fixup: quality description in readviz

browser/src/ShortTandemRepeatPage/ShortTandemRepeatAlleleSizeDistributionPlot.tsx

@@ -12,6 +12,11 @@ import { TooltipAnchor } from '@gnomad/ui'
 import { GNOMAD_POPULATION_NAMES } from '@gnomad/dataset-metadata/gnomadPopulations'
 import { PopulationId } from '@gnomad/dataset-metadata/gnomadPopulations'
 import { colorByLabels } from './ShortTandemRepeatColorBySelect'
+import {
+  genotypeQualityKeys,
+  GenotypeQuality,
+  qualityDescriptionLabels,
+} from './qualityDescription'
 
 // The 100% width/height container is necessary the component
 // to size to fit its container vs staying at its initial size.
@@ -36,17 +41,6 @@ export type ScaleType =
   | 'linear-truncated-1000'
   | 'log'
 
-export const genotypeQualityKeys = [
-  'low',
-  'medium-low',
-  'medium',
-  'medium-high',
-  'high',
-  'not-reviewed',
-] as const
-
-export type GenotypeQuality = (typeof genotypeQualityKeys)[number]
-
 export const qScoreKeys = [
   '0',
   '0.1',
@@ -118,15 +112,6 @@ const colorMap: Record<ColorBy | '', Record<string, string>> = {
   },
 } as const
 
-const qualityDescriptionLabels: Record<GenotypeQuality, string> = {
-  low: 'Low',
-  'medium-low': 'Medium-low',
-  medium: 'Medium',
-  'medium-high': 'Medium-high',
-  high: 'High',
-  'not-reviewed': 'Not reviewed',
-}
-
 const qScoreLabels: Record<QScoreBin, string> = {
   '0': '0 to 0.05',
   '0.1': '0.05 to 0.15',

browser/src/ShortTandemRepeatPage/ShortTandemRepeatPage.tsx

@@ -16,7 +16,6 @@ import ShortTandemRepeatPopulationOptions from './ShortTandemRepeatPopulationOpt
 import ShortTandemRepeatColorBySelect from './ShortTandemRepeatColorBySelect'
 import ShortTandemRepeatAlleleSizeDistributionPlot, {
   ColorBy,
-  GenotypeQuality,
   QScoreBin,
   Sex,
   ScaleType,
@@ -38,6 +37,7 @@ import {
 } from './shortTandemRepeatHelpers'
 import ShortTandemRepeatAdjacentRepeatSection from './ShortTandemRepeatAdjacentRepeatSection'
 import { PopulationId } from '@gnomad/dataset-metadata/gnomadPopulations'
+import { GenotypeQuality } from './qualityDescription'
 
 type ShortTandemRepeatReferenceRegion = {
   chrom: string

browser/src/ShortTandemRepeatPage/ShortTandemRepeatReads.tsx

@@ -10,8 +10,8 @@ import Delayed from '../Delayed'
 import StatusMessage from '../StatusMessage'
 import useRequest from '../useRequest'
 import ControlSection from '../VariantPage/ControlSection'
-
 import { ShortTandemRepeat } from './ShortTandemRepeatPage'
+import { GenotypeQuality, qualityDescriptionLabels } from './qualityDescription'
 
 const ShortTandemRepeatReadImageWrapper = styled.div`
   width: 100%;
@@ -48,6 +48,7 @@ type ShortTandemRepeatReadProps = {
     age?: string
     pcr_protocol: string
     path: string
+    quality_description: GenotypeQuality
   }
 }
 
@@ -83,6 +84,9 @@ const ShortTandemRepeatRead = ({ read }: ShortTandemRepeatReadProps) => {
             'None'
           )}
         </AttributeListItem>
+        <AttributeListItem label="Genotype quality: manual review">
+          {qualityDescriptionLabels[read.quality_description]}
+        </AttributeListItem>
       </AttributeList>
       <ShortTandemRepeatReadImageWrapper>
         <ShortTandemRepeatReadImage
@@ -168,6 +172,7 @@ const fetchReads = ({ datasetId, shortTandemRepeatId, filter, limit, offset }: a
               age
               pcr_protocol
               path
+	      quality_description
             }
           }
         }

browser/src/ShortTandemRepeatPage/qualityDescription.ts

@@ -0,0 +1,19 @@
+export const genotypeQualityKeys = [
+  'low',
+  'medium-low',
+  'medium',
+  'medium-high',
+  'high',
+  'not-reviewed',
+] as const
+
+export type GenotypeQuality = (typeof genotypeQualityKeys)[number]
+
+export const qualityDescriptionLabels: Record<GenotypeQuality, string> = {
+  low: 'Low',
+  'medium-low': 'Medium-low',
+  medium: 'Medium',
+  'medium-high': 'Medium-high',
+  high: 'High',
+  'not-reviewed': 'Not reviewed',
+}

reads/reads-data/create_short_tandem_repeat_reads_db.py

@@ -41,7 +41,8 @@ def _format_read(read, index, locus):
         "pcr_protocol": read["PcrProtocol"],
         "filename": read["ReadvizFilename"] or None,
         "q": read["Q"],
-        "quality_description": read["ManualReviewGenotypeQualitySummary"],
+        # some quality_description values in the raw data have odd capitalization, so we lowercase it
+        "quality_description": read["ManualReviewGenotypeQualitySummary"].lower(),
     }
 
 

reads/src/resolveShortTandemRepeatReads.js

@@ -149,7 +149,8 @@ const resolveShortTandemRepeatReads = async (
       \`sex\`,
       \`age\`,
       \`pcr_protocol\`,
-      \`filename\`
+      \`filename\`,
+      \`quality_description\`
     FROM
       \`reads\`
     WHERE
@@ -207,6 +208,7 @@ const resolveShortTandemRepeatReads = async (
       age: row.age,
       pcr_protocol: row.pcr_protocol,
       path: `${publicPath}/${id}/${row.filename}`,
+      quality_description: row.quality_description,
     }
   })
 }

reads/src/schema.js

@@ -108,6 +108,7 @@ const ShortTandemRepeatReadType = new GraphQLObjectType({
     age: { type: GraphQLString },
     pcr_protocol: { type: new GraphQLNonNull(GraphQLString) },
     path: { type: new GraphQLNonNull(GraphQLString) },
+    quality_description: { type: new GraphQLNonNull(GraphQLString) },
   },
 })
 

reads/start.sh

@@ -8,3 +8,4 @@ DEFAULT_PORT="8000"
 export PORT=${PORT:-$DEFAULT_PORT}
 
 pnpm nodemon ./src/server.js
+#pnpm node -r ts-node/register --inspect ./src/server.js