Add glob::glob file expansion

lazear / sage

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Add glob::glob file expansion #134

Open acesnik opened 2 months ago

acesnik commented 2 months ago

https://github.com/lazear/sage/issues/133

acesnik commented 2 months ago

I tested this out on a simple bash commandline.

It works for pattern matching mzMLs, e.g. *.mzML.
When nothing matches, it returns Error:mzml_pathsmust be set. For more information try '--help'.
With a malformed glob, e.g. L[*.mzML, it returns Glob pattern error: Pattern syntax error near position 1: invalid range pattern. This might create some undesirable behavior, treating every path as a glob request... What do you think?

acesnik commented 2 months ago

Yep, sounds good and made the change. :)

lazear commented 1 month ago

After some quick testing, this appears to break s3 support if the url is specified via CLI - IMO the best way to do this will be to move this logic into the sage-cloudpath crate for now. This would also enable glob paths to work when specified via the JSON configuration file.

We could then implement a method on the CloudPath enum that handles globs for both S3 (via list-objects) and local files (via glob)