def get_context():
return json.dumps({
"references":
data_handler.get_references(),
"datasets":
get_content(data_handler.datasets.all()),
"services":
list(
map(lambda Service: Service.frontend_information(),
get_services())),
"experiments":
get_content(data_handler.experiments.all())
})
def __init__(self, data_handler, data_directory, constants):
self.data_handler = data_handler
self.experiment_statuses = constants["experiment"]
self.docker_client = Docker(data_directory)
self.tasks = []
self.current_task = None
self.services = get_services()
self.scheduler = BackgroundScheduler()
self.scheduler.add_job(func=self.check_run,
trigger="interval",
seconds=5,
timezone="Europe/Berlin")
self.scheduler.start()
logging.getLogger('apscheduler').setLevel("ERROR")
def start_node(config: dict):
import services
services = services.get_services()
logger = get_logger("Node_" + str(uuid.uuid4()))
loop = asyncio.new_event_loop()
async def run(config):
await asyncio.gather(
call_service(nats_host=config.get('nats_host'),
nats_port=config.get('nats_port'),
service_topic=config.get('service_topic'),
response_topic=config.get('response_topic'),
loop=loop,
logger=logger,
services=services), synchronize(services, logger))
loop.run_until_complete(run(config))
loop.run_forever()
import os
import sys
import bonobo
import bonobo_sqlalchemy
from bonobo.config import use_context
@use_context
def extract(context):
context.set_output_fields(['id', 'value'])
for i in range(1000):
yield i, 'value for {}'.format(i)
def get_graph(**options):
graph = bonobo.Graph()
graph.add_chain(extract, bonobo_sqlalchemy.InsertOrUpdate('example'))
return graph
# The __main__ block actually execute the graph.
if __name__ == '__main__':
sys.path.append(os.path.dirname(__file__))
import commands, services
with commands.parse_args() as options:
bonobo.run(get_graph(**options), services=services.get_services())
def configurate_extension(self):
from services import get_services
for view, urls in get_services():
self.extension.add_resource(view, urls)
def get_aligner_soft_clips(self):
aligner_id = self.content["pipeline"]["alignment"]["id"]
aligner = next(service for service in get_services()
if service.id == aligner_id)
return aligner.soft_clips_exist
def main():
bonobo.run(get_graph(), services=services.get_services())
if __name__ == "__main__":
# Initialize API
config.load_kube_config()
api = client.CoreV1Api()
beta_api = client.ExtensionsV1beta1Api()
print("\n\nDelete all deployments in default namespace")
deployments_list = deployments.get_deployments(beta_api)
for deployment in deployments_list:
if deployments.namespace(deployment) == 'default':
deployments.delete_deployment(beta_api, deployment)
print("\n\nDelete all services in default namespace")
services_list = services.get_services(api)
for service in services_list:
if services.namespace(service) == 'default' and services.name(
service) != 'kubernetes':
services.delete_service(api, service)
print("\n\nDelete all pods in default namespace")
pods_list = pods.get_pods_list(api)
for pod in pods_list:
if pods.namespace(pod) == 'default':
pods.delete_pod(api, pod)
pods_deleted = check_empty_namespace(api, 'default')
if pods_deleted:
print("All pods in default namespace successfully deleted")
else: