def check_policy(policy, result):
pysba = PysbAssembler()
pysba.add_statements([stmt])
pysba.make_model(policies=policy)
mc = ModelChecker(pysba.model, [stmt])
checks = mc.check_model()
assert len(checks) == 1
assert isinstance(checks[0], tuple)
assert checks[0][0] == stmt
assert checks[0][1] == result
def test_pysb_assembler_phospho_policies():
a = Agent('A', db_refs={'HGNC': '1'})
b = Agent('B', db_refs={'HGNC': '2'})
st = Phosphorylation(a, b, 'T', '185')
pa = PysbAssembler()
pa.add_statements([st])
# Try two step
pa.make_model(policies='two_step')
mc = ModelChecker(pa.model, [st])
results = mc.check_model()
assert len(results) == 1
assert isinstance(results[0], tuple)
assert results[0][0] == st
assert results[0][1] == True
# Try one step
pa.make_model(policies='one_step')
mc = ModelChecker(pa.model, [st])
results = mc.check_model()
assert len(results) == 1
assert isinstance(results[0], tuple)
assert results[0][0] == st
assert results[0][1] == True
# Try interactions_only
pa.make_model(policies='interactions_only')
mc = ModelChecker(pa.model, [st])
results = mc.check_model()
assert len(results) == 1
assert isinstance(results[0], tuple)
assert results[0][0] == st
assert results[0][1] == False
def test_check_ubiquitination():
xiap = Agent('XIAP', db_refs={'HGNC': '592'})
casp3 = Agent('CASP3', db_refs={'HGNC': '1504'})
stmt = Ubiquitination(xiap, casp3)
pysba = PysbAssembler()
pysba.add_statements([stmt])
pysba.make_model(policies='one_step')
mc = ModelChecker(pysba.model, [stmt])
checks = mc.check_model()
assert len(checks) == 1
assert isinstance(checks[0], tuple)
assert checks[0][0] == stmt
assert checks[0][1] == True
def check_stmts(stmts):
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model(policies='one_step')
stmts_to_check = [
Activation(egfr, kras, 'gtpbound'),
Activation(egfr, braf, 'kinase')
]
mc = ModelChecker(pa.model, stmts_to_check)
results = mc.check_model()
assert len(results) == len(stmts_to_check)
assert isinstance(results[0], tuple)
assert results[0][1] == True
assert results[1][1] == True
def test_check_rule_subject1():
mek = Agent('MEK1', db_refs={'HGNC': '6840'})
erk = Agent('ERK2', db_refs={'HGNC': '6871'})
stmt = Phosphorylation(mek, erk)
pysba = PysbAssembler()
pysba.add_statements([stmt])
pysba.make_model(policies='one_step')
# Check against stmt: should not validate ERK phosphorylates ERK
stmt_to_check = Phosphorylation(erk, erk)
mc = ModelChecker(pysba.model, [stmt_to_check])
checks = mc.check_model()
assert len(checks) == 1
assert checks[0][0] == stmt_to_check
assert checks[0][1] == False
def test_rasgap_activation():
nf1 = Agent('NF1', db_refs={'HGNC':'1'})
ras = Agent('KRAS', db_refs={'HGNC':'2'})
rasgap_stmt = RasGap(nf1, ras)
act_stmt = Inhibition(nf1, ras, 'gtpbound')
# Check that the activation is satisfied by the RasGap
pysba = PysbAssembler()
pysba.add_statements([rasgap_stmt])
pysba.make_model(policies='one_step')
mc = ModelChecker(pysba.model, [act_stmt])
checks = mc.check_model()
assert len(checks) == 1
assert checks[0][0] == act_stmt
assert checks[0][1] == True
# TODO TODO TODO
"""
def test_check_activation():
a = Agent('A')
b = Agent('B')
c = Agent('C')
st1 = Activation(a, b)
st2 = Inhibition(b, c, 'kinase')
stmts = [st1, st2]
# Create the model
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model(policies='one_step')
mc = ModelChecker(pa.model, stmts)
results = mc.check_model()
assert len(results) == len(stmts)
assert isinstance(results[0], tuple)
assert results[0][1] == True
assert results[1][1] == True
def test_rasgef_rasgtp():
sos = Agent('SOS1', db_refs={'HGNC':'1'})
ras = Agent('KRAS', activity=ActivityCondition('gtpbound', True),
db_refs={'HGNC':'2'})
raf = Agent('BRAF', db_refs={'HGNC':'3'})
rasgef_stmt = RasGef(sos, ras)
rasgtp_stmt = RasGtpActivation(ras, raf, 'kinase')
act_stmt = Activation(sos, raf, 'kinase')
# Check that the activation is satisfied by the RasGef
pysba = PysbAssembler()
pysba.add_statements([rasgef_stmt, rasgtp_stmt])
pysba.make_model(policies='one_step')
mc = ModelChecker(pysba.model, [act_stmt])
checks = mc.check_model()
assert len(checks) == 1
assert checks[0][0] == act_stmt
assert checks[0][1] == True
def test_grounded_modified_enzyme():
"""Check if the model checker can use semantic annotations to match mods
on the enzyme, not just the substrate, of a phosphorylation statement."""
