def test_dds_job_input_files_post(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'dds-job-input-file1'
mock_requests.post.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
dds_input_file = api.dds_job_input_files_post(
project_id='123',
file_id='456',
destination_path='data.txt',
sequence_group=1,
sequence=2,
dds_user_credentials=4,
stage_group_id=5,
size=1000)
self.assertEqual(dds_input_file, 'dds-job-input-file1')
expected_json = {
'project_id': '123',
'file_id': '456',
'destination_path': 'data.txt',
'sequence_group': 1,
'sequence': 2,
'dds_user_credentials': 4,
'stage_group': 5,
'size': 1000,
}
mock_requests.post.assert_called_with('someurl/dds-job-input-files/',
headers=self.expected_headers,
json=expected_json)
def test_workflow_versions_post(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'worflow_version1'
mock_requests.post.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
# def workflow_versions_post(self, workflow, version, workflow_type, description, workflow_path, url, version_info_url, fields):
worflow_version = api.workflow_versions_post(
workflow=1,
version='v2.1.0',
workflow_type='zipped',
description='my desc',
workflow_path='dir/workflow.cwl',
url='https://example.com/v2.1.0.zip',
version_info_url='https://example.com/info.md',
fields=['field1'])
self.assertEqual(worflow_version, 'worflow_version1')
expected_post_payload = {
'workflow': 1,
'version': 'v2.1.0',
'description': 'my desc',
'url': 'https://example.com/v2.1.0.zip',
'type': 'zipped',
'workflow_path': 'dir/workflow.cwl',
'version_info_url': 'https://example.com/info.md',
'fields': ['field1']
}
mock_requests.post.assert_called_with(
'someurl/admin/workflow-versions/',
headers=self.expected_headers,
json=expected_post_payload)
def test_workflow_configurations_post(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'workflowconfiguration1'
mock_requests.post.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
workflow_configuration = api.workflow_configurations_post(
tag='myconfig',
workflow=1,
share_group=2,
default_job_strategy=3,
system_job_order={})
self.assertEqual(workflow_configuration, 'workflowconfiguration1')
expected_post_payload = {
'tag': 'myconfig',
'workflow': 1,
'share_group': 2,
'default_job_strategy': 3,
'system_job_order': {}
}
mock_requests.post.assert_called_with(
'someurl/admin/workflow-configurations/',
headers=self.expected_headers,
json=expected_post_payload)
def test_delete_job(self, mock_requests):
mock_response = Mock(status_code=200)
mock_requests.delete.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
api.delete_job(job_id=123)
mock_requests.delete.assert_called_with('someurl/jobs/123',
headers=self.expected_headers)
def test_delete_connection_error(self, mock_requests):
mock_requests.exceptions.ConnectionError = ValueError
mock_requests.delete.side_effect = ValueError("Some Error")
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
with self.assertRaises(BespinException) as raised_exception:
api._delete_request('test')
self.assertEqual(
str(raised_exception.exception).strip(),
'Failed to connect to someurl\nSome Error')
def test_workflow_configurations_list_no_filtering(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = ['workflowconfig1']
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
items = api.workflow_configurations_list()
mock_requests.get.assert_called_with(
'someurl/workflow-configurations/', headers=self.expected_headers)
self.assertEqual(items, ['workflowconfig1'])
def test_vm_strategy_get(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'jobstrategy1'
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
response = api.job_strategy_get(123)
self.assertEqual(response, 'jobstrategy1')
mock_requests.get.assert_called_with('someurl/job-strategies/123/',
headers=self.expected_headers)
def test_share_group_get_for_name(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = ['sharegroup1']
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
response = api.share_group_get_for_name(name='myname')
self.assertEqual(response, 'sharegroup1')
mock_requests.get.assert_called_with(
'someurl/share-groups/?name=myname', headers=self.expected_headers)
def test_jobs_list(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = ['job1', 'job2']
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
jobs = api.jobs_list()
self.assertEqual(jobs, ['job1', 'job2'])
mock_requests.get.assert_called_with('someurl/jobs/',
headers=self.expected_headers)
def test_workflows_list_with_filter(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = ['workflow1', 'workflow2']
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
workflows = api.workflows_list(tag="mytag")
self.assertEqual(workflows, ['workflow1', 'workflow2'])
mock_requests.get.assert_called_with('someurl/workflows/?tag=mytag',
headers=self.expected_headers)
def test_dds_user_credentials_list(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = ['agentcred1']
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
items = api.dds_user_credentials_list()
self.assertEqual(items, ['agentcred1'])
mock_requests.get.assert_called_with('someurl/dds-user-credentials/',
headers=self.expected_headers)
def test_workflow_get(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'workflow1'
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
workflow = api.workflow_get('12')
self.assertEqual(workflow, 'workflow1')
mock_requests.get.assert_called_with('someurl/workflows/12/',
headers=self.expected_headers)
def test_workflow_version_get(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'workflowversion1'
