Failed to upload volume to Server. Message:: Status: 500; Response: Internal Server Error #1663
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Hi, Is the volume part of the datastore? can you see it in the dataset folder? From the logs:
It seems the system didn't find the volume associate with the label you wanted to upload. |
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Filename had to be sanitized (you cannot have : in the filename). |
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The file does not exist anymore
…On Mon, Apr 1, 2024 at 3:15 PM Andres Diaz-Pinto ***@***.***> wrote:
Hi,
Is the volume part of the datastore? can you see it in the dataset folder?
From the logs:
FileNotFoundError: [Errno 2] No such file or directory: '3: Abdomen +C
3.00 Br40.nii.gz'
It seems the system didn't find the volume associate with the label you
wanted to upload.
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I know that, but the file does not exist anymore
…On Mon, Apr 1, 2024 at 8:37 PM Andras Lasso ***@***.***> wrote:
Filename had to be sanitized (you cannot have : in the filename).
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Describe the bug
Failed to upload volume to Server.
Message:: Status: 500; Response: Internal Server Error
Server logs
..+.+...+........+.........+...+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++..+...+........+.......+.....+...+....+........+......+.+........+.+..+...+.+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++........+.........+......+......+.+..+.......+...+..+.+.....+...+......+....+..+.......+..+....+.....+....+............+...+.....+.+.....+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
........+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++...+...+.+..+.........+.+..+...+...+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++.+.....+...+.......+......+.....+....+...+...+..+...+....+...+..+.+.....+.......+..+...+.+..+............+.+.....+.......+..+.+...........+....+......+........+......+.+..................+..+......+...................+........+.+..+..........+...+.........+..+.........+.......+..+.+..+.......+...+........+.+...+..+.........+..........+...........+....+.....+....+......+.....+....+......+...........+......+.......+.....+...+...+.......+.....+..........+.........+...+..+...+...+......................+..+...+.+......+......+...+..............+...+...+....+..+.........+....+..+.+...+.........+..+...+...+.............+......+........................+.....+.........+...+......................+..+.+...+..............+.+..+....+......+..+...+.............+.....+.........+.......+...+...+.....+.............+............+.....+....+...+......+............+.....+...+......+...+.+......+......+..+......+.+.....+...+.......+...+..+...............+...............+....+..+...+....+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
You are about to be asked to enter information that will be incorporated
into your certificate request.
What you are about to enter is what is called a Distinguished Name or a DN.
There are quite a few fields but you can leave some blank
For some fields there will be a default value,
If you enter '.', the field will be left blank.
Country Name (2 letter code) [AU]:
State or Province Name (full name) [Some-State]:
Locality Name (eg, city) []:
Organization Name (eg, company) [Internet Widgits Pty Ltd]:
Organizational Unit Name (eg, section) []:
Common Name (e.g. server FQDN or YOUR name) []:
Email Address []:
Using PYTHONPATH=C:\Users\bz197\anaconda3\envs;
""
[2024-03-28 09:26:42,713] [13068] [MainThread] [INFO] (main:285) - USING:: version = False
[2024-03-28 09:26:42,713] [13068] [MainThread] [INFO] (main:285) - USING:: app = C:\Users\bz197\MONAILabel\apps\radiology
[2024-03-28 09:26:42,713] [13068] [MainThread] [INFO] (main:285) - USING:: studies = C:\Users\bz197\MONAILabel\datasets\Task09_Spleen\imagesTr
[2024-03-28 09:26:42,714] [13068] [MainThread] [INFO] (main:285) - USING:: verbose = INFO
[2024-03-28 09:26:42,714] [13068] [MainThread] [INFO] (main:285) - USING:: conf = [['models', 'deepedit']]
[2024-03-28 09:26:42,714] [13068] [MainThread] [INFO] (main:285) - USING:: host = 0.0.0.0
[2024-03-28 09:26:42,714] [13068] [MainThread] [INFO] (main:285) - USING:: port = 8000
[2024-03-28 09:26:42,715] [13068] [MainThread] [INFO] (main:285) - USING:: uvicorn_app = monailabel.app:app
[2024-03-28 09:26:42,715] [13068] [MainThread] [INFO] (main:285) - USING:: ssl_keyfile = uvicorn-selfsigned.key
