feat: Use Seqvar and LinearStrucvar whenever possible (#366) (#378)

bihealth · Jan 10, 2024 · c35ae0f · c35ae0f
1 parent a587af1
commit c35ae0f
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Showing 9 changed files with 72 additions and 102 deletions.
diff --git a/frontend/src/api/__tests__/acmgSeqvar.spec.ts b/frontend/src/api/__tests__/acmgSeqvar.spec.ts
@@ -52,7 +52,7 @@ describe.concurrent('AcmgSeqVar Client', () => {
     fetchMocker.mockResponse(JSON.stringify(mockAcmgRating))
 
     const client = new AcmgSeqVarClient()
-    const result = await client.fetchAcmgRating(seqVar.toName())
+    const result = await client.fetchAcmgRating(seqVar)
 
     expect(result).toEqual(mockAcmgRating)
   })
@@ -66,7 +66,7 @@ describe.concurrent('AcmgSeqVar Client', () => {
     })
 
     const client = new AcmgSeqVarClient()
-    const result = await client.fetchAcmgRating(seqVar.toName())
+    const result = await client.fetchAcmgRating(seqVar)
 
     expect(result).toEqual({ status: 500 })
   })
@@ -75,7 +75,7 @@ describe.concurrent('AcmgSeqVar Client', () => {
     fetchMocker.mockResponse(JSON.stringify(mockAcmgRating))
 
     const client = new AcmgSeqVarClient()
-    const result = await client.saveAcmgRating(seqVar.toName(), mockAcmgRating)
+    const result = await client.saveAcmgRating(seqVar, mockAcmgRating)
 
     expect(result).toEqual(mockAcmgRating)
   })
@@ -89,7 +89,7 @@ describe.concurrent('AcmgSeqVar Client', () => {
     })
 
     const client = new AcmgSeqVarClient()
-    const result = await client.saveAcmgRating(seqVar.toName(), mockAcmgRating)
+    const result = await client.saveAcmgRating(seqVar, mockAcmgRating)
 
     expect(result).toEqual({ status: 500 })
   })
@@ -98,7 +98,7 @@ describe.concurrent('AcmgSeqVar Client', () => {
     fetchMocker.mockResponse(JSON.stringify(mockAcmgRating))
 
     const client = new AcmgSeqVarClient()
-    const result = await client.updateAcmgRating(seqVar.toName(), mockAcmgRating)
+    const result = await client.updateAcmgRating(seqVar, mockAcmgRating)
 
     expect(result).toEqual(mockAcmgRating)
   })
@@ -112,7 +112,7 @@ describe.concurrent('AcmgSeqVar Client', () => {
     })
 
     const client = new AcmgSeqVarClient()
-    const result = await client.updateAcmgRating(seqVar.toName(), mockAcmgRating)
+    const result = await client.updateAcmgRating(seqVar, mockAcmgRating)
 
     expect(result).toEqual({ status: 500 })
   })
@@ -121,7 +121,7 @@ describe.concurrent('AcmgSeqVar Client', () => {
     fetchMocker.mockResponse(JSON.stringify({}))
 
     const client = new AcmgSeqVarClient()
-    const result = await client.deleteAcmgRating(seqVar.toName())
+    const result = await client.deleteAcmgRating(seqVar)
 
     expect(result).toEqual({})
   })
@@ -135,7 +135,7 @@ describe.concurrent('AcmgSeqVar Client', () => {
     })
 
     const client = new AcmgSeqVarClient()
-    const result = await client.deleteAcmgRating(seqVar.toName())
+    const result = await client.deleteAcmgRating(seqVar)
 
     expect(result).toEqual({ status: 500 })
   })

diff --git a/frontend/src/api/__tests__/annonars.spec.ts b/frontend/src/api/__tests__/annonars.spec.ts
@@ -5,9 +5,12 @@ import { AnnonarsClient } from '@/api/annonars'
 import * as BRCA1geneInfo from '@/assets/__tests__/BRCA1GeneInfo.json'
 import * as BRCA1VariantInfo from '@/assets/__tests__/BRCA1VariantInfo.json'
 import * as EMPSearchInfo from '@/assets/__tests__/EMPSearchInfo.json'
+import { SeqvarImpl } from '@/lib/genomicVars'
 
 const fetchMocker = createFetchMock(vi)
 
