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broadinstitute · Oct 31, 2023 · 415490e · 415490e
1 parent 190e815
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Showing 50 changed files with 754 additions and 707 deletions.
diff --git a/browser/src/ClinvarVariantsTrack/ClinvarVariantTrack.tsx b/browser/src/ClinvarVariantsTrack/ClinvarVariantTrack.tsx
@@ -134,7 +134,7 @@ const ClinvarVariantTrack = ({ referenceGenome, transcripts, variants }: Props)
       // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
       includedConsequenceCategories[getCategoryFromConsequence(v.major_consequence)] &&
       (!showOnlyGnomad || v.in_gnomad) &&
-      (v.gold_stars >= starFilter)
+      v.gold_stars >= starFilter
   )
 
   return (
@@ -229,7 +229,7 @@ const ClinvarVariantTrack = ({ referenceGenome, transcripts, variants }: Props)
             <label htmlFor="star-filtering">
               Filter by{' '}
               {/* @ts-expect-error TS(2786) FIXME: 'ExternalLink' cannot be used as a JSX component. */}
-              <ExternalLink href='https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/'>
+              <ExternalLink href="https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/">
                 review status
               </ExternalLink>
               : &nbsp;

diff --git a/browser/src/ConstraintTable/ConstraintTable.tsx b/browser/src/ConstraintTable/ConstraintTable.tsx
@@ -43,8 +43,8 @@ const transcriptDetails = (
       transcriptId = geneOrTranscript.canonical_transcript_id
       const canonicalTranscript = transcriptId
         ? geneOrTranscript.transcripts.find(
-          (transcript) => transcript.transcript_id === transcriptId
-        )
+            (transcript) => transcript.transcript_id === transcriptId
+          )
         : null
       transcriptVersion = canonicalTranscript ? canonicalTranscript.transcript_version : null
       transcriptDescription = 'Ensembl canonical'

diff --git a/browser/src/ConstraintTable/GnomadConstraintTable.tsx b/browser/src/ConstraintTable/GnomadConstraintTable.tsx
@@ -79,7 +79,11 @@ Graph.defaultProps = {
   color: undefined,
 }
 
-const renderOEMetrics = (constraint: GnomadConstraint, category: ConstraintFieldWithOEMetrics, highlightColor: string | null) => {
+const renderOEMetrics = (
+  constraint: GnomadConstraint,
+  category: ConstraintFieldWithOEMetrics,
+  highlightColor: string | null
+) => {
   const value = constraint[`oe_${category}` as OEMetricField]
   const lower = constraint[`oe_${category}_lower` as OEMetricField]
   const upper = constraint[`oe_${category}_upper` as OEMetricField]
@@ -150,7 +154,10 @@ export type GnomadConstraint = {
 }
 
 type ConstraintFieldWithOEMetrics = 'lof' | 'mis' | 'syn'
-type OEMetricField = `oe_${ConstraintFieldWithOEMetrics}` | `oe_${ConstraintFieldWithOEMetrics}_lower` | `oe_${ConstraintFieldWithOEMetrics}_upper`
+type OEMetricField =
+  | `oe_${ConstraintFieldWithOEMetrics}`
+  | `oe_${ConstraintFieldWithOEMetrics}_lower`
+  | `oe_${ConstraintFieldWithOEMetrics}_upper`
 
 type GnomadConstraintTableProps = {
   constraint: GnomadConstraint
@@ -249,15 +256,22 @@ const GnomadConstraintTable = ({ constraint }: GnomadConstraintTableProps) => {
           {constraintFlags.map((flag) => {
             let flagDescription
             if (flag in CONSTRAINT_FLAG_DESCRIPTIONS) {
-              {/* @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message */ }
+              {
+                /* @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message */
+              }
               flagDescription = CONSTRAINT_FLAG_DESCRIPTIONS[flag]
             } else {
-              flagDescription = <span>Gene constraint flag: <code>{flag}</code></span>
+              flagDescription = (
+                <span>
+                  Gene constraint flag: <code>{flag}</code>
+                </span>
+              )
             }
-            return <p key={flag} style={{ maxWidth: '460px' }}>
-              <Badge level="info">Note</Badge> {flagDescription}
-            </p>
-
+            return (
+              <p key={flag} style={{ maxWidth: '460px' }}>
+                <Badge level="info">Note</Badge> {flagDescription}
+              </p>
+            )
           })}
           <p>
             <Link

