feat: adding api/mehari

package.json

@@ -48,6 +48,7 @@
   "dependencies": {
     "@mdi/font": "^7.4.47",
     "@protobuf-ts/runtime": "^2.9.3",
+    "@reactgular/chunks": "^1.0.1",
     "@types/luxon": "^3.4.2",
     "luxon": "^3.4.4",
     "title-case": "^4.3.1",
@@ -97,6 +98,7 @@
     "vite-plugin-sass-dts": "^1.3.17",
     "vitest": "^1.2.2",
     "vitest-canvas-mock": "^0.3.3",
+    "vitest-fetch-mock": "^0.2.2",
     "vue-tsc": "^1.8.27"
   }
 }

src/api/mehari/client.spec.ts

@@ -0,0 +1,125 @@
+import fs from 'fs'
+import path from 'path'
+import { beforeEach, describe, expect, it, vi } from 'vitest'
+import createFetchMock from 'vitest-fetch-mock'
+
+import { SeqvarImpl } from '@/lib/genomicVars'
+
+import { LinearStrucvarImpl } from '../../lib/genomicVars'
+import { MehariClient } from './client'
+import { SeqvarResult, StrucvarResult } from './types'
+
+/** Fixture Seqvar */
+const seqvar = new SeqvarImpl('grch37', '1', 123, 'A', 'G')
+
+/** Fixture with BRCA1 seqvar consequence. */
+const seqvarCsqResponseBrca1 = JSON.parse(
+  fs.readFileSync(path.resolve(__dirname, './fixture.seqvarCsqResponse.BRCA1.json'), 'utf8')
+)
+
+/** Fixture Strucvar affecting BRCA1 */
+const strucvar = new LinearStrucvarImpl('DEL', 'grch37', 'chr17', 43044295, 43044297)
+
+/** Fixture with strucvar (BRCA1) consequence */
+const strucvarCsqResponseBrca1 = JSON.parse(
+  fs.readFileSync(path.resolve(__dirname, './fixture.strucvarCsqResponse.BRCA1.json'), 'utf8')
+)
+
+/** Initialize mock for `fetch()`. */
+const fetchMocker = createFetchMock(vi)
+
+describe.concurrent('MehariClient/seqvar', () => {
+  beforeEach(() => {
+    fetchMocker.enableMocks()
+    fetchMocker.resetMocks()
+  })
+
+  it('fetches TxCsq info correctly', async () => {
+    // arrange:
+    fetchMocker.mockResponseOnce(JSON.stringify(seqvarCsqResponseBrca1))
+
+    // act:
+    const client = new MehariClient()
+    const result = await client.retrieveSeqvarsCsq(seqvar, 'HGNC:1100')
+
+    // assert:
+    expect(JSON.stringify(result)).toEqual(
+      JSON.stringify(SeqvarResult.fromJson(seqvarCsqResponseBrca1))
+    )
+  })
+
+  it('fetches TxCsq info correctly without HGNC id', async () => {
+    // arrange:
+    fetchMocker.mockResponseOnce(JSON.stringify(seqvarCsqResponseBrca1))
+
+    // act:
+    const client = new MehariClient()
+    const result = await client.retrieveSeqvarsCsq(seqvar)
+
+    // assert:
+    expect(JSON.stringify(result)).toEqual(
+      JSON.stringify(SeqvarResult.fromJson(seqvarCsqResponseBrca1))
+    )
+  })
+
+  it('fails to fetch variant info with wrong variant', async () => {
+    // arrange:
+    const seqVarInvalid = new SeqvarImpl('grch37', '1', 123, 'A', 'T')
+    fetchMocker.mockResponse((req) => {
+      if (req.url.includes('alternative=G')) {
+        return Promise.resolve(JSON.stringify(seqvarCsqResponseBrca1))
+      }
+      return Promise.reject('failed to fetch seqvar')
+    })
+
+    // act:
+    const client = new MehariClient()
+    // (with guard)
+    await expect(async () => await client.retrieveSeqvarsCsq(seqVarInvalid)).rejects.toThrow(
+      'failed to fetch seqvar'
+    )
+
+    // assert:
+  })
+})
+
+describe.concurrent('MehariClient/strucvar', () => {
+  beforeEach(() => {
+    fetchMocker.enableMocks()
+    fetchMocker.resetMocks()
+  })
+
+  it('fetches strucvar info correctly', async () => {
+    // arrange:
+    fetchMocker.mockResponseOnce(JSON.stringify(strucvarCsqResponseBrca1))
+
+    // act:
+    const client = new MehariClient()
+    const result = await client.retrieveStrucvarsCsq(strucvar)
+
+    // assert:
+    expect(JSON.stringify(result)).toEqual(
+      JSON.stringify(StrucvarResult.fromJson(strucvarCsqResponseBrca1))
+    )
+  })
+
+  it('fails to fetch variant info with wrong variant', async () => {
+    // arrange:
+    const strucVarInvalid = new LinearStrucvarImpl('DUP', 'grch37', 'chr17', 43044295, 43044297)
+    fetchMocker.mockResponse((req) => {
+      if (req.url.includes('DEL')) {
+        return Promise.resolve(JSON.stringify(strucvarCsqResponseBrca1))
+      }
+      return Promise.reject('failed to fetch strucvar')
+    })
+
+    // act:
+    const client = new MehariClient()
+    // (with guard)
+    await expect(async () => await client.retrieveStrucvarsCsq(strucVarInvalid)).rejects.toThrow(
+      'failed to fetch strucvar'
+    )
+
+    // assert:
+  })
+})

