Handling empty prefix

[hiraksarkar]

https://github.com/scverse/spatialdata-io/blame/bc17abc065c39e07d6b17affaf2c4b95adbaafea/src/spatialdata_io/readers/visium_hd.py#L357

Currently visium_hd function can't handle empty file prefixes. In other words,

binned_outputs       feature_slice.h5     molecule_info.h5              probe_set.csv  web_summary.html
cloupe_008um.cloupe  metrics_summary.csv  possorted_genome_bam.bam.bai  spatial

This would be unreadable by the function. Can this be fixed. Alternatively I raise a pull request.

[ddiez]

Same problem with me. The problem is here where the assignment of the dataset_id is done. Perhaps if dataset_id is None and the guessing returns empty then do not add "_". Something like this?

if dataset_id is None:
        dataset_id = _infer_dataset_id(path)

if dataset_id is "":
  filename_prefix = ""
else
  filename_prefix = f"{dataset_id}_"

@hiraksarkar A temporary solution for me to avoid renaming the files was to create a symlink to feature_slice.h5. Something like ln -s feature_slice.h5 id_ feature_slice.h5 where id is whatever label works for your project.

[ddiez]

@hiraksarkar just realized you offered a PR so probably didn't need my "temporary solution". Sorry for the noise although perhaps it is useful for someone else until this is fixed!

[LucaMarconato]

Thanks for reporting the bug and for the discussion. @hiraksarkar, if you could make a PR it would be wonderful, thank you! Happy to review it 😊

[ddiez]

Thanks @LucaMarconato sounds great. @hiraksarkar will you do the PR? If not, I can do it myself although I have not tested yet my proposed solution.

[ddiez]

Was the PR for this finally submitted? @LucaMarconato @hiraksarkar