(signed_edges)
return self.graph
def get_graph(self,
include_variants=False,
symmetric_variant_links=False,
include_components=True,
symmetric_component_links=True):
"""Convert a PyBELGraph to a graph with signed nodes."""
# This import is done here rather than at the top level to avoid
# making pybel an implicit dependency of the model checker
from indra.assemblers.pybel.assembler import belgraph_to_signed_graph
if self.graph:
return self.graph
signed_edges = belgraph_to_signed_graph(
self.model,
include_variants=include_variants,
symmetric_variant_links=symmetric_variant_links,
include_components=include_components,
symmetric_component_links=symmetric_component_links)
self.graph = signed_edges_to_signed_nodes(signed_edges)
return self.graph
def get_graph(self,
include_variants=False,
symmetric_variant_links=False,
include_components=True,
symmetric_component_links=True,
edge_filter_func=None):
"""Convert a PyBELGraph to a graph with signed nodes."""
# This import is done here rather than at the top level to avoid
# making pybel an implicit dependency of the model checker
from indra.assemblers.pybel.assembler import belgraph_to_signed_graph
if self.graph:
return self.graph
# NOTE edge_filter_func is not currently used in PyBEL
signed_edges = belgraph_to_signed_graph(
self.model,
include_variants=include_variants,
symmetric_variant_links=symmetric_variant_links,
include_components=include_components,
symmetric_component_links=symmetric_component_links,
propagate_annotations=True)
self.graph = signed_edges_to_signed_nodes(signed_edges,
copy_edge_data={'belief'})
self.get_nodes_to_agents()
return self.graph
def db_dump_to_pybel_sg(stmts_list=None,
pybel_model=None,
belief_dump=None,
default_belief=0.1,
sign_in_edges=False):
"""Create a signed pybel graph from an evidenceless dump from the db
Parameters
----------
stmts_list : list[indra.statements.Statement]
Provide a list of statements if they are already loaded. By default
the latest available pa statements dump is downloaded from s3.
Default: None.
pybel_model : pybel.BELGraph
If provided, skip generating a new pybel model from scratch
belief_dump : dict
If provided, reset the belief scores associated with the statements
supporting the edges.
default_belief : float
Only used if belief_dump is provided. When no belief score is
available, reset to this belief score. Default: 0.1.
sign_in_edges : bool
If True, check that all edges are stored with an index corresponding
to the sign of the edge. Default: False.
Returns
-------
tuple(DiGraph, MultiDiGraph)
"""
# Get statement dump:
# Look for latest file on S3 and pickle.loads it
if pybel_model is None:
pb_model = _custom_pb_assembly(stmts_list)
else:
logger.info('Pybel model provided')
pb_model = pybel_model
# If belief dump is provided, reset beliefs to the entries in it
if belief_dump:
logger.info('Belief dump provided, resetting belief scores')
missing_hash = 0
changed_belief = 0
no_hash = 0
logger.info(f'Looking for belief scores among {len(pb_model.edges)} '
f'edges')
for edge in pb_model.edges:
ed = pb_model.edges[edge]
if ed and ed.get('stmt_hash'):
h = ed['stmt_hash']
if h in belief_dump:
ed['belief'] = belief_dump[h]
changed_belief += 1
else:
logger.warning(f'No belief found for {h}')
ed['belief'] = default_belief
missing_hash += 1
else:
no_hash += 1
logger.info(f'{no_hash} edges did not have hashes')
logger.info(f'{changed_belief} belief scores were changed')
logger.info(f'{missing_hash} edges did not have a belief entry')
# Get a signed edge graph
logger.info('Getting a PyBEL signed edge graph')
pb_signed_edge_graph = belgraph_to_signed_graph(
pb_model,
symmetric_variant_links=True,
symmetric_component_links=True,
propagate_annotations=True)
if sign_in_edges:
for u, v, ix in pb_signed_edge_graph.edges:
ed = pb_signed_edge_graph.edges[(u, v, ix)]
if 'sign' in ed and ix != ed['sign']:
pb_signed_edge_graph.add_edge(u, v, ed['sign'], **ed)
pb_signed_edge_graph.remove_edge(u, v, ix)
# Map hashes to edges
logger.info('Getting hash to signed edge mapping')
seg_hash_edge_dict = {}
for edge in pb_signed_edge_graph.edges:
if pb_signed_edge_graph.edges[edge].get('stmt_hash'):
seg_hash_edge_dict[pb_signed_edge_graph.edges[edge]
['stmt_hash']] = edge
pb_signed_edge_graph.graph['edge_by_hash'] = seg_hash_edge_dict
# Get the signed node graph
logger.info('Getting a signed node graph from signed edge graph')
pb_signed_node_graph = signed_edges_to_signed_nodes(pb_signed_edge_graph,
copy_edge_data=True)
# Map hashes to edges for signed nodes
logger.info('Getting hash to edge mapping')
sng_hash_edge_dict = {}
for edge in pb_signed_node_graph.edges:
if pb_signed_node_graph.edges[edge].get('stmt_hash'):
sng_hash_edge_dict[pb_signed_node_graph.edges[edge]
['stmt_hash']] = edge
pb_signed_node_graph.graph['edge_by_hash'] = sng_hash_edge_dict
logger.info('Done assembling signed edge and signed node PyBEL graphs')
return pb_signed_edge_graph, pb_signed_node_graph
