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Return metabolite and protein to Analyte Type valid values #312

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adamjtaylor opened this issue Oct 17, 2023 · 3 comments · Fixed by #336
Closed

Return metabolite and protein to Analyte Type valid values #312

adamjtaylor opened this issue Oct 17, 2023 · 3 comments · Fixed by #336
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@adamjtaylor
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These were removed in #311 to fix #309. They should be returned once Schematic v23.10.1 is running on mtDCA prod.

Before deployment to confirm in cli and in staging that the Biospecimen template can be generated

@aclayton555 aclayton555 added the effort-mid This one needs your brain label Dec 4, 2023
@aclayton555
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Implement in DEC, but review and perform testing mid-sprint.

@adamjtaylor adamjtaylor changed the title Return metabolite and lipid to Assay Type valid values Return metabolite and lipid to Analyte Type valid values Jan 4, 2024
@adamjtaylor adamjtaylor changed the title Return metabolite and lipid to Analyte Type valid values Return metabolite and protein to Analyte Type valid values Jan 4, 2024
@adamjtaylor
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@elv-sb can I get a sanity check on our approach here

Our valid values are
cfDNA Analyte, DNA Analyte, RNA Analyte, Total RNA Analyte, Tissue Block Analyte, Tissue Section Analyte, PBMCs or Plasma or Serum Analyte, cDNA Libraries Analyte, PBMCs, Plasma, Serum Analyte

The PVs are
Image

As I see it out options are

  1. Use old valid values (lower case)
  2. Use title case values for Metabolite and Lipid to match the PV
  3. Remap all valid values to the CDE

Note that to date the only uses are

SELECT DISTINCT Analyte_Type FROM htan-dcc.combined_assays.Biospecimen LIMIT 1000

  • RNA Analyte
  • Tissue Block Analyte
  • Tissue Section Analyte
  • DNA Analyte

AND

SELECT DISTINCT Analyte_Type FROM htan-dcc.combined_assays.MassSpectrometryLevel1 LIMIT 1000

  • Tissue Block Analyte

Note that there is a seperate attribute used by Molecular Test: Test Analyte Type which has different valid values all together

@adamjtaylor
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I have opened a PR that does option i but to disscuss in review today

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