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Allow search of gene symbols that look like CAIDs
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@phildarnowsky-broad
phildarnowsky-broad committed Oct 30, 2024
1 parent cb77f51 commit f89a77b
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Showing 2 changed files with 168 additions and 60 deletions.
72 changes: 71 additions & 1 deletion browser/src/search.spec.ts
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
import { beforeEach, describe, expect, jest, it } from '@jest/globals'
import { beforeEach, describe, expect, jest, it, test } from '@jest/globals'

import { fetchSearchResults } from './search'

Expand Down Expand Up @@ -150,4 +150,74 @@ describe('fetchSearchResults', () => {
},
])
})

describe('looking up a query formatted like a CAID', () => {
test('returns links to any genes with matching symbols as well as the presumptive CAID, disambiguating if needed', async () => {
// @ts-expect-error TS(2339) FIXME: Property 'mockReturnValue' does not exist on type ... Remove this comment to see the full error message
global.fetch.mockReturnValue(
Promise.resolve({
json: () =>
Promise.resolve({
data: {
gene_search: [
{ ensembl_id: 'ENSG000004', symbol: 'CA327' },
{ ensembl_id: 'ENSG000001', symbol: 'CA321' },
{ ensembl_id: 'ENSG000005', symbol: 'CA3213' },
{ ensembl_id: 'ENSG000006', symbol: 'CA32' },
{ ensembl_id: 'ENSG000003', symbol: 'CA325' },
],
},
}),
})
)

expect(await fetchSearchResults('gnomad_r4', 'CA3')).toEqual([
{ label: 'CA3', value: `/variant/CA3?dataset=gnomad_r4` },
{
label: 'CA32',
value: '/gene/ENSG000006?dataset=gnomad_r4',
},
{
label: 'CA321',
value: '/gene/ENSG000001?dataset=gnomad_r4',
},
{
label: 'CA3213',
value: '/gene/ENSG000005?dataset=gnomad_r4',
},
{
label: 'CA325',
value: '/gene/ENSG000003?dataset=gnomad_r4',
},
{
label: 'CA327',
value: '/gene/ENSG000004?dataset=gnomad_r4',
},
])

expect(await fetchSearchResults('gnomad_r4', 'CA32')).toEqual([
{ label: 'CA32 (variant)', value: `/variant/CA32?dataset=gnomad_r4` },
{
label: 'CA32 (ENSG000006)',
value: '/gene/ENSG000006?dataset=gnomad_r4',
},
{
label: 'CA321',
value: '/gene/ENSG000001?dataset=gnomad_r4',
},
{
label: 'CA3213',
value: '/gene/ENSG000005?dataset=gnomad_r4',
},
{
label: 'CA325',
value: '/gene/ENSG000003?dataset=gnomad_r4',
},
{
label: 'CA327',
value: '/gene/ENSG000004?dataset=gnomad_r4',
},
])
})
})
})
156 changes: 97 additions & 59 deletions browser/src/search.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,80 @@ import {
isRsId,
} from '@gnomad/identifiers'

import { DatasetId, referenceGenome } from '@gnomad/dataset-metadata/metadata'
import {
DatasetId,
ReferenceGenome,
referenceGenome as getReferenceGenome,
} from '@gnomad/dataset-metadata/metadata'
import { isStructuralVariantId } from './identifiers'

export const fetchSearchResults = (datasetId: DatasetId, query: string) => {
const fetchGeneSymbolSearchResults = (query: string, referenceGenome: ReferenceGenome) => {
return fetch('/api/', {
body: JSON.stringify({
query: `
query GeneSearch($query: String!, $referenceGenome: ReferenceGenomeId!) {
gene_search(query: $query, reference_genome: $referenceGenome) {
ensembl_id
symbol
}
}
`,
variables: { query, referenceGenome },
}),
method: 'POST',
headers: { 'Content-Type': 'application/json' },
}).then((response) => response.json())
}

type GeneSearchResult = { data: { gene_search: { ensembl_id: string; symbol: string }[] } }

const parseGeneSearchResults = (
response: GeneSearchResult,
query: string,
datasetId: DatasetId,
startingGeneSymbolCounts: Record<string, number> = {}
): [SearchResultItem[], Record<string, number>] => {
const genes = response.data.gene_search
const geneSymbolCounts = { ...startingGeneSymbolCounts }

genes.forEach((gene) => {
if (geneSymbolCounts[gene.symbol] === undefined) {
geneSymbolCounts[gene.symbol] = 0
}
geneSymbolCounts[gene.symbol] += 1
})

