def test_normalize(self):
filename_xls_1 = path.join(self.tempdir, 'model-1.xlsx')
filename_xls_2 = path.join(self.tempdir, 'model-2.xlsx')
model = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.0')
Writer().run(filename_xls_1, model, data_repo_metadata=False)
# with same destination
with __main__.App(argv=['normalize', filename_xls_1]) as app:
app.run()
model2 = Reader().run(filename_xls_1)[Model][0]
self.assertTrue(model2.is_equal(model))
# with different destination
with __main__.App(
argv=['normalize', filename_xls_1, '--dest', filename_xls_2
]) as app:
app.run()
model2 = Reader().run(filename_xls_2)[Model][0]
self.assertTrue(model2.is_equal(model))
def test_convert_sloppy(self):
filename_xls1 = os.path.join(self.tempdir, 'model1.xlsx')
filename_xls2 = os.path.join(self.tempdir, 'model2.xlsx')
filename_csv = os.path.join(self.tempdir, 'model-*.csv')
Writer().run(filename_xls1, self.model, data_repo_metadata=False)
wb = read_workbook(filename_xls1)
row = wb['!!Model'].pop(3)
wb['!!Model'].insert(4, row)
write_workbook(filename_xls1, wb)
with self.assertRaisesRegex(ValueError, "The rows of worksheet '!!Model' must be defined in this order"):
convert(filename_xls1, filename_csv)
env = EnvironmentVarGuard()
env.set('CONFIG__DOT__wc_lang__DOT__io__DOT__strict', '0')
with env:
convert(filename_xls1, filename_csv)
self.assertTrue(os.path.isfile(os.path.join(self.tempdir, 'model-Model.csv')))
self.assertTrue(os.path.isfile(os.path.join(self.tempdir, 'model-Taxon.csv')))
model = Reader().run(filename_csv)[Model][0]
self.assertTrue(model.is_equal(self.model))
convert(filename_csv, filename_xls2)
model = Reader().run(filename_xls2)[Model][0]
self.assertTrue(model.is_equal(self.model))
def test_read_write(self):
fixture_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'example-model.xlsx')
model = Reader().run(fixture_filename)[Model][0]
self.assertEqual(model.validate(), None)
# compare excel files
Writer().run(self.filename, model, data_repo_metadata=False)
original = read_workbook(fixture_filename)
copy = read_workbook(self.filename)
remove_ws_metadata(original)
remove_ws_metadata(copy)
original.pop('!!' + obj_tables.core.TOC_SHEET_NAME)
copy.pop('!!' + obj_tables.core.TOC_SHEET_NAME)
# note that models must be sorted by id for this assertion to hold
for sheet in original.keys():
for i_row, (copy_row, original_row) in enumerate(zip(copy[sheet], original[sheet])):
self.assertEqual(copy_row, original_row,
msg='Rows {} of {} sheets are not equal'.format(i_row, sheet))
self.assertEqual(copy[sheet], original[sheet], msg='{} sheets are not equal'.format(sheet))
self.assertEqual(copy, original)
# compare models
model2 = Reader().run(self.filename)[Model][0]
self.assertTrue(model2.is_equal(model))
self.assertTrue(model.difference(model2) == '')
def test_convert(self):
filename_xls1 = os.path.join(self.tempdir, 'model1.xlsx')
filename_xls2 = os.path.join(self.tempdir, 'model2.xlsx')
filename_csv = os.path.join(self.tempdir, 'model-*.csv')
Writer().run(filename_xls1, self.model, data_repo_metadata=False)
convert(filename_xls1, filename_csv)
self.assertTrue(os.path.isfile(os.path.join(self.tempdir, 'model-Model.csv')))
self.assertTrue(os.path.isfile(os.path.join(self.tempdir, 'model-Taxon.csv')))
model = Reader().run(filename_csv)[Model][0]
self.assertTrue(model.is_equal(self.model))
convert(filename_csv, filename_xls2)
model = Reader().run(filename_xls2)[Model][0]
self.assertTrue(model.is_equal(self.model))
def setUp(self):
self.model = model = Model(id='test', version='0.1')
c = model.compartments.create(id='comp')
c.init_density = model.parameters.create(id='density_compartment_1', value=1100,
units=unit_registry.parse_units('g l^-1'))
