Unidock pipeline fails to read ligand index

[davide-grheco]

Describe the bug

When a large ligand index is provided, the software fails to work.

This is because the whole file is read and pathlib attempts to resolve it to a path. This incurs in an OS error.
I solved it removing one of the two lines here, but a more elegant solution should not be too hard to find.

https://github.com/dptech-corp/Uni-Dock/blob/ab4d8cd46886949da10e62a5f10cd5d8839ef76f/unidock_tools/src/unidock_tools/application/unidock_pipeline.py#L215C1-L218C73

Traceback:

Traceback (most recent call last):                                                                                                                                                                                                                                                                                          
  File "/conda/unidock/bin/unidocktools", line 8, in <module>                                                                                                                                                                                                                    
    sys.exit(main_cli())                                                                                                                                      
             ^^^^^^^^^^                                                                                                                                       
  File "/conda/unidock/lib/python3.12/site-packages/unidock_tools/main.py", line 32, in main_cli                   
    name_module_dict[args["cmd"]].main(args)                                                                                                                  
  File "/conda/unidock/lib/python3.12/site-packages/unidock_tools/application/unidock_pipeline.py", line 216, in main
    if line.strip() and Path(line.strip()).exists()]                                                                                                          
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                                                           
  File "/conda/unidock/lib/python3.12/pathlib.py", line 860, in exists                                             
    self.stat(follow_symlinks=follow_symlinks)                                                                                                                
  File "/conda/unidock/lib/python3.12/pathlib.py", line 840, in stat                                               
    return os.stat(self, follow_symlinks=follow_symlinks)                                                                                                     
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                                                     
OSError: [Errno 36] File name too long: '

Expected behavior

No response

To Reproduce

Install unidocktools, prepare an index file with a large number of files.

seq 30000 > ligands.txt
unidocktools unidock_pipeline -i ligands.txt (other required parameters)

Environment

No response

Additional Context

No response

[dp-yuanyn]

@davide-grheco Thanks for your report, this problem has been solved in #127.