mek_s202 = Agent('MEK1', mods=[ModCondition('phosphorylation', 'S', '202')],
db_refs={'HGNC': '6840'})
mek_phos = Agent('MEK1', mods=[ModCondition('phosphorylation', None, None)],
db_refs={'HGNC': '6840'})
erk = Agent('ERK2', db_refs={'HGNC': '6871'})
stmt_to_model = Phosphorylation(mek_s202, erk, None, None)
stmt_to_check = Phosphorylation(mek_phos, erk, None, None)
pa = PysbAssembler()
pa.add_statements([stmt_to_model])
pa.make_model(policies='one_step')
mc = ModelChecker(pa.model, [stmt_to_check])
results = mc.check_model()
assert len(results) == 1
assert results[0][0] == stmt_to_check
assert results[0][1] == True
def test_rasgef_rasgtp_phos():
sos = Agent('SOS1', db_refs={'HGNC':'1'})
ras = Agent('KRAS', activity=ActivityCondition('gtpbound', True),
db_refs={'HGNC':'2'})
raf = Agent('BRAF', db_refs={'HGNC':'3'})
mek = Agent('MEK', db_refs={'HGNC': '4'})
rasgef_stmt = RasGef(sos, ras)
rasgtp_stmt = RasGtpActivation(ras, raf, 'kinase')
phos = Phosphorylation(raf, mek)
stmt_to_check = Phosphorylation(sos, mek)
# Assemble and check
pysba = PysbAssembler()
pysba.add_statements([rasgef_stmt, rasgtp_stmt, phos])
pysba.make_model(policies='one_step')
mc = ModelChecker(pysba.model, [stmt_to_check])
checks = mc.check_model()
assert len(checks) == 1
assert checks[0][0] == stmt_to_check
assert checks[0][1] == True
def test_eidos_to_pysb():
stmts = __get_stmts_from_remote_jsonld()
pa = PysbAssembler()
# Make sure these don't error
pa.add_statements(stmts)
pa.make_model()
for fmt in ['kappa', 'sbml', 'sbgn']:
exp_str = pa.export_model(fmt)
assert exp_str, "Got no exported model from eidos->psyb to %s." % fmt
return
def check_policy(policy, result):
pysba = PysbAssembler()
pysba.add_statements([stmt])
pysba.make_model(policies=policy)
mc = ModelChecker(pysba.model, [stmt])
checks = mc.check_model()
assert len(checks) == 1
assert isinstance(checks[0], tuple)
assert checks[0][0] == stmt
assert checks[0][1] == result
def test_stmt_from_rule():
mek = Agent('MEK1', db_refs={'HGNC': '6840'})
erk = Agent('ERK2', db_refs={'HGNC': '6871'})
st = Phosphorylation(mek, erk, 'T', '185')
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
rule_name = pa.model.rules[0].name
stmt = _stmt_from_rule(pa.model, rule_name, [st])
assert (stmt == st)
def test_model_check_data():
# Create a set of statements
a = Agent('A', db_refs={'HGNC': '1'})
b = Agent('B', db_refs={'HGNC': '2'})
b_phos = Agent('B',
mods=[ModCondition('phosphorylation')],
db_refs={'HGNC': '2'})
c = Agent('C', db_refs={'HGNC': '3'})
c_phos = Agent('C',
mods=[ModCondition('phosphorylation')],
db_refs={'HGNC': '3'})
d = Agent('D', db_refs={'HGNC': '4'})
d_phos = Agent('D',
mods=[ModCondition('phosphorylation')],
db_refs={'HGNC': '4'})
# Two paths from A to D: One going through B and another through C
st1 = Phosphorylation(a, b)
st2 = Phosphorylation(b_phos, d)
st3 = Phosphorylation(a, c)
st4 = Phosphorylation(c_phos, d)
# Statements/Data agents for checking
stmt_to_check = Phosphorylation(a, d)
agent_obs = [b_phos, c_phos, d_phos]
# Make model
pa = PysbAssembler()
pa.add_statements([st1, st2, st3, st4])
pa.make_model(policies='one_step')
mc = ModelChecker(pa.model, [stmt_to_check], agent_obs)
results = mc.check_model(max_paths=5)
mc.get_im().draw('im.pdf', prog='dot')
# Create observable
assert len(results) == 1
pr = results[0][1]
