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", "{}/../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))