def test_medium_adapter_ec_model(eciML1515):
eciML1515, biomass_reaction, is_ec_model = eciML1515
medium = [
{
"name": "glc",
"identifier": "MNXM41",
"namespace": "metanetx.chemical"
},
{
"name": "nh4",
"identifier": "MNXM15",
"namespace": "metanetx.chemical"
},
{
"name": "o2",
"identifier": "MNXM4",
"namespace": "metanetx.chemical"
},
]
operations, warnings, errors = apply_medium(eciML1515, is_ec_model, medium)
# 2 warnings are expected: trace metals (CHEBI:25517 and CHEBI:25368) not found in
# model, as eciML1515 does not have CHEBI ids.
assert len(warnings) == 2
assert len(errors) == 0
assert set(eciML1515.medium) == {
"EX_glc__D_e_REV",
"EX_nh4_e_REV",
"EX_o2_e_REV",
}
assert eciML1515.reactions.EX_glc__D_e_REV.upper_bound == +10
assert eciML1515.reactions.EX_nh4_e_REV.upper_bound == +1000
assert eciML1515.reactions.EX_o2_e_REV.upper_bound == +1000
def test_medium_adapter(iJO1366):
iJO1366, biomass_reaction, is_ec_model = iJO1366
medium = [
{
"name": "Foo",
"identifier": "CHEBI:63041",
"namespace": "chebi"
},
{
"name": "Bar",
"identifier": "CHEBI:91249",
"namespace": "chebi"
},
{
"name": "Baz",
"identifier": "CHEBI:86244",
"namespace": "chebi"
},
{
"name": "Goo",
"identifier": "CHEBI:131387",
"namespace": "chebi"
},
]
operations, warnings, errors = apply_medium(iJO1366, is_ec_model, medium)
# 30 warnings are expected; 29 unique compounds not found in the model and 1
# unmapped ion from the salts mapping
assert len(warnings) == 30
assert len(errors) == 0
assert set(iJO1366.medium) == {
"EX_fe2_e",
"EX_fe3_e",
"EX_h2o_e",
"EX_mobd_e",
"EX_nh4_e",
"EX_so4_e",
"EX_ni2_e",
"EX_mn2_e",
"EX_cl_e",
}
assert all(
iJO1366.reactions.get_by_id(r).lower_bound == -1000
for r in iJO1366.medium)
def model_modify(
model_id,
medium,
genotype,
fluxomics,
metabolomics,
uptake_secretion_rates,
molar_yields,
growth_rate,
):
if not request.is_json:
abort(415, "Non-JSON request content is not supported")
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)
# Use the context manager to undo all modifications to the shared model instance on
# completion.
with model_wrapper.model as model:
# Build list of operations to perform on the model
operations = []
warnings = []
errors = []
if medium:
results = apply_medium(model, medium)
operations.extend(results[0])
warnings.extend(results[1])
errors.extend(results[2])
if genotype:
results = apply_genotype(model, genotype)
operations.extend(results[0])
warnings.extend(results[1])
errors.extend(results[2])
if (
fluxomics
or metabolomics
or uptake_secretion_rates
or molar_yields
or growth_rate
):
results = apply_measurements(
model,
model_wrapper.biomass_reaction,
fluxomics,
metabolomics,
uptake_secretion_rates,
molar_yields,
growth_rate,
)
operations.extend(results[0])
warnings.extend(results[1])
errors.extend(results[2])
if errors:
# If any errors occured during modifications, discard generated operations
# and return the error messages to the client for follow-up
return {"errors": errors}, 400
else:
return {"operations": operations, "warnings": warnings}