[2024-03-28 09:26:42,715] [13068] [MainThread] [INFO] (main:285) - USING:: ssl_certfile = uvicorn-selfsigned.crt
[2024-03-28 09:26:42,716] [13068] [MainThread] [INFO] (main:285) - USING:: ssl_keyfile_password = None
[2024-03-28 09:26:42,716] [13068] [MainThread] [INFO] (main:285) - USING:: ssl_ca_certs = None
[2024-03-28 09:26:42,716] [13068] [MainThread] [INFO] (main:285) - USING:: workers = None
[2024-03-28 09:26:42,716] [13068] [MainThread] [INFO] (main:285) - USING:: limit_concurrency = None
[2024-03-28 09:26:42,717] [13068] [MainThread] [INFO] (main:285) - USING:: access_log = False
[2024-03-28 09:26:42,717] [13068] [MainThread] [INFO] (main:285) - USING:: root_path = /
[2024-03-28 09:26:42,717] [13068] [MainThread] [INFO] (main:285) - USING:: log_level = info
[2024-03-28 09:26:42,717] [13068] [MainThread] [INFO] (main:285) - USING:: log_config = None
[2024-03-28 09:26:42,718] [13068] [MainThread] [INFO] (main:285) - USING:: dryrun = False
[2024-03-28 09:26:42,718] [13068] [MainThread] [INFO] (main:285) - USING:: action = start_server
[2024-03-28 09:26:42,718] [13068] [MainThread] [INFO] (main:296) -
Allow Origins: ['']
[2024-03-28 09:26:43,539] [13068] [MainThread] [INFO] (uvicorn.error:74) - Started server process [13068]
[2024-03-28 09:26:43,540] [13068] [MainThread] [INFO] (uvicorn.error:48) - Waiting for application startup.
[2024-03-28 09:26:43,540] [13068] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: C:\Users\bz197\MONAILabel\apps\radiology; studies: C:\Users\bz197\MONAILabel\datasets\Task09_Spleen\imagesTr; conf: {'models': 'deepedit'}
[2024-03-28 09:26:43,598] [13068] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2024-03-28 09:26:43,612] [13068] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2024-03-28 09:26:43,613] [13068] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2024-03-28 09:26:43,614] [13068] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2024-03-28 09:26:43,615] [13068] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2024-03-28 09:26:43,616] [13068] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2024-03-28 09:26:43,618] [13068] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2024-03-28 09:26:43,619] [13068] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2024-03-28 09:26:43,620] [13068] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2024-03-28 09:26:43,620] [13068] [MainThread] [INFO] (main:93) - +++ Adding Model: deepedit => lib.configs.deepedit.DeepEdit
[2024-03-28 09:26:44,326] [13068] [MainThread] [INFO] (lib.configs.deepedit:141) - EPISTEMIC Enabled: False; Samples: 5
[2024-03-28 09:26:44,326] [13068] [MainThread] [INFO] (main:96) - +++ Using Models: ['deepedit']
[2024-03-28 09:26:44,327] [13068] [MainThread] [INFO] (monailabel.interfaces.app:135) - Init Datastore for: C:\Users\bz197\MONAILabel\datasets\Task09_Spleen\imagesTr
[2024-03-28 09:26:44,327] [13068] [MainThread] [INFO] (monailabel.datastore.local:130) - Auto Reload: True; Extensions: ['.nii.gz', '.nii', '.nrrd', '.jpg', '.png', '.tif', '.svs', '*.xml']
[2024-03-28 09:26:44,349] [13068] [MainThread] [INFO] (monailabel.datastore.local:577) - Invalidate count: 0
[2024-03-28 09:26:44,349] [13068] [MainThread] [INFO] (monailabel.datastore.local:151) - Start observing external modifications on datastore (AUTO RELOAD)
[2024-03-28 09:26:44,353] [13068] [MainThread] [INFO] (main:126) - +++ Adding Inferer:: deepedit => <lib.infers.deepedit.DeepEdit object at 0x000001A0480DCC40>
[2024-03-28 09:26:44,354] [13068] [MainThread] [INFO] (main:126) - +++ Adding Inferer:: deepedit_seg => <lib.infers.deepedit.DeepEdit object at 0x000001A04825E610>
[2024-03-28 09:26:44,354] [13068] [MainThread] [INFO] (main:191) - {'deepedit': <lib.infers.deepedit.DeepEdit object at 0x000001A0480DCC40>, 'deepedit_seg': <lib.infers.deepedit.DeepEdit object at 0x000001A04825E610>, 'Histogram+GraphCut': <monailabel.scribbles.infer.HistogramBasedGraphCut object at 0x000001A0481ADE50>, 'GMM+GraphCut': <monailabel.scribbles.infer.GMMBasedGraphCut object at 0x000001A04831C3A0>}
[2024-03-28 09:26:44,355] [13068] [MainThread] [INFO] (main:206) - +++ Adding Trainer:: deepedit => <lib.trainers.deepedit.DeepEdit object at 0x000001A04831C4C0>
[2024-03-28 09:26:44,355] [13068] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: C:\Users\bz197.cache\monailabel\sessions
[2024-03-28 09:26:44,355] [13068] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2024-03-28 09:26:44,356] [13068] [MainThread] [INFO] (monailabel.interfaces.app:469) - App Init - completed
[2024-03-28 09:26:44,356] [timeloop] [INFO] Starting Timeloop..