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
item = api.workflow_version_get(workflow_version=123)
self.assertEqual(item, 'workflowversion1')
mock_requests.get.assert_called_with('someurl/workflow-versions/123/',
headers=self.expected_headers)
def test_job_strategies_list(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = ['jobstrategy1']
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
response = api.job_strategies_list(name='somename')
self.assertEqual(response, ['jobstrategy1'])
mock_requests.get.assert_called_with(
'someurl/job-strategies/?name=somename',
headers=self.expected_headers)
def test_job_templates_create_job(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'job_template_filled_in'
mock_requests.post.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
result = api.job_templates_create_job(job_file_payload={'a': '1'})
self.assertEqual(result, 'job_template_filled_in')
mock_requests.post.assert_called_with(
'someurl/job-templates/create-job/',
headers=self.expected_headers,
json={'a': '1'})
def test_job_templates_init(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'job_template1'
mock_requests.post.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
result = api.job_templates_init(tag="exome/v1/human")
self.assertEqual(result, 'job_template1')
expected_post_payload = {'tag': 'exome/v1/human'}
mock_requests.post.assert_called_with('someurl/job-templates/init/',
headers=self.expected_headers,
json=expected_post_payload)
def test_restart_job(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'job1'
mock_requests.post.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
item = api.restart_job(job_id=123)
self.assertEqual(item, 'job1')
mock_requests.post.assert_called_with('someurl/jobs/123/restart/',
headers=self.expected_headers,
json={})
def test_stage_group_post(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'stagegroup1'
mock_requests.post.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
stage_group = api.stage_group_post()
self.assertEqual(stage_group, 'stagegroup1')
mock_requests.post.assert_called_with('someurl/job-file-stage-groups/',
headers=self.expected_headers,
json={})
def test_workflow_version_find_by_tag_version(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = [
'filtered',
]
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
item = api.workflow_version_find_by_tag_version('exomeseq', 'v3')
self.assertEqual(item, 'filtered')
mock_requests.get.assert_called_with(
'someurl/workflow-versions/?workflow__tag=exomeseq&version=v3',
headers=self.expected_headers)
def test_workflow_versions_list_with_filter(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = [
'workflowversion1', 'workflowversion2'
]
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
items = api.workflow_versions_list(workflow_tag='exomeseq')
self.assertEqual(items, ['workflowversion1', 'workflowversion2'])
mock_requests.get.assert_called_with(
'someurl/workflow-versions/?workflow__tag=exomeseq',
headers=self.expected_headers)
def test_workflow_version_find_by_tag_version_raises_empty(
self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = []
mock_requests.get.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
with self.assertRaises(WorkflowNotFound) as context:
api.workflow_version_find_by_tag_version('exomeseq', 'v3')
self.assertIn('No workflow version found matching exomeseq/v3',
str(context.exception))
mock_requests.get.assert_called_with(
'someurl/workflow-versions/?workflow__tag=exomeseq&version=v3',
headers=self.expected_headers)
def test_workflow_post(self, mock_requests):
mock_response = Mock(status_code=200)
mock_response.json.return_value = 'workflow1'
mock_requests.post.return_value = mock_response
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
workflow = api.workflow_post(name="myname", tag="mytag")
self.assertEqual(workflow, 'workflow1')
mock_requests.post.assert_called_with('someurl/admin/workflows/',
headers=self.expected_headers,
json={
'name': 'myname',
'tag': 'mytag'
})
def test_workflow_version_tool_details_post(self, mock_requests):
mock_response = Mock(status_code=201)
mock_response.json.return_value = 'details1'
mock_requests.post.return_value = mock_response
workflow_version_id = '3'
contents = [{'docker_image': 'ubuntu:latest'}]
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
tool_details = api.workflow_version_tool_details_post(
workflow_version_id, contents)
self.assertEqual(tool_details, 'details1')
mock_requests.post.assert_called_with(
'someurl/admin/workflow-version-tool-details/',
headers=self.expected_headers,
json={
'workflow_version': '3',
'details': contents
})
def _create_api(self):
config = ConfigFile().read_or_create_config()
return BespinApi(config, user_agent_str=self.user_agent_str)
def test_check_response_raising_exceptions(self):
api = BespinApi(config=self.mock_config,
user_agent_str=self.mock_user_agent_str)
mock_response = Mock()
mock_response.json.return_value = {'field1': ['bad']}
mock_response.raise_for_status.side_effect = requests.HTTPError()
mock_response.status_code = 400
with self.assertRaises(BespinClientErrorException):
api._check_response(mock_response)
mock_response.status_code = 401
with self.assertRaises(BespinClientErrorException):
api._check_response(mock_response)
mock_response.status_code = 404
with self.assertRaises(NotFoundException):
api._check_response(mock_response)
mock_response = Mock()
mock_response.json.return_value = {}
mock_response.raise_for_status.return_value = None
mock_response.status_code = 200
api._check_response(mock_response)
mock_response.status_code = 201
api._check_response(mock_response)