feat: adding api/variantValidator (#38)

src/api/variantValidator/client.spec.ts

@@ -0,0 +1,54 @@
+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 { VariantValidatorClient } from './client'
+import { Response } from './types'
+
+/** Fixture Seqvar */
+const seqvar = new SeqvarImpl('grch37', '6', 24302274, 'T', 'C')
+
+/** Fixture with response from API. */
+const responseManeBrca1Json = JSON.parse(
+  fs.readFileSync(path.resolve(__dirname, './fixture.maneResponse.BRCA1.json'), 'utf8')
+)
+
+/** Initialize mock for `fetch()`. */
+const fetchMocker = createFetchMock(vi)
+
+describe.concurrent('VariantValidator', () => {
+  beforeEach(() => {
+    fetchMocker.enableMocks()
+    fetchMocker.resetMocks()
+  })
+
+  it('handles response correctly', async () => {
+    // arrange:
+    fetchMocker.mockResponseOnce(JSON.stringify(responseManeBrca1Json))
+
+    // act:
+    const client = new VariantValidatorClient()
+    const result = await client.fetchVvResults(seqvar)
+
+    // assert:
+    expect(result).toMatchSnapshot()
+  })
+
+  it('throws in case of fetching problems', async () => {
+    // arrange:
+    fetchMocker.mockResponse(() => {
+      return Promise.reject(new Error('failed to fetch from VariantValidator'))
+    })
+
+    // act:
+    const client = new VariantValidatorClient()
+    // (with guard)
+    await expect(async () => await client.fetchVvResults(seqvar)).rejects.toThrow(
+      'failed to fetch from VariantValidator'
+    )
+
+    // assert:
+  })
+})

src/api/variantValidator/client.ts

@@ -0,0 +1,36 @@
+import type { Seqvar } from '../../lib/genomicVars'
+
+/** Base URL for VariantValidator. */
+const API_BASE_URL = `/remote/variantvalidator`
+
+/**
+ * Client for the VariantValidator API.
+ */
+export class VariantValidatorClient {
+  private apiBaseUrl: string
+
+  constructor(apiBaseUrl?: string) {
+    this.apiBaseUrl = apiBaseUrl ?? API_BASE_URL
+  }
+
+  /**
+   * Call variant validator API via proxy.
+   *
+   * @param seqvar The `Seqvar` object to be validated.
+   * @returns The response from the API.
+   * @throws Error if the API call fails.
+   */
+  async fetchVvResults(seqvar: Seqvar): Promise<any> {
+    const { genomeBuild, chrom, pos, del, ins } = seqvar
+    const release = genomeBuild === 'grch37' ? 'hg19' : 'hg38'
+    const url =
+      `${this.apiBaseUrl}/${release}/` +
+      `${chrom}-${pos}-${del}-${ins}/mane?content-type=application%2Fjson`
+
+    const response = await fetch(url, { method: 'GET' })
+    if (!response.ok) {
+      throw new Error(`Failed to fetch ACMG rating for ${seqvar.userRepr}`)
+    }
+    return await response.json()
+  }
+}