t0 = model.species_types.create(id='s0', type=onto['WC:metabolite'])
t1 = model.species_types.create(id='s1', type=onto['WC:metabolite'])
t2 = model.species_types.create(id='s2', type=onto['WC:metabolite'])
s0 = model.species.create(id='s0[comp]', species_type=t0, compartment=c)
s1 = model.species.create(id='s1[comp]', species_type=t1, compartment=c)
s2 = model.species.create(id='s2[comp]', species_type=t2, compartment=c)
self.submodel = submodel = model.submodels.create(id='submodel',
framework=onto['WC:stochastic_simulation_algorithm'])
self.r0 = r0 = model.reactions.create(id='r0', reversible=True, submodel=submodel)
r0.participants.create(species=s0, coefficient=-2)
r0.participants.create(species=s1, coefficient=3)
r0_f = r0.rate_laws.create(id='r0-forward', direction=RateLawDirection.forward, model=model)
a = model.parameters.create(id='a', value=1., units=unit_registry.parse_units('s^-1'))
r0_f.expression, error = RateLawExpression.deserialize('a', {Parameter: {'a': a}})
assert error is None, str(error)
r0_b = r0.rate_laws.create(id='r0-backward', direction=RateLawDirection.backward,
model=model)
b = model.parameters.create(id='b', value=1., units=unit_registry.parse_units('s^-1'))
r0_b.expression, error = RateLawExpression.deserialize('b', {Parameter: {'b': b}})
assert error is None, str(error)
r0.references.create(id='ref_0', model=model)
r0.identifiers.create(namespace='x', id='y')
self.r1 = r1 = model.reactions.create(id='r1', reversible=False, submodel=submodel)
r1.participants.create(species=s1, coefficient=-3)
r1.participants.create(species=s2, coefficient=4)
r1_f = r1.rate_laws.create(id='r1-forward', direction=RateLawDirection.forward, model=model)
c = model.parameters.create(id='c', value=1., units=unit_registry.parse_units('s^-1'))
r1_f.expression, error = RateLawExpression.deserialize('c', {Parameter: {'c': c}})
assert error is None, str(error)
r1.references.create(id='ref_1', model=model)
r1.identifiers.create(namespace='xx', id='yy')
self.tempdir = tempfile.mkdtemp()
# check model's integrity by writing and reading with validate=True
filename = os.path.join(self.tempdir, 'model_for_tranformation.xlsx')
Writer().run(filename, model, data_repo_metadata=False)
# turn off validate_element_charge_balance validation so that simple species and reactions validate
with EnvironUtils.temp_config_env([(['wc_lang', 'validation', 'validate_element_charge_balance'],
'False')]):
model_read = Reader().run(filename, validate=True)[Model][0]
self.assertTrue(model_read.is_equal(model))
def test_write_read(self):
filename = os.path.join(self.tempdir, 'model.xlsx')
Writer().run(filename, self.model, data_repo_metadata=False)
model = Reader().run(filename)[Model][0]
self.assertEqual(model.validate(), None)
self.assertTrue(model.is_equal(self.model))
self.assertEqual(self.model.difference(model), '')
def test(self):
test_model = Model(id='model', version='0.0.1', wc_lang_version='0.0.1')
submodel = test_model.submodels.create(id='submodel')
filename_yaml = os.path.join(self.tempdir, 'model.yaml')
Writer().run(filename_yaml, test_model)
model = Reader().run(filename_yaml)[Model][0]
self.assertEqual(model.validate(), None)
self.assertTrue(model.is_equal(test_model))
self.assertEqual(test_model.difference(model), '')
def test_export_import(self):
filename = path.join(path.dirname(__file__), 'fixtures',
'sbml-io.xlsx')
filename_transformed = path.join(path.dirname(__file__), 'fixtures',
'sbml-io-transformed.xlsx')
sbml_dir = self.tempdir
filename_2 = path.join(self.tempdir, 'export.xlsx')
with __main__.App(argv=['export', filename, sbml_dir]) as app:
app.run()
with __main__.App(argv=['import', sbml_dir, filename_2]) as app:
