Project-MONAI / Project-MONAI/MONAILabel

Github access rate limit reached, please provide personal auth token by setting env MONAI_ZOO_AUTH_TOKEN or --conf auth_token <personal auth token>

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Python
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Description

(monailabel) huyao@vvm-XPS-8960:~$ monailabel start_server --app /home/huyao/apps/monaibundle --studies /home/huyao/data/Task08_HepaticVessel/imagesTr --conf models swin_unetr_btcv_segmentation
Using PYTHONPATH=/home/huyao/anaconda3/envs:

[2024-05-08 10:13:55,639] [1657753] [MainThread] [INFO] (main:285) - USING:: version = False
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: app = /home/huyao/apps/monaibundle
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: studies = /home/huyao/data/Task08_HepaticVessel/imagesTr
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: verbose = INFO
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: conf = [['models', 'swin_unetr_btcv_segmentation']]
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: host = 0.0.0.0
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: port = 8000
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: uvicorn_app = monailabel.app:app
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: ssl_keyfile = None
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: ssl_certfile = None
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: ssl_keyfile_password = None
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: ssl_ca_certs = None
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: workers = None
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: limit_concurrency = None
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: access_log = False
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: root_path = /
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: log_level = info
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: log_config = None
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: dryrun = False
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:285) - USING:: action = start_server
[2024-05-08 10:13:55,640] [1657753] [MainThread] [INFO] (main:296) -
Allow Origins: ['*']
[2024-05-08 10:13:55,853] [1657753] [MainThread] [INFO] (uvicorn.error:74) - Started server process [1657753]
[2024-05-08 10:13:55,853] [1657753] [MainThread] [INFO] (uvicorn.error:48) - Waiting for application startup.
[2024-05-08 10:13:55,853] [1657753] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: /home/huyao/apps/monaibundle; studies: /home/huyao/data/Task08_HepaticVessel/imagesTr; conf: {'models': 'swin_unetr_btcv_segmentation'}
[2024-05-08 10:13:55,861] [1657753] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>


Github access rate limit reached, please provide personal auth token by setting env MONAI_ZOO_AUTH_TOKEN
or --conf auth_token
[2024-05-08 10:13:55,882] [1657753] [MainThread] [ERROR] (uvicorn.error:123) - Traceback (most recent call last):
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/urllib3/connection.py", line 174, in _new_conn
conn = connection.create_connection(
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/urllib3/util/connection.py", line 95, in create_connection
raise err
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/urllib3/util/connection.py", line 85, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/urllib3/connectionpool.py", line 715, in urlopen
httplib_response = self._make_request(
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/urllib3/connectionpool.py", line 404, in _make_request
self._validate_conn(conn)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/urllib3/connectionpool.py", line 1058, in _validate_conn
conn.connect()
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/urllib3/connection.py", line 363, in connect
self.sock = conn = self._new_conn()
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/urllib3/connection.py", line 186, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7ab4c2324100>: Failed to establish a new connection: [Errno 111] Connection refused

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/requests/adapters.py", line 489, in send
resp = conn.urlopen(
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/urllib3/connectionpool.py", line 799, in urlopen
retries = retries.increment(
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/urllib3/util/retry.py", line 592, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='raw.githubusercontent.com', port=443): Max retries exceeded with url: /Project-MONAI/model-zoo/dev/models/model_info.json (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7ab4c2324100>: Failed to establish a new connection: [Errno 111] Connection refused'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/monailabel/utils/others/generic.py", line 261, in get_zoo_bundle
zoo_info = get_all_bundles_list(auth_token=auth_token)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/monai/bundle/scripts.py", line 624, in get_all_bundles_list
bundles_info = _get_all_bundles_info(repo=repo, tag=tag, auth_token=auth_token)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/monai/bundle/scripts.py", line 568, in _get_all_bundles_info
resp = requests_get(request_url)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/requests/sessions.py", line 587, in request
resp = self.send(prep, **send_kwargs)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/requests/sessions.py", line 701, in send
r = adapter.send(request, **kwargs)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/requests/adapters.py", line 565, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='raw.githubusercontent.com', port=443): Max retries exceeded with url: /Project-MONAI/model-zoo/dev/models/model_info.json (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7ab4c2324100>: Failed to establish a new connection: [Errno 111] Connection refused'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/starlette/routing.py", line 677, in lifespan
async with self.lifespan_context(app) as maybe_state:
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/starlette/routing.py", line 566, in aenter
await self._router.startup()
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/starlette/routing.py", line 654, in startup
await handler()
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/monailabel/app.py", line 108, in startup_event
instance = app_instance()
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/monailabel/interfaces/utils/app.py", line 50, in app_instance
app = c(app_dir=app_dir, studies=studies, conf=conf)
File "/home/huyao/apps/monaibundle/main.py", line 36, in init
self.models = get_bundle_models(app_dir, conf)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/monailabel/utils/others/generic.py", line 354, in get_bundle_models
bundles = get_zoo_bundle(model_dir, conf, models, conf_key)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/site-packages/monailabel/utils/others/generic.py", line 269, in get_zoo_bundle
exit(-1)
File "/home/huyao/anaconda3/envs/monailabel/lib/python3.9/_sitebuiltins.py", line 26, in call
raise SystemExit(code)
SystemExit: -1

[2024-05-08 10:13:55,882] [1657753] [MainThread] [ERROR] (uvicorn.error:59) - Application startup failed. Exiting.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the command shown in the report and inspect get_zoo_bundle in monailabel/utils/others/generic.py, along with the model-zoo lookup in monai/bundle/scripts.py. Check how MONAI_ZOO_AUTH_TOKEN and the auth_token configuration reach get_all_bundles_list. Done means the model-zoo lookup handles the reported access failure and server startup behavior is verified with an authenticated request.

Written by the indexing model from the issue text.

Assessment

Tech stack
github, python
Domain
api, backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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