src/api/mehari/client.ts

@@ -0,0 +1,65 @@
+import type { LinearStrucvar, Seqvar } from '../../lib/genomicVars'
+import { SeqvarResult, StrucvarResult } from './types'
+
+/** API base URL to use. */
+const API_BASE_URL = '/internal/proxy/pubtator3-api'
+
+/**
+ * Client for Mehari API requests.
+ */
+export class MehariClient {
+  private apiBaseUrl: string
+
+  constructor(apiBaseUrl?: string) {
+    this.apiBaseUrl = apiBaseUrl ?? API_BASE_URL
+  }
+
+  /**
+   * Retrieve consequences for sequence variants.
+   *
+   * @param seqvar Sequence variant to retrieve consequences for.
+   * @param hgncId HGNC ID of gene to restrict results to.
+   * @returns The response from the API.
+   * @throws Error if the API request fails.
+   */
+  async retrieveSeqvarsCsq(seqvar: Seqvar, hgncId?: string): Promise<SeqvarResult> {
+    const { genomeBuild, chrom, pos, del, ins } = seqvar
+    const hgncSuffix = hgncId ? `&hgnc_id=${hgncId}` : ''
+    const url =
+      `${this.apiBaseUrl}seqvars/csq?genome_release=${genomeBuild}&` +
+      `chromosome=${chrom}&position=${pos}&reference=${del}&` +
+      `alternative=${ins}${hgncSuffix}`
+
+    const response = await fetch(url, {
+      method: 'GET'
+    })
+    if (!response.ok) {
+      throw new Error(`Failed to fetch sequence variant consequences: ${response.statusText}`)
+    }
+    const responseJson = await response.json()
+    return SeqvarResult.fromJson(responseJson)
+  }
+
+  /**
+   * Retrieve consequences for structural variants.
+   *
+   * @param strucvar Structural variant to retrieve consequences for.
+   * @returns The response from the API.
+   * @throws Error if the API request fails.
+   */
+  async retrieveStrucvarsCsq(strucvar: LinearStrucvar): Promise<StrucvarResult> {
+    const { genomeBuild, chrom, start, stop, svType } = strucvar
+    const url =
+      `${this.apiBaseUrl}strucvars/csq?genome_release=${genomeBuild}&` +
+      `chromosome=${chrom}&start=${start}&stop=${stop}&sv_type=${svType}`
+
+    const response = await fetch(url, {
+      method: 'GET'
+    })
+    if (!response.ok) {
+      throw new Error(`Failed to fetch structural variant consequences: ${response.statusText}`)
+    }
+    const responseJson = await response.json()
+    return StrucvarResult.fromJson(responseJson)
+  }
+}

