def test_anvil_workspace_page(self, mock_logger):
# Requesting to load data from a workspace without an existing project
url = reverse(
anvil_workspace_page,
args=[TEST_WORKSPACE_NAMESPACE, TEST_NO_PROJECT_WORKSPACE_NAME])
collaborator_response = self._check_login_permissions(url, mock_logger)
self.assertEqual(collaborator_response.get('Content-Type'),
'text/html')
initial_json = self.get_initial_page_json(collaborator_response)
self.assertEqual(initial_json['user']['username'],
'test_user_collaborator')
response = self.client.post(url)
self.assertEqual(response.status_code, 302)
self.assertEqual(
response.url, '/create_project_from_workspace/{}/{}'.format(
TEST_WORKSPACE_NAMESPACE, TEST_NO_PROJECT_WORKSPACE_NAME))
self.mock_get_ws_access_level.assert_called_with(
self.manager_user, TEST_WORKSPACE_NAMESPACE,
TEST_NO_PROJECT_WORKSPACE_NAME)
# Test error handling when token refresh fails
self.mock_get_ws_access_level.side_effect = TerraRefreshTokenFailedException(
'Failed to refresh token')
response = self.client.post(url)
self.assertEqual(response.status_code, 302)
self.assertEqual(
response.url, '/login/google-oauth2?next=/workspace/{}/{}'.format(
TEST_WORKSPACE_NAMESPACE, TEST_NO_PROJECT_WORKSPACE_NAME))
self.mock_get_ws_access_level.assert_called_with(
self.manager_user, TEST_WORKSPACE_NAMESPACE,
TEST_NO_PROJECT_WORKSPACE_NAME)
# Requesting to load data for an existing project
self.mock_get_ws_access_level.reset_mock()
url = reverse(anvil_workspace_page,
args=[TEST_WORKSPACE_NAMESPACE, TEST_WORKSPACE_NAME])
response = self.client.post(url)
self.assertEqual(response.status_code, 302)
self.assertEqual(response.url, '/project/R0001_1kg/project_page')
self.mock_get_ws_access_level.assert_not_called()
# Test login locally
remove_token(
self.manager_user
) # The user will be same as logging in locally after the access token is removed
response = self.client.post(url)
self.assertEqual(response.status_code, 302)
self.assertEqual(
response.url,
'/login/google-oauth2?next=/workspace/my-seqr-billing/anvil-1kg%2520project%2520n%25C3%25A5me%2520with%2520uni%25C3%25A7%25C3%25B8de'
)
self.mock_get_ws_access_level.assert_not_called()
def test_is_google_authenticated(self, mock_social_auth_key):
user = User.objects.get(username='******')
r = is_google_authenticated(user)
self.assertTrue(r)
remove_token(user)
r = is_google_authenticated(user)
self.assertTrue(r)
local_user = User.objects.get(username='******')
r = is_google_authenticated(local_user)
self.assertFalse(r)
mock_social_auth_key.__bool__.return_value = False
r = is_google_authenticated(user)
self.assertFalse(r)
def test_is_anvil_authenticated(self, mock_social_auth_key,
mock_terra_url):
mock_social_auth_key.__bool__.return_value = False
mock_terra_url.__bool__.return_value = True
user = User.objects.get(username='******')
r = is_anvil_authenticated(user)
self.assertFalse(r)
mock_social_auth_key.__bool__.return_value = True
mock_terra_url.__bool__.return_value = False
r = is_anvil_authenticated(user)
self.assertFalse(r)
mock_terra_url.__bool__.return_value = True
r = is_anvil_authenticated(user)
self.assertTrue(r)
remove_token(user)
r = is_anvil_authenticated(user)
self.assertFalse(r)
def logout_view(request):
user = request.user
remove_token(user)
logout(request)
logger.info('Logged out {}'.format(user.email), extra={'user': user})
return redirect('/login')
def test_create_project_from_workspace(self, mock_file_exist, mock_email,
mock_add_service_account,
mock_has_service_account,
mock_load_file, mock_api_logger,
mock_sleep, mock_utils_logger):
# Requesting to load data from a workspace without an existing project
url = reverse(
create_project_from_workspace,
args=[TEST_WORKSPACE_NAMESPACE, TEST_NO_PROJECT_WORKSPACE_NAME])
# Test user doesn't login
response = self.client.post(url)
self.assertEqual(response.status_code, 302)
self.assertEqual(
response.url,
'/login/google-oauth2?next=/api/create_project_from_workspace/submit/{}/{}'
.format(TEST_WORKSPACE_NAMESPACE, TEST_NO_PROJECT_WORKSPACE_NAME))
# Test the user needs sufficient workspace permissions
self.check_manager_login(url)
mock_utils_logger.warning.assert_called_with(
'User does not have sufficient permissions for workspace {}/{}'.
