def abort(workflow_id, host, port):
server = cromwell.Server(host, port)
if not server.is_accessible():
msg = "Could not access the cromwell server! Please ensure it is up!"
raise Exception(msg)
status = server.abort_workflow(workflow_id)
print(json.dumps(status, indent=4, sort_keys=True))
def execution_status(workflow_id, host, port):
server = cromwell.Server(host, port)
if not server.is_accessible():
msg = "Could not access the cromwell server! Please ensure it is up!"
raise Exception(msg)
status_summary = server.get_workflow_execution_status(workflow_id)
creport.display_workflow_execution_status(workflow_id, status_summary)
def outputs(workflow_id, host, port):
server = cromwell.Server(host, port)
if not server.is_accessible():
msg = "Could not access the cromwell server! Please ensure it is up!"
raise Exception(msg)
metadata = server.get_workflow_input_outputs(workflow_id)
pretty_metadata = json.dumps(metadata, indent=4, sort_keys=True)
print(pretty_metadata)
def metadata_lite(workflow_id, output, host, port):
cromwell.Server.get_workflow_metadata_lite = \
utils.memoize(cromwell.Server.get_workflow_metadata_lite)
server = cromwell.Server(host, port)
if not server.is_accessible():
msg = "Could not access the cromwell server! Please ensure it is up!"
raise Exception(msg)
metadata = server.get_workflow_metadata_lite(workflow_id)
pretty_metadata = json.dumps(metadata, indent=4, sort_keys=True)
if output:
with open(output, 'w') as f:
print(pretty_metadata, file=f)
else:
print(pretty_metadata)
def _get_cromwell_server(host, port):
# setup the server object
# decorate the cromwell.Server class function
cromwell.Server.get_workflow_metadata = \
utils.memoize(cromwell.Server.get_workflow_metadata)
server = cromwell.Server(host, port)
logging.info("Checking if we have access to the cromwell server")
if not server.is_accessible():
msg = "Could not access the cromwell server! Please ensure it is up!"
logging.error(msg)
raise Exception(msg)
return server
def estimate_workflow_cost(metadata_path=None,
workflow_id=None,
sku_path=None,
host='localhost',
port=8000,
tier_scheme='all'):
# setup the server object
# decorate the cromwell.Server class function
cromwell.Server.get_workflow_metadata = \
utils.memoize(cromwell.Server.get_workflow_metadata)
server = cromwell.Server(host, port)
logging.info("Checking if we have access to the cromwell server")
if not server.is_accessible():
msg = "Could not access the cromwell server! Please ensure it is up!"
logging.error(msg)
raise Exception(msg)
# setup the google services and skus information
gcloud.GoogleServices.get_available_compute_types = \
utils.memoize(gcloud.GoogleServices.get_available_compute_types)
google = gcloud.GoogleServices(sku_path)
# derive the metadata
metadata = None
if metadata_path:
msg = "Loading the workflow metadata from : {}".format(metadata_path)
logging.info(msg)
with open(metadata_path) as f:
metadata = json.load(f)
else:
logging.info("Fetching metadata from cromwell")
metadata = server.get_workflow_metadata(workflow_id)
logging.info("Fetched metadata from cromwell")
if metadata is None:
msg = "Could not derive workflow metadata"
logger.error(msg)
raise Exception(msg)
# perform the calculations
estimator = cromwell.CostEstimator(server, google)
logging.info("Starting cost calculations")
cost = estimator.calculate_cost(metadata, tier_scheme)
logging.info("Finished cost calculations")
return cost
def test(self):
server = cromwell.Server()
self.assertEqual(server.host, 'localhost')
self.assertEqual(server.port, 8000)
self.__class__.server = server