def test_evidence_assembly():
ev1 = Evidence(pmid='1')
ev2 = Evidence(pmid='2')
ev3 = Evidence(pmid='3')
Evidence(pmid='4')
st1 = Activation(Agent('a'), Agent('b'), evidence=[ev1])
st2 = Inhibition(Agent('a'), Agent('c'), evidence=[ev1, ev2, ev3])
sa = SifAssembler([st1, st2])
sa.make_model()
assert len(sa.graph.nodes()) == 3
assert len(sa.graph.edges()) == 2
sa.set_edge_weights('support_pmid')
from indra.util import _require_python3
from indra.assemblers.sif import SifAssembler
import indra.tools.assemble_corpus as ac
stmts = ac.load_statements('output/preassembled.pkl')
stmts = ac.filter_belief(stmts, 0.95)
stmts = ac.filter_direct(stmts)
sa = SifAssembler(stmts)
sa.make_model(True, True, False)
sa.set_edge_weights('support_all')
fname = 'model_high_belief_v2.sif'
with open(fname, 'wt') as fh:
for s, t, d in sa.graph.edges(data=True):
source = sa.graph.nodes[s]['name']
target = sa.graph.nodes[t]['name']
fh.write('%s %f %s\n' % (source, d['weight'], target))