format(TEST_WORKSPACE_NAMESPACE, TEST_NO_PROJECT_WORKSPACE_NAME))
# Test missing required fields in the request body
response = self.client.post(url,
content_type='application/json',
data=json.dumps({}))
self.assertEqual(response.status_code, 400)
self.assertEqual(
response.reason_phrase,
'Field(s) "genomeVersion, uploadedFileId, dataPath" are required')
self.mock_get_ws_access_level.assert_called_with(
self.manager_user,
TEST_WORKSPACE_NAMESPACE,
TEST_NO_PROJECT_WORKSPACE_NAME,
meta_fields=['workspace.bucketName'])
data = {
'genomeVersion': '38',
'uploadedFileId': 'test_temp_file_id',
'dataPath': '/test_path',
}
response = self.client.post(url,
content_type='application/json',
data=json.dumps(data))
self.assertEqual(response.status_code, 400)
self.assertEqual(
response.reason_phrase,
'Must agree to grant seqr access to the data in the associated workspace.'
)
# Test parsing sample data error
mock_load_file.return_value = LOAD_SAMPLE_DATA + BAD_SAMPLE_DATA
response = self.client.post(url,
content_type='application/json',
data=json.dumps(REQUEST_BODY))
self.assertEqual(response.status_code, 400)
response_json = response.json()
self.assertListEqual(response_json['errors'], [
'NA19679 is the mother of NA19674 but doesn\'t have a separate record in the table'
])
# Test adding service account exception
mock_load_file.return_value = LOAD_SAMPLE_DATA
mock_add_service_account.side_effect = TerraAPIException(
'Failed to grant seqr service account access to the workspace {}/{}'
.format(TEST_WORKSPACE_NAMESPACE,
TEST_NO_PROJECT_WORKSPACE_NAME), 400)
response = self.client.post(url,
content_type='application/json',
data=json.dumps(REQUEST_BODY))
self.assertEqual(response.status_code, 400)
self.assertEqual(
response.json()['error'],
'Failed to grant seqr service account access to the workspace {}/{}'
.format(TEST_WORKSPACE_NAMESPACE, TEST_NO_PROJECT_WORKSPACE_NAME))
# Test adding service account never processes
mock_add_service_account.reset_mock(side_effect=True)
mock_add_service_account.return_value = True
mock_has_service_account.return_value = False
response = self.client.post(url,
content_type='application/json',
data=json.dumps(REQUEST_BODY))
self.assertEqual(response.status_code, 400)
self.assertEqual(
response.json()['error'],
'Failed to grant seqr service account access to the workspace')
mock_has_service_account.assert_called_with(
self.manager_user, TEST_WORKSPACE_NAMESPACE,
TEST_NO_PROJECT_WORKSPACE_NAME)
self.assertEqual(mock_has_service_account.call_count, 3)
self.assertEqual(mock_sleep.call_count, 3)
# Test bad data path
mock_sleep.reset_mock()
mock_has_service_account.reset_mock()
mock_has_service_account.return_value = True
mock_file_exist.return_value = False
response = self.client.post(
url,
content_type='application/json',
data=json.dumps(REQUEST_BODY_NO_SLASH_DATA_PATH))
self.assertEqual(response.status_code, 400)
self.assertEqual(response.json()['error'],
'Data file or path test_no_slash_path is not found.')
