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Update EHR MHC query to point to new aggregated data #219

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Merged
bbimber merged 1 commit into from
Jul 23, 2021
Merged

Update EHR MHC query to point to new aggregated data #219

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60 changes: 7 additions & 53 deletions onprc_reports/resources/queries/sequenceanalysis/MHC_Data_Unified.sql
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Original file line number Diff line number Diff line change
@@ -1,57 +1,11 @@
SELECT
s.subjectId as Id,
s.allele,
--s.primerPairs,
s.shortName,
s.totalRecords as testsPerformed,
s.status as result,
cast('SSP' as varchar) as type

FROM assay.SSP_assay.SSP.SSP_Summary s
WHERE s.subjectId is not null

UNION ALL

SELECT
a.subjectId as Id,
a.marker as allele,
t.subjectId as Id,
t.marker as allele,
null as shortName,
count(*) as totalTests,
cast('POS' as varchar) as result,
cast('SBT' as varchar) as type

FROM assay.GenotypeAssay.Genotype.Data a
WHERE a.run.assayType = 'SBT'
GROUP BY a.subjectid, a.marker

UNION ALL

SELECT
DISTINCT s.subjectId as Id,
p.ref_nt_name as allele,
null as shortName,
1 as totalTests,
cast('NEG' as varchar) as result,
cast('SBT' as varchar) as type

--we want any IDs with SBT data, but lacking data for these special-cased markers
FROM genotypeassays.primer_pairs p
FULL JOIN (SELECT DISTINCT subjectId FROM assay.GenotypeAssay.Genotype.Data s WHERE s.run.assayType = 'SBT') s ON (1=1)
LEFT JOIN assay.GenotypeAssay.Genotype.Data a ON (a.run.assayType = 'SBT' AND p.ref_nt_name = a.marker AND a.subjectid = s.subjectid)
WHERE a.rowid IS NULL AND (p.ref_nt_name LIKE 'Mamu-A%' OR p.ref_nt_name LIKE 'Mamu-B%')
sum(t.totalTests) as totalTests,
t.result,
GROUP_CONCAT(distinct t.assaytype) as type

-- NOTE: eventually this will be the only source of data. However, disable for now so that we can populate this
-- table on the production server without polluting the results people see.
-- UNION ALL
--
-- SELECT
--
-- t.subjectId as Id,
-- t.marker as allele,
-- null as shortName,
-- count(*) as totalTests,
-- t.result,
-- GROUP_CONCAT(distinct t.assaytype) as type
--
-- FROM geneticscore.mhc_data t
-- GROUP BY t.subjectid, t.marker, t.result
FROM geneticscore.mhc_data t
GROUP BY t.subjectid, t.marker, t.result