res = pr.paths[0:2]
assert len(res) == 2
p1 = [('A_phosphorylation_B_phospho', 1),
('B_phospho_phosphorylation_D_phospho', 1), ('D_phospho_p_obs', 1)]
assert p1 in res
p2 = [('A_phosphorylation_C_phospho', 1),
('C_phospho_phosphorylation_D_phospho', 1), ('D_phospho_p_obs', 1)]
assert p2 in res
# Now, a vector linking agents with values, expressed at first as
# +/- 1
# This data should ensure that the path through B should be more highly
# ranked than the path through C
data = {b_phos: 1, c_phos: -1, d_phos: 1}
paths = results[0][1].paths
scored_paths = mc.score_paths(paths, data)
assert scored_paths[0][0] == p1
assert scored_paths[0][1] == 0
assert scored_paths[1][0] == p2
def test_check_ubiquitination():
xiap = Agent('XIAP', db_refs={'HGNC': '592'})
casp3 = Agent('CASP3', db_refs={'HGNC': '1504'})
stmt = Ubiquitination(xiap, casp3)
pysba = PysbAssembler()
pysba.add_statements([stmt])
pysba.make_model(policies='one_step')
mc = ModelChecker(pysba.model, [stmt])
checks = mc.check_model()
assert len(checks) == 1
assert isinstance(checks[0], tuple)
assert checks[0][0] == stmt
assert checks[0][1] == True
def test_check_rule_subject1():
mek = Agent('MEK1', db_refs={'HGNC': '6840'})
erk = Agent('ERK2', db_refs={'HGNC': '6871'})
stmt = Phosphorylation(mek, erk)
pysba = PysbAssembler()
pysba.add_statements([stmt])
pysba.make_model(policies='one_step')
# Check against stmt: should not validate ERK phosphorylates ERK
stmt_to_check = Phosphorylation(erk, erk)
mc = ModelChecker(pysba.model, [stmt_to_check])
checks = mc.check_model()
assert len(checks) == 1
assert checks[0][0] == stmt_to_check
assert checks[0][1] == False
def check_stmts(stmts):
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model(policies='one_step')
stmts_to_check = [
Activation(egfr, kras, 'gtpbound'),
Activation(egfr, braf, 'kinase')
]
mc = ModelChecker(pa.model, stmts_to_check)
results = mc.check_model()
assert len(results) == len(stmts_to_check)
assert isinstance(results[0], tuple)
assert results[0][1] == True
assert results[1][1] == True
def test_prune_influence_map():
kin = Agent('Kin', db_refs={'HGNC': '1'})
phos = Agent('Phos', db_refs={'HGNC': '2'})
subs = Agent('Substrate', db_refs={'HGNC': '3'})
st1 = Phosphorylation(kin, subs)
st2 = Dephosphorylation(phos, subs)
pa = PysbAssembler()
pa.add_statements([st1, st2])
pa.make_model(policies='one_step')
mc = ModelChecker(pa.model, [st1])
mc.prune_influence_map()
im = mc.get_im()
assert len(im.nodes()) == 3
assert len(im.edges()) == 2
def test_activate_via_mod():
mek = Agent('MEK1', db_refs={'HGNC': '6840'})
erk = Agent('ERK2', db_refs={'HGNC': '6871'})
erka = Agent('ERK2',
mods=[ModCondition('phosphorylation', 'T', '185')],
db_refs={'HGNC': '6871'})
st1 = Phosphorylation(mek, erk, 'T', '185')
st2 = ActiveForm(erka, 'activity', True)
st3 = Activation(mek, erk)
pa = PysbAssembler()
pa.add_statements([st1, st2])
pa.make_model()
mc = ModelChecker(pa.model, [st3])
checks = mc.check_model()
# Make sure it checks out to True
assert (checks[0][1].path_found)
def test_rasgap_activation():
nf1 = Agent('NF1', db_refs={'HGNC': '1'})
ras = Agent('KRAS', db_refs={'HGNC': '2'})
rasgap_stmt = RasGap(nf1, ras)
act_stmt = Inhibition(nf1, ras, 'gtpbound')
# Check that the activation is satisfied by the RasGap
pysba = PysbAssembler()
pysba.add_statements([rasgap_stmt])
