def run(auth: CromwellAuth, metadata: str = None, uuid: str = None):
if metadata is not None:
with open(args.metadata) as data_file:
metadata = json.load(data_file)
# cli top level parsing ensures metadata is set otherwise
else:
response = CromwellAPI.metadata(
uuid=uuid,
auth=auth,
expandSubWorkflows=True,
raise_for_status=True,
)
metadata = response.json()
if auth.service_key_content is None:
raise exceptions.CromwellAuthenticationError(
"task_runtime requires a service account key")
print_task_runtime_data(metadata, auth.service_key_content)
def get_wf_metadata(cromwell_auth,
wf_id,
include_keys=None,
exclude_keys=None):
result = CromwellAPI.metadata(wf_id,
cromwell_auth,
includeKey=include_keys,
excludeKey=exclude_keys)
try:
result.raise_for_status()
except requests.exceptions.HTTPError as e:
logging.error("Unable to fetch metadata for wf: {0}".format(wf_id))
logging.error("Message from cromwell server:\n{0}".format(
result.json()))
raise
return result.json()
def test_metadata_returns_200(self, mock_request):
workflow_id = '12345abcde'
test_include_key = 'workflow'
def _request_callback(request, context):
context.status_code = 200
context.headers['test'] = 'header'
return {'id': '12345abcde', 'actualWorkflowLanguageVersion': 'draft-2'}
for cromwell_auth in self.auth_options:
mock_request.get(
'{0}/api/workflows/v1/{1}/metadata?expandSubWorkflows=false&includeKey={2}'.format(
cromwell_auth.url, workflow_id, test_include_key
),
json=_request_callback,
)
result = CromwellAPI.metadata(
workflow_id, cromwell_auth, includeKey=test_include_key
)
self.assertEqual(result.status_code, 200)
self.assertEqual(result.json()['id'], workflow_id)
def get_status(self):
return pd.DataFrame(
[[_a, cwt.metadata(_a, self.auth_obj).json()['status']]
for _a in self.resp_list])
def sync_metadata(self):
self.metadata = CromwellAPI.metadata(
self.wf_id,
self.auth,
includeKey=["outputs", "labels", "status", "inputs"],
raise_for_status=True).json()
