def test_bound_condition_mapping_multi():
# Test with multiple agents
akt = Agent('pkbA', db_refs={'TEXT': 'Akt', 'UP': 'XXXXXX'})
erk = Agent('ERK1', db_refs={'TEXT': 'ERK1'})
akt.bound_conditions = [BoundCondition(erk)]
stmt = Phosphorylation(akt, erk)
mapped_stmts = gm.map_stmts([stmt])
s = mapped_stmts[0]
mapped_akt = mapped_stmts[0].enz
mapped_erk1 = mapped_akt.bound_conditions[0].agent
mapped_erk2 = mapped_stmts[0].sub
assert mapped_akt.db_refs['TEXT'] == 'Akt'
assert mapped_akt.db_refs['FPLX'] == 'AKT'
for e in (mapped_erk1, mapped_erk2):
assert e.db_refs['TEXT'] == 'ERK1'
assert e.db_refs['HGNC'] == '6877'
assert e.db_refs['UP'] == 'P27361'
def test_bound_condition_mapping_agent_json():
# Test with agent/json mapping
akt = Agent('pkbA', db_refs={'TEXT': 'p-Akt', 'UP': 'XXXXXX'})
erk = Agent('ERK1', db_refs={'TEXT': 'ERK1'})
akt.bound_conditions = [BoundCondition(erk)]
stmt = Phosphorylation(None, akt)
mapped_stmts = gm.map_stmts([stmt])
s = mapped_stmts[0]
mapped_akt = mapped_stmts[0].sub
mapped_erk = mapped_akt.bound_conditions[0].agent
#assert mapped_akt.db_refs['TEXT'] == 'p-AKT', mapped_akt.db_refs
assert mapped_akt.db_refs['FPLX'] == 'AKT', mapped_akt.db_refs
assert mapped_erk.db_refs['TEXT'] == 'ERK1'
assert mapped_erk.db_refs['HGNC'] == '6877'
assert mapped_erk.db_refs['UP'] == 'P27361'
def test_bound_condition_mapping_agent_json():
# Test with agent/json mapping
akt = Agent('pkbA', db_refs={'TEXT': 'p-Akt', 'UP': 'XXXXXX'})
erk = Agent('ERK1', db_refs={'TEXT': 'ERK1'})
akt.bound_conditions = [BoundCondition(erk)]
stmt = Phosphorylation(None, akt)
gm = GroundingMapper(default_grounding_map, default_agent_map)
mapped_stmts = gm.map_agents([stmt])
s = mapped_stmts[0]
mapped_akt = mapped_stmts[0].sub
mapped_erk = mapped_akt.bound_conditions[0].agent
#assert mapped_akt.db_refs['TEXT'] == 'p-AKT', mapped_akt.db_refs
assert mapped_akt.db_refs['FPLX'] == 'AKT', mapped_akt.db_refs
assert mapped_erk.db_refs['TEXT'] == 'ERK1'
assert mapped_erk.db_refs['HGNC'] == '6877'
assert mapped_erk.db_refs['UP'] == 'P27361'
def test_bound_condition_mapping_multi():
# Test with multiple agents
akt = Agent('pkbA', db_refs={'TEXT': 'Akt', 'UP': 'XXXXXX'})
erk = Agent('ERK1', db_refs={'TEXT': 'ERK1'})
akt.bound_conditions = [BoundCondition(erk)]
stmt = Phosphorylation(akt, erk)
gm = GroundingMapper(default_grounding_map)
mapped_stmts = gm.map_agents([stmt])
s = mapped_stmts[0]
mapped_akt = mapped_stmts[0].enz
mapped_erk1 = mapped_akt.bound_conditions[0].agent
mapped_erk2 = mapped_stmts[0].sub
assert mapped_akt.db_refs['TEXT'] == 'Akt'
assert mapped_akt.db_refs['FPLX'] == 'AKT'
for e in (mapped_erk1, mapped_erk2):
assert e.db_refs['TEXT'] == 'ERK1'
assert e.db_refs['HGNC'] == '6877'
assert e.db_refs['UP'] == 'P27361'
def test_bound_condition_mapping():
# Verify that the grounding mapper grounds the agents within a bound
# condition
akt = Agent('pkbA', db_refs={'TEXT': 'Akt', 'UP': 'XXXXXX'})
erk = Agent('ERK1', db_refs={'TEXT': 'ERK1'})
akt.bound_conditions = [BoundCondition(erk)]
stmt = Phosphorylation(None, akt)
mapped_stmts = gm.map_stmts([stmt])
s = mapped_stmts[0]
mapped_akt = mapped_stmts[0].sub
mapped_erk = mapped_akt.bound_conditions[0].agent
assert mapped_akt.db_refs['TEXT'] == 'Akt'
assert mapped_akt.db_refs['FPLX'] == 'AKT'
assert mapped_erk.db_refs['TEXT'] == 'ERK1'
assert mapped_erk.db_refs['HGNC'] == '6877'
assert mapped_erk.db_refs['UP'] == 'P27361'
def test_bound_condition_mapping():
# Verify that the grounding mapper grounds the agents within a bound
# condition
akt = Agent('pkbA', db_refs={'TEXT': 'Akt', 'UP': 'XXXXXX'})
erk = Agent('ERK1', db_refs={'TEXT': 'ERK1'})
akt.bound_conditions = [BoundCondition(erk)]
stmt = Phosphorylation(None, akt)
gm = GroundingMapper(default_grounding_map)
mapped_stmts = gm.map_agents([stmt])
s = mapped_stmts[0]
mapped_akt = mapped_stmts[0].sub
mapped_erk = mapped_akt.bound_conditions[0].agent
assert mapped_akt.db_refs['TEXT'] == 'Akt'
assert mapped_akt.db_refs['FPLX'] == 'AKT'
assert mapped_erk.db_refs['TEXT'] == 'ERK1'
assert mapped_erk.db_refs['HGNC'] == '6877'
assert mapped_erk.db_refs['UP'] == 'P27361'