def start():
"""
Start the bcl2fastq-ws app
"""
app_svc = AppService.create(__package__)
app_svc.start(routes(config=app_svc.config_svc))
def start():
"""
Start the bcl2fastq-ws app
"""
app_svc = AppService.create(__package__)
app_svc.start(routes(config=app_svc.config_svc))
def start():
app_svc = AppService.create(__package__)
process_svc = ProcessService(app_svc.config_svc)
# Setup the routing. Help will be automatically available at /api, and will
# be based on the doc strings of the get/post/put/delete methods
app_svc.start(routes(process_svc=process_svc, config_svc=app_svc.config_svc))
def test_can_load_configuration(self):
app_svc = AppService.create("arteria-test", None, True)
self.assertIsNotNone(app_svc.config_svc)
app_config = app_svc.config_svc.get_app_config()
logger_config = app_svc.config_svc.get_logger_config()
self.assertTrue(app_config["port"] == 10000)
self.assertTrue(logger_config["version"] == 1)
def test_can_load_configuration(self):
app_svc = AppService.create("arteria-test", None, True)
self.assertIsNotNone(app_svc.config_svc)
app_config = app_svc.config_svc.get_app_config()
logger_config = app_svc.config_svc.get_logger_config()
self.assertTrue(app_config["port"] == 10000)
self.assertTrue(logger_config["version"] == 1)
def test_can_load_configuration(self):
app_svc = AppService.create("arteria-test", "{}/../templates/".format(self.this_file_path))
self.assertIsNotNone(app_svc.config_svc)
app_config = app_svc.config_svc.get_app_config()
logger_config = app_svc.config_svc.get_logger_config()
self.assertTrue(app_config["port"] == 10000)
self.assertTrue(logger_config["version"] == 1)
def start():
app_svc = AppService.create(__package__)
process_svc = ProcessService(app_svc.config_svc)
# Setup the routing. Help will be automatically available at /api, and will
# be based on the doc strings of the get/post/put/delete methods
app_svc.start(
routes(process_svc=process_svc, config_svc=app_svc.config_svc))
def test_can_load_configuration(self):
app_svc = AppService.create(
"arteria-test", "{}/../templates/".format(self.this_file_path))
self.assertIsNotNone(app_svc.config_svc)
app_config = app_svc.config_svc.get_app_config()
logger_config = app_svc.config_svc.get_logger_config()
self.assertTrue(app_config["port"] == 10000)
self.assertTrue(logger_config["version"] == 1)
def start():
app_svc = AppService.create(__package__)
process_svc = ProcessService(app_svc.config_svc)
# Setup the routing. Help will be automatically available at /api, and will
# be based on the doc strings of the get/post/put/delete methods
args = dict(process_svc=process_svc, config_svc=app_svc.config_svc)
routes = [(r"/api/1.0/(?:qc|report)/run/([\w_-]+)", RunHandler, args),
(r"/api/1.0/(?:qc|report)/status/(\d*)", StatusHandler, args)]
app_svc.start(routes)
def start():
"""
Start the delivery-ws app
"""
app_svc = AppService.create(__package__)
config = app_svc.config_svc
composed_service = compose_application(config)
app_svc.start(routes(**composed_service))
def start():
app_svc = AppService.create(__package__)
# Setup the routing. Help will be automatically available at /api, and will
# be based on the doc strings of the get/post/put/delete methods
args = dict(config_svc=app_svc.config_svc)
routes = [
(r"/api/1.0/echo/([\w_-]+)", EchoHandler, args)
]
app_svc.start(routes)
def start():
"""
Start the checksum-ws app
"""
app_svc = AppService.create(__package__)
number_of_cores_to_use = app_svc.config_svc["number_of_cores"]
runner_service = LocalQAdapter(nbr_of_cores=number_of_cores_to_use, interval = 2, priority_method = "fifo")
app_svc.start(routes(config=app_svc.config_svc, runner_service = runner_service))
def start():
app_svc = AppService.create(__package__)
process_svc = ProcessService(app_svc.config_svc)
# Setup the routing. Help will be automatically available at /api, and will
# be based on the doc strings of the get/post/put/delete methods
args = dict(process_svc=process_svc, config_svc=app_svc.config_svc)
routes = [
(r"/api/1.0/(?:qc|report)/run/([\w_-]+)", RunHandler, args),
(r"/api/1.0/(?:qc|report)/status/(\d*)", StatusHandler, args)
]
app_svc.start(routes)
