Closed adamjtaylor closed 7 months ago
Implement in DEC, but review and perform testing mid-sprint.
@elv-sb can I get a sanity check on our approach here
metabolite
and protein
as valid values for Analyte Type
(lower case).source
column cites the CADSR CDE Molecular Specimen Type
https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2513915&version=2.0Protein
(note capitalization)but not
Metabolite, or indeed
Lipid`.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
As I see it out options are
Note that to date the only uses are
SELECT DISTINCT Analyte_Type FROM
htan-dcc.combined_assays.BiospecimenLIMIT 1000
AND
SELECT DISTINCT Analyte_Type FROM
htan-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
I have opened a PR that does option i but to disscuss in review today
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