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_difference(self):
now = datetime.datetime.now().replace(microsecond=0)
model1 = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.0',
created=now,
updated=now)
filename1 = path.join(self.tempdir, 'model1.xlsx')
Writer().run(filename1, model1, data_repo_metadata=False)
model2 = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.0',
created=now,
updated=now)
filename2 = path.join(self.tempdir, 'model2.xlsx')
Writer().run(filename2, model2, data_repo_metadata=False)
model3 = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.1',
created=now,
updated=now)
filename3 = path.join(self.tempdir, 'model3.xlsx')
Writer().run(filename3, model3, data_repo_metadata=False)
with CaptureOutput(relay=False) as capturer:
with __main__.App(
argv=['difference', filename1, filename2]) as app:
app.run()
self.assertEqual(capturer.get_text(), 'Models are identical')
with CaptureOutput(relay=False) as capturer:
with __main__.App(argv=[
'difference', filename1, filename2, '--compare-files'
]) as app:
app.run()
self.assertEqual(capturer.get_text(), 'Models are identical')
with CaptureOutput(relay=False) as capturer:
with __main__.App(
argv=['difference', filename1, filename3]) as app:
app.run()
diff = (
'Objects (Model: "model", Model: "model") have different attribute values:\n '
'`wc_lang_version` are not equal:\n 0.0.0 != 0.0.1')
self.assertEqual(capturer.get_text(), diff)
with CaptureOutput(relay=False) as capturer:
with __main__.App(argv=[
'difference', filename1, filename3, '--compare-files'
]) as app:
app.run()
diff = 'Sheet !!Model:\n Row 7:\n Cell B: 0.0.0 != 0.0.1'
self.assertEqual(capturer.get_text(), diff)
def test_get_version(self):
with CaptureOutput(relay=False) as capturer:
with __main__.App(argv=['-v']) as app:
with self.assertRaises(SystemExit):
app.run()
self.assertEqual(capturer.get_text(), wc_lang.__version__)
with CaptureOutput(relay=False) as capturer:
with __main__.App(argv=['--version']) as app:
with self.assertRaises(SystemExit):
app.run()
self.assertEqual(capturer.get_text(), wc_lang.__version__)
def test_merge_models(self):
in_paths = [
path.join(self.tempdir, 'in-0.xlsx'),
path.join(self.tempdir, 'in-1.xlsx'),
]
out_path = path.join(self.tempdir, 'out.xlsx')
# write models
model_0 = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.1')
model_0.species_types.create(id='a')
model_1 = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.1')
model_1.species_types.create(id='b')
Writer().run(in_paths[0], model_0, data_repo_metadata=False)
Writer().run(in_paths[1], model_1, data_repo_metadata=False)
# merge models
with __main__.App(argv=[
'merge-models', '-p', in_paths[0], '-s', in_paths[1], '-o',
out_path
]) as app:
app.run()
# read merged model
merged_model = Reader().run(out_path)[Model][0]
# verify merged model
self.assertEqual(len(merged_model.species_types), 2)
self.assertNotEqual(merged_model.species_types.get_one(id='a'), None)
self.assertNotEqual(merged_model.species_types.get_one(id='b'), None)
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_create_template(self):
filename = path.join(self.tempdir, 'template.xlsx')
with __main__.App(
argv=['create-template', filename, '--ignore-repo-metadata'
]) as app:
app.run()
self.assertTrue(path.isfile(filename))
def test_transform_exception(self):
source = path.join(self.tempdir, 'source.xlsx')
model = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.0')
Writer().run(source, model, data_repo_metadata=False)
dest = path.join(self.tempdir, 'dest.xlsx')
with self.assertRaisesRegex(SystemExit,
'Please select at least one transform'):
with __main__.App(argv=['transform', source, dest]) as app:
app.run()
def test_validate(self):
model = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.1')
self.assertEqual(Validator().run(model, get_related=True), None)
filename = path.join(self.tempdir, 'model.xlsx')
Writer().run(filename, model, data_repo_metadata=False)
with CaptureOutput(relay=False) as capturer:
with __main__.App(argv=['validate', filename]) as app:
app.run()
self.assertEqual(capturer.get_text(), 'Model is valid')
def test_convert(self):
filename_xls = path.join(self.tempdir, 'model.xlsx')
filename_csv = path.join(self.tempdir, 'model-*.csv')
model = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.0')
Writer().run(filename_xls, model, data_repo_metadata=False)
with __main__.App(argv=['convert', filename_xls, filename_csv]) as app:
app.run()
self.assertTrue(path.isfile(path.join(self.tempdir,
'model-Model.csv')))
def test_transform(self):
source = path.join(self.tempdir, 'source.xlsx')
model = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.0')
Writer().run(source, model, data_repo_metadata=False)
dest = path.join(self.tempdir, 'dest.xlsx')
with __main__.App(argv=[
'transform', source, dest, '--transform',
'MergeAlgorithmicallyLikeSubmodels'
]) as app:
app.run()
self.assertTrue(path.isfile(dest))
def test_update_version_metadata(self):
filename = path.join(self.tempdir, 'model.xlsx')
model = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.0')
self.assertNotEqual(model.wc_lang_version, wc_lang.__version__)
Writer().run(filename, model, data_repo_metadata=False)
with __main__.App(argv=[
'update-version-metadata', filename, '--ignore-repo-metadata'
]) as app:
app.run()
model = Reader().run(filename)[Model][0]
self.assertEqual(model.wc_lang_version, wc_lang.__version__)
def test_migration_handlers(self):
with CaptureOutput(relay=False, termination_delay=0.1) as capturer:
with __main__.App(argv=['make-changes-template']) as app:
app.run()
m = re.search(
r"Created and added template schema changes file: '(.+)'",
capturer.get_text())
filename = m.group(1)
self.assertTrue(os.path.isfile(filename))
# remove schema changes file from the git repo
repo = git.Repo('.')
repo.index.remove([filename])
os.remove(filename)
dir = os.path.dirname(filename)
try:
os.rmdir(dir)
except OSError as ex:
pass
def test_validate_exception(self):
model = Model(id='model',
name='test model',
version='0.0.1a',
wc_lang_version='0.0.1')
model.parameters.append(
Parameter(id='param_1',
value=1.,
units=unit_registry.parse_units('dimensionless')))
model.parameters.append(
Parameter(id='param_1',
value=1.,
units=unit_registry.parse_units('dimensionless')))
self.assertNotEqual(Validator().run(model, get_related=True), None)
filename = path.join(self.tempdir, 'model.xlsx')
Writer().run(filename, model, data_repo_metadata=False)
with self.assertRaisesRegex(SystemExit, '^Model is invalid: '):
with __main__.App(argv=['validate', filename]) as app:
app.run()
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))
