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Enable STRs in v4 #1305

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merged 5 commits into from
Nov 17, 2023
Merged

Enable STRs in v4 #1305

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4872de0
Add STR index for v4
mattsolo1 Nov 17, 2023
e13a374
Update STR metadata helper
mattsolo1 Nov 17, 2023
e8222bc
Use metadata helper on STR page
mattsolo1 Nov 17, 2023
79507ba
Update homepage to use v4 in STR links
mattsolo1 Nov 17, 2023
fc48ca4
Update snapshots
mattsolo1 Nov 17, 2023
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15 changes: 10 additions & 5 deletions browser/src/HomePage.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -156,16 +156,21 @@ export default () => (
</ListItem>
{/* @ts-expect-error TS(2746) FIXME: This JSX tag's 'children' prop expects a single ch... Remove this comment to see the full error message */}
<ListItem>
{/* @ts-expect-error TS(2786) FIXME: 'ExternalLink' cannot be used as a JSX component. */}
<ExternalLink href="https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r3">
Short tandem repeat
</ExternalLink>{' '}
<Link
preserveSelectedDataset={false}
to={{
pathname: '/short-tandem-repeats',
search: queryString.stringify({ dataset: 'gnomad_r4' }),
}}
>
Short tandem repeat{' '}
</Link>
locus:{' '}
<Link
preserveSelectedDataset={false}
to={{
pathname: 'short-tandem-repeat/ATXN1',
search: queryString.stringify({ dataset: 'gnomad_r3' }),
search: queryString.stringify({ dataset: 'gnomad_r4' }),
}}
>
ATXN1
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2 changes: 1 addition & 1 deletion browser/src/RegionPage/__snapshots__/RegionPageContainer.spec.tsx.snap
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Expand Up @@ -772,7 +772,7 @@ exports[`RegionPageContainer with dataset gnomad_r4 queries API with correct par
variables={
{
"chrom": "12",
"includeShortTandemRepeats": false,
"includeShortTandemRepeats": true,
"referenceGenome": "GRCh38",
"shortTandemRepeatDatasetId": "gnomad_r3",
"start": 345,
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4 changes: 2 additions & 2 deletions browser/src/ShortTandemRepeatsPage/ShortTandemRepeatsPage.tsx
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Expand Up @@ -2,7 +2,7 @@ import React from 'react'

import { BaseTable, ExternalLink, Page } from '@gnomad/ui'

import { DatasetId, labelForDataset } from '@gnomad/dataset-metadata/metadata'
import { DatasetId, hasShortTandemRepeats, labelForDataset } from '@gnomad/dataset-metadata/metadata'
import DocumentTitle from '../DocumentTitle'
import GnomadPageHeading from '../GnomadPageHeading'
import Link from '../Link'
Expand Down Expand Up @@ -133,7 +133,7 @@ const ShortTandemRepeatsPageContainer = ({ datasetId }: ShortTandemRepeatsPageCo
>
Pathogenic Short Tandem Repeats
</GnomadPageHeading>
{datasetId === 'gnomad_r3' ? (
{hasShortTandemRepeats(datasetId) ? (
<Query
operationName={operationName}
query={query}
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11 changes: 5 additions & 6 deletions browser/src/__snapshots__/HomePage.spec.tsx.snap
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Expand Up @@ -444,19 +444,18 @@ exports[`Home Page has no unexpected changes 1`] = `
className="c7"
>
<a
className="c9"
href="https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r3"
rel="noopener noreferrer"
target="_blank"
className="-Link c8"
href="/short-tandem-repeats?dataset=gnomad_r4"
onClick={[Function]}
>
Short tandem repeat

</a>

locus:

<a
className="-Link c8"
href="short-tandem-repeat/ATXN1?dataset=gnomad_r3"
href="short-tandem-repeat/ATXN1?dataset=gnomad_r4"
onClick={[Function]}
>
ATXN1
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8 changes: 4 additions & 4 deletions dataset-metadata/metadata.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -207,9 +207,9 @@ const metadataForDataset = (datasetId: DatasetId): DatasetMetadata => ({
transcriptsHaveExomeCoverage: !datasetId.startsWith('gnomad_r3') && datasetId !== 'gnomad_sv_r4',
referenceGenome:
datasetId.startsWith('gnomad_r3') ||
datasetId.startsWith('gnomad_r4') ||
datasetId === 'gnomad_sv_r4' ||
datasetId === 'gnomad_cnv_r4'
datasetId.startsWith('gnomad_r4') ||
datasetId === 'gnomad_sv_r4' ||
datasetId === 'gnomad_cnv_r4'
? 'GRCh38'
: 'GRCh37',
genesHaveGenomeCoverage: !datasetId.startsWith('gnomad_cnv'),
Expand Down Expand Up @@ -245,7 +245,7 @@ const metadataForDataset = (datasetId: DatasetId): DatasetMetadata => ({
hasRelatedVariants: datasetId !== 'gnomad_r2_1',
showAllIndividualsInAgeDistributionByDefault: datasetId !== 'exac',
hasExons: !datasetId.startsWith('gnomad_sv'),
hasShortTandemRepeats: datasetId.startsWith('gnomad_r3') || datasetId === 'gnomad_sv_r4',
hasShortTandemRepeats: datasetId.startsWith('gnomad_r3') || datasetId.startsWith('gnomad_r4') || datasetId === "gnomad_sv_r4",
hasMitochondrialGenomeCoverage: !(datasetId === 'exac' || datasetId.startsWith('gnomad_r2')),
hasMitochondrialVariants: !(datasetId === 'exac' || datasetId.startsWith('gnomad_r2')),
hasNonCodingReadData: !(datasetId === 'exac' || datasetId.startsWith('gnomad_r2')),
Expand Down
1 change: 1 addition & 0 deletions graphql-api/src/queries/short-tandem-repeat-queries.ts
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Expand Up @@ -5,6 +5,7 @@ import { fetchAllSearchResults } from './helpers/elasticsearch-helpers'

const SHORT_TANDEM_REPEAT_INDICES = {
gnomad_r3: 'gnomad_v3_short_tandem_repeats',
gnomad_r4: 'gnomad_v3_short_tandem_repeats',
}

const SUMMARY_FIELDS = [
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