src/api/mehari/fixture.seqvarCsqResponse.BRCA1.json

@@ -0,0 +1,98 @@
+{
+  "version": { "tx_db": "0.5.0", "mehari": "0.7.0" },
+  "query": {
+    "genome_release": "grch37",
+    "chromosome": "chr17",
+    "position": 41197751,
+    "reference": "G",
+    "alternative": "T",
+    "hgnc_id": null
+  },
+  "result": [
+    {
+      "consequences": ["MissenseVariant"],
+      "putative_impact": "Moderate",
+      "gene_symbol": "BRCA1",
+      "gene_id": "HGNC:1100",
+      "feature_type": { "SoTerm": { "term": "Transcript" } },
+      "feature_id": "NM_007294.4",
+      "feature_biotype": "Coding",
+      "rank": { "ord": 23, "total": 23 },
+      "hgvs_t": "c.5536C>A",
+      "hgvs_p": "p.Q1846K",
+      "tx_pos": { "ord": 5649, "total": 7088 },
+      "cds_pos": { "ord": 5536, "total": 5592 },
+      "protein_pos": { "ord": 1846, "total": 1864 },
+      "distance": -1440,
+      "messages": null
+    },
+    {
+      "consequences": ["MissenseVariant"],
+      "putative_impact": "Moderate",
+      "gene_symbol": "BRCA1",
+      "gene_id": "HGNC:1100",
+      "feature_type": { "SoTerm": { "term": "Transcript" } },
+      "feature_id": "NM_007297.4",
+      "feature_biotype": "Coding",
+      "rank": { "ord": 22, "total": 22 },
+      "hgvs_t": "c.5395C>A",
+      "hgvs_p": "p.Q1799K",
+      "tx_pos": { "ord": 5589, "total": 7028 },
+      "cds_pos": { "ord": 5395, "total": 5451 },
+      "protein_pos": { "ord": 1799, "total": 1817 },
+      "distance": -1440,
+      "messages": null
+    },
+    {
+      "consequences": ["MissenseVariant"],
+      "putative_impact": "Moderate",
+      "gene_symbol": "BRCA1",
+      "gene_id": "HGNC:1100",
+      "feature_type": { "SoTerm": { "term": "Transcript" } },
+      "feature_id": "NM_007298.3",
+      "feature_biotype": "Coding",
+      "rank": { "ord": 22, "total": 22 },
+      "hgvs_t": "c.2224C>A",
+      "hgvs_p": "p.Q742K",
+      "tx_pos": { "ord": 2243, "total": 3682 },
+      "cds_pos": { "ord": 2224, "total": 2280 },
+      "protein_pos": { "ord": 742, "total": 760 },
+      "distance": -1440,
+      "messages": null
+    },
+    {
+      "consequences": ["MissenseVariant"],
+      "putative_impact": "Moderate",
+      "gene_symbol": "BRCA1",
+      "gene_id": "HGNC:1100",
+      "feature_type": { "SoTerm": { "term": "Transcript" } },
+      "feature_id": "NM_007300.4",
+      "feature_biotype": "Coding",
+      "rank": { "ord": 24, "total": 24 },
+      "hgvs_t": "c.5599C>A",
+      "hgvs_p": "p.Q1867K",
+      "tx_pos": { "ord": 5712, "total": 7151 },
+      "cds_pos": { "ord": 5599, "total": 5655 },
+      "protein_pos": { "ord": 1867, "total": 1885 },
+      "distance": -1440,
+      "messages": null
+    },
+    {
+      "consequences": ["ThreePrimeUtrVariant"],
+      "putative_impact": "Modifier",
+      "gene_symbol": "BRCA1",
+      "gene_id": "HGNC:1100",
+      "feature_type": { "SoTerm": { "term": "Transcript" } },
+      "feature_id": "NM_007299.4",
+      "feature_biotype": "Coding",
+      "rank": { "ord": 22, "total": 22 },
+      "hgvs_t": "c.*50C>A",
+      "hgvs_p": "p.?",
+      "tx_pos": { "ord": 2257, "total": 3696 },
+      "cds_pos": { "ord": 50, "total": 2100 },
+      "protein_pos": null,
+      "distance": -1440,
+      "messages": null
+    }
+  ]
+}