pysba.make_model(policies='one_step')
mc = ModelChecker(pysba.model, [act_stmt])
checks = mc.check_model()
assert len(checks) == 1
assert checks[0][0] == act_stmt
assert checks[0][1] == True
# TODO TODO TODO
"""
def test_rasgef_activation():
sos = Agent('SOS1', db_refs={'HGNC': '1'})
ras = Agent('KRAS', db_refs={'HGNC': '2'})
rasgef_stmt = RasGef(sos, ras)
act_stmt = Activation(sos, ras, 'gtpbound')
# Check that the activation is satisfied by the RasGef
pysba = PysbAssembler()
pysba.add_statements([rasgef_stmt])
pysba.make_model(policies='one_step')
mc = ModelChecker(pysba.model, [act_stmt])
checks = mc.check_model()
assert len(checks) == 1
assert checks[0][0] == act_stmt
assert checks[0][1].paths == [[('SOS1_activates_KRAS', 1),
('KRAS_gtpbound_active_obs', 1)]]
# TODO TODO TODO
"""
def test_check_activation():
a = Agent('A')
b = Agent('B')
c = Agent('C')
st1 = Activation(a, b)
st2 = Inhibition(b, c, 'kinase')
stmts = [st1, st2]
# Create the model
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model(policies='one_step')
mc = ModelChecker(pa.model, stmts)
results = mc.check_model()
assert len(results) == len(stmts)
assert isinstance(results[0], tuple)
assert results[0][1] == True
assert results[1][1] == True
def test_observables():
mek = Agent('MEK1', db_refs={'HGNC': '6840'})
erk = Agent('ERK2', db_refs={'HGNC': '6871'})
erkp = Agent('ERK2',
mods=[ModCondition('phosphorylation', 'T', '185')],
db_refs={'HGNC': '6871'})
st1 = Phosphorylation(mek, erk, 'T', '185')
st2 = ActiveForm(erkp, 'activity', True)
st3 = Activation(mek, erk)
pa = PysbAssembler()
pa.add_statements([st1, st2])
pa.make_model()
mc = ModelChecker(pa.model, [st1, st3], agent_obs=[erkp])
checks = mc.check_model()
assert checks[0][1].path_found
assert checks[1][1].path_found
# Only 1 observable should be created
assert len(mc.model.observables) == 1
def test_rasgef_rasgtp():
sos = Agent('SOS1', db_refs={'HGNC': '1'})
ras = Agent('KRAS',
activity=ActivityCondition('gtpbound', True),
db_refs={'HGNC': '2'})
raf = Agent('BRAF', db_refs={'HGNC': '3'})
rasgef_stmt = RasGef(sos, ras)
rasgtp_stmt = RasGtpActivation(ras, raf, 'kinase')
act_stmt = Activation(sos, raf, 'kinase')
# Check that the activation is satisfied by the RasGef
pysba = PysbAssembler()
pysba.add_statements([rasgef_stmt, rasgtp_stmt])
pysba.make_model(policies='one_step')
mc = ModelChecker(pysba.model, [act_stmt])
checks = mc.check_model()
assert len(checks) == 1
assert checks[0][0] == act_stmt
assert checks[0][1] == True
def test_check_activation():
a = Agent('A', db_refs={'HGNC': '1'})
b = Agent('B', db_refs={'HGNC': '2'})
c = Agent('C', db_refs={'HGNC': '3'})
st1 = Activation(a, b)
st2 = Inhibition(b, c, 'kinase')
stmts = [st1, st2]
# Create the model
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model(policies='one_step')
mc = ModelChecker(pa.model, stmts)
results = mc.check_model()
assert len(results) == len(stmts)
assert isinstance(results[0], tuple)
assert results[0][1].paths == [[('A_activates_B_activity', 1),
('B_activity_active_obs', 1)]]
assert results[1][1].paths == [[('B_deactivates_C_kinase', 1),
('C_kinase_active_obs', -1)]]
def test_grounded_modified_enzyme():
"""Check if the model checker can use semantic annotations to match mods
on the enzyme, not just the substrate, of a phosphorylation statement."""
