def test_missing_activity2():
stmts = [Inhibition(drug, raf), Activation(raf, mek)]
md = ModelDiagnoser(stmts)
suggs = md.get_missing_activities()
assert len(suggs) == 1
assert suggs[0].subj.name == 'RAF'
assert suggs[0].subj.activity
assert suggs[0].subj.activity.activity_type == 'activity'
def test_missing_activity2():
stmts = [Inhibition(drug, raf), Activation(raf, mek)]
md = ModelDiagnoser(stmts)
suggs = md.get_missing_activities()
assert len(suggs) == 1
assert suggs[0].subj.name == 'RAF'
assert suggs[0].subj.activity
assert suggs[0].subj.activity.activity_type == 'activity'
def test_missing_activity1():
stmts = [Activation(raf, mek), Phosphorylation(mek, erk)]
md = ModelDiagnoser(stmts)
suggs = md.get_missing_activities()
assert len(suggs) == 1
assert suggs[0].enz.name == 'MEK'
assert suggs[0].enz.activity
assert suggs[0].enz.activity.activity_type == 'activity'
def test_missing_activity1():
stmts = [Activation(raf, mek), Phosphorylation(mek, erk)]
md = ModelDiagnoser(stmts)
suggs = md.get_missing_activities()
assert len(suggs) == 1
assert suggs[0].enz.name == 'MEK'
assert suggs[0].enz.activity
assert suggs[0].enz.activity.activity_type == 'activity'
def test_check_model():
explain = Activation(raf, erk)
mek_active = Agent('MEK', db_refs={'FPLX': 'MEK'},
activity=ActivityCondition('activity', True))
model_stmts = [Activation(raf, mek), Activation(mek_active, erk)]
# Build the pysb model
pa = PysbAssembler()
pa.add_statements(model_stmts)
pa.make_model(policies='one_step')
md = ModelDiagnoser(model_stmts, pa.model, explain)
result = md.check_explanation()
assert result['has_explanation'] is True
path = result['explanation_path']
assert len(path) == 2
assert path[0] == model_stmts[0]
assert path[1] == model_stmts[1]
def test_check_model():
explain = Activation(raf, erk)
mek_active = Agent('MEK',
db_refs={'FPLX': 'MEK'},
activity=ActivityCondition('activity', True))
model_stmts = [Activation(raf, mek), Activation(mek_active, erk)]
# Build the pysb model
pa = PysbAssembler()
pa.add_statements(model_stmts)
pa.make_model(policies='one_step')
md = ModelDiagnoser(model_stmts, pa.model, explain)
result = md.check_explanation()
assert result['has_explanation'] is True
path = result['explanation_path']
assert len(path) == 2
assert path[0] == model_stmts[0]
assert path[1] == model_stmts[1]
def run_diagnoser(self, res, model_stmts, model_exec):
# Use a model diagnoser to identify explanations given the executable
# model, the current statements, and the explanation goal
if self.explain:
md = ModelDiagnoser(model_stmts, model=model_exec,
explain=self.explain)
md_result = md.check_explanation()
res.update(md_result)
# If we got a proposal for a statement, get a specific
# recommendation
connect_stmts = res.get('connect_stmts')
if connect_stmts:
u_stmt, v_stmt = connect_stmts
stmt_suggestions, sugg_subj, sugg_obj = \
md.suggest_statements(u_stmt, v_stmt)
if stmt_suggestions:
agents = [a.name for a in stmt_suggestions[0].agent_list()
if a is not None]
if len(set(agents)) > 1:
res['stmt_suggestions'] = stmt_suggestions
res['stmt_suggestions_subj'] = sugg_subj
res['stmt_suggestions_obj'] = sugg_obj
md = ModelDiagnoser(model_stmts)
acts = md.get_missing_activities()
if acts:
logger.info('Missing activities found: %s' % acts)
res['stmt_corrections'] = acts
def test_propose_statement():
jun = Agent('JUN', db_refs={'HGNC':'6204', 'UP': 'P05412'})
explain = Activation(raf, jun)
erk_active = Agent('ERK', db_refs={'FPLX': 'ERK'},
activity=ActivityCondition('activity', True))
# Leave out MEK activates ERK
model_stmts = [Activation(raf, mek), Activation(erk_active, jun)]
# Build the pysb model
pa = PysbAssembler()
pa.add_statements(model_stmts)
pa.make_model(policies='one_step')
md = ModelDiagnoser(model_stmts, pa.model, explain)
result = md.check_explanation()
assert result['has_explanation'] is False
assert result.get('explanation_path') is None
inf_prop = result.get('connect_rules')
assert inf_prop == ('RAF_activates_MEK_activity',
'ERK_act_activates_JUN_activity'), inf_prop
stmt_prop = result.get('connect_stmts')
assert stmt_prop == (model_stmts[0], model_stmts[1])
stmt_suggestions = md.suggest_statements(*stmt_prop)
def test_propose_statement():
jun = Agent('JUN', db_refs={'HGNC': '6204', 'UP': 'P05412'})
explain = Activation(raf, jun)
erk_active = Agent('ERK',
db_refs={'FPLX': 'ERK'},
activity=ActivityCondition('activity', True))
# Leave out MEK activates ERK
model_stmts = [Activation(raf, mek), Activation(erk_active, jun)]
# Build the pysb model
pa = PysbAssembler()
pa.add_statements(model_stmts)
pa.make_model(policies='one_step')
md = ModelDiagnoser(model_stmts, pa.model, explain)
result = md.check_explanation()
assert result['has_explanation'] is False
assert result.get('explanation_path') is None
inf_prop = result.get('connect_rules')
assert inf_prop == ('RAF_activates_MEK_activity',
'ERK_act_activates_JUN_activity'), inf_prop
stmt_prop = result.get('connect_stmts')
assert stmt_prop == (model_stmts[0], model_stmts[1])
stmt_suggestions = md.suggest_statements(*stmt_prop)
def run_diagnoser(self, res, model_stmts, model_exec):
# Use a model diagnoser to identify explanations given the executable
# model, the current statements, and the explanation goal
if self.explain:
md = ModelDiagnoser(model_stmts, model=model_exec,
explain=self.explain)
md_result = md.check_explanation()
res.update(md_result)
# If we got a proposal for a statement, get a specific
# recommendation
connect_stmts = res.get('connect_stmts')
if connect_stmts:
u_stmt, v_stmt = connect_stmts
stmt_suggestions = md.suggest_statements(u_stmt, v_stmt)
if stmt_suggestions:
agents = [a.name for a in stmt_suggestions[0].agent_list()
if a is not None]
if len(set(agents)) > 1:
res['stmt_suggestions'] = stmt_suggestions
md = ModelDiagnoser(model_stmts)
acts = md.get_missing_activities()
if acts:
res['stmt_corrections'] = acts
def test_missing_activity3():
stmts = [Activation(raf, mek), Activation(raf, erk)]
md = ModelDiagnoser(stmts)
suggs = md.get_missing_activities()
assert len(suggs) == 0
def test_missing_activity3():
stmts = [Activation(raf, mek), Activation(raf, erk)]
md = ModelDiagnoser(stmts)
suggs = md.get_missing_activities()
assert len(suggs) == 0