def test_if_compose_oauth_options_for_jes_backend_cromwell_can_deal_with_null_workflow_options(
self, ):
test_url = 'https://fake_url'
test_service_account_key = 'data/fake_account_key.json'
with open(test_service_account_key, 'r') as f:
test_service_account_key_content = json.load(f)
test_auth = CromwellAuth(
url=test_url,
header={"Authorization": "bearer fake_token"},
auth=None,
service_key_content=test_service_account_key_content,
)
result_options = utils.compose_oauth_options_for_jes_backend_cromwell(
test_auth)
result_options_in_dict = json.loads(result_options.getvalue())
assert (result_options_in_dict['google_project'] ==
test_service_account_key_content['project_id'])
assert (result_options_in_dict['google_compute_service_account'] ==
test_service_account_key_content['client_email'])
assert result_options_in_dict[
'user_service_account_json'] == json.dumps(
test_service_account_key_content)
def test_compose_oauth_options_for_jes_backend_cromwell_add_required_fields_to_workflow_options(
self, ):
test_url = 'https://fake_url'
test_service_account_key = 'data/fake_account_key.json'
with open(test_service_account_key, 'r') as f:
test_service_account_key_content = json.load(f)
test_auth = CromwellAuth(
url=test_url,
header={"Authorization": "bearer fake_token"},
auth=None,
service_key_content=test_service_account_key_content,
)
result_options = utils.compose_oauth_options_for_jes_backend_cromwell(
test_auth, self.options_file_BytesIO)
# use .decode('utf-8') for Python3.5 compatibility
result_options_in_dict = json.loads(
result_options.getvalue().decode('utf-8'))
assert (
# use .decode('utf-8') for Python3.5 compatibility
result_options_in_dict['read_from_cache'] == json.loads(
self.options_file_BytesIO.getvalue().decode('utf-8'))
['read_from_cache'])
assert (result_options_in_dict['google_project'] ==
test_service_account_key_content['project_id'])
assert (result_options_in_dict['google_compute_service_account'] ==
test_service_account_key_content['client_email'])
assert result_options_in_dict[
'user_service_account_json'] == json.dumps(
test_service_account_key_content)
def submit(
cls: 'CromwellAPI',
auth: CromwellAuth,
wdl_file: Union[str, io.BytesIO],
inputs_files: Union[List[Union[str, io.BytesIO]], str,
io.BytesIO] = None,
options_file: Union[str, io.BytesIO] = None,
dependencies: Union[str, List[str], io.BytesIO] = None,
label_file: Union[str, io.BytesIO] = None,
collection_name: str = None,
on_hold: bool = False,
validate_labels: bool = False,
raise_for_status: bool = False,
) -> requests.Response:
""" Submits a workflow to Cromwell.
Args:
auth: authentication class holding auth information to a
Cromwell server.
wdl_file: The workflow source file to submit for execution. Could be either the
path to the file (str) or the file content in io.BytesIO.
inputs_files: The input data in JSON
format. Could be either the path to the file (str) or the file content in io.BytesIO. This could also
be a list of unlimited input file paths/contents, each of them should have a type of
Union[str, io.BytesIO].
options_file: The Cromwell options file for workflows. Could be either
the path to the file (str) or the file content in io.BytesIO.
dependencies: Workflow dependency files. Could be the path to
the zipped file (str) containing dependencies, a list of paths(List[str]) to all dependency files to be
zipped or a zipped file in io.BytesIO.
label_file: A collection of key/value pairs for workflow labels in JSON
format, could be either the path to the JSON file (str) or the file content in io.BytesIO.
collection_name: Collection in SAM that the workflow should belong to, if use CaaS.
on_hold: Whether to submit the workflow in "On Hold" status.
validate_labels: If True, validate cromwell labels.
raise_for_status: Whether to check and raise for status based on the response.
Raises:
requests.exceptions.HTTPError: This will be raised when raise_for_status is True and Cromwell returns
a response that satisfies 400 <= response.status_code < 600.
Returns:
HTTP response from Cromwell.
"""
submission_manifest = utilities.prepare_workflow_manifest(
wdl_file=wdl_file,
inputs_files=inputs_files,
options_file=options_file,
dependencies=dependencies,
label_file=label_file,
collection_name=collection_name,
on_hold=on_hold,
)
if auth.service_key_content:
submission_manifest[
'workflowOptions'] = utilities.compose_oauth_options_for_jes_backend_cromwell(
auth, submission_manifest.get('workflowOptions'))
if validate_labels and label_file is not None:
validate_cromwell_label(submission_manifest['labels'])
response = requests.post(
auth.url + cls._submit_endpoint,
files=submission_manifest,
auth=auth.auth,
headers=auth.header,
)
if raise_for_status:
cls._check_and_raise_status(response)
return response
