def test_metadata_when_type_changed_case2(self, mock_check_extension, \
mock_get_storage_backend, mock_move_resource_to_final_location):
resource_path = os.path.join(VAL_TESTDIR, 'test_matrix.tsv')
mock_move_resource_to_final_location.return_value = resource_path
mock_f = mock.MagicMock()
mock_f.get_local_resource_path.return_value = resource_path
mock_get_storage_backend.return_value = mock_f
mock_check_extension.return_value = True
r = Resource.objects.create(
name = 'test_annotation_valid.tsv',
owner = self.regular_user_1,
is_active=True,
path = resource_path,
resource_type = '*'
)
validate_resource(r, '*')
rm = ResourceMetadata.objects.get(resource=r)
self.assertTrue(rm.observation_set is None)
r.save()
validate_resource(r, 'MTX')
rm = ResourceMetadata.objects.get(resource=r)
obs_set = rm.observation_set
samples = [x['id'] for x in obs_set['elements']]
expected = ['SW1_Control','SW2_Control','SW3_Control','SW4_Treated','SW5_Treated','SW6_Treated']
self.assertCountEqual(samples, expected)
def test_proper_exceptions_raised_case3(self, \
mock_check_extension, \
mock_get_storage_backend, \
mock_handle_valid_resource, \
mock_get_resource_type_instance):
'''
If unexpected errors (like connecting to cloud storage occur), check that we raise exceptions
that provide helpful errors.
Here, we test if the `get_resource_type` function raises an exception from an unknown
resource type (a keyError).
'''
mock_check_extension.return_value = True
mock_get_resource_type_instance.side_effect = [KeyError('abc'),]
all_resources = Resource.objects.all()
unset_resources = []
for r in all_resources:
if not r.resource_type:
unset_resources.append(r)
if len(unset_resources) == 0:
raise ImproperlyConfigured('Need at least one'
' Resource without a type to test properly.'
)
unset_resource = unset_resources[0]
with self.assertRaisesRegex(Exception, 'ZZZ'):
validate_resource(unset_resource, 'ZZZ')
mock_handle_valid_resource.assert_not_called()
mock_get_storage_backend.assert_not_called()
mock_get_resource_type_instance.assert_called()
def test_metadata_when_type_changed(self, mock_check_extension, \
mock_get_storage_backend, mock_move_resource_to_final_location):
'''
Checks that the update of resource metadata is updated. Related to a bug where
a file was initially set to a general type (and thus the metadata was effectively empty).
After trying to validate it as an annotation type, it was raising json serializer errors.
'''
resource_path = os.path.join(VAL_TESTDIR, 'test_annotation_valid.tsv')
mock_move_resource_to_final_location.return_value = resource_path
mock_check_extension.return_value = True
mock_f = mock.MagicMock()
mock_f.get_local_resource_path.return_value = resource_path
mock_get_storage_backend.return_value = mock_f
r = Resource.objects.create(
name = 'test_annotation_valid.tsv',
owner = self.regular_user_1,
is_active=True,
path = resource_path,
resource_type = '*'
)
validate_resource(r, '*')
rm = ResourceMetadata.objects.get(resource=r)
self.assertTrue(rm.observation_set is None)
validate_resource(r, 'ANN')
rm = ResourceMetadata.objects.get(resource=r)
self.assertFalse(rm.observation_set is None)
def test_proper_exceptions_raised_case1(self, \
mock_check_extension, \
mock_get_storage_backend, \
mock_handle_valid_resource, \
mock_get_resource_type_instance):
'''
If unexpected errors (like connecting to cloud storage occur), check that we raise exceptions
that provide helpful errors.
Here, we test if the `check_extension` function raises an exception
'''
mock_check_extension.side_effect = [Exception('something unexpected!')]
all_resources = Resource.objects.all()
unset_resources = []
for r in all_resources:
if not r.resource_type:
unset_resources.append(r)
if len(unset_resources) == 0:
raise ImproperlyConfigured('Need at least one'
' Resource without a type to test properly.'
)
unset_resource = unset_resources[0]
with self.assertRaisesRegex(Exception, 'file extension'):
validate_resource(unset_resource, 'MTX')
mock_handle_valid_resource.assert_not_called()
mock_get_storage_backend.assert_not_called()
mock_get_resource_type_instance.assert_not_called()
def test_invalid_handler_called(self, mock_check_extension, \
mock_get_storage_backend, \
mock_handle_invalid_resource, mock_get_resource_type_instance):
'''
Here we test that a failure to validate the resource calls the proper
handler function.
'''
all_resources = Resource.objects.all()
unset_resources = []
for r in all_resources:
if not r.resource_type:
unset_resources.append(r)
if len(unset_resources) == 0:
raise ImproperlyConfigured('Need at least one'
' Resource without a type to test properly.'
)
unset_resource = unset_resources[0]
mock_resource_class_instance = mock.MagicMock()
mock_resource_class_instance.validate_type.return_value = (False, 'some string')
mock_get_resource_type_instance.return_value = mock_resource_class_instance
mock_storage_backend = mock.MagicMock()
mock_storage_backend.get_local_resource_path.return_value = 'foo'
mock_get_storage_backend.return_value = mock_storage_backend
mock_check_extension.return_value = True
validate_resource(unset_resource, 'MTX')
mock_handle_invalid_resource.assert_called()
def validate_resource(resource_pk, requested_resource_type):
'''
This function only performs validation of the resource.
