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_add_reaction(e_coli_core):
e_coli_core, biomass_reaction, is_ec_model = e_coli_core
assert not e_coli_core.reactions.has_id("FOOBAR")
apply_operations(
e_coli_core,
[{
"operation": "add",
"type": "reaction",
"data": {
"id": "FOOBAR",
"name": "Foo Bar",
"metabolites": {
"accoa_c": -1.0,
"cit_c": 1.0,
"coa_c": 1.0,
"h2o_c": -1.0,
"h_c": 1.0,
"oaa_c": -1.0,
},
"lower_bound": 0.0,
"upper_bound": 1000.0,
"gene_reaction_rule": "b0720",
},
}],
)
assert e_coli_core.reactions.FOOBAR.bounds == (0.0, 1000.0)
def test_knockout_reaction(e_coli_core):
e_coli_core, biomass_reaction, is_ec_model = e_coli_core
assert e_coli_core.reactions.CS.bounds != (0.0, 0.0)
apply_operations(e_coli_core, [{
"operation": "knockout",
"type": "reaction",
"id": "CS"
}])
assert e_coli_core.reactions.CS.bounds == (0.0, 0.0)
def test_knockout_gene(e_coli_core):
e_coli_core, biomass_reaction, is_ec_model = e_coli_core
assert e_coli_core.genes.b4025.functional
assert all(
[r.bounds != (0.0, 0.0) for r in e_coli_core.genes.b4025.reactions])
apply_operations(e_coli_core, [{
"operation": "knockout",
"type": "gene",
"id": "b4025"
}])
assert not e_coli_core.genes.b4025.functional
assert all(
[r.bounds == (0.0, 0.0) for r in e_coli_core.genes.b4025.reactions])
def test_modify_reaction(e_coli_core):
e_coli_core, biomass_reaction, is_ec_model = e_coli_core
assert e_coli_core.reactions.CS.bounds == (0.0, 1000.0)
apply_operations(
e_coli_core,
[{
"operation": "modify",
"type": "reaction",
"id": "CS",
"data": {
"id": "CS",
"lower_bound": -20.0,
"upper_bound": 20.0
},
}],
)
assert e_coli_core.reactions.CS.bounds == (-20.0, 20)
def test_add_reaction_unknown_metabolites(e_coli_core):
e_coli_core, biomass_reaction, is_ec_model = e_coli_core
assert not e_coli_core.metabolites.has_id("foo_c")
assert not e_coli_core.metabolites.has_id("bar_c")
apply_operations(
e_coli_core,
[{
"operation": "add",
"type": "reaction",
"data": {
"id": "FOOBAR",
"name": "Foo Bar",
"metabolites": {
"foo_c": -1.0,
"bar_c": 1.0
},
"lower_bound": -1000.0,
"upper_bound": 1000.0,
"gene_reaction_rule": "",
},
}],
)
assert e_coli_core.metabolites.has_id("foo_c")
assert e_coli_core.metabolites.has_id("bar_c")