mock_file_exist.assert_called_with(
'gs://test_bucket/test_no_slash_path')
mock_has_service_account.assert_called_with(
self.manager_user, TEST_WORKSPACE_NAMESPACE,
TEST_NO_PROJECT_WORKSPACE_NAME)
self.assertEqual(mock_has_service_account.call_count, 1)
self.assertEqual(mock_sleep.call_count, 1)
# Test valid operation
mock_sleep.reset_mock()
mock_has_service_account.reset_mock()
mock_add_service_account.return_value = False
mock_file_exist.return_value = True
response = self.client.post(url,
content_type='application/json',
data=json.dumps(REQUEST_BODY))
self.assertEqual(response.status_code, 200)
project = Project.objects.get(
workspace_namespace=TEST_WORKSPACE_NAMESPACE,
workspace_name=TEST_NO_PROJECT_WORKSPACE_NAME)
response_json = response.json()
self.assertEqual(project.guid, response_json['projectGuid'])
self.assertListEqual([
project.genome_version, project.description,
project.workspace_namespace, project.workspace_name
], [
'38', 'A test project', TEST_WORKSPACE_NAMESPACE,
TEST_NO_PROJECT_WORKSPACE_NAME
])
mock_add_service_account.assert_called_with(
self.manager_user, TEST_WORKSPACE_NAMESPACE,
TEST_NO_PROJECT_WORKSPACE_NAME)
mock_has_service_account.assert_not_called()
mock_sleep.assert_not_called()
mock_file_exist.assert_called_with('gs://test_bucket/test_path')
email_body = """
[email protected] requested to load data from AnVIL workspace "{namespace}/{name}" at "gs://test_bucket/test_path" to seqr project
{{project_name}} (guid: {guid})
The sample IDs to load are attached.
""".format(namespace=TEST_WORKSPACE_NAMESPACE,
name=TEST_NO_PROJECT_WORKSPACE_NAME,
guid=project.guid)
mock_email.assert_called_with(
subject='AnVIL data loading request',
body=email_body.format(
project_name=TEST_NO_PROJECT_WORKSPACE_NAME),
to=['*****@*****.**', '*****@*****.**'],
attachments=[('{}_sample_ids.tsv'.format(project.guid),
'NA19675\nNA19678\nHG00735')])
html_project_name = '<a href="http://testserver/project/{guid}/project_page">{name}</a>'.format(
name=TEST_NO_PROJECT_WORKSPACE_NAME, guid=project.guid)
mock_email.return_value.attach_alternative.assert_called_with(
email_body.format(project_name=html_project_name), 'text/html')
mock_email.return_value.send.assert_called()
# Test project exist
url = reverse(
create_project_from_workspace,
args=[TEST_WORKSPACE_NAMESPACE, TEST_NO_PROJECT_WORKSPACE_NAME])
response = self.client.post(url)
self.assertEqual(response.status_code, 400)
self.assertEqual(
response.reason_phrase,
'Project "{name}" for workspace "{namespace}/{name}" exists.'.
format(namespace=TEST_WORKSPACE_NAMESPACE,
name=TEST_NO_PROJECT_WORKSPACE_NAME))
# Test sending email exception
url = reverse(
create_project_from_workspace,
args=[TEST_WORKSPACE_NAMESPACE, TEST_NO_PROJECT_WORKSPACE_NAME2])
mock_email.side_effect = Exception(
'Something wrong while sending email.')
response = self.client.post(url,
content_type='application/json',
data=json.dumps(REQUEST_BODY))
self.assertEqual(response.status_code, 200)
mock_api_logger.error.assert_called_with(
'Exception while sending email to user test_user_manager. Something wrong while sending email.'
)
# Test logged in locally
remove_token(
self.manager_user
) # The user will look like having logged in locally after the access token is removed
response = self.client.post(url)
self.assertEqual(response.status_code, 302)
self.assertEqual(
response.url,
'/login/google-oauth2?next=/api/create_project_from_workspace/submit/my-seqr-billing/anvil-no-project-workspace2'
)
def logout_view(request):
user = request.user
remove_token(user)
logout(request)
logger.info('Logged out {}'.format(user.email), user)
return redirect('/')
