def get(self, tracking_id):
logger.debug("get tracking details")
self.check_token()
tracking_id = utils.decrypt_value(tracking_id)
tracking = utils.encrypt_ids(db.get_export_tracking(tracking_id))
self.send_response(data=tracking)
def post(self, tracking_id):
logger.debug("requeue import tracking")
self.check_token()
values = self.post_values()
self.require_arguments(values, ['state'])
state = values['state']
try:
tracking_id = utils.decrypt_value(tracking_id)
tracking = db.get_import_tracking(tracking_id)
print(tracking)
tracking['state'] = state
for k in ['id', 'create_time', 'update_time']:
del tracking[k]
tracking[
'log'] = f"requeue import tracker {tracking_id} and changed state to {state}"
tracking_id = db.add_import_tracking(tracking)
tracking_id = utils.encrypt_value(tracking_id)
submit_mq_job(tracking_id, "import")
self.send_response_200()
except Exception as e:
logger.error(f"Request import tracking error {e}")
import stacktrace
self.send_response_404()
def patch(self, tracking_id):
logger.debug("patch tracking details")
self.check_token()
data = self.post_values()
self.valid_arguments(data, ['state', 'export_id', 'tmpfile', 'show'])
# need to decrypt the id otherwise things blow up!
tracking_id = utils.decrypt_value(tracking_id)
db.update_export_tracking(tracking_id, data)
return self.send_response_204()
def get_session_key(self):
if DEV:
session_key = 'ed42604e029aab1a5b1644a93288a9fa'
else:
cookie = self.get_cookie("galaxysession")
if cookie is None or cookie == '':
return None
session_key = utils.decrypt_value(cookie)
return session_key
def get(self, import_id=None):
logger.debug("get history imports")
self.check_token()
if import_id is None:
logger.debug('getting by history_id')
filter = self.arguments()
self.require_arguments(filter, [
'history_id',
])
history_id = utils.decrypt_value(filter['history_id'])
imp = db.get_latest_import_for_history(history_id)
else:
logger.debug('getting by export_id')
import_id = utils.decrypt_value(import_id)
imp = db.get_import(import_id)
if len(imp):
imp = imp[0]
imp = utils.encrypt_ids(imp)
return self.send_response(data=imp)
else:
return self.send_response_404()
def get(self, export_id=None):
logger.debug("get history exports")
self.check_token()
if export_id is None:
logger.debug('getting by history_id')
filter = self.arguments()
self.require_arguments(filter, [
'history_id',
])
history_id = utils.decrypt_value(filter['history_id'])
export = db.get_latest_export_for_history(history_id)
else:
logger.debug('getting by export_id')
export_id = utils.decrypt_value(export_id)
export = db.get_export(export_id)
if len(export):
export = export[0]
export = utils.encrypt_ids(export)
return self.send_response(data=export)
else:
return self.send_response_404()
def get(self, ):
logger.debug("get jobs list")
self.check_token()
filter = self.arguments()
logger.debug(f'arguments {filter}')
self.valid_arguments(filter, ['time_delta', 'user_id'])
time_delta = filter.get('time_delta', "60m") #default 1 hour
time_delta = utils.timedelta_to_sec(time_delta)
user_id = filter.get('user_id', None)
if user_id is not None:
user_id = utils.decrypt_value(user_id)
jobs = db.get_jobs(time_delta=time_delta, user_id=user_id)
return self.send_response(data=utils.list_encrypt_ids(jobs))
def patch(self, tracking_id):
logger.debug("patch tracking details")
user = self.get_user()
if user is None:
self.send_response_404()
data = self.arguments()
self.require_arguments(data, ['show'])
# need to decrypt the id otherwise things blow up!
tracking_id = utils.decrypt_value(tracking_id)
tracking = db.get_export_tracking(tracking_id)
logger.debug(tracking)
if user['email'] != tracking['user_email']:
self.send_response_401()
db.update_export_tracking(tracking_id, data)
return self.send_response_204()
async def get(self, export_id=None):
logger.debug("get history download")
self.check_token()
# chunk size to read
chunk_size = 1024 * 1024 * 1 # 1 MiB
export_id = utils.decrypt_value(export_id)
export = db.get_export(export_id)[0]
try:
dataset = db.get_dataset(export['dataset_id'])
filename = utils.construct_file_path(obj_id=dataset['id'],
file_dir=galaxy_file_path)
logger.debug("start the download")
with open(filename, 'rb') as f:
while True:
chunk = f.read(chunk_size)
if not chunk:
break
try:
self.write(chunk) # write the cunk to response
await self.flush() # flush the current chunk to socket
except iostream.StreamClosedError:
# this means the client has closed the connection
# so break the loop
break
finally:
# deleting the chunk is very important because
# if many clients are downloading files at the
# same time, the chunks in memory will keep
# increasing and will eat up the RAM
del chunk
time.sleep(0)
except Exception as e:
logger.error(e)
self.send_response_400(data={'error': str(e)})
logger.debug("download completed")
def get(self):
logger.debug("proxy export list")
# Will not check token here as relying on the session id instead
# self.check_token()
user = self.get_user()
if user is None:
self.send_response_404()
# cannot proxy to it-self, read directly from the database
if no_proxy:
logger.debug('accessing the data directly')
# print( user )
trackings = db.get_export_trackings(
user_email=user['email'],
instance=instances[instance_id]['name'])
else:
logger.debug('accessing the data using the proxy')
trackings, _ = api_requests.get_user_instance_exports(
master_url, user['email'], instance_id)
results = []
for tracking in trackings:
history_id = utils.decrypt_value(tracking['history_id'])
history = db.get_history(history_id)[0]
results.append({
'name': history['name'],
'id': tracking['id'],
'state': tracking['state'],
'create_time': tracking['create_time'],
'destination': tracking['destination'],
'update_time': tracking['update_time'],
'show': tracking['show'],
})
results = utils.list_encrypt_ids(results)
return self.send_response(data=results)
def get(self, user_id):
logger.debug("get user")
self.check_token()
user_id = utils.decrypt_value(user_id)
user = db.get_user(id=user_id)
if user is None or user == []:
return self.send_response_404()
user = user[0]
api_key = db.get_api_key(user['id'])
if api_key is None or api_key == []:
new_key = utils.create_uuid(32)
db.add_api_key(user['id'], new_key)
user['api_key'] = new_key
else:
user['api_key'] = api_key['key']
print(user)
user = utils.encrypt_ids(user)
return self.send_response(data=user)
def get(self, value):
logger.debug("decrypt value")
self.check_token()
return self.send_response(data={'value': utils.decrypt_value(value)})
def test_decrypt_str():
utils.init('Secret_key')
d = utils.decrypt_value('bc729496af0697be')
assert d == '42'
