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Computational Crystallography Toolbox
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mod_input searches for tar in the whole pathname of files instead the filetype #733

Open ravescovi opened 2 years ago

ravescovi commented 2 years ago

I have files named: random_start/test_raf/Cocoa_proc/int-2-Cocoa_3_37023.pickle because of the 'tar' in start mod_input keeps trying to open the pickles as tar.

https://github.com/cctbx/cctbx_project/blob/c6e33af78a268d0d867080fcb70ae0b682d1e133/prime/postrefine/mod_input.py#L598

A solution would be to look for 

if p.endswith('tar') : is_tar = True
dwpaley commented 2 years ago

The "normal" way would be using os.path.splitext, but should this also be true for .tar.gz etc?

ravescovi commented 2 years ago

I think the splittext would fail on tar.gz indeed. Some possible solutions would be to use os.path.basename() (that would remove the path for the file, similar to splittext) or tarfile.is_tarfile() which would be more generic.

bkpoon commented 2 years ago

I like the tarfile.is_tarfile() approach. @ravescovi can you make a pull request?

ravescovi commented 2 years ago

Hey, Sorry for the late response. Yes, I will do a PR later this month if that is ok with you.

On Tue, Feb 22, 2022 at 1:48 PM Billy K. Poon @.***> wrote:

I like the tarfile.is_tarfile() approach. @ravescovi https://github.com/ravescovi can you make a pull request?

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