diff --git a/browser/src/CopyNumberVariantList/CopyNumberVariantFilterControls.tsx b/browser/src/CopyNumberVariantList/CopyNumberVariantFilterControls.tsx
@@ -56,9 +56,7 @@ type Props = {
 const CopyNumberVariantFilterControls = ({ onChange, colorKey, value }: Props) => (
   <SettingsWrapper>
     <CategoryFiltersWrapper>
-      <CategoryFilterLabel>
-        Classes
-      </CategoryFilterLabel>
+      <CategoryFilterLabel>Classes</CategoryFilterLabel>
       <CategoryFilterControl
         categories={cnvTypes.map((type) => ({
           id: type,

diff --git a/browser/src/CopyNumberVariantList/CopyNumberVariantPlot.tsx b/browser/src/CopyNumberVariantList/CopyNumberVariantPlot.tsx
@@ -45,13 +45,12 @@ const CopyNumberVariantPlot = ({
   // If one endpoint is undefined, which should only happen if the SV extends outside the visible region,
   // offset the start/stop coordinate to make room for the arrow marker at the end of the bar.
 
-    if (!startIsDefined) {
-      startX += arrowWidth
-    }
-    if (!stopIsDefined) {
-      stopX -= arrowWidth
-    }
-
+  if (!startIsDefined) {
+    startX += arrowWidth
+  }
+  if (!stopIsDefined) {
+    stopX -= arrowWidth
+  }
 
   return (
     <svg height={trackHeight} width={width} style={{ overflow: 'visible' }}>
@@ -76,21 +75,21 @@ const CopyNumberVariantPlot = ({
         strokeWidth={1}
       />
       (
-        <React.Fragment>
-          {!startIsDefined && (
-            <path
-              d={`M ${startX} ${barY} l -${arrowWidth} ${halfBarHeight} l ${arrowWidth} ${halfBarHeight} z`}
-              fill={color}
-            />
-          )}
-          <rect x={startX} y={barY} width={stopX - startX} height={barHeight} fill={color} />
-          {!stopIsDefined && (
-            <path
-              d={`M ${stopX} ${barY} l ${arrowWidth} ${halfBarHeight} l -${arrowWidth} ${halfBarHeight} z`}
-              fill={color}
-            />
-          )}
-        </React.Fragment>
+      <React.Fragment>
+        {!startIsDefined && (
+          <path
+            d={`M ${startX} ${barY} l -${arrowWidth} ${halfBarHeight} l ${arrowWidth} ${halfBarHeight} z`}
+            fill={color}
+          />
+        )}
+        <rect x={startX} y={barY} width={stopX - startX} height={barHeight} fill={color} />
+        {!stopIsDefined && (
+          <path
+            d={`M ${stopX} ${barY} l ${arrowWidth} ${halfBarHeight} l -${arrowWidth} ${halfBarHeight} z`}
+            fill={color}
+          />
+        )}
+      </React.Fragment>
       )
     </svg>
   )

diff --git a/browser/src/CopyNumberVariantList/CopyNumberVariantPropType.ts b/browser/src/CopyNumberVariantList/CopyNumberVariantPropType.ts
@@ -28,11 +28,11 @@ type CopyNumberVariantPropType = {
 }
 
 const PopulationPropType = PropTypes.shape({
-    id: PropTypes.string.isRequired,
-    sc: PropTypes.number.isRequired,
-    sn: PropTypes.number.isRequired,
-    sf: PropTypes.number.isRequired,
-  })
+  id: PropTypes.string.isRequired,
+  sc: PropTypes.number.isRequired,
+  sn: PropTypes.number.isRequired,
+  sf: PropTypes.number.isRequired,
+})
 
 // @ts-expect-error TS(2322) FIXME: Type 'Requireable<InferProps<{ ac: Validator<numbe... Remove this comment to see the full error message
 const CopyNumberVariantPropType: PropTypes.Requireable<CopyNumberVariantPropType> = PropTypes.shape(

diff --git a/browser/src/CopyNumberVariantList/CopyNumberVariants.tsx b/browser/src/CopyNumberVariantList/CopyNumberVariants.tsx
@@ -31,19 +31,9 @@ const Wrapper = styled.div`
   margin-bottom: 1em;
 `
 
-
 const HUMAN_CHROMOSOMES = [...Array.from(new Array(22), (x: any, i: any) => `${i + 1}`), 'X', 'Y']
 
