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@gregcaporaso gregcaporaso commented Mar 8, 2023

Still to-do:

  • unit tests
  • should the formats be called MetadataFormat and MetadataDirectoryFormat (i.e., drop the Immutable from the beginning of both, since there is nothing about the formats that differs from our regular metadata files)? looking for input on this

fixes #292

A little example of how this can be used:

$ qiime tools import \
  --type ImmutableMetadata \
  --input-format ImmutableMetadataFormat \
  --input-path sample-metadata.tsv \
  --output-path sample-metadata.qza
$ qiime metadata tabulate \
  --m-input-file sample-metadata.qza \
  --o-visualization sample-metadata.qzv
$ qiime tools export \
  --input-path sample-metadata.qza \
  --output-path md/

@gregcaporaso gregcaporaso marked this pull request as ready for review March 8, 2023 23:49
@gregcaporaso gregcaporaso requested a review from lizgehret March 9, 2023 17:00
@lizgehret lizgehret self-assigned this Mar 9, 2023
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@lizgehret lizgehret left a comment

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Generally this all looks good @gregcaporaso! In terms of your question about whether this should be named ImmutableMetadata vs Metadata - I am leaning towards ImmutableMetadata just because that is a bit clearer in the intention behind adding this type and associated formats. I think that would also help folks distinguish between the Metadata class within QIIME 2 🤷‍♀️

@lizgehret lizgehret assigned gregcaporaso and unassigned lizgehret Mar 9, 2023
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That makes sense to me @lizgehret! I think we can merge this one when you're ready.

@lizgehret lizgehret merged commit 05d433c into qiime2:master Mar 27, 2023
@lizgehret lizgehret changed the title adds ImmutableMetadata semantic type and supporting formats NEW: adds ImmutableMetadata semantic type and supporting formats Mar 27, 2023
@gregcaporaso gregcaporaso deleted the issue-292 branch March 27, 2023 17:30
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add ImmutableMetadata semantic type

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