def get_wf_status(cromwell_auth, wf_id, log_on_fail=True):
result = CromwellAPI.status(wf_id, cromwell_auth)
try:
result.raise_for_status()
except requests.exceptions.HTTPError as e:
err_msg = "Message from cromwell server: {0}".format(
result.json()["message"])
if log_on_fail:
logging.error(err_msg)
raise WFStatusCheckFailException(err_msg)
return result.json()["status"]
def test_status(self, mock_request):
def _request_callback_status(request, context):
context.status_code = 200
context.headers['test'] = 'header'
return {'status': 'Succeeded'}
workflow_id = "01234"
for cromwell_auth in self.auth_options:
mock_request.get(
cromwell_auth.url + '/api/workflows/v1/{}/status'.format(workflow_id),
json=_request_callback_status,
)
result = CromwellAPI.status(workflow_id, cromwell_auth)
self.assertEqual(result.json()['status'], 'Succeeded')
def calculate_metric(template_values, scan_values):
merged_values = {
k: v
for (k, v) in (template_values.items() + scan_values.items())
}
merged_json_file, merged_json_path = tempfile.mkstemp()
with open(merged_json_path, 'w') as f:
json.dump(merged_values, f)
cromwell_auth = CromwellAuth(url=args.cromwell_server,
header={'Authorization': 'bearer fake_token'},
auth=None)
with open(args.workflow_wdl, 'r') as w, open(merged_json_path, 'r') as j:
submit = CromwellAPI.submit(cromwell_auth, w, j)
workflow_id = submit.json()['id']
logger.info('Submitted workflow: ' + workflow_id)
time.sleep(5)
logger.info('Waiting for workflow to complete...')
# Query workflow status indefinitely until success or failure returned.
# If success returned, attempt to retrieve objective_value from metadata and return.
# If failure returned or if exception raised during metadata retreival, return bad_value.
try:
while True:
try:
CromwellAPI.wait([workflow_id],
cromwell_auth,
timeout_minutes=600,
poll_interval_seconds=20,
verbose=False)
response = CromwellAPI.status(workflow_id, cromwell_auth)
status = response.json()['status']
if status == 'Succeeded':
logger.info('Workflow succeeded...')
break
except WorkflowFailedException:
logger.info('Workflow failed, returning bad value...')
return bad_value
except Exception as e:
logger.info(e)
logger.info(
'Cromwell exception, retrying wait and status check...')
logger.info('Getting metadata...')
session = retry_session(retries=10)
metadata = session.post(
url=cromwell_auth.url +
CromwellAPI._metadata_endpoint.format(uuid=workflow_id),
auth=cromwell_auth.auth,
headers=cromwell_auth.header)
workflow_name = metadata.json()['workflowName']
objective_value = metadata.json()['outputs'][
'{}.objective_value'.format(workflow_name)]
return objective_value
except Exception as e:
logger.info(e)
logger.info(
'Cromwell exception during metadata retrieval, returning bad value...'
)
return bad_value
