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Update default structural dataset to SVs v4 #1260

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merged 5 commits into from
Nov 6, 2023
Merged

Update default structural dataset to SVs v4 #1260

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5f9f5c8
update default structual dataset for v4 sv
elissa-alarmani Nov 3, 2023
250d5db
update snapshots
elissa-alarmani Nov 3, 2023
346d685
add logic to keep v2 dataset defaults
elissa-alarmani Nov 6, 2023
c400270
add additional snapshots
elissa-alarmani Nov 6, 2023
7fe952a
add eslint fix
elissa-alarmani Nov 6, 2023
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26 changes: 17 additions & 9 deletions browser/src/DatasetSelector.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,6 @@ import queryString from 'query-string'
import React, { Component } from 'react'
import { Link, withRouter } from 'react-router-dom'
import styled from 'styled-components'

import sampleCounts from '@gnomad/dataset-metadata/sampleCounts'

import {
Expand All @@ -16,6 +15,7 @@ import {
referenceGenome,
hasCopyNumberVariants,
shortVariantDatasetId,
isV2,
} from '@gnomad/dataset-metadata/metadata'

const NavigationMenuWrapper = styled.ul`
Expand Down Expand Up @@ -457,14 +457,14 @@ const DatasetSelector = withRouter(({ datasetOptions, history, selectedDataset }
const shortVariantDatasets = [
{
id: 'current_short_variant',
isActive: hasShortVariants(selectedDataset) && !hasCopyNumberVariants(selectedDataset),
isActive: hasShortVariants(selectedDataset),
label: labelForDataset(topLevelShortVariantDataset),
url: datasetLink(topLevelShortVariantDataset),
childReferenceGenome: referenceGenome(topLevelShortVariantDataset),
},
{
id: 'other_short_variant',
isActive: hasShortVariants(selectedDataset) && !hasCopyNumberVariants(selectedDataset),
isActive: hasShortVariants(selectedDataset),
label: 'More datasets',
children: [] as ChildDataset[],
},
Expand Down Expand Up @@ -589,17 +589,25 @@ const DatasetSelector = withRouter(({ datasetOptions, history, selectedDataset }
}

if (includeStructuralVariants || includeCopyNumberVariants) {
const topLevelStructuralVariantDataset = hasStructuralVariants(selectedDataset)
? selectedDataset
: 'gnomad_sv_r2_1'
const topLevelStructuralVariantDataset: any = (() => {
if (isV2(selectedDataset)) {
return 'gnomad_sv_r2_1'
}

if (hasStructuralVariants(selectedDataset)) {
return selectedDataset
}

return 'gnomad_sv_r4'
})()

const topLevelCopyNumberVariantDataset = hasCopyNumberVariants(selectedDataset)
? selectedDataset
: 'gnomad_cnv_r4'

const currentDataset = hasStructuralVariants(selectedDataset)
? topLevelStructuralVariantDataset
: topLevelCopyNumberVariantDataset
const currentDataset = hasCopyNumberVariants(selectedDataset)
? topLevelCopyNumberVariantDataset
: topLevelStructuralVariantDataset

datasets.push(
{
Expand Down
52 changes: 26 additions & 26 deletions browser/src/GenePage/__snapshots__/GenePage.spec.tsx.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7647,12 +7647,12 @@ exports[`GenePage with non-SV dataset "exac" has no unexpected changes 1`] = `
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -10621,12 +10621,12 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1" has no unexpected changes 1`
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r2_1"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v2.1
</a>
</li>
<li
Expand Down Expand Up @@ -12209,12 +12209,12 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1_controls" has no unexpected c
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r2_1"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v2.1
</a>
</li>
<li
Expand Down Expand Up @@ -13797,12 +13797,12 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1_non_cancer" has no unexpected
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r2_1"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v2.1
</a>
</li>
<li
Expand Down Expand Up @@ -15385,12 +15385,12 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1_non_neuro" has no unexpected
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r2_1"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v2.1
</a>
</li>
<li
Expand Down Expand Up @@ -16973,12 +16973,12 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1_non_topmed" has no unexpected
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r2_1"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v2.1
</a>
</li>
<li
Expand Down Expand Up @@ -18561,12 +18561,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3" has no unexpected changes 1`]
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -20065,12 +20065,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3_controls_and_biobanks" has no u
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -21569,12 +21569,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3_non_cancer" has no unexpected c
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -23073,12 +23073,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3_non_neuro" has no unexpected ch
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -24577,12 +24577,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3_non_topmed" has no unexpected c
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -26081,12 +26081,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3_non_v2" has no unexpected chang
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -27585,12 +27585,12 @@ exports[`GenePage with non-SV dataset "gnomad_r4" has no unexpected changes 1`]
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down
28 changes: 14 additions & 14 deletions browser/src/MitochondrialVariantPage/__snapshots__/MitochondrialVariantPage.spec.tsx.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8454,12 +8454,12 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3 has no unexpected chang
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -16675,12 +16675,12 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3_controls_and_biobanks h
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -24896,12 +24896,12 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3_non_cancer has no unexp
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -33117,12 +33117,12 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3_non_neuro has no unexpe
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -41338,12 +41338,12 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3_non_topmed has no unexp
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -49559,12 +49559,12 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3_non_v2 has no unexpecte
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down Expand Up @@ -57780,12 +57780,12 @@ exports[`MitochondrialVariantPage with dataset gnomad_r4 has no unexpected chang
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD CNVs v4.0
gnomAD SVs v4.0
</a>
</li>
<li
Expand Down
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