typing related error in metadata embedding.

[bpinsard]

Summary

Updating heudiconv from master branch, I have the following error showing up which seems related to #656 changes.

230505-14:27:39,460 nipype.workflow WARNING:                                                                                                              
         [Node] Error on "embedder" (/scratch/tmp/embedmetab5y9u753/embedder)                                                                             
Embedding failed: Exception raised while executing Node embedder.                                                                                         
                                                                                                                                                          
Traceback (most recent call last):                                                                                                                        
  File "/data/neuromod/virtualenvs/neuromod_data/lib/python3.7/site-packages/nipype/utils/functions.py", line 34, in create_function_from_source          
    exec(function_source, ns)                                                                                                                             
  File "<string>", line 4, in <module>                                                                                                                    
TypeError: unsupported operand type(s) for |: 'type' and 'type'                                                                                           
                                                                                                                                                          
The above exception was the direct cause of the following exception:                                                                                      
                                                                                                                                                          
Traceback (most recent call last):                                                                                                                        
  File "/data/neuromod/virtualenvs/neuromod_data/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 398, in run                            
    runtime = self._run_interface(runtime)                                                                                                                
  File "/data/neuromod/virtualenvs/neuromod_data/lib/python3.7/site-packages/nipype/interfaces/utility/wrappers.py", line 133, in _run_interface          
    self.inputs.function_str, self.imports                                                                                                                
  File "/data/neuromod/virtualenvs/neuromod_data/lib/python3.7/site-packages/nipype/utils/functions.py", line 44, in create_function_from_source          
    raise RuntimeError(msg) from e                                                                                                                        
RuntimeError: Error executing function                                                                                                                    
def embed_dicom_and_nifti_metadata(                                                                                                                       
    dcmfiles: List[str],                                                                                                                                  
    niftifile: str,                                                                                                                                       
    infofile: str | Path,                                                                                                                                 
    bids_info: Optional[Dict[str, Any]],                                                                                                                  
) -> None:                                                                                                                                                
    """Embed metadata from nifti (affine etc) and dicoms into infofile (json)                                                                             
                                                                                                                                                          
    `niftifile` should exist. Its affine's orientation information is used while                                                                          
    establishing new `NiftiImage` out of dicom stack and together with `bids_info`                                                                        
    (if provided) is dumped into json `infofile`                                                                                                          
                                                                                                                                                          
    Parameters                                                                                                                                            
    ----------                                                                                                                                            
    dcmfiles                                                                                                                                              
    niftifile                                                                                                                                             
    infofile                                                                                                                                              
    bids_info: dict                                                                                                                                       
      Additional metadata to be embedded. `infofile` is overwritten if exists,                                                                            
      so here you could pass some metadata which would overload (at the first                                                                             
      level of the dict structure, no recursive fancy updates) what is obtained                                                                           
      from nifti and dicoms                                                                                                                               
                                                                                                                                                          
    """                                                                                                                                                   
    # These imports need to be within the body of the function so that they                                                                               
    # will be available when executed by nipype:                                                                                                          
    import json                                                                                                                                           
    import os.path                                                                
...
...

Platform details:

Choose one:

• Local environment: ubuntu-22.04 python3.7.16

• Container

• Heudiconv version:

0.5.3.post808+g6cc9f29

[jwodder]

@bpinsard I believe #673 should fix this. Can you test it and see?

[bpinsard]

Perfect, that' fixed on my side. Thanks!

[github-actions]

🚀 Issue was released in v0.13.0 🚀

[github-actions]

🚀 Issue was released in v0.13.0 🚀