feat: Retrieval of affected genes in SV from mehari (#56) (#107)

frontend/src/api/__tests__/mehari.spec.ts

@@ -3,6 +3,7 @@ import createFetchMock from 'vitest-fetch-mock'
 
 import { MehariClient } from '@/api/mehari'
 import * as BRCA1TxInfo from '@/assets/__tests__/BRCA1TxInfo.json'
+import * as SVInfo from '@/assets/__tests__/ExampleSVTxInfo.json'
 
 const fetchMocker = createFetchMock(vi)
 
@@ -16,15 +17,22 @@ describe.concurrent('Mehari Client', () => {
     fetchMocker.mockResponseOnce(JSON.stringify(BRCA1TxInfo))
 
     const client = new MehariClient()
-    const result = await client.retrieveTxCsq('grch37', 'chr17', 43044295, 'A', 'G', 'HGNC:1100')
+    const result = await client.retrieveSeqvarsCsq(
+      'grch37',
+      'chr17',
+      43044295,
+      'A',
+      'G',
+      'HGNC:1100'
+    )
     expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1TxInfo))
   })
 
   it('fetches TxCsq info correctly without HGNC id', async () => {
     fetchMocker.mockResponseOnce(JSON.stringify(BRCA1TxInfo))
 
     const client = new MehariClient()
-    const result = await client.retrieveTxCsq('grch37', 'chr17', 43044295, 'A', 'G')
+    const result = await client.retrieveSeqvarsCsq('grch37', 'chr17', 43044295, 'A', 'G')
     expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1TxInfo))
   })
 
@@ -37,7 +45,28 @@ describe.concurrent('Mehari Client', () => {
     })
 
     const client = new MehariClient()
-    const result = await client.retrieveTxCsq('grch37', 'chr17', 43044295, 'A', 'T')
+    const result = await client.retrieveSeqvarsCsq('grch37', 'chr17', 43044295, 'A', 'T')
+    expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
+  })
+
+  it('fetches Structur Variant info correctly', async () => {
+    fetchMocker.mockResponseOnce(JSON.stringify(SVInfo))
+
+    const client = new MehariClient()
+    const result = await client.retrieveStrucvarsCsq('grch37', 'chr17', 43044295, 43044297, 'DEL')
+    expect(JSON.stringify(result)).toEqual(JSON.stringify(SVInfo))
+  })
+
+  it('fails to fetch variant info with wrong variant', async () => {
+    fetchMocker.mockResponse((req) => {
+      if (req.url.includes('alternative=G')) {
+        return Promise.resolve(JSON.stringify(SVInfo))
+      }
+      return Promise.resolve(JSON.stringify({ status: 400 }))
+    })
+
+    const client = new MehariClient()
+    const result = await client.retrieveStrucvarsCsq('grch37', 'chr17', 43044295, 43044297, 'INS')
     expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
   })
 })

frontend/src/api/mehari.ts

@@ -11,7 +11,7 @@ export class MehariClient {
     this.csrfToken = csrfToken ?? null
   }
 
-  async retrieveTxCsq(
+  async retrieveSeqvarsCsq(
     genomeRelease: string,
     chromosome: string,
     pos: number,
@@ -30,4 +30,20 @@ export class MehariClient {
     })
     return await response.json()
   }
+
+  async retrieveStrucvarsCsq(
+    genomeRelease: string,
+    chromosome: string,
+    start: number,
+    stop: number,
+    sv_type: string
+  ): Promise<any> {
+    const url =
+      `${this.apiBaseUrl}strucvars/csq?genome_release=${genomeRelease}&` +
+      `chromosome=${chromosome}&start=${start}&stop=${stop}&sv_type=${sv_type}`
+    const response = await fetch(url, {
+      method: 'GET'
+    })
+    return await response.json()
+  }
 }