-
-const DEFAULT_COLUMNS = [
-  'source',
-  'class',
-  'pos',
-  'length',
-  'sc',
-  'sn',
-  'sf',
-]
+const DEFAULT_COLUMNS = ['source', 'class', 'pos', 'length', 'sc', 'sn', 'sf']
 
 const sortVariants = (variants: any, { sortKey, sortOrder }: any) => {
   const sortColumn = copyNumberVariantTableColumns.find((column: any) => column.key === sortKey)
@@ -158,7 +148,7 @@ const CopyNumberVariants = ({ context, exportFileName, variants }: CopyNumberVar
     }
   }, [])
 
-    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+  // eslint-disable-next-line @typescript-eslint/no-unused-vars
   const [colorKey, setColorKey] = useState('type')
   const trackColor = useCallback(
     // @ts-expect-error TS(7006) FIXME: Parameter 'variant' implicitly has an 'any' type.
@@ -196,7 +186,6 @@ const CopyNumberVariants = ({ context, exportFileName, variants }: CopyNumberVar
     return copy
   })
 
-
   return (
     <div>
       <Wrapper>
@@ -251,7 +240,10 @@ const CopyNumberVariants = ({ context, exportFileName, variants }: CopyNumberVar
               // @ts-expect-error TS(2322) FIXME: Type '{ ref: MutableRefObject<null>; cellData: { c... Remove this comment to see the full error message
               cellData={{
                 colorKey,
-                highlightWords: filter.searchText.split(',').map((s) => s.trim()).filter((term) => term !== ''),
+                highlightWords: filter.searchText
+                  .split(',')
+                  .map((s) => s.trim())
+                  .filter((term) => term !== ''),
               }}
               columns={renderedTableColumns}
               numRowsRendered={numRowsRendered}

diff --git a/browser/src/CopyNumberVariantList/copyNumberVariantTableColumns.tsx b/browser/src/CopyNumberVariantList/copyNumberVariantTableColumns.tsx
@@ -64,7 +64,7 @@ const copyNumberVariantTableColumns = [
       if (variantType === 'DEL') {
         return 'deletion'
       }
-        return 'duplication'
+      return 'duplication'
     },
     render: renderType,
   },

diff --git a/browser/src/CopyNumberVariantPage/CopyNumberVariantAttributeList.tsx b/browser/src/CopyNumberVariantPage/CopyNumberVariantAttributeList.tsx
@@ -62,7 +62,7 @@ const CopyNumberVariantAttributeList = ({ variant }: CopyNumberVariantAttributeL
     {/* @ts-expect-error TS(2604) FIXME: JSX element type 'AttributeList.Item' does not hav... Remove this comment to see the full error message */}
     <AttributeList.Item label="Class">
       {/* @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message */}
-      {cnvTypeLabels[variant.type]} 
+      {cnvTypeLabels[variant.type]}
     </AttributeList.Item>
   </AttributeList>
 )

diff --git a/browser/src/CopyNumberVariantPage/CopyNumberVariantPopulationsTable.tsx b/browser/src/CopyNumberVariantPage/CopyNumberVariantPopulationsTable.tsx
@@ -5,22 +5,20 @@ import { populationName } from '@gnomad/dataset-metadata/gnomadPopulations'
 import { CNVPopulationsTable } from './CNVPopulationsTable'
 
 type CopyNumberVariantPopulation = {
-    id: string,
-    sc: number,
-    sn: number,
-    sf: number,
-    name: string
+  id: string
+  sc: number
+  sn: number
+  sf: number
+  name: string
 }
 
 type Subpopulations = {
-    [key: string]: CopyNumberVariantPopulation[];
+  [key: string]: CopyNumberVariantPopulation[]
 }
 
-
 const nestPopulations = (populations: CopyNumberVariantPopulation[]) => {
   const popIndices = []
   const subpopulations: Subpopulations = {}
-
 
   for (let i = 0; i < populations.length; i += 1) {
     const pop = populations[i]
@@ -74,12 +72,7 @@ const CopyNumberVariantPopulationsTable = ({ variant }: CopyNumberVariantPopulat
     sf: 'Site Frequency',
   }
 
