Application startup failed #1143

vincentochs · 2022-11-14T08:16:14Z

vincentochs
Nov 14, 2022

Hello together,

I followed this instruction:

https://www.youtube.com/watch?v=8y1OBQs2wis&list=PLxkMXif0j08xNt1qK3thZ3Ee7u3XoKsCp&index=10

I was wondering how to do that in 3DSlicer

I have done the same steps for installation

git clone https://github.com/Project-MONAI/MONAILabel
pip install -r MONAILabel/requirements.txt
export PATH=$PATH:pwd/MONAILabel/monailabel/scripts

and then when running:

monailabel start_server --app apps/radiology --studies datasets/Task09_Spleen/imagesTr --conf models deepedit

I get the same error:

ModuleNotFoundError: No module named 'monailabel.tasks.infer.deepgrow_pipeline'

[2022-11-08 15:32:07,293] [2498248] [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting

Here are my loggs:

(monailabel-env) vincent.ochs@dbe-cia-sl19-01:~$ monailabel start_server --app apps/radiology --studies datasets/Task09_Spleen/imagesTr --conf models deepedit
Using PYTHONPATH=/home/vincent.ochs/miniconda3/envs:

2022-11-10 14:31:24,422 - USING:: version = False
2022-11-10 14:31:24,423 - USING:: app = /home/vincent.ochs/apps/radiology
2022-11-10 14:31:24,423 - USING:: studies = /home/vincent.ochs/datasets/Task09_Spleen/imagesTr
2022-11-10 14:31:24,423 - USING:: verbose = INFO
2022-11-10 14:31:24,423 - USING:: conf = [['models', 'deepedit']]
2022-11-10 14:31:24,423 - USING:: host = 0.0.0.0
2022-11-10 14:31:24,423 - USING:: port = 8000
2022-11-10 14:31:24,423 - USING:: uvicorn_app = monailabel.app:app
2022-11-10 14:31:24,423 - USING:: ssl_keyfile = None
2022-11-10 14:31:24,423 - USING:: ssl_certfile = None
2022-11-10 14:31:24,423 - USING:: ssl_keyfile_password = None
2022-11-10 14:31:24,423 - USING:: ssl_ca_certs = None
2022-11-10 14:31:24,423 - USING:: workers = None
2022-11-10 14:31:24,423 - USING:: limit_concurrency = None
2022-11-10 14:31:24,423 - USING:: access_log = False
2022-11-10 14:31:24,423 - USING:: log_config = None
2022-11-10 14:31:24,423 - USING:: dryrun = False
2022-11-10 14:31:24,423 - USING:: action = start_server
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_API_STR = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_APP_DIR = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_STUDIES = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}'
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DATASTORE = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH = 
2022-11-10 14:31:24,423 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}'
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_READ_ONLY = False
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '["*.nii.gz", "*.nii", "*.nrrd", "*.jpg", "*.png", "*.tif", "*.svs", "*.xml"]'
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]'
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH = 
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600
2022-11-10 14:31:24,424 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True
2022-11-10 14:31:24,424 - 
Allow Origins: ['*']
[2022-11-10 14:31:24,804] [3714814] [MainThread] [INFO] (uvicorn.error:75) - Started server process [3714814]
[2022-11-10 14:31:24,804] [3714814] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2022-11-10 14:31:24,804] [3714814] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /home/vincent.ochs/apps/radiology; studies: /home/vincent.ochs/datasets/Task09_Spleen/imagesTr; conf: {'models': 'deepedit'}
[2022-11-10 14:31:25,030] [3714814] [MainThread] [ERROR] (uvicorn.error:119) - Traceback (most recent call last):
  File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/routing.py", line 635, in lifespan
    async with self.lifespan_context(app):
  File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/routing.py", line 530, in __aenter__
    await self._router.startup()
  File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/routing.py", line 612, in startup
    await handler()
  File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/app.py", line 106, in startup_event
    instance = app_instance()
  File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/interfaces/utils/app.py", line 44, in app_instance
    c = get_class_of_subclass_from_file("main", main_py, "MONAILabelApp")
  File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/utils/others/class_utils.py", line 55, in get_class_of_subclass_from_file
    return get_class_of_subclass(module_from_file(module_name, file_path), class_c)
  File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/utils/others/class_utils.py", line 27, in module_from_file
    spec.loader.exec_module(module)
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/home/vincent.ochs/apps/radiology/main.py", line 29, in <module>
    from monailabel.tasks.infer.deepgrow_pipeline import InferDeepgrowPipeline
ModuleNotFoundError: No module named 'monailabel.tasks.infer.deepgrow_pipeline'

[2022-11-10 14:31:25,030] [3714814] [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.

When going into MONAILabel and running your suggested command I get the following results

(monailabel-env) vincent.ochs@dbe-cia-sl19-01:~/MONAILabel$ ./monailabel/scripts/monailabel start_server --app apps/radiology --studies datasets/Task09_Spleen/imagesTr --conf models deepedit
Using PYTHONPATH=/home/vincent.ochs/MONAILabel:

APP Directory apps/radiology NOT Found

diazandr3s · 2022-11-14T12:29:51Z

diazandr3s
Nov 14, 2022
Maintainer

Hi @vincentochs,

You should specify the path to the radiology app.

If using the GitHub repo, the radiology app is located at ./sample-apps/radiology. From what I can see you're trying to start the server from apps/radiology. It should be:

./monailabel/scripts/monailabel start_server --app ./sample-apps/radiology --studies datasets/Task09_Spleen/imagesTr --conf models deepedit

Regarding this error:

ModuleNotFoundError: No module named 'monailabel.tasks.infer.deepgrow_pipeline'
[2022-11-10 14:31:25,030] [3714814] [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.

Have you removed the deepgrow_pipeline.py file inside infers? Please pull the latest changes from GitHub and try again.

Hope this helps,

1 reply

vincentochs Nov 15, 2022
Author

Hi @diazandr3s

Thanks for your help!
It worked and its running now.

Thank you! :)

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