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[ENH]: Unix path expansion directives support for PatternDataGrabber #345

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merged 4 commits into from
May 22, 2024

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@synchon synchon commented May 21, 2024

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This PR adds support for specifying Unix path expansion directives like [], [!] for PatternDataGrabber patterns. This is an improvement which is needed for supporting FreeSurfer data type. For example, fsaverage directory is at the same level as subjects like sub-0001 for AOMIC datasets and [!f] allows to not glob the fsaverage directory without overriding get_elements() method. As the .mgz and other outputs of FreeSurfer are not unique by subject (and/or task / session) prefix, globbing doesn't work as usual (at least for the AOMIC datasets). This also enables one to have the pattern: .../T1.mg[z] to make it work.

@synchon synchon self-assigned this May 21, 2024
@synchon synchon added enhancement New feature or request dataset Issues or pull requests related to datagrabbers or datasets labels May 21, 2024
@synchon synchon added this to the 0.0.5 (alpha 4) milestone May 21, 2024
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synchon commented May 21, 2024

Needs to go before #344

@synchon synchon requested a review from fraimondo May 21, 2024 13:39
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2024-05-22 17:37 UTC

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Can you also improve the docs to reflect this change?

@synchon synchon force-pushed the feat/unix-path-expansion-pattern-dg branch from 3bbf98b to 80a5a4a Compare May 22, 2024 13:25
@synchon synchon requested a review from fraimondo May 22, 2024 14:11
@synchon synchon merged commit 52ab2fd into main May 22, 2024
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@synchon synchon deleted the feat/unix-path-expansion-pattern-dg branch May 22, 2024 17:18
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