fixup(browser): appease typecheck

broadinstitute · Oct 21, 2024 · 8cc0010 · 8cc0010
1 parent 72dad5d
commit 8cc0010
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Showing 5 changed files with 20 additions and 26 deletions.
diff --git a/browser/src/GenePage/GenePage.tsx b/browser/src/GenePage/GenePage.tsx
@@ -523,6 +523,7 @@ const GenePage = ({ datasetId, gene, geneId }: Props) => {
         {showTranscripts && (
           <TrackWrapper>
             <GeneTranscriptsTrack
+              datasetId={datasetId}
               isTissueExpressionAvailable={!!gene.pext}
               gene={gene}
               includeNonCodingTranscripts={includeNonCodingTranscripts}

diff --git a/browser/src/GenePage/GeneTranscriptsTrack.tsx b/browser/src/GenePage/GeneTranscriptsTrack.tsx
@@ -14,7 +14,7 @@ import Link from '../Link'
 import sortedTranscripts from './sortedTranscripts'
 import TranscriptsTissueExpression from './TranscriptsTissueExpression'
 import { Gene } from './GenePage'
-import { hasStructuralVariants } from '../../../dataset-metadata/metadata'
+import { DatasetId, hasStructuralVariants } from '../../../dataset-metadata/metadata'
 import { GtexTissueDetail, TranscriptWithTissueExpression } from './TissueExpressionTrack'
 
 const TranscriptsInfoWrapper = styled.div`
@@ -36,6 +36,7 @@ const RightPanel = styled.div`
 `
 
 type GeneTranscriptsTrack = {
+  datasetId: DatasetId
   isTissueExpressionAvailable: boolean
   gene: Gene
   includeNonCodingTranscripts: boolean
@@ -45,6 +46,7 @@ type GeneTranscriptsTrack = {
 }
 
 const GeneTranscriptsTrack = ({
+  datasetId,
   isTissueExpressionAvailable,
   gene,
   includeNonCodingTranscripts,
@@ -177,7 +179,7 @@ const GeneTranscriptsTrack = ({
                       tooltip={`Mean expression across all tissues = ${meanExpression.toFixed(
                         2
                       )} TPM\nMost expressed in ${
-                        gtexTissues[tissueMostExpressedIn]!.fullName
+                        gtexTissues[tissueMostExpressedIn as GtexTissueName]!.fullName
                       } (${maxExpression.toFixed(2)} TPM)`}
                     >
                       <rect

diff --git a/browser/src/GenePage/TissueExpressionTrack.tsx b/browser/src/GenePage/TissueExpressionTrack.tsx
@@ -9,7 +9,7 @@ import { Track } from '@gnomad/region-viewer'
 import { RegionsPlot } from '@gnomad/track-regions'
 import { Badge, Button, Modal, SearchInput, Select, TooltipAnchor } from '@gnomad/ui'
 
-import { ALL_GTEX_TISSUES, AllGtexTissues, GtexTissueName } from '../gtex'
+import { ALL_GTEX_TISSUES, GtexTissueName, GtexTissues } from '../gtex'
 import InfoButton from '../help/InfoButton'
 
 import { logButtonClick } from '../analytics'
@@ -68,7 +68,7 @@ const TRACK_HEIGHT = 20
 const heightScale = scaleLinear().domain([0, 1]).range([0, TRACK_HEIGHT]).clamp(true)
 
 type PextRegionsPlotProps = {
-  gtexTissues: Partial<AllGtexTissues>
+  gtexTissues: Partial<GtexTissues>
   color: string
   regions: {
     start: number
@@ -153,7 +153,7 @@ type ExpressedTissue = {
 }
 
 type IndividualTissueTrackProps = {
-  gtexTissues: Partial<AllGtexTissues>
+  gtexTissues: Partial<GtexTissues>
   exons: {
     start: number
     stop: number
@@ -167,7 +167,7 @@ type IndividualTissueTrackProps = {
   maxTranscriptExpressionInTissue: number
   maxMeanTranscriptExpressionInAnyTissue: number
   meanTranscriptExpressionInTissue: number
-  tissue: string
+  tissue: GtexTissueName
   transcriptWithMaxExpressionInTissue: {
     transcript_id: string
     transcript_version: string
@@ -221,8 +221,7 @@ const IndividualTissueTrack = ({
                     )} (${transcriptWithMaxExpressionInTissue!.transcript_id}.${
                       transcriptWithMaxExpressionInTissue!.transcript_version
                     })`
-                  : // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
-                    `Gene is not expressed in ${gtexTissues[tissue].fullName}`
+                  : `Gene is not expressed in ${gtexTissues[tissue]!.fullName}`
               }
             >
               <rect x={12} y={2} width={25} height={27} fill="none" pointerEvents="visible" />
@@ -256,8 +255,7 @@ const IndividualTissueTrack = ({
           <PlotWrapper key={tissue}>
             <PextRegionsPlot
               gtexTissues={gtexTissues}
-              // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
-              color={gtexTissues[tissue].color}
+              color={gtexTissues[tissue]!.color}
               regions={getPlotRegions(
                 expressionRegions,
                 (r: any) =>
@@ -602,7 +600,7 @@ const TissueExpressionTrack = ({
                 return (
                   <IndividualTissueTrack
                     gtexTissues={gtexTissues}
-                    key={`${tissue}-${datasetId}`}
+                    key={`${tissue}`}
                     exons={exons}
                     expressionRegions={expressionRegions}
                     maxTranscriptExpressionInTissue={