app.run()
model = Reader().run(filename_transformed)[Model][0]
model_2 = Reader().run(filename_2)[Model][0]
self.assertTrue(model_2.is_equal(model))
def test_write_read_sloppy(self):
filename = os.path.join(self.tempdir, 'model.xlsx')
Writer().run(filename, self.model, data_repo_metadata=False)
wb = read_workbook(filename)
row = wb['!!Model'].pop(3)
wb['!!Model'].insert(4, row)
write_workbook(filename, wb)
with self.assertRaisesRegex(ValueError, "The rows of worksheet '!!Model' must be defined in this order"):
Reader().run(filename)
env = EnvironmentVarGuard()
env.set('CONFIG__DOT__wc_lang__DOT__io__DOT__strict', '0')
with env:
model = Reader().run(filename)[Model][0]
self.assertEqual(model.validate(), None)
self.assertTrue(model.is_equal(self.model))
self.assertEqual(self.model.difference(model), '')
def do_test_dfba_obj_expr(self, obj_expression, reversible_rxns, expected_obj_expr,
dfba_obj_reaction_id='unused'):
model, submodel, dfba_rxn = self.prep_dfba_obj_test(obj_expression, reversible_rxns,
expected_obj_expr,
dfba_obj_reaction_id=dfba_obj_reaction_id)
SplitReversibleReactionsTransform().run(model)
self.assertEqual(len(model.dfba_objs), 1)
self.assertEqual(model.dfba_objs[0], submodel.dfba_obj)
# make DfbaObjectiveExpression & DfbaObjective from expected_obj_expr, and compare
all_reactions = {Reaction: {rxn.id: rxn for rxn in model.reactions},
DfbaObjReaction: {dfba_obj_reaction_id: dfba_rxn}}
expected_dfba_obj_expr, error = DfbaObjectiveExpression.deserialize(expected_obj_expr,
all_reactions)
self.assertEqual(error, None)
transformed_dfba_obj = submodel.dfba_obj
submodel.dfba_obj = None
dfba_obj = DfbaObjective(id='dfba-obj-submodel',
submodel=submodel,
expression=expected_dfba_obj_expr)
self.assertEqual(dfba_obj.validate(), None)
# the list of ObjTablesTokens captures the semantics of a parsed expression
self.assertEqual(dfba_obj.expression._parsed_expression._obj_tables_tokens,
transformed_dfba_obj.expression._parsed_expression._obj_tables_tokens)
# test io
model, _, _ = self.prep_dfba_obj_test(obj_expression, reversible_rxns, expected_obj_expr,
dfba_obj_reaction_id=dfba_obj_reaction_id)
SplitReversibleReactionsTransform().run(model)
filename = os.path.join(self.tempdir, 'split_rxn_model.xlsx')
Writer().run(filename, model, data_repo_metadata=False)
# turn off validate_element_charge_balance validation so that simple species and reactions validate
with EnvironUtils.temp_config_env([(['wc_lang', 'validation', 'validate_element_charge_balance'],
'False')]):
model_read = Reader().run(filename, validate=True)[Model][0]
self.assertTrue(model_read.is_equal(model))
def test_cut_submodels(self):
timestamp = datetime.datetime(2018, 1, 1, 12, 0, 0)
model = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.1',
created=timestamp,
updated=timestamp)
model.submodels.create(id='submodel_1')
model.submodels.create(id='submodel_2')
model.references.create(id='ref_0')
model.references.create(id='ref_1', submodels=model.submodels[0:1])
model.references.create(id='ref_2', submodels=model.submodels[1:2])
model.references.create(id='ref_3', submodels=model.submodels[0:2])
in_path = path.join(self.tempdir, 'in.xlsx')
Writer().run(in_path, model, data_repo_metadata=False)
out_path = path.join(self.tempdir, 'out')
with __main__.App(argv=['cut-submodels', in_path, out_path]) as app:
app.run()
model_0 = Reader().run(path.join(out_path, 'core.xlsx'))[Model][0]
model_1 = Reader().run(path.join(out_path,
'submodel_1.xlsx'))[Model][0]
model_2 = Reader().run(path.join(out_path,
'submodel_2.xlsx'))[Model][0]
exp_model_0 = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.1',
created=timestamp,
updated=timestamp)
exp_model_0.references.create(id='ref_0')
