Project-MONAI / Project-MONAI/MONAILabel
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- Dominant language
- Python
- Stars
- 891
- Forks
- 269
- Avg merge
- 15h 41m
- Merged PRs (30d)
- 1
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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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