Note that it calls the `resource_utilities.validate_resource`
function which does NOT perform a save on the passed Resource
instance
'''
resource = resource_utilities.get_resource_by_pk(resource_pk)
try:
resource_utilities.validate_resource(resource, requested_resource_type)
except Exception as ex:
logger.info(
'Caught an exception raised by the validate_resource function.')
alert_admins(str(ex))
resource.status = str(ex)
resource.is_active = True
resource.save()
def test_proper_exceptions_raised_case4(self, \
mock_check_extension, \
mock_get_storage_backend, \
mock_handle_valid_resource, \
mock_get_resource_type_instance):
'''
If unexpected errors (like connecting to cloud storage occur), check that we raise exceptions
that provide helpful errors.
Here, we test if the get_local_resource_path (a method of the storage backend) fails
for some unexpected reason, such as failure to connect to cloud storage
'''
mock_check_extension.return_value = True
# here we mock there being a problem with the storage backend (maybe bucket storage
# service is temporarily offline?)
mock_storage_backend = mock.MagicMock()
mock_storage_backend.get_local_resource_path.side_effect = [Exception('something bad')]
mock_get_storage_backend.return_value = mock_storage_backend
mock_resource_class_instance = mock.MagicMock()
mock_resource_class_instance.performs_validation.return_value = True
mock_get_resource_type_instance.return_value = mock_resource_class_instance
all_resources = Resource.objects.all()
unset_resources = []
for r in all_resources:
if not r.resource_type:
unset_resources.append(r)
if len(unset_resources) == 0:
raise ImproperlyConfigured('Need at least one'
' Resource without a type to test properly.'
)
unset_resource = unset_resources[0]
expected_message_partial = ('An unexpected issue occurred when'
' moving the file for inspection')
with self.assertRaisesRegex(Exception, expected_message_partial):
validate_resource(unset_resource, 'MTX')
mock_resource_class_instance.validate_type.assert_not_called()
mock_handle_valid_resource.assert_not_called()
def test_proper_steps_taken_with_wildcard_resource(self, mock_check_extension, \
mock_get_storage_backend, \
mock_handle_valid_resource, \
mock_get_resource_type_instance):
'''
Here we test that a esource type with a "wildcard" type goes through the proper
steps. That is, we should skip the validation, etc.
'''
all_resources = Resource.objects.all()
r = all_resources[0]
mock_check_extension.return_value = True
g = GeneralResource()
mock_get_resource_type_instance.return_value = g
validate_resource(r, WILDCARD)
mock_handle_valid_resource.assert_called()
mock_get_storage_backend.assert_not_called()
def test_proper_exceptions_raised_case5(self, \
mock_check_extension, \
mock_get_storage_backend, \
mock_handle_valid_resource, \
mock_get_resource_type_instance):
'''
If unexpected errors (like connecting to cloud storage occur), check that we raise exceptions
that provide helpful errors.
Here, we test if the validation method fails unexpectedly.
'''
mock_check_extension.return_value = True
mock_local_path = '/some/local/path.txt'
mock_storage_backend = mock.MagicMock()
mock_storage_backend.get_local_resource_path.return_value = mock_local_path
mock_get_storage_backend.return_value = mock_storage_backend
mock_resource_class_instance = mock.MagicMock()
mock_resource_class_instance.performs_validation.return_value = True
mock_resource_class_instance.validate_type.side_effect = [Exception('something unexpected.')]
mock_get_resource_type_instance.return_value = mock_resource_class_instance
all_resources = Resource.objects.all()
unset_resources = []
for r in all_resources:
if not r.resource_type:
unset_resources.append(r)
if len(unset_resources) == 0:
raise ImproperlyConfigured('Need at least one'
' Resource without a type to test properly.'
)
unset_resource = unset_resources[0]
with self.assertRaisesRegex(Exception, Resource.UNEXPECTED_VALIDATION_ERROR):
validate_resource(unset_resource, 'MTX')
mock_handle_valid_resource.assert_not_called()
def test_proper_valid_handler_called(self, \
mock_check_extension, \
mock_get_storage_backend, \
mock_handle_valid_resource, \
mock_get_resource_type_instance):
'''
Here we test that a successful validation calls the proper
handler function.
'''
mock_local_path = '/some/local/path.txt'
mock_storage_backend = mock.MagicMock()
mock_storage_backend.get_local_resource_path.return_value = mock_local_path
mock_get_storage_backend.return_value = mock_storage_backend
mock_resource_class_instance = mock.MagicMock()
mock_resource_class_instance.performs_validation.return_value = True
mock_resource_class_instance.validate_type.return_value = (True, 'some string')
mock_get_resource_type_instance.return_value = mock_resource_class_instance
mock_check_extension.return_value = True
all_resources = Resource.objects.all()
unset_resources = []
for r in all_resources:
if not r.resource_type:
unset_resources.append(r)
if len(unset_resources) == 0:
raise ImproperlyConfigured('Need at least one'
' Resource without a type to test properly.'
)
unset_resource = unset_resources[0]
validate_resource(unset_resource, 'MTX')
mock_handle_valid_resource.assert_called()