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MAINT: adds FeatureData[Selection] type, UNIXListFormat, IDSelectionDirectoryFormat #282

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MAINT: adds FeatureData[Selection] type, UNIXListFormat, IDSelectionDirectoryFormat #282

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@lizgehret lizgehret commented Oct 10, 2022 •
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This PR adds the following type/formats from genome-sampler and their accompanying transformers:

New file/directory formats:
UNIXListFormat
IDSelection
IDSelectionDirectoryFormat
IDMetadataFormat

New Semantic Type:
FeatureData[Selection]

@lizgehret lizgehret requested a review from Oddant1 October 10, 2022 22:58
@lizgehret lizgehret changed the title new: NewlineListFileFormat and InclusionExclusionDirectoryFormat new: adds FeatureData[Selection] type, UNIXListFormat, IDSelectionDirectoryFormat Oct 11, 2022
@lizgehret lizgehret mentioned this pull request Oct 11, 2022
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@lizgehret lizgehret removed the request for review from Oddant1 October 12, 2022 18:54
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This PR has been moved to the 'rainy day activities' board because it still needs unit tests added, and isn't needed for any immediate projects/goals for the 2022.11 release.

@lizgehret lizgehret changed the title new: adds FeatureData[Selection] type, UNIXListFormat, IDSelectionDirectoryFormat MAINT: adds FeatureData[Selection] type, UNIXListFormat, IDSelectionDirectoryFormat Dec 11, 2023
@gregcaporaso gregcaporaso self-assigned this Dec 11, 2023
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Reminder to merge caporaso-lab/genome-sampler#98 after this is merged.

gregcaporaso
gregcaporaso reviewed Dec 11, 2023
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q2_types/feature_data/_format.py
return [s.strip() for s in fh]


class IDMetadataFormat(model.TextFileFormat):
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@gregcaporaso gregcaporaso Dec 11, 2023 •
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We didn't have the ImmutableMetadata type/format when we created this - we could probably update genome-sampler to not use this anymore, but I think we'll need to keep the type/format around for working with previously generated artifacts. (Note to self to create a genome-sampler issue for this, nothing really to do here.)

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After some discussion with @ebolyen we decided to convert this to a draft PR. The IDSelection type is likely relevant to revisit at some point, but with only the one use case in genome-sampler, we're not yet sure that this is an implementation that we want to commit to. If/when we circle back to the idea of supporting selections of IDs (sample or feature) with a semantic type, we can use this code or refactor to meet the needs that we identify at that time.

@gregcaporaso gregcaporaso marked this pull request as draft December 12, 2023 19:22
@gregcaporaso gregcaporaso removed their assignment Dec 13, 2023
@lizgehret lizgehret self-assigned this Jul 11, 2024
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closing this as the current implementation isn't needed - will revisit with a revised edition in the future when it's needed.

@lizgehret lizgehret closed this Jul 17, 2024
@lizgehret lizgehret deleted the featuredata-selection branch July 17, 2024 17:22
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@lizgehret @gregcaporaso @Oddant1