def test_can_get_next(self):
# TODO: These integration tests are semi-manual, as they expect certain data
logger = MagicMock()
client = RunfolderClient(["http://testarteria1:10800"], logger)
result = client.next_ready()
self.assertNotEqual(result, None)
self.assertTrue('path' in result)
self.assertTrue('host' in result)
self.assertTrue('link' in result)
self.assertTrue('state' in result)
self.assertEqual(result['state'], 'ready')
def test_can_get_next(self):
# TODO: These integration tests are semi-manual, as they expect certain data
logger = MagicMock()
client = RunfolderClient(["http://testarteria1:10800"], logger)
result = client.next_ready()
self.assertNotEqual(result, None)
self.assertTrue('path' in result)
self.assertTrue('host' in result)
self.assertTrue('link' in result)
self.assertTrue('state' in result)
self.assertEqual(result['state'], 'ready')
def setup(self):
self._infolog("setup")
try:
self._load_config()
client_urls = self.config["runfolder_svc_urls"]
self._client = RunfolderClient(client_urls, self._logger)
self._infolog("Created client: {0}".format(self._client))
except Exception as ex:
# TODO: It seems that st2 isn't logging the entire exception, or
# they're not in /var/log/st2
self._logger.error(str(ex))
self._infolog("setup finished")
class RunfolderSensor(PollingSensor):
def __init__(self, sensor_service, config=None, poll_interval=None, trigger='arteria.runfolder_ready'):
super(RunfolderSensor, self).__init__(sensor_service=sensor_service,
config=config,
poll_interval=poll_interval)
self._logger = self._sensor_service.get_logger(__name__)
self._infolog("__init__")
self._client = None
self._trigger = trigger
self._hostconfigs = {}
def setup(self):
self._infolog("setup")
client_urls = self._config["runfolder_service_url"]
self._client = RunfolderClient(client_urls, self._logger)
self._infolog("Created client: {0}".format(self._client))
self._infolog("setup finished")
def poll(self):
self._infolog("poll")
self._infolog("Checking for available runfolders")
result = self._client.next_ready()
self._infolog("Result from client: {0}".format(result))
if result:
self._handle_result(result)
def cleanup(self):
self._infolog("cleanup")
def add_trigger(self, trigger):
self._infolog("add_trigger")
def update_trigger(self, trigger):
self._infolog("update_trigger")
def remove_trigger(self, trigger):
self._infolog("remove_trigger")
def _handle_result(self, result):
self._infolog("_handle_result")
trigger = self._trigger
runfolder_path = result['response']['path']
runfolder_name = os.path.split(runfolder_path)[1]
payload = {
'host': result['response']['host'],
'runfolder': runfolder_path,
'runfolder_name': runfolder_name,
'link': result['response']['link'],
'timestamp': datetime.utcnow().isoformat(),
'destination': ""
}
if result['requesturl'] in self._hostconfigs:
payload['destination'] = self._hostconfigs[result['requesturl']].get('dest_folder', "")
payload['remote_user'] = self._hostconfigs[result['requesturl']].get('remote_user', "")
payload['user_key'] = self._hostconfigs[result['requesturl']].get('user_key', "")
self._sensor_service.dispatch(trigger=trigger, payload=payload, trace_tag=runfolder_name)
def _infolog(self, msg):
self._logger.info("[arteria-packs." + self.__class__.__name__ + "] " + msg)
def setup(self):
self._infolog("setup")
try:
self._load_config()
client_urls = self.config["runfolder_svc_urls"]
self._client = RunfolderClient(client_urls, self._logger)
self._infolog("Created client: {0}".format(self._client))
except Exception as ex:
# TODO: It seems that st2 isn't logging the entire exception, or
# they're not in /var/log/st2
self._logger.error(str(ex))
self._infolog("setup finished")
def setup(self):
self._infolog("setup")
try:
self._load_config()
client_urls = [x['url'] for x in self.config["incoming_svc_urls"]]
# copy all further keys of every item over to self._hostconfigs
for x in self.config["incoming_svc_urls"]:
self._hostconfigs[x['url']] = {}
for y in x:
if y != 'url':
self._hostconfigs[x['url']][y] = x[y]