mek_s202 = Agent('MEK1',
mods=[ModCondition('phosphorylation', 'S', '202')],
db_refs={'HGNC': '6840'})
mek_phos = Agent('MEK1',
mods=[ModCondition('phosphorylation', None, None)],
db_refs={'HGNC': '6840'})
erk = Agent('ERK2', db_refs={'HGNC': '6871'})
stmt_to_model = Phosphorylation(mek_s202, erk, None, None)
stmt_to_check = Phosphorylation(mek_phos, erk, None, None)
pa = PysbAssembler()
pa.add_statements([stmt_to_model])
pa.make_model(policies='one_step')
mc = ModelChecker(pa.model, [stmt_to_check])
results = mc.check_model()
assert len(results) == 1
assert results[0][0] == stmt_to_check
assert results[0][1] == True
def test_rasgef_rasgtp_phos():
sos = Agent('SOS1', db_refs={'HGNC': '1'})
ras = Agent('KRAS',
activity=ActivityCondition('gtpbound', True),
db_refs={'HGNC': '2'})
raf = Agent('BRAF', db_refs={'HGNC': '3'})
mek = Agent('MEK', db_refs={'HGNC': '4'})
rasgef_stmt = RasGef(sos, ras)
rasgtp_stmt = RasGtpActivation(ras, raf, 'kinase')
phos = Phosphorylation(raf, mek)
stmt_to_check = Phosphorylation(sos, mek)
# Assemble and check
pysba = PysbAssembler()
pysba.add_statements([rasgef_stmt, rasgtp_stmt, phos])
pysba.make_model(policies='one_step')
mc = ModelChecker(pysba.model, [stmt_to_check])
checks = mc.check_model()
assert len(checks) == 1
assert checks[0][0] == stmt_to_check
assert checks[0][1] == True
def test_rasgap_rasgtp():
nf1 = Agent('NF1', db_refs={'HGNC': '1'})
ras = Agent('KRAS', db_refs={'HGNC': '2'})
ras_g = Agent('KRAS',
activity=ActivityCondition('gtpbound', True),
db_refs={'HGNC': '2'})
raf = Agent('BRAF', db_refs={'HGNC': '3'})
rasgap_stmt = RasGap(nf1, ras)
rasgtp_stmt = RasGtpActivation(ras_g, raf, 'kinase')
act_stmt = Inhibition(nf1, raf, 'kinase')
# Check that the activation is satisfied by the RasGap
pysba = PysbAssembler()
pysba.add_statements([rasgap_stmt, rasgtp_stmt])
pysba.make_model(policies='one_step')
mc = ModelChecker(pysba.model, [act_stmt])
checks = mc.check_model()
assert len(checks) == 1
assert checks[0][0] == act_stmt
assert checks[0][1].paths == [[('NF1_deactivates_KRAS', 1),
('KRAS_activates_BRAF_kinase', -1),
('BRAF_kinase_active_obs', -1)]]