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[python] Early error for dataframe objects presented as obsm etc. on ingest #2118

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johnkerl opened this issue Feb 8, 2024 · 1 comment · Fixed by #2131
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[python] Early error for dataframe objects presented as obsm etc. on ingest #2118

johnkerl opened this issue Feb 8, 2024 · 1 comment · Fixed by #2131
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@johnkerl
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johnkerl commented Feb 8, 2024

The obsm, obsp, varm, and varp must be 2D arrays, not dataframes. In those cases when an input AnnData object does contain a dataframe in any of these slots, the ingest fails (as it should) but it fails partway through the ingest, and it fails with a stack trace.

  • We should have a type-check early on in from_anndata (next to the other existing error checks) -- before the ingest starts -- not within the ingest-matrix function at which point the experiment-level ingest would crash partway through
  • The error message should be user-friendly
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johnkerl commented Feb 8, 2024

@jp-dark or delegate will handle this for the upcoming sprint.

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