[BUG] generateNetwork raises TypeError when links_file is supplied

[jasmin-guven]

Describe the bug
Supplying a links_file to generateNetwork raises a TypeError. The error is raised because on line 407 the wrong variable is given to the default_kwargs dictionary:

    # Create a dictionary of default keyword arguments.
    default_kwargs = {
        "name": f"{work_dir}/outputs/lomap",
        "links_file": lf,
        "output": True,
        "output_no_graph": True,
        "output_no_images": True,
        "threed": True,
        "max3d": 3.0,
        "time": 3,
        "parallel": 10,
    }

To fix, I just changed lf to links_file and it works:

    # Create a dictionary of default keyword arguments.
    default_kwargs = {
        "name": f"{work_dir}/outputs/lomap",
        "links_file": links_file,
        "output": True,
        "output_no_graph": True,
        "output_no_images": True,
        "threed": True,
        "max3d": 3.0,
        "time": 3,
        "parallel": 10,
    }

To Reproduce
Steps to reproduce the behavior:

1. Run the code :

transformations, lomap_scores = bss.Align.generateNetwork(ligands, plot_network=False, names=names, work_dir=workdir, links_file="/home/jguven/projects/irap/inputs/ligands/table_1_links.txt") 

2. This is the exception that was raised / this is what went wrong.

╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ in <module>:6                                                                                    │
│                                                                                                  │
│   3 names = [functions.get_filenames(file) for file in files]                                    │
│   4 table_1_links_file = table_1_workdir + "table_1_links.txt"                                   │
│   5 ligands = [bss.IO.readMolecules(file)[0] for file in files]                                  │
│ ❱ 6 transformations, lomap_scores = bss.Align.generateNetwork(ligands, plot_network=False, n     │
│   7                                                                                              │
│                                                                                                  │
│ /home/jguven/Software/miniconda3/envs/obss-d/lib/python3.9/site-packages/BioSimSpace/Align/_alig │
│ n.py:421 in generateNetwork                                                                      │
│                                                                                                  │
│    418 │   total_kwargs = {**default_kwargs, **kwargs}                                           │
│    419 │                                                                                         │
│    420 │   # Create the DBMolecules object.                                                      │
│ ❱  421 │   db_mol = _lomap.DBMolecules(f"{work_dir}/inputs", **total_kwargs)                     │
│    422 │                                                                                         │
│    423 │   # Create the similarity matrices.                                                     │
│    424 │   strict, loose = db_mol.build_matrices()                                               │
│                                                                                                  │
│ /home/jguven/Software/miniconda3/envs/obss-d/lib/python3.9/site-packages/lomap/dbmol.py:295 in   │
│ __init__                                                                                         │
│                                                                                                  │
│    292 │   │   │   self.inv_dic_mapping[mol.getName()] = mol.getID()                             │
│    293 │   │                                                                                     │
│    294 │   │   if self.options['links_file']:                                                    │
│ ❱  295 │   │   │   self.parse_links_file(self.options['links_file'])                             │
│    296 │   │                                                                                     │
│    297 │   │   if self.options['known_actives_file']:                                            │
│    298 │   │   │   self.parse_known_actives_file(self.options['known_actives_file'])             │
│                                                                                                  │
│ /home/jguven/Software/miniconda3/envs/obss-d/lib/python3.9/site-packages/lomap/dbmol.py:459 in   │
│ parse_links_file                                                                                 │
│                                                                                                  │
│    456 │                                                                                         │
│    457 │   def parse_links_file(self, links_file):                                               │
│    458 │   │   try:                                                                              │
│ ❱  459 │   │   │   with open(links_file, "r") as lf:                                             │
│    460 │   │   │   │   for line in lf:                                                           │
│    461 │   │   │   │   │   mols = line.split()                                                   │
│    462 │   │   │   │   │   if (len(mols) < 2 or len(mols) > 4):                                  │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
TypeError: expected str, bytes or os.PathLike object, not TextIOWrapper

Context

• OS: Linux Ubuntu 22.04 LTS
• Version of Python: 3.9.18
• Version of BioSimSpace: 2023.5.0.dev
• I confirm that I have checked this bug still exists in the latest released version of BioSimSpace: [yes]

[lohedges]

Thanks for this. I'm not sure when this got changed. Will fix tomorrow.

[lohedges]

Ah, this issue here is that the user supplied links file is modified and written to the inputs directory. We need to pass the path to the new file in the default_kwargs dictionary. In your case, you are re-using the input one, which isn't always guaranteed to work given the remapping of file names.

[lohedges]

I've pushed a fix here. If you are able to test, that would be great.