[BUG] OS error when building deploy app

[filipmu]

Describe the bug

Get an OSError: source code not available when creating the deploy application.

OSError                                   Traceback (most recent call last)
Cell In[6], line 1
----> 1 app = App()

File /opt/conda/lib/python3.10/site-packages/monai/deploy/core/application.py:95, in Application.__init__(self, runtime_env, do_run, path)
     93     self.path = Path(path)
     94 else:
---> 95     self.path = get_class_file_path(self.__class__)
     97 # Set the runtime environment
     98 if str(self.path) == "ipython":

File /opt/conda/lib/python3.10/site-packages/monai/deploy/utils/importutil.py:116, in get_class_file_path(cls)
    100 """Get the file path of a class.
    101 
    102 If the file path is not available, it tries to see each frame information
   (...)
    112     A file path of the class.
    113 """
    115 try:
--> 116     return Path(inspect.getfile(cls))
    117 except TypeError:
    118     # If in IPython shell, use inspect.stack() to get the caller's file path
    119     stack = inspect.stack()

File /opt/conda/lib/python3.10/site-packages/torch/package/package_importer.py:691, in _patched_getfile(object)
    689     if object.__module__ in _package_imported_modules:
    690         return _package_imported_modules[object.__module__].__file__
--> 691 return _orig_getfile(object)

File /opt/conda/lib/python3.10/inspect.py:785, in getfile(object)
    783             return module.__file__
    784         if object.__module__ == '__main__':
--> 785             raise OSError('source code not available')
    786     raise TypeError('{!r} is a built-in class'.format(object))
    787 if ismethod(object):

OSError: source code not available

Steps/Code to reproduce bug

Run this notebook in jupyterlab.

Expected behavior

No stack trace, successful instantiation.

Environment details (please complete the following information)

• OS/Platform: Linux jupyter-u63dd2b35b6fb5b--w646fbf22bc325c 5.15.0-1035-azure #42-Ubuntu SMP Tue Feb 28 19:41:23 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
• Python Version:Python 3.10.10
• Method of MONAI Deploy App SDK install: pip
• SDK Version:monai-deploy-app-sdk-0.5.0

Additional context

[MMelQin]

Thank you @filipmu for reporting the issue, and sorry for the late reply.

I tried to run the Jupyter Notebook that you provided, but I could not even go as far as you had, failing at instantiating the object, app = App(). It is observed that the example code has only ONE operator, and in the compose function the call to add_flow failed for me. In this case, please change the statement to add operator only, self.add_operator(load_pil_op).

Also, in the example the application object was created, but its run function was not called. So, I made the change to add operator, adding a line to call run function with local data, app.run(input="input/AbdomenCT_007000.jpeg", output="output").

A line was also added to print the image array in the operator, print(f"arrry {image_arr!r}").

The pillow package needs to be in the requirements too, if not already installed in the virtual env.

These changes allowed me to execute the whole book without errors, and see the console output:

Going to initiate execution of operator LoadPILOperator
Executing operator LoadPILOperator (Process ID: 65396, Operator ID: bdac6aa2-0812-4fe8-880b-6d93ac872f2d)
arrry array([[101, 101, 101, ..., 101, 101, 101],
       [101, 101, 101, ..., 101, 101, 101],
       [101, 101, 101, ..., 101, 101, 101],
       ...,
       [101, 101, 101, ..., 101, 101, 101],
       [101, 101, 101, ..., 101, 101, 101],
       [101, 101, 101, ..., 101, 101, 101]], dtype=uint8)
Done performing execution of operator LoadPILOperator

[filipmu]

Hi @MMelQin - I made your suggested change (self.add_operator(load_pil_op)) but still could not create the app object. Received the same error relating to ipython. My colleague suggested a fix to handle a change in python 3.10 - a change to the inspect.getfile function. Fix would be to change that line with expect (TypeError, OSError). I made the fix locally and this allowed me to create the app object with no errors.

Calling the app object resulted in an error that matched issue 410 so I downgraded typeguard~=2.12.1 and then calling it ran with no errors.

I'll submit a PR for the change.

[MMelQin]

Thanks @filipmu for the update. In my venv I have Python 3.8 and ipython 8.11.0, hence did not encounter the path issue.

It is great to get a PR from you!

[MMelQin]

Addressed in release 0.5.1