def _bc_agent_from_up_list(self, up_id_list):
# Return the first agent with the remaining agents as a bound condition
agents_list = [self._agent_from_up_id(up_id) for up_id in up_id_list]
agent = agents_list[0]
agent.bound_conditions = \
[BoundCondition(a, True) for a in agents_list[1:]]
return agent
def test_cljson_stmt():
gtp = Agent('GTP')
kras_bound = Agent("KRAS", bound_conditions=[BoundCondition(gtp, True)])
braf = Agent('BRAF')
stmt = Phosphorylation(kras_bound, braf, position='373')
cj = Bioagent.make_cljson(stmt)
stmt2 = Bioagent.get_statement(cj)
assert stmt.equals(stmt2)
def test_bound_condition_deep_refinement():
"""A statement with more specific bound context should be supported by a
less specific statement."""
src = Agent('SRC', db_refs={'HGNC': '11283'})
gtp1 = Agent('GTP', db_refs={'CHEBI': '15996'})
gtp2 = Agent('GTP',
mods=[ModCondition('phosphorylation')],
db_refs={'CHEBI': '15996'})
nrasgtp1 = Agent('NRAS',
db_refs={'HGNC': '7989'},
bound_conditions=[BoundCondition(gtp1, True)])
nrasgtp2 = Agent('NRAS',
db_refs={'HGNC': '7989'},
bound_conditions=[BoundCondition(gtp2, True)])
st1 = Phosphorylation(src, nrasgtp1, 'tyrosine', '32')
st2 = Phosphorylation(src, nrasgtp2, 'tyrosine', '32')
# The top-level list should contain only one statement, the more specific
# modification, supported by the less-specific modification.
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
assert len(stmts) == 1
assert stmts[0].equals(st2)
assert len(stmts[0].supported_by) == 1
assert stmts[0].supported_by[0].equals(st1)
def test_bound_condition_norefinement():
"""A statement with more specific bound context should be supported by a
less specific statement."""
src = Agent('SRC', db_refs={'HGNC': '11283'})
gtp = Agent('GTP', db_refs={'CHEBI': '15996'})
nras = Agent('NRAS', db_refs={'HGNC': '7989'})
nrasgtp = Agent('NRAS',
db_refs={'HGNC': '7989'},
bound_conditions=[BoundCondition(gtp, True)])
st1 = Phosphorylation(src, nras, 'tyrosine', '32')
st2 = Phosphorylation(src, nrasgtp)
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
# The bound condition is more specific in st2 but the modification is less
# specific. Therefore these statements should not be combined.
assert len(stmts) == 2
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():
# 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'
from kqml import KQMLList
from indra.statements import Agent, Activation, BoundCondition, stmts_to_json, \
ActivityCondition, Phosphorylation
from bioagents.tests.util import get_request
from bioagents.bionlg.bionlg_module import BioNLG_Module
from bioagents.tests.integration import _IntegrationTest
kras = Agent('KRAS')
braf = Agent('BRAF')
map2k1 = Agent('MAP2K1')
mapk3 = Agent('MAPK3')
gtp = Agent('GTP')
active_braf = Agent('BRAF', activity=ActivityCondition('activity', True))
kras_bound = Agent("KRAS", bound_conditions=[BoundCondition(gtp, True)])
class _NlgTestBase(_IntegrationTest):
message_funcs = ['statements']
# Define these in the sub-classes with statements, and sentences that
# correspond to those statements.
statements = []
sentences = []
def __init__(self, *args, **kwargs):
super().__init__(BioNLG_Module)
def create_statements(self):
content = KQMLList('INDRA-TO-NL')
