def test_remove_dangling_basket_variables_study_specific(self):
"""Can we clean up BasketVariables belonging to a specific study?"""
other_study = StudyFactory(name="a_different_study")
dataset = DatasetFactory(name="a_different_study")
dataset.study = other_study
dataset.save()
new_variable = Variable()
new_variable.name = "a_different_variable"
new_variable.dataset = dataset
basket_variable = BasketVariable(basket_id=self.basket.id,
variable_id=self.variable.id)
new_basket = Basket()
new_basket.study = other_study
new_basket.user = self.basket.user
new_basket.save()
new_basket_variable = BasketVariable()
new_basket_variable.variable = new_variable
new_basket_variable.basket = new_basket
new_basket_variable.save()
basket_variable.save()
variable_id = basket_variable.variable.id
basket_variable.variable.delete()
new_variable.delete()
basket_variable.clean_basket_variables(
study_name=self.basket.study.name)
with self.assertRaises(BasketVariable.DoesNotExist):
BasketVariable.objects.get(variable__id=variable_id)
def test_variable_import_without_concept_csv(self):
csv_path = Study().import_path()
concept_path = csv_path.joinpath("concepts.csv")
os.remove(concept_path)
some_dataset = DatasetFactory(name="some-dataset")
some_dataset.save()
TEST_CASE.assertIsNone(
StudyImportManager(study=some_dataset.study).fix_concepts_csv())
TEST_CASE.assertFalse(concept_path.exists())
def test_no_parameter(self) -> None:
other_study = StudyFactory(name="some-other-study")
dataset = DatasetFactory(name="some-dataset")
other_dataset = DatasetFactory(name="some-other-dataset",
study=other_study)
response = self.client.get(self.API_PATH)
content = json.loads(response.content)
self.assertEqual(2, content["count"])
result_dataset_names = [
result["name"] for result in content["results"]
]
self.assertIn(getattr(dataset, "name"), result_dataset_names)
self.assertIn(getattr(other_dataset, "name"), result_dataset_names)
def test_variable_import(self):
some_dataset = DatasetFactory(name="some-dataset")
some_dataset.save()
ConceptFactory(name="some-concept").save()
ConceptFactory(name="orphaned-concept").save()
variable_path = Path(
"tests/functional/test_data/some-study/ddionrails/variables.csv")
variable_path = variable_path.absolute()
VariableImport.run_import(variable_path, study=some_dataset.study)
with open(variable_path, "r", encoding="utf8") as csv_file:
variable_names = {row["name"] for row in csv.DictReader(csv_file)}
result = Variable.objects.filter(name__in=list(variable_names))
TEST_CASE.assertNotEqual(0, len(result))
TEST_CASE.assertEqual(len(variable_names), len(result))
def _dataset(request, db):
"""A dataset in the database"""
_factory = DatasetFactory(
name="some-dataset", label="Some Dataset", description="This is some dataset"
)
if request.instance:
request.instance.dataset = _factory
return _factory
def test_study_name_parameter(self) -> None:
dataset = DatasetFactory(name="some-dataset")
study_name = getattr(dataset.study, "name")
response = self.client.get(self.API_PATH + f"?study={study_name}")
content = json.loads(response.content)
self.assertEqual(1, content["count"])
self.assertEqual(getattr(dataset, "name"),
content["results"][0]["name"])
def test_variable_import_with_orphaned_concept(self):
csv_path = Study().import_path()
concept_path = csv_path.joinpath("concepts.csv")
some_dataset = DatasetFactory(name="some-dataset")
some_dataset.save()
StudyImportManager(study=some_dataset.study).fix_concepts_csv()
ConceptFactory(name="some-concept").save()
variable_path = csv_path.joinpath("variables.csv")
variable_path = variable_path.absolute()
ConceptImport(concept_path).run_import(filename=concept_path)
VariableImport.run_import(variable_path, study=some_dataset.study)
with open(variable_path, "r", encoding="utf8") as csv_file:
variable_names = {row["name"] for row in csv.DictReader(csv_file)}
result = Variable.objects.filter(name__in=list(variable_names))
TEST_CASE.assertNotEqual(0, len(result))
TEST_CASE.assertEqual(len(variable_names), len(result))
def test_clean_method_fails(self, basket):
""" BasketVariable clean method should raise an ValidationError when basket and variable study do not match """
other_study = StudyFactory(name="some-other-study")
other_dataset = DatasetFactory(name="some-other-dataset",
study=other_study)
other_variable = VariableFactory(name="some-other-variable",
dataset=other_dataset)
basket_variable = BasketVariable(basket_id=basket.id,
variable_id=other_variable.id)
with pytest.raises(ValidationError):
basket_variable.clean()
assert 0 == BasketVariable.objects.count()
def test_query_parameter_study(self):
"""Define study parameter behavior."""
dataset = DatasetFactory(name="different-dataset")
study = StudyFactory(name="different-study")
study_name = study.name
dataset.study = study
dataset.save()
variable_list = []
for number in range(1, 11):
_variable = VariableFactory(name=str(number))
_variable.dataset = dataset
_variable.save()
variable_list.append(_variable)
for number in range(11, 21):
_variable = VariableFactory(name=str(number))
variable_list.append(_variable)
response = self.client.get(self.API_PATH + f"?study={study_name}")
content = json.loads(response.content)
self.assertEqual(10, len(content))
def test_clean_method_fails(self):
"""Ensure the correct error raising of the BasketVariable clean method.
BasketVariable clean method should raise a ValidationError
when basket and variable study do not match.
"""
other_study = StudyFactory(name="some-other-study")
other_dataset = DatasetFactory(name="some-other-dataset",
study=other_study)
other_variable = VariableFactory(name="some-other-variable",
dataset=other_dataset)
basket_variable = BasketVariable(basket_id=self.basket.id,
variable_id=other_variable.id)
with pytest.raises(ValidationError):
basket_variable.clean()
expected = 0
self.assertEqual(expected, BasketVariable.objects.count())
def dataset(db):
""" A dataset in the database """
return DatasetFactory(name="some-dataset",
label="Some Dataset",
description="This is some dataset")
def setUp(self):
self.dataset = DatasetFactory(name="test-dataset")
self.study = self.dataset.study
return super().setUp()