def model_simulate(model_id, method, objective_id, objective_direction, operations):
try:
model_wrapper = storage.get(model_id)
except Unauthorized as error:
abort(401, error.message)
except Forbidden as error:
abort(403, error.message)
except ModelNotFound as error:
abort(404, error.message)
model = model_wrapper.model
# Use the context manager to undo all modifications to the shared model instance on
# completion.
with model:
apply_operations(model, operations)
try:
flux_distribution, growth_rate = simulate(
model,
model_wrapper.biomass_reaction,
method,
objective_id,
objective_direction,
)
except OptimizationError:
return jsonify({"status": model.solver.status})
else:
return jsonify(
{
"status": model.solver.status,
"flux_distribution": flux_distribution,
"growth_rate": growth_rate,
}
)
def test_tmy_result(e_coli_core, objective):
e_coli_core, biomass_reaction = e_coli_core
to_return = ["fluxes", "tmy", "model", "growth-rate", "removed-reactions"]
result = simulate(
e_coli_core, biomass_reaction, "fba", None, None, [objective], to_return
)
assert set(result) == set(to_return)
def test_simulation_methods(e_coli_core, method):
e_coli_core, biomass_reaction = e_coli_core
for method in METHODS:
fluxes, growth_rate = simulate(
e_coli_core, biomass_reaction, method, None, None
)
if method not in {"fva", "pfba-fva"}:
reactions_ids = [i.id for i in e_coli_core.reactions]
assert set(fluxes) == set(reactions_ids)