const formattedGenes = genes
.sort((gene1, gene2) => {
const symbolPrefix = query.toUpperCase()
const symbol1 = gene1.symbol.toUpperCase()
const symbol2 = gene2.symbol.toUpperCase()

if (symbol1.startsWith(symbolPrefix) && !symbol2.startsWith(symbolPrefix)) {
return -1
}

if (!symbol1.startsWith(symbolPrefix) && symbol2.startsWith(symbolPrefix)) {
return 1
}
return symbol1.localeCompare(symbol2)
})
.map((gene) => ({
label:
geneSymbolCounts[gene.symbol] > 1 ? `${gene.symbol} (${gene.ensembl_id})` : gene.symbol,

value: `/gene/${gene.ensembl_id}?dataset=${datasetId}`,
}))

return [formattedGenes, geneSymbolCounts]
}

type SearchResultItem = { label: string; value: string }

export const fetchSearchResults = (
datasetId: DatasetId,
query: string
): Promise<SearchResultItem[]> => {
if (datasetId.startsWith('gnomad_sv')) {
// ==============================================================================================
// Structural Variants
Expand Down Expand Up @@ -49,14 +119,26 @@ export const fetchSearchResults = (datasetId: DatasetId, query: string) => {
])
}

// Some gene symbols also match the format for variant CAIDs, so we have
// to cover that as a special case
if (/^CA[0-9]+$/i.test(query)) {
const caid = query.toUpperCase()
return Promise.resolve([
{
label: caid,
value: `/variant/${caid}?dataset=${datasetId}`,
},
])
return fetchGeneSymbolSearchResults(query, getReferenceGenome(datasetId))
.then((response) => {
if (!response?.data?.gene_search) {
return []
}
return response
})
.then((response) => parseGeneSearchResults(response, query, datasetId, { [caid]: 1 }))
.then(([geneSearchResults, geneSymbolCounts]) => {
const variantItem = {
label: geneSymbolCounts[caid] > 1 ? `${caid} (variant)` : caid,
value: `/variant/${caid}?dataset=${datasetId}`,
}

return [variantItem, ...geneSearchResults]
})
}

if (/^[0-9]+$/.test(query)) {
Expand Down Expand Up @@ -132,60 +214,16 @@ export const fetchSearchResults = (datasetId: DatasetId, query: string) => {
// ==============================================================================================

if (/^[A-Z][A-Z0-9-]*$/.test(upperCaseQuery)) {
return fetch('/api/', {
body: JSON.stringify({
query: `
query GeneSearch($query: String!, $referenceGenome: ReferenceGenomeId!) {
gene_search(query: $query, reference_genome: $referenceGenome) {
ensembl_id
symbol
}
}
`,
variables: { query, referenceGenome: referenceGenome(datasetId) },
}),
method: 'POST',
headers: { 'Content-Type': 'application/json' },
})
.then((response) => response.json())
return fetchGeneSymbolSearchResults(query, getReferenceGenome(datasetId))
.then((response) => {
if (!response.data.gene_search) {
if (!response?.data?.gene_search) {
throw new Error('Unable to retrieve search results')
}

const genes = response.data.gene_search as { ensembl_id: string; symbol: string }[]

const geneSymbolCounts: Record<string, number> = {}
genes.forEach((gene) => {
if (geneSymbolCounts[gene.symbol] === undefined) {
geneSymbolCounts[gene.symbol] = 0
}
geneSymbolCounts[gene.symbol] += 1
})

return genes
.sort((gene1, gene2) => {
const symbolPrefix = query.toUpperCase()
const symbol1 = gene1.symbol.toUpperCase()
const symbol2 = gene2.symbol.toUpperCase()

if (symbol1.startsWith(symbolPrefix) && !symbol2.startsWith(symbolPrefix)) {
return -1
}

if (!symbol1.startsWith(symbolPrefix) && symbol2.startsWith(symbolPrefix)) {
return 1
}
return symbol1.localeCompare(symbol2)
})
.map((gene) => ({
label:
geneSymbolCounts[gene.symbol] > 1
? `${gene.symbol} (${gene.ensembl_id})`
: gene.symbol,

value: `/gene/${gene.ensembl_id}?dataset=${datasetId}`,
}))
return response
})
.then((response) => {
const [geneSearchResults] = parseGeneSearchResults(response, query, datasetId)
return geneSearchResults
})
}

Expand Down

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