def test_cache(monkeypatch, tmp_path, bigg_models, biomodels):
"""Test that remote models are properly cached."""
config = Configuration()
monkeypatch.setattr(config, "cache_directory", tmp_path)
remote_model = load_model("e_coli_core")
cached_model = load_model("e_coli_core", repositories=[bigg_models, biomodels])
bigg_models.get_sbml.assert_not_called()
biomodels.get_sbml.assert_not_called()
assert len(cached_model.metabolites) == len(remote_model.metabolites)
assert len(cached_model.reactions) == len(remote_model.reactions)
def build_test_model():
model = load_model("e_coli_core")
pH_I_T_dict = {
"pH": {"c": 7.5, "e": 7, "p": 7},
"I": {"c": 0.25, "e": 0, "p": 0},
"T": {"c": 298.15, "e": 298.15, "p": 298.15},
}
del_psi_dict = {
"c": {"c": 0, "e": 0, "p": 150},
"e": {"c": 0, "e": 0, "p": 0},
"p": {"c": -150, "e": 0, "p": 0},
}
del_psi = pd.DataFrame.from_dict(data=del_psi_dict)
comp_info = pd.DataFrame.from_dict(data=pH_I_T_dict)
Excl = [rxn.id for rxn in model.boundary] + [
"BIOMASS_Ecoli_core_w_GAM",
"O2t",
"H2Ot",
]
tfa_model = tmodel(
model, Exclude_list=Excl, compartment_info=comp_info, membrane_potential=del_psi
)
for met in tfa_model.metabolites:
kegg_id = "bigg.metabolite:" + met.id[:-2]
met.Kegg_id = kegg_id
tfa_model.update()
return tfa_model
def test_remote_load(model_id: str, num_metabolites: int, num_reactions: int):
"""Test that sample models can be loaded from remote repositories (e2e)."""
model = load_model(model_id, cache=False)
assert len(model.metabolites) == num_metabolites
assert len(model.reactions) == num_reactions
def test_unknown_model():
"""Expect that a not found error is raised (e2e)."""
load_model("MODELWHO?", cache=False)
def test_biomodels_access(biomodels):
"""Test that SBML would be retrieved from the BioModels repository."""
load_model("BIOMD0000000633", cache=False, repositories=[biomodels])
biomodels.get_sbml.assert_called_once_with(model_id="BIOMD0000000633")
def test_bigg_access(bigg_models):
"""Test that SBML would be retrieved from the BiGG Models repository."""
load_model("e_coli_core", cache=False, repositories=[bigg_models])
bigg_models.get_sbml.assert_called_once_with(model_id="e_coli_core")