[2024-03-28 09:26:44,356] [13068] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2024-03-28 09:26:44,357] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x000001A04814B4C0>
[2024-03-28 09:26:44,357] [13068] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x000001A04814B4C0>
[2024-03-28 09:26:44,358] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2024-03-28 09:26:44,358] [13068] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2024-03-28 09:26:44,358] [13068] [MainThread] [INFO] (uvicorn.error:62) - Application startup complete.
[2024-03-28 09:26:44,359] [13068] [MainThread] [INFO] (uvicorn.error:217) - Uvicorn running on https://0.0.0.0:8000 (Press CTRL+C to quit)
[2024-03-28 09:27:24,851] [13068] [MainThread] [INFO] (monailabel.endpoints.datastore:68) - Image: 3: Abdomen +C 3.00 Br40; File: <starlette.datastructures.UploadFile object at 0x000001A048340310>; params: {"client_id": "user-xyz"}
[2024-03-28 09:27:24,911] [13068] [MainThread] [INFO] (monailabel.datastore.local:439) - Adding Image: 3: Abdomen +C 3.00 Br40 => C:\Users\bz197\AppData\Local\Temp\tmpd9ju61ai.nii.gz
[2024-03-28 09:27:24,924] [13068] [MainThread] [ERROR] (uvicorn.error:434) - Exception in ASGI application
Traceback (most recent call last):
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\uvicorn\protocols\http\h11_impl.py", line 429, in run_asgi
result = await app( # type: ignore[func-returns-value]
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\uvicorn\middleware\proxy_headers.py", line 78, in call
return await self.app(scope, receive, send)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\fastapi\applications.py", line 276, in call
await super().call(scope, receive, send)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\starlette\applications.py", line 122, in call
await self.middleware_stack(scope, receive, send)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\starlette\middleware\errors.py", line 184, in call
raise exc
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\starlette\middleware\errors.py", line 162, in call
await self.app(scope, receive, _send)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\starlette\middleware\cors.py", line 84, in call
await self.app(scope, receive, send)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\starlette\middleware\exceptions.py", line 79, in call
raise exc
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\starlette\middleware\exceptions.py", line 68, in call
await self.app(scope, receive, sender)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\fastapi\middleware\asyncexitstack.py", line 21, in call
raise e
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\fastapi\middleware\asyncexitstack.py", line 18, in call
await self.app(scope, receive, send)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\starlette\routing.py", line 718, in call
await route.handle(scope, receive, send)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\starlette\routing.py", line 276, in handle
await self.app(scope, receive, send)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\starlette\routing.py", line 66, in app
response = await func(request)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\fastapi\routing.py", line 237, in app
raw_response = await run_endpoint_function(
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\fastapi\routing.py", line 163, in run_endpoint_function
return await dependant.call(**values)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\monailabel\endpoints\datastore.py", line 216, in api_add_image
return add_image(background_tasks, image, params, file, user.username)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\monailabel\endpoints\datastore.py", line 82, in add_image
image_id = instance.datastore().add_image(image_id, image_file, save_params)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\site-packages\monailabel\datastore\local.py", line 445, in add_image
shutil.copy(image_filename, dest)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\shutil.py", line 427, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "C:\Users\bz197\anaconda3\envs\monailabel_env\lib\shutil.py", line 266, in copyfile
with open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '3: Abdomen +C 3.00 Br40.nii.gz'
Expected behavior
It doesn't suppose to show error when uploading the label
Screenshots
Environment
Ensuring you use the relevant python executable, please paste the output of:
Additional context
Add any other context about the problem here.
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