self._client = RunfolderClient(client_urls, self._logger)
self._infolog("Created client: {0}".format(self._client))
except Exception as ex:
# TODO: It seems that st2 isn't logging the entire exception, or
# they're not in /var/log/st2
self._logger.error(str(ex))
self._infolog("setup finished")
class RunfolderSensor(PollingSensor):
def __init__(self,
sensor_service,
config=None,
poll_interval=None,
trigger='arteria-packs.runfolder_ready'):
super(RunfolderSensor, self).__init__(sensor_service=sensor_service,
config=config,
poll_interval=poll_interval)
self._logger = self._sensor_service.get_logger(__name__)
self._infolog("__init__")
self._client = None
self._trigger = trigger
self._hostconfigs = {}
def setup(self):
self._infolog("setup")
try:
self._load_config()
client_urls = self.config["runfolder_svc_urls"]
self._client = RunfolderClient(client_urls, self._logger)
self._infolog("Created client: {0}".format(self._client))
except Exception as ex:
# TODO: It seems that st2 isn't logging the entire exception, or
# they're not in /var/log/st2
self._logger.error(str(ex))
self._infolog("setup finished")
def poll(self):
try:
self._infolog("poll")
self._infolog("Checking for available runfolders")
result = self._client.next_ready()
self._infolog("Result from client: {0}".format(result))
if result:
self._handle_result(result)
except Exception as ex:
self._logger.error(str(ex))
def cleanup(self):
self._infolog("cleanup")
def add_trigger(self, trigger):
self._infolog("add_trigger")
def update_trigger(self, trigger):
self._infolog("update_trigger")
def remove_trigger(self, trigger):
self._infolog("remove_trigger")
def _handle_result(self, result):
self._infolog("_handle_result")
trigger = self._trigger
runfolder_path = result['response']['path']
runfolder_name = os.path.split(runfolder_path)[1]
payload = {
'host': result['response']['host'],
'runfolder': runfolder_path,
'runfolder_name': runfolder_name,
'link': result['response']['link'],
'timestamp': datetime.utcnow().isoformat(),
'destination': ""
}
if result['requesturl'] in self._hostconfigs:
payload['destination'] = self._hostconfigs[
result['requesturl']].get('dest_folder', "")
payload['remote_user'] = self._hostconfigs[
result['requesturl']].get('remote_user', "")
payload['user_key'] = self._hostconfigs[result['requesturl']].get(
'user_key', "")
self._sensor_service.dispatch(trigger=trigger,
payload=payload,
trace_tag=runfolder_name)
def _load_config(self):
config_path = "/opt/stackstorm/packs/arteria-packs/config.yaml"
with open(config_path) as stream:
self.config = yaml.load(stream)
self._infolog("Loaded configuration from {}".format(config_path))
def _infolog(self, msg):
self._logger.info("[arteria-packs." + self.__class__.__name__ + "] " +
msg)
def test_server_down_only_logs(self):
logger = MagicMock()
client = RunfolderClient(["http://testarteria1-notavailable:10800"], logger)
result = client.next_ready()
self.assertEqual(result, None)
class RunfolderSensor(PollingSensor):
def __init__(self, sensor_service, config=None, poll_interval=None, trigger='snpseq_packs.runfolder_ready'):
super(RunfolderSensor, self).__init__(sensor_service=sensor_service,
config=config,
poll_interval=poll_interval)
self._logger = self._sensor_service.get_logger(__name__)
self._infolog("__init__")
self._client = None
self._trigger = trigger
self._hostconfigs = {}
def setup(self):
self._infolog("setup")
try:
self._load_config()
client_urls = self.config["runfolder_svc_urls"]
self._client = RunfolderClient(client_urls, self._logger)
self._infolog("Created client: {0}".format(self._client))
except Exception as ex:
# TODO: It seems that st2 isn't logging the entire exception, or
# they're not in /var/log/st2
self._logger.error(str(ex))
self._infolog("setup finished")
def poll(self):
try:
self._infolog("poll")
self._infolog("Checking for available runfolders")
result = self._client.next_ready()
self._infolog("Result from client: {0}".format(result))
if result:
self._handle_result(result)
except Exception as ex:
self._logger.error(str(ex))