+const seqVar = new SeqvarImpl('grch37', '1', 123, 'A', 'G')
+
 describe.concurrent('Annonars Client', () => {
   beforeEach(() => {
     fetchMocker.enableMocks()
@@ -39,7 +42,7 @@ describe.concurrent('Annonars Client', () => {
     fetchMocker.mockResponseOnce(JSON.stringify(BRCA1VariantInfo))
 
     const client = new AnnonarsClient()
-    const result = await client.fetchVariantInfo('grch37', 'chr17', 43044295, 'A', 'G')
+    const result = await client.fetchVariantInfo(seqVar)
     expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1VariantInfo))
   })
 
@@ -52,11 +55,12 @@ describe.concurrent('Annonars Client', () => {
     })
 
     const client = new AnnonarsClient()
-    const result = await client.fetchVariantInfo('grch38', 'chr17', 43044295, 'A', 'G')
+    const result = await client.fetchVariantInfo(seqVar)
     expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1VariantInfo))
   })
 
   it('fails to fetch variant info with wrong variant', async () => {
+    const seqVarInvalid = new SeqvarImpl('grch37', '1', 123, 'A', 'T')
     fetchMocker.mockResponse((req) => {
       if (req.url.includes('alternative=G')) {
         return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
@@ -65,7 +69,7 @@ describe.concurrent('Annonars Client', () => {
     })
 
     const client = new AnnonarsClient()
-    const result = await client.fetchVariantInfo('grch37', 'chr17', 43044295, 'A', 'T')
+    const result = await client.fetchVariantInfo(seqVarInvalid)
     expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
   })
 

diff --git a/frontend/src/api/__tests__/mehari.spec.ts b/frontend/src/api/__tests__/mehari.spec.ts
@@ -4,9 +4,14 @@ 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'
+import { SeqvarImpl } from '@/lib/genomicVars'
+import { LinearStrucvarImpl } from '@/lib/genomicVars'
 
 const fetchMocker = createFetchMock(vi)
 
+const seqVar = new SeqvarImpl('grch37', '1', 123, 'A', 'G')
+const strucVar = new LinearStrucvarImpl('DEL', 'grch37', 'chr17', 43044295, 43044297)
+
 describe.concurrent('Mehari Client', () => {
   beforeEach(() => {
     fetchMocker.enableMocks()
@@ -17,26 +22,20 @@ describe.concurrent('Mehari Client', () => {
     fetchMocker.mockResponseOnce(JSON.stringify(BRCA1TxInfo))
 
     const client = new MehariClient()
-    const result = await client.retrieveSeqvarsCsq(
-      'grch37',
-      'chr17',
-      43044295,
-      'A',
-      'G',
-      'HGNC:1100'
-    )
+    const result = await client.retrieveSeqvarsCsq(seqVar, '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.retrieveSeqvarsCsq('grch37', 'chr17', 43044295, 'A', 'G')
+    const result = await client.retrieveSeqvarsCsq(seqVar)
     expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1TxInfo))
   })
 
   it('fails to fetch variant info with wrong variant', async () => {
+    const seqVarInvalid = new SeqvarImpl('grch37', '1', 123, 'A', 'T')
     fetchMocker.mockResponse((req) => {
       if (req.url.includes('alternative=G')) {
         return Promise.resolve(JSON.stringify(BRCA1TxInfo))
@@ -45,28 +44,29 @@ describe.concurrent('Mehari Client', () => {
     })
 
     const client = new MehariClient()
-    const result = await client.retrieveSeqvarsCsq('grch37', 'chr17', 43044295, 'A', 'T')
+    const result = await client.retrieveSeqvarsCsq(seqVarInvalid)
     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')
+    const result = await client.retrieveStrucvarsCsq(strucVar)
     expect(JSON.stringify(result)).toEqual(JSON.stringify(SVInfo))
   })
 
   it('fails to fetch variant info with wrong variant', async () => {
+    const strucVarInvalid = new LinearStrucvarImpl('DUP', 'grch37', 'chr17', 43044295, 43044297)
     fetchMocker.mockResponse((req) => {
-      if (req.url.includes('alternative=G')) {
+      if (req.url.includes('DEL')) {
         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')
+    const result = await client.retrieveStrucvarsCsq(strucVarInvalid)
     expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
   })
 })
diff --git a/frontend/src/api/acmgSeqvar.ts b/frontend/src/api/acmgSeqvar.ts
@@ -1,4 +1,5 @@
 import { API_V1_BASE_PREFIX } from '@/api/common'
+import type { SeqvarImpl } from '@/lib/genomicVars'
 import { type AcmgRatingBackend } from '@/stores/seqvarAcmgRating'
 
