ncihtan / data-models

Schema.org Data Models for HTAN
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Return `metabolite` and `protein` to `Analyte Type` valid values #312

Closed adamjtaylor closed 7 months ago

adamjtaylor commented 10 months ago

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 commented 8 months ago

Implement in DEC, but review and perform testing mid-sprint.

adamjtaylor commented 7 months ago

@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 FROMhtan-dcc.combined_assays.BiospecimenLIMIT 1000

AND

SELECT DISTINCT Analyte_Type FROMhtan-dcc.combined_assays.MassSpectrometryLevel1LIMIT 1000

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

adamjtaylor commented 7 months ago

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