def test_metabolite_summary_to_table_previous_solution(model, opt_solver, met):
"""Test metabolite summary._to_table() of previous solution."""
model.solver = opt_solver
solution = pfba(model)
expected_entry = [
'PRODUCING CYTBD 100 43.6 2.0 h_c + 0.5 o2_c + '
'q8h2_c --> h2o_c + 2.0 h_'
]
with captured_output() as (out, _):
print(model.metabolites.get_by_id(met).summary(solution))
check_in_line(out.getvalue(), expected_entry)
def test_metabolite_summary_to_table_with_fva(model, opt_solver, fraction,
met):
"""Test metabolite summary._to_table() (using FVA)."""
# pytest.xfail("FVA currently buggy")
model.solver = opt_solver
model.optimize()
expected_entry = [
'PRODUCING PFK 100 7.48 6.17 9.26 '
'atp_c + f6p_c --> adp_c + fdp_c + h_c'
]
with captured_output() as (out, _):
print(model.metabolites.get_by_id(met).summary(fva=fraction))
check_line(out.getvalue(), expected_entry)
def test_model_summary_to_table_previous_solution(model, opt_solver, names):
"""Test Summary._to_table() of previous solution."""
model.solver = opt_solver
solution = model.optimize()
rxn_test = model.exchanges[0]
if names:
met_test = list(rxn_test.metabolites.keys())[0].name
else:
met_test = list(rxn_test.metabolites.keys())[0].id
solution.fluxes[rxn_test.id] = 321
with captured_output() as (out, _):
print(model.summary(solution, names=names))
check_in_line(out.getvalue(), [met_test + '321'])
def test_reaction_summary_to_table(model, rxn, names):
"""Test reaction summary._to_table()."""
if names:
expected_entry = [
' adhE '
'Coenzyme A -1 c '
]
else:
expected_entry = [
' accoa_c '
'1 c '
]
with captured_output() as (out, _):
print(model.reactions.get_by_id(rxn).summary(names=names))
check_in_line(out.getvalue(), expected_entry)
def test_model_summary_to_table_with_fva(model, opt_solver, fraction):
"""Test model summary._to_table() (using FVA)."""
if opt_solver == "optlang-gurobi":
pytest.xfail("FVA currently buggy")
# test non-fva version (these should be fixed for textbook model)
expected_entry = [
' o2_e 21.8 19.9 23.7 h2o_e '
'29.2 25 30.7 Biomass_Ecoli_core '
'0.874 '
]
model.solver = opt_solver
solution = model.optimize()
with captured_output() as (out, _):
print(model.summary(solution, fva=fraction))
check_in_line(out.getvalue(), expected_entry)
def test_metabolite_summary_to_table(model, opt_solver, met, names):
"""Test metabolite summary._to_table()."""
model.solver = opt_solver
model.optimize()
if names:
expected_entry = [
'PRODUCING cytochrome oxidase bd '
'(ubiquinol-8: 2 protons) 100 43.6 '
'2.0 H+ + 0.5 O2 + Ubiquinol-8 --> H2O + 2.0 H+'
]
else:
expected_entry = [
'PRODUCING CYTBD 100 43.6 2.0 h_c + '
'0.5 o2_c + q8h2_c --> h2o_c + 2.0 h_'
]
with captured_output() as (out, _):
print(model.metabolites.get_by_id(met).summary(names=names))
check_in_line(out.getvalue(), expected_entry)
def test_model_summary_to_table(model, opt_solver, names):
"""Test model.summary()._to_table()."""
model.solver = opt_solver
# test non-fva version (these should be fixed for textbook model)
if names:
expected_entry = [
' O2 21.8 H2O 29.2 '
'Biomass Objective Function with GAM 0.874 '
]
else:
expected_entry = [
' o2_e 21.8 h2o_e 29.2 '
'Biomass_Ecoli_core 0.874 '
]
model.optimize()
with captured_output() as (out, _):
print(model.summary(names=names))
check_in_line(out.getvalue(), expected_entry)