def start():
app_svc = AppService.create(__package__)
runfolder_svc = RunfolderService(app_svc.config_svc)
# Setup the routing. Help will be automatically available at /api, and will be based on
# the doc strings of the get/post/put/delete methods
args = dict(runfolder_svc=runfolder_svc, config_svc=app_svc.config_svc)
routes = [
(r"/api/1.0/runfolders", ListAvailableRunfoldersHandler, args),
(r"/api/1.0/runfolders/next", NextAvailableRunfolderHandler, args),
(r"/api/1.0/runfolders/path(/.*)", RunfolderHandler, args),
(r"/api/1.0/runfolders/test/markasready/path(/.*)", TestFakeSequencerReadyHandler, args)
]
app_svc.start(routes)
def get_app(self):
# Get an as similar app as possible, tough note that we don't use the
# app service start method to start up the the application
path_to_this_file = os.path.abspath(
os.path.dirname(os.path.realpath(__file__)))
app_svc = AppService.create(
product_name="test_delivery_service",
config_root="{}/../../config/".format(path_to_this_file))
config = app_svc.config_svc
composed_application = compose_application(config)
routes = app_routes(**composed_application)
if self.mock_delivery:
def mock_delivery(cmd):
project_id = f"snpseq{random.randint(0, 10**10):010d}"
dds_output = f"""Current user: bio
Project created with id: {project_id}
User forskare was associated with Project {project_id} as Owner=True. An e-mail notification has not been sent.
Invitation sent to [email protected]. The user should have a valid account to be added to a
project"""
log.debug(f"Mock is called with {cmd}")
shell = False
if any(cmd[0].endswith(delivery_prgm)
for delivery_prgm in ['dds', 'moverinfo', 'to_outbox']):
new_cmd = ['sleep', str(self.mock_duration)]
if cmd[0].endswith('dds') and 'project' in cmd:
new_cmd += ['&&', 'echo', f'"{dds_output}"']
new_cmd = " ".join(new_cmd)
shell = True
else:
new_cmd = cmd
log.debug(f"Running mocked {new_cmd}")
p = Subprocess(new_cmd,
stdout=PIPE,
stderr=PIPE,
stdin=PIPE,
shell=shell)
return Execution(pid=p.pid, process_obj=p)
self.patcher = mock.patch(
'delivery.services.external_program_service'
'.ExternalProgramService.run',
wraps=mock_delivery)
return Application(routes)
def start():
app_svc = AppService.create(__package__)
runfolder_svc = RunfolderService(app_svc.config_svc)
# Setup the routing. Help will be automatically available at /api, and will be based on
# the doc strings of the get/post/put/delete methods
args = dict(runfolder_svc=runfolder_svc, config_svc=app_svc.config_svc)
routes = [(r"/api/1.0/runfolders", ListAvailableRunfoldersHandler, args),
(r"/api/1.0/runfolders/next",
NextAvailableRunfolderHandler, args),
(r"/api/1.0/runfolders/path(/.*)", RunfolderHandler, args),
(r"/api/1.0/runfolders/test/markasready/path(/.*)",
TestFakeSequencerReadyHandler, args)]
app_svc.start(routes)
def start():
"""
Start the checksum-ws app
"""
app_svc = AppService.create(__package__)
number_of_cores_to_use = app_svc.config_svc["number_of_cores"]
runner_service = LocalQAdapter(nbr_of_cores=number_of_cores_to_use,
interval=2,
priority_method="fifo")
app_svc.start(
routes(config=app_svc.config_svc, runner_service=runner_service))
def start():
"""
Start the archive-upload-ws app
"""
app_svc = AppService.create(__package__)
number_of_cores_to_use = app_svc.config_svc["number_of_cores"]
whitelist = app_svc.config_svc["whitelisted_warnings"]
runner_service = LocalQAdapter(nbr_of_cores=number_of_cores_to_use,
whitelisted_warnings=whitelist,
interval=2,
priority_method="fifo")
app_svc.start(
routes(config=app_svc.config_svc, runner_service=runner_service))
def get_app(self):
# Get an as similar app as possible, tough note that we don't use the
# app service start method to start up the the application
path_to_this_file = os.path.abspath(
os.path.dirname(os.path.realpath(__file__)))
app_svc = AppService.create(
product_name="test_delivery_service",
config_root="{}/../../config/".format(path_to_this_file))
config = app_svc.config_svc
composed_application = compose_application(config)
# TODO Later swap the "real" delivery service here for mock one.
return Application(app_routes(**composed_application))