-  return (
-    <CNVPopulationsTable
-      columnLabels={columnLabels}
-      populations={populations}
-     />
-  )
+  return <CNVPopulationsTable columnLabels={columnLabels} populations={populations} />
 }
 
 export default CopyNumberVariantPopulationsTable
diff --git a/browser/src/CoverageTrack.tsx b/browser/src/CoverageTrack.tsx
@@ -89,7 +89,7 @@ type OwnCoverageTrackProps = {
   filenameForExport?: (...args: any[]) => any
   height?: number
   maxCoverage?: number
-  datasetId: DatasetId,
+  datasetId: DatasetId
 }
 
 type CoverageTrackState = any
@@ -107,7 +107,7 @@ class CoverageTrack extends Component<CoverageTrackProps, CoverageTrackState> {
   plotElement: any
 
   state = {
-    selectedMetric: isV4(this.props.datasetId) ? "over_30" : "mean",
+    selectedMetric: isV4(this.props.datasetId) ? 'over_30' : 'mean',
   }
 
   plotRef = (el: any) => {
@@ -203,19 +203,19 @@ class CoverageTrack extends Component<CoverageTrackProps, CoverageTrackState> {
     )
     return totalBases < 100
       ? this.renderBars({
-        isPositionDefined,
-        scaleCoverageMetric,
-        scalePosition,
-        totalBases,
-        width,
-      })
+          isPositionDefined,
+          scaleCoverageMetric,
+          scalePosition,
+          totalBases,
+          width,
+        })
       : this.renderArea({
-        isPositionDefined,
-        scaleCoverageMetric,
-        scalePosition,
-        totalBases,
-        width,
-      })
+          isPositionDefined,
+          scaleCoverageMetric,
+          scalePosition,
+          totalBases,
+          width,
+        })
   }
 
   render() {

diff --git a/browser/src/DatasetSelector.tsx b/browser/src/DatasetSelector.tsx
@@ -450,7 +450,7 @@ const DatasetSelector = withRouter(({ datasetOptions, history, selectedDataset }
   })
 
   const topLevelShortVariantDataset = shortVariantDatasetId(selectedDataset)
-  
+
   let datasets: any = []
 
   if (includeShortVariants) {
@@ -601,9 +601,9 @@ const DatasetSelector = withRouter(({ datasetOptions, history, selectedDataset }
       ? selectedDataset
       : 'gnomad_cnv_r4'
 
-      const currentDataset = hasStructuralVariants(selectedDataset)
-    ? topLevelStructuralVariantDataset
-    : topLevelCopyNumberVariantDataset
+    const currentDataset = hasStructuralVariants(selectedDataset)
+      ? topLevelStructuralVariantDataset
+      : topLevelCopyNumberVariantDataset
 
     datasets.push(
       {
@@ -653,7 +653,7 @@ const DatasetSelector = withRouter(({ datasetOptions, history, selectedDataset }
             childReferenceGenome: referenceGenome('gnomad_cnv_r4'),
           },
         ],
-      },
+      }
     )
   }
 

diff --git a/browser/src/DownloadsPage/TableOfContents.tsx b/browser/src/DownloadsPage/TableOfContents.tsx
@@ -88,9 +88,9 @@ const DownloadsPageTableOfContents = () => {
   }
 
   type ContentItem = {
-    link: string,
-    indent: string,
-    text: string,
+    link: string
+    indent: string
+    text: string
   }
 
   return (

diff --git a/browser/src/GenePage/GenePage.tsx b/browser/src/GenePage/GenePage.tsx
@@ -34,7 +34,9 @@ import GnomadPageHeading from '../GnomadPageHeading'
 import InfoButton from '../help/InfoButton'
 import Link from '../Link'
 import RegionalConstraintTrack from '../RegionalConstraintTrack'
-import RegionalMissenseConstraintTrack, { RegionalMissenseConstraint} from '../RegionalMissenseConstraintTrack'
+import RegionalMissenseConstraintTrack, {
+  RegionalMissenseConstraint,
+} from '../RegionalMissenseConstraintTrack'
 import RegionCoverageTrack from '../RegionPage/RegionCoverageTrack'
 import RegionViewer from '../RegionViewer/ZoomableRegionViewer'
 import { TrackPage, TrackPageSection } from '../TrackPage'
@@ -592,8 +594,8 @@ const GenePage = ({ datasetId, gene, geneId }: Props) => {
         {/* eslint-disable-next-line no-nested-ternary */}
         {hasStructuralVariants(datasetId) ? (
           <StructuralVariantsInGene datasetId={datasetId} gene={gene} zoomRegion={zoomRegion} />
-          // eslint-disable-next-line no-nested-ternary
-        ) : hasCopyNumberVariants(datasetId) ? (
+        ) : // eslint-disable-next-line no-nested-ternary
+        hasCopyNumberVariants(datasetId) ? (
           <CopyNumberVariantsInGene datasetId={datasetId} gene={gene} zoomRegion={zoomRegion} />
         ) : gene.chrom === 'M' ? (
           <MitochondrialVariantsInGene datasetId={datasetId} gene={gene} zoomRegion={zoomRegion} />