def submit_to_cromwell(args):
# Get authentication (as no authentication)
auth = CromwellAuth.from_no_authentication(
url="http://localhost:{}".format(args.webservice_port))
response = api.submit(auth=auth,
wdl_file=args.workflow_source,
inputs_files=args.workflow_inputs,
dependencies=args.workflow_dependencies,
validate_labels=True)
# FIXME - need to test this first a bit
print(response)
def run_wdl(ls: Server, params: Tuple[RunWDLParams]):
wdl_uri = params[0].wdl_uri
wdl_path = urlparse(wdl_uri).path
_, wdl = _parse_wdl(ls, wdl_uri)
if not wdl:
return ls.show_message('Unable to submit: WDL contains error(s)', MessageType.Error)
config = _get_client_config(ls)
auth = CromwellAuth.from_no_authentication(config.cromwell.url)
workflow = cromwell_api.submit(
auth, wdl_path, raise_for_status=True,
).json()
id = workflow['id']
title = 'Workflow {} for {}'.format(id, wdl_path)
_progress(ls, 'start', {
'id': id,
'title': title,
'cancellable': True,
'message': workflow['status'],
})
status: str = ''
while True:
if status != workflow['status']:
status = workflow['status']
if status == 'Succeeded':
message_type = MessageType.Info
elif status in ('Aborting', 'Aborted'):
message_type = MessageType.Warning
elif status == 'Failed':
message_type = MessageType.Error
else:
_progress(ls, 'report', {
'id': id,
'message': status,
})
continue
_progress(ls, 'done', {
'id': id,
})
message = '{}: {}'.format(title, status)
ls.show_message(message, message_type)
diagnostics = _parse_failures(wdl, wdl_uri, id, auth)
return ls.publish_diagnostics(wdl_uri, diagnostics)
sleep(config.cromwell.pollSec)
if id in ls.aborting_workflows:
workflow = cromwell_api.abort(
id, auth, raise_for_status=True,
).json()
ls.aborting_workflows.remove(id)
continue
try:
workflow = cromwell_api.status(
id, auth, raise_for_status=True,
).json()
except HTTPError as e:
ls.show_message_log(str(e), MessageType.Error)