def test_cli_tool():
""" Test the command line interface parser of scrumpy files """
output_file = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for n in range(10)) + '.json'
output_file_path = os.path.join(tempfile.gettempdir(), output_file)
# Test loading of scrumpy models
model = load_model(scrumpy_model_path)
assert isinstance(model, cobra.Model)
runner = CliRunner()
result = runner.invoke(gsmodutils.utils.scrumpy.scrumpy_to_cobra, [
scrumpy_model_path,
'MetaSal',
'--output',
output_file_path,
'--fixed_fluxes',
scrumpy_biomass_path,
'--name',
'samonella scrumpy model',
'--objective',
'Glc_tx',
])
assert result.exit_code == 0
model = load_model(output_file_path)
assert isinstance(model, cobra.Model)
solution = model.optimize()
assert solution.objective_value != 0.0
os.remove(output_file_path)
# Check the number of reactions is correct
assert len(model.reactions) == 1229 # 1158 ??
# Check the number of metabolites is correct
assert len(model.metabolites) == 1130 # 1129
# Number of transporters + metabolites should equal scrumpy's number of metabolites
assert len(model.exchanges) == 71 # 67
result = runner.invoke(gsmodutils.utils.scrumpy.scrumpy_to_cobra, [
scrumpy_model_path,
'MetaSal',
'--output',
output_file_path,
'--media',
scrumpy_media_path,
'--name',
'samonella scrumpy model',
'--objective',
'Glc_tx',
])
def build_universal_model(path,
use_cache=True,
cache_location='.metacyc_universal.json'):
"""
Constructs a universal model from all the reactions in the metacyc database
:param path: path to folder containing metacyc dat files
:param use_cache: optionally store the resulting model in cached form
:return:
"""
try:
if use_cache and os.path.exists(cache_location):
model = load_model(cache_location)
return model
except (IOError, TypeError):
pass # This means cached model couldn't be loaded, we'll create a new one
db = parse_db(path)
model = Model()
for reaction_id in db['reactions']:
try:
add_reaction(model, reaction_id, db)
except KeyError:
# Exception handling ignores badly formatted reactions
pass
if use_cache:
save_json_model(model, cache_location)
return model
def test_load_model():
""" Force exceptions to be thrown """
with pytest.raises(IOError):
load_model('/this/path/does/not/exist')
with pytest.raises(TypeError):
# Create a fake file, format is not valid
with tempfile.NamedTemporaryFile() as fp:
load_model(fp.name, file_format="foo")
with FakeProjectContext() as ctx:
model = ctx.project.model
load_medium(model, {}, copy=True)
with pytest.raises(TypeError):
load_medium(model, set())
with pytest.raises(TypeError):
load_medium(set(), dict())
def _load_cobra_model(self):
"""
Loads the cobra model
:return: cobra.Model instance of self
"""
if self.model_path is not None and not os.path.exists(self.model_path):
raise IOError("Model file not found")
if self.design is not None:
return self.design.load()
return load_model(self.model_path)
def validate_model_file(model_path):
"""
Simple wrapper to load a model from a given path (handles JSON and SBML)
"""
model = load_model(model_path)
return validate_model(model)