def main():
parser = argparse.ArgumentParser(description='consumes a mq ')
parser.add_argument('-c',
'--config',
required=True,
help="conductor config file ",
default="conductor.yml")
parser.add_argument('-l',
'--logfile',
default=None,
help="Logfile to write to, default is stdout")
parser.add_argument('-v',
'--verbose',
default=4,
action="count",
help="Increase the verbosity of logging output")
args = parser.parse_args()
config = init(args.config)
if args.logfile:
logger.init(name='nga_runner', log_file=args.logfile, rotate_logs=True)
else:
logger.init(name='nga_runner')
logger.set_log_level(args.verbose)
logger.info(f'startup (v:{version})')
api_requests.set_token(config['key'])
global mq
mq.connect(uri=config['mq_uri'], prefetch_count=1)
try:
mq.consume(route='default', callback=do_work)
except KeyboardInterrupt:
mq.channel.stop_consuming()
# Wait for all to complete
# logger.debug('waiting for threads')
mq.channel.close()
def init(config_file) -> {}:
config = config_utils.readin_config_file(config_file)
logger.info("init from config ")
# set incoming and proxy keys
api_requests.set_token(config.get('proxy_key', None))
global master_url, nels_url, instances, master_api, tmp_dir, sleep_time
master_url = config['master_url'].rstrip("/")
nels_url = config['nels_url'].rstrip("/")
instances = {}
master_api = api_requests.ApiRequests(master_url, config['key'])
global nels_storage_client_key, nels_storage_client_secret, nels_storage_url, sleep_time
nels_storage_client_key = config['nels_storage_client_key']
nels_storage_client_secret = config['nels_storage_client_secret']
nels_storage_url = config['nels_storage_url'].rstrip("/")
tmp_dir = config.get('tmp_dir', tmp_dir)
sleep_time = config.get('sleep_time', sleep_time)
tmp_instances = config['instances']
for iid in tmp_instances:
if 'active' not in tmp_instances[
iid] or not tmp_instances[iid]['active']:
continue
instances[iid] = tmp_instances[iid]
instance = tmp_instances[iid]
instance['api'] = api_requests.ApiRequests(
instance['nga_url'].rstrip("/"), instance['nga_key'])
instances[instance['name']] = instance
return config
def init(config_file: dict) -> None:
# Initialises setup from config file and galaxy config file and
# also initialites global variables (galaxy_url, master_url, nels_url, instance_id, tos_grace_period),
# sets (proxy_keys, instances, no_proxy)
config = config_utils.readin_config_file(config_file)
galaxy_config = config_utils.readin_config_file(config['galaxy_config'])
galaxy_init(galaxy_config)
logger.info("init from config ")
# set incoming and proxy keys
tornado.set_token(config.get('key', None))
api_requests.set_token(config.get('proxy_key', None))
global galaxy_url, master_url, nels_url, instance_id
galaxy_url = config['galaxy_url'].rstrip("/")
master_url = config['master_url'].rstrip("/")
instance_id = config['id'].rstrip("/")
nels_url = config['nels_url'].rstrip("/")
if 'tos_server' in config and config['tos_server']:
logger.info("Running with the tos-server")
db.create_tos_table()
global tos_grace_period
tos_grace_period = config.get('grace_period', 14)
if 'master' in config and config['master']:
logger.info("Running with the master API")
db.create_export_tracking_table()
db.create_export_tracking_logs_table()
db.create_import_tracking_table()
db.create_import_tracking_logs_table()
mq.connect(uri=config['mq_uri'])
global proxy_keys, instances, no_proxy
proxy_keys = {}
instances = {}
no_proxy = True
tmp_instances = config['instances']
for iid in tmp_instances:
if 'active' not in tmp_instances[
iid] or not tmp_instances[iid]['active']:
continue
instances[iid] = tmp_instances[iid]
instance = tmp_instances[iid]
instances[instance['name']] = instance
instances[instance['name']]['api'] = api_requests.ApiRequests(
instance['nga_url'].rstrip("/"), instance['nga_key'])
if instance['proxy_key'] in proxy_keys.keys():
logger.warn(
f"Proxy key for {instance['name']} is also used for {proxy_keys[instance['proxy_key']]}"
)
proxy_keys[instance['proxy_key']] = instance['name']
# global mq
return config
def test_encrypt():
requests.set_token(token)
r = requests.encrypt(base_url, 13)
assert True
def test_get_user_history_exports():
requests.set_token(token)
r = requests.get_user_history_exports(base_url, 3)
assert True
def test_get_history_export():
requests.set_token(token)
r = requests.get_history_export(base_url, 13)
assert True
def test_get_info():
requests.set_token(token)
r = requests.get_info(base_url)
assert True
def test_get_users():
requests.set_token(token)
r = requests.get_users(base_url)
assert True
def test_request_get():
requests.set_token(token)
response, return_token = requests.request_get(base_url)
assert return_token == token
def test_request_delete():
requests.set_token(token)
response, return_token = requests.request_delete(base_url, {'user': '******'})
assert return_token == token
def test_get_all_exports():
requests.set_token(token)
r = requests.get_instance_exports(base_url, user)
assert True
def test_get_user_exports():
requests.set_token(token)
r = requests.get_user_exports(base_url, user)
assert True
def test_update_export():
requests.set_token(token)
r = requests.update_export(base_url, 3, data={"state": "new"})
assert True
def test_set_token():
requests.set_token(token)
def test_add_bulk_history_export():
requests.set_token(token)
data = {"nels_id": 3, "selectedFiles": ["goes_here"]}
r = requests.add_bulk_export(base_url, instance, user, data)
assert True