def cleanup(self):
self._infolog("cleanup")
def add_trigger(self, trigger):
self._infolog("add_trigger")
def update_trigger(self, trigger):
self._infolog("update_trigger")
def remove_trigger(self, trigger):
self._infolog("remove_trigger")
def _handle_result(self, result):
self._infolog("_handle_result")
trigger = self._trigger
runfolder_path = result['response']['path']
runfolder_name = os.path.split(runfolder_path)[1]
payload = {
'host': result['response']['host'],
'runfolder': runfolder_path,
'runfolder_name': runfolder_name,
'link': result['response']['link'],
'timestamp': datetime.utcnow().isoformat(),
'destination': ""
}
if result['requesturl'] in self._hostconfigs:
payload['destination'] = self._hostconfigs[result['requesturl']].get('dest_folder', "")
payload['remote_user'] = self._hostconfigs[result['requesturl']].get('remote_user', "")
payload['user_key'] = self._hostconfigs[result['requesturl']].get('user_key', "")
self._sensor_service.dispatch(trigger=trigger, payload=payload, trace_tag=runfolder_name)
def _load_config(self):
config_path = "/opt/stackstorm/packs/snpseq_packs/config.yaml"
with open(config_path) as stream:
self.config = yaml.load(stream)
self._infolog("Loaded configuration from {}".format(config_path))
def _infolog(self, msg):
self._logger.info("[snpseq_packs." + self.__class__.__name__ + "] " + msg)
class RunfolderSensor(PollingSensor):
def __init__(self,
sensor_service,
config=None,
poll_interval=None,
trigger='arteria.runfolder_ready'):
super(RunfolderSensor, self).__init__(sensor_service=sensor_service,
config=config,
poll_interval=poll_interval)
self._logger = self._sensor_service.get_logger(__name__)
self._infolog("__init__")
self._client = None
self._trigger = trigger
self._hostconfigs = {}
def setup(self):
self._infolog("setup")
client_urls = self._config["runfolder_service_url"]
self._client = RunfolderClient(client_urls, self._logger)
self._infolog("Created client: {0}".format(self._client))
self._infolog("setup finished")
def poll(self):
self._infolog("poll")
self._infolog("Checking for available runfolders")
result = self._client.next_ready()
self._infolog("Result from client: {0}".format(result))
if result:
self._handle_result(result)
def cleanup(self):
self._infolog("cleanup")
def add_trigger(self, trigger):
self._infolog("add_trigger")
def update_trigger(self, trigger):
self._infolog("update_trigger")
def remove_trigger(self, trigger):
self._infolog("remove_trigger")
def _handle_result(self, result):
self._infolog("_handle_result")
trigger = self._trigger
runfolder_path = result['response']['path']
runfolder_name = os.path.split(runfolder_path)[1]
payload = {
'host': result['response']['host'],
'runfolder': runfolder_path,
'runfolder_name': runfolder_name,
'link': result['response']['link'],
'timestamp': datetime.utcnow().isoformat(),
'destination': ""
}
if result['requesturl'] in self._hostconfigs:
payload['destination'] = self._hostconfigs[
result['requesturl']].get('dest_folder', "")
payload['remote_user'] = self._hostconfigs[
result['requesturl']].get('remote_user', "")
payload['user_key'] = self._hostconfigs[result['requesturl']].get(
'user_key', "")
self._sensor_service.dispatch(trigger=trigger,
payload=payload,
trace_tag=runfolder_name)
def _infolog(self, msg):
self._logger.info("[arteria-packs." + self.__class__.__name__ + "] " +
msg)
def setup(self):
self._infolog("setup")
client_urls = self._config["runfolder_service_url"]
self._client = RunfolderClient(client_urls, self._logger)
self._infolog("Created client: {0}".format(self._client))
self._infolog("setup finished")
def setup(self):
self._infolog("setup")
client_urls = self._config["runfolder_service_url"]
self._client = RunfolderClient(client_urls, self._logger)
self._infolog("Created client: {0}".format(self._client))
self._infolog("setup finished")
def test_server_down_only_logs(self):
logger = MagicMock()
client = RunfolderClient(["http://testarteria1-notavailable:10800"],
logger)
result = client.next_ready()
self.assertEqual(result, None)
