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Add full support for (fetch|with)_assay_covariates to FacileData API #2

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lianos opened this issue Apr 24, 2019 · 0 comments
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lianos commented Apr 24, 2019

Currently the assay_sample_info_tbl holds "libsize" and "normfactor" columns which make sense for RNA-seq-like count data, however we can't store other types of assay information on the sample level anywhere.

One way to fix this is to make a new assay_sample_covariate EAV table where we can add arbitrary covariates to the samples, like the sample_covariate table.

Once we do this, we'd remove the "libsize" and "normfactor" columns from assay_sample_info_tbl and put them as long covariates in the assay_sample_covariate table.

We would then remove the fetch_sample_statistics faciledata API function.

  • Create the assay_sample_covariate EAV table in the faciledata sql schema
  • Move libsize and normfactor for dataset,sample_id,assay_name combinations into that table
  • drop "libsize" and "normfactor" from assay_sample_info_tbl
  • remove fetch_sample_statistics from FacileData API
@lianos lianos added the enhancement New feature or request label Apr 24, 2019
@lianos lianos changed the title Create an assay_sample_covariate EAV db table Add full support for (fetch|with)_assay_covariates to FacileData API Apr 24, 2019
@lianos lianos self-assigned this Jan 14, 2020
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