diff --git a/browser/src/GenePage/TranscriptsTissueExpression.tsx b/browser/src/GenePage/TranscriptsTissueExpression.tsx
@@ -4,7 +4,7 @@ import styled from 'styled-components'
 
 import { Select } from '@gnomad/ui'
 
-import { AllGtexTissues } from '../gtex'
+import { GtexTissues } from '../gtex'
 
 import sortedTranscripts from './sortedTranscripts'
 import TranscriptsTissueExpressionPlot from './TranscriptsTissueExpressionPlot'
@@ -21,7 +21,7 @@ const isTranscriptCoding = (transcript: any) =>
   transcript.exons.some((exon: any) => exon.feature_type === 'CDS')
 
 type TranscriptsTissueExpressionProps = {
-  gtexTissues: Partial<AllGtexTissues>
+  gtexTissues: Partial<GtexTissues>
   transcripts: TranscriptWithTissueExpression[]
   includeNonCodingTranscripts: boolean
   preferredTranscriptId?: string

diff --git a/browser/src/GenePage/TranscriptsTissueExpressionPlot.tsx b/browser/src/GenePage/TranscriptsTissueExpressionPlot.tsx
@@ -4,8 +4,8 @@ import React from 'react'
 import { AxisBottom, AxisLeft } from '@visx/axis'
 
 import { TooltipAnchor } from '@gnomad/ui'
-import { AllGtexTissueNames, AllGtexTissues } from '../gtex'
 import { TranscriptWithTissueExpression } from './TissueExpressionTrack'
+import { GtexTissueName, GtexTissues } from '../gtex'
 
 const mergeOverlappingRegions = (regions: any) => {
   if (regions.length === 0) {
@@ -121,8 +121,8 @@ const margin = {
 }
 
 type TranscriptsTissueExpressionPlotProps = {
-  gtexTissues: Partial<AllGtexTissues>
-  tissues?: AllGtexTissueNames[]
+  gtexTissues: Partial<GtexTissues>
+  tissues?: GtexTissueName[]
   transcripts: TranscriptWithTissueExpression[]
   starredTranscriptId?: string
 }
@@ -133,7 +133,7 @@ const TranscriptsTissueExpressionPlot = ({
   transcripts,
   starredTranscriptId,
 }: TranscriptsTissueExpressionPlotProps) => {
-  type RenderedTissue = AllGtexTissueNames | 'Mean' | 'Median'
+  type RenderedTissue = GtexTissueName | 'Mean' | 'Median'
   const renderedTissues: RenderedTissue[] = ['Mean', 'Median', ...tissues!]
 
   const transcriptsWithMeanAndMedianExpression = transcripts.map((transcript) => {
@@ -148,7 +148,7 @@ const TranscriptsTissueExpressionPlot = ({
     return {
       ...transcript,
       gtex_tissue_expression: {
-        ...(gtexTissueExpressionObject as Partial<Record<AllGtexTissueNames, number>>),
+        ...(gtexTissueExpressionObject as Partial<Record<GtexTissueName, number>>),
         Mean: mean(expressionValues),
         Median: median(expressionValues),
       },
@@ -279,7 +279,7 @@ const TranscriptsTissueExpressionPlot = ({
         // @ts-expect-error TS(2322) FIXME: Type 'ScaleOrdinal<string, unknown, never>' is not... Remove this comment to see the full error message
         scale={xAxisScale}
         stroke="#333"
-        tickFormat={(tissue: AllGtexTissueNames) => {
+        tickFormat={(tissue: GtexTissueName) => {
           return gtexTissues[tissue] ? gtexTissues[tissue]!.fullName : tissue
         }}
         tickLabelProps={(value) => ({
@@ -354,11 +354,4 @@ const TranscriptsTissueExpressionPlot = ({
   )
 }
 
-// TranscriptsTissueExpressionPlot.defaultProps = {
-//   tissues: Object.entries(GTEX_TISSUE_NAMES)
-//     .sort((t1: any, t2: any) => t1[1].localeCompare(t2[1]))
-//     .map((t: any) => t[0]),
-//   starredTranscriptId: null,
-// }
-
 export default TranscriptsTissueExpressionPlot