 /**
@@ -33,11 +34,11 @@ export class AcmgSeqVarClient {
   /**
    * Obtains the ACMG rating for a variant.
    *
-   * @param variantName The variant to retrieve the ACMG rating for.
+   * @param seqvar The variant to retrieve the ACMG rating for.
    * @returns The ACMG rating for the variant.
    */
-  async fetchAcmgRating(variantName: string): Promise<any> {
-    const url = `${this.apiBaseUrl}acmgSeqvar/get?seqvar=${variantName}`
+  async fetchAcmgRating(seqvar: SeqvarImpl): Promise<any> {
+    const url = `${this.apiBaseUrl}acmgSeqvar/get?seqvar=${seqvar.toName()}`
     const response = await fetch(url, {
       method: 'GET',
       mode: 'cors',
@@ -50,11 +51,11 @@ export class AcmgSeqVarClient {
    * Save the ACMG rating for a variant.
    */
   async saveAcmgRating(
-    variantName: string,
+    seqVar: SeqvarImpl,
     acmgRating: AcmgRatingBackend
   ): Promise<AcmgRatingBackend> {
     const postData = `{
-      "seqvar_name": "${variantName}",
+      "seqvar_name": "${seqVar.toName()}",
       "acmg_rank": ${JSON.stringify(acmgRating)}
     }`
     const response = await fetch(`${this.apiBaseUrl}acmgSeqvar/create`, {
@@ -74,11 +75,11 @@ export class AcmgSeqVarClient {
    * Update the ACMG rating for a variant.
    */
   async updateAcmgRating(
-    variantName: string,
+    seqVar: SeqvarImpl,
     acmgRating: AcmgRatingBackend
   ): Promise<AcmgRatingBackend> {
     const postData = `{
-      "seqvar_name": "${variantName}",
+      "seqvar_name": "${seqVar.toName()}",
       "acmg_rank": ${JSON.stringify(acmgRating)}
     }`
     const response = await fetch(`${this.apiBaseUrl}acmgSeqvar/update`, {
@@ -97,8 +98,8 @@ export class AcmgSeqVarClient {
   /**
    * Delete the ACMG rating for a variant.
    */
-  async deleteAcmgRating(variantName: string): Promise<AcmgRatingBackend> {
-    const response = await fetch(`${this.apiBaseUrl}acmgSeqvar/delete?seqvar=${variantName}`, {
+  async deleteAcmgRating(seqVar: SeqvarImpl): Promise<AcmgRatingBackend> {
+    const response = await fetch(`${this.apiBaseUrl}acmgSeqvar/delete?seqvar=${seqVar.toName()}`, {
       method: 'DELETE',
       mode: 'cors',
       credentials: 'include'

diff --git a/frontend/src/api/annonars.ts b/frontend/src/api/annonars.ts
@@ -1,6 +1,7 @@
 import { chunks } from '@reactgular/chunks'
 
 import { API_INTERNAL_BASE_PREFIX_ANNONARS } from '@/api/common'
+import type { LinearStrucvar, Seqvar } from '@/lib/genomicVars'
 
 const API_BASE_URL = `${API_INTERNAL_BASE_PREFIX_ANNONARS}/`
 
@@ -28,28 +29,19 @@ export class AnnonarsClient {
   /**
    * Fetch variant information via annonars and mehari REST APIs.
    *
-   * @param genomeRelease GRCh37 or GRCh38.
-   * @param chromosome Chromosome, e.g., `"chr1"`.
-   * @param pos Position of the variant.
-   * @param reference Reference nucleotide, e.g., `"A"`.
-   * @param alternative Alternative nucleotide, e.g., `"G"`.
+   * @param seqvar The variant to retrieve the information for.
    */
-  async fetchVariantInfo(
-    genomeRelease: string,
-    chromosome: string,
-    pos: number,
-    reference: string,
-    alternative: string
-  ): Promise<any> {
-    let chrom = chromosome.replace('chr', '')
-    if (genomeRelease !== 'grch37') {
-      chrom = `chr${chrom}`
+  async fetchVariantInfo(seqvar: Seqvar): Promise<any> {
+    const { genomeBuild, chrom, pos, del, ins } = seqvar
+    let chromosome = chrom.replace('chr', '')
+    if (genomeBuild !== 'grch37') {
+      chromosome = `chr${chrom}`
     }
 
     const