From 1d151f83d68a8f2d8bd7c0fd559032b0a3bb3a9d Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 23 Jul 2021 09:46:55 -0700
Subject: [PATCH] Update EHR MHC query to point to new aggregated data

---
 .../sequenceanalysis/MHC_Data_Unified.sql     | 60 +++----------------
 1 file changed, 7 insertions(+), 53 deletions(-)

diff --git a/onprc_reports/resources/queries/sequenceanalysis/MHC_Data_Unified.sql b/onprc_reports/resources/queries/sequenceanalysis/MHC_Data_Unified.sql
index 623d4dc06..61902e571 100644
--- a/onprc_reports/resources/queries/sequenceanalysis/MHC_Data_Unified.sql
+++ b/onprc_reports/resources/queries/sequenceanalysis/MHC_Data_Unified.sql
@@ -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
\ No newline at end of file
+FROM geneticscore.mhc_data t
+GROUP BY t.subjectid, t.marker, t.result