self.assertTrue(model_0.is_equal(exp_model_0))
exp_model_1 = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.1',
created=timestamp,
updated=timestamp)
exp_model_1.submodels.create(id='submodel_1')
exp_model_1.references.create(id='ref_1',
submodels=exp_model_1.submodels)
exp_model_1.references.create(id='ref_3',
submodels=exp_model_1.submodels)
self.assertTrue(model_1.is_equal(exp_model_1))
exp_model_2 = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.1',
created=timestamp,
updated=timestamp)
exp_model_2.submodels.create(id='submodel_2')
exp_model_2.references.create(id='ref_2',
submodels=exp_model_2.submodels)
exp_model_2.references.create(id='ref_3',
submodels=exp_model_2.submodels)
self.assertTrue(model_2.is_equal(exp_model_2))
def test_make_test_model(self):
'''
Simple SSA model tests:
no reactions: simulation terminates immediately
1 species:
one reaction consume species, at constant rate: consume all reactant, in time given by rate
2 species:
one reaction: convert all reactant into product, in time given by rate
a pair of symmetrical reactions with constant rates: maintain steady state, on average
a pair of symmetrical reactions rates given by reactant population: maintain steady state, on average
a pair of symmetrical reactions rates given by product population: exhaust on species,
with equal chance for each species
** ring of futile reactions with balanced rates: maintain steady state, on average
'''
# test get_model_type_params
expected_params_list = [(0, 0, False, RateLawType.constant),
(1, 1, False, RateLawType.constant),
(2, 1, False, RateLawType.constant),
(2, 1, True, RateLawType.constant),
(2, 1, True, RateLawType.reactant_pop),
(2, 1, True, RateLawType.product_pop)]
for model_type, expected_params in zip(self.model_types,
expected_params_list):
params = MakeModel.get_model_type_params(model_type)
self.assertEqual(params, expected_params)
# test make_test_model
for model_type in self.model_types:
for num_submodels in [1, 10]:
model = MakeModel.make_test_model(
model_type,
num_submodels=num_submodels,
transform_prep_and_check=False)
self.assertEqual(model.validate(), None)
# test round-tripping
file = model_type.replace(' ', '_').replace(',', '')
file = "{}_{}_submodels.xlsx".format(file, num_submodels)
filename = os.path.join(self.test_dir, file)
Writer().run(filename, model, data_repo_metadata=False)
round_trip_model = Reader().run(filename)[Model][0]
self.assertEqual(round_trip_model.validate(), None)
self.assertTrue(round_trip_model.is_equal(model, tol=1e-8))
self.assertEqual(model.difference(round_trip_model, tol=1e-8),
'')
# unittest one of the models made
# TODO (ARTHUR): test with multiple submodels
# TODO (ARTHUR): test observables
# TODO (ARTHUR): test functions
model = MakeModel.make_test_model(self.model_types[4])
self.assertEqual(model.id, 'test_model')
comp = model.compartments[0]
self.assertEqual(comp.id, 'compt_1')
species_type_ids = set([st.id for st in model.species_types])
self.assertEqual(species_type_ids, set(['spec_type_0', 'spec_type_1']))
species_ids = set([s.id for s in comp.species])
self.assertEqual(species_ids,
set(['spec_type_0[compt_1]', 'spec_type_1[compt_1]']))
submodel = model.submodels[0]
# reaction was split by SplitReversibleReactionsTransform
ratelaw_elements = set()
for r in submodel.reactions:
self.assertFalse(r.reversible)
rl = r.rate_laws[0]
ratelaw_elements.add((rl.direction, rl.expression.expression))
expected_rate_laws = set([
# direction, expression.expression
(RateLawDirection.forward,
'k_cat_1_1_for * spec_type_0[compt_1] / Avogadro / volume_compt_1'
), # forward
(RateLawDirection.forward,
'k_cat_1_1_bck * spec_type_1[compt_1] / Avogadro / volume_compt_1'
), # backward, but reversed
])
self.assertEqual(ratelaw_elements, expected_rate_laws)
participant_elements = set()
for r in submodel.reactions:
r_list = []
for part in r.participants:
r_list.append((part.species.id, part.coefficient))
participant_elements.add(tuple(sorted(r_list)))
expected_participants = set([
# id, coefficient
tuple(
sorted((('spec_type_0[compt_1]', -1), ('spec_type_1[compt_1]',
1)))), # forward
tuple(
sorted((('spec_type_1[compt_1]', -1), ('spec_type_0[compt_1]',
1)))), # reversed
])
self.assertEqual(participant_elements, expected_participants)
# test exceptions
with self.assertRaises(ValueError):
MakeModel.make_test_model('3 reactions')
with self.assertRaises(ValueError):
MakeModel.make_test_model(self.model_types[0], num_submodels=0)
def test_successful_roundtrip(self):
"""
Args:
species_coefficient_creation_method (:obj:`str`): name of method to use to get or create
an instance of :obj:`wc_lang.SpeciesCoefficient`
"""
model = Model(id='test_model', version='0.0.0')
comp = model.compartments.create(id='compartment_1')
comp.init_density = model.parameters.create(
id='density_compartment_1',
value=1100,
units=unit_registry.parse_units('g l^-1'))
species_type_1 = model.species_types.create(
id='species_type_1',
structure=ChemicalStructure(
empirical_formula=EmpiricalFormula('CHO'), charge=1))
species_type_2 = model.species_types.create(
id='species_type_2',
structure=ChemicalStructure(
empirical_formula=EmpiricalFormula('C3H3O3'), charge=3))
species_1 = comp.species.create(species_type=species_type_1,
model=model)
species_2 = comp.species.create(species_type=species_type_2,
model=model)
species_1.id = species_1.gen_id()
species_2.id = species_2.gen_id()
submdl = model.submodels.create(id='submodel_1')
# create a DistributionInitConcentration so that Species are provided to ExpressionAttribute.deserialize()
species_1.distribution_init_concentration = DistributionInitConcentration(
model=model, mean=1, units=unit_registry.parse_units('M'))
species_1.distribution_init_concentration.id = species_1.distribution_init_concentration.gen_id(
)
objects = {Species: {}}
objects[Species][species_1.id] = species_1
observable_1 = Expression.make_obj(model, Observable, 'observable_1',
species_1.id, objects)
objects = {Observable: {'observable_1': observable_1}}
observable_2 = Expression.make_obj(model, Observable, 'observable_2',
'obs_1', objects)
param_1 = model.parameters.create(
id='param_1',
value=1.,
units=unit_registry.parse_units('dimensionless'))
param_2 = model.parameters.create(
id='param_2', value=1., units=unit_registry.parse_units('s^-1'))
objects = {
Parameter: {
'param_1': param_1,
'param_2': param_2,
},
}
func_1 = Expression.make_obj(model, Function, 'func_1', 'param_1',
objects)
func_1.units = unit_registry.parse_units('dimensionless')
rxn_species_coeffs = [
species_1.species_coefficients.get_or_create(coefficient=-3.),
species_2.species_coefficients.get_or_create(coefficient=1.),
]
rxn = submdl.reactions.create(id='reaction_1', model=model)
rxn.participants.extend(rxn_species_coeffs)
rl = rxn.rate_laws.create(direction=RateLawDirection.forward,
units=unit_registry.parse_units('s^-1'),
model=model)
rl.id = rl.gen_id()
rl.expression, error = RateLawExpression.deserialize(
'param_2', objects)
self.assertEqual(error, None)
errors = obj_tables.Validator().run(model, get_related=True)
self.assertEqual(errors, None, str(errors))
filename = os.path.join(self.tmp_dir, 'model.xlsx')
Writer().run(filename, model, data_repo_metadata=False)
model_2 = Reader().run(filename)[Model][0]
self.assertEqual(model.difference(model_2), '')
self.assertTrue(model_2.is_equal(model))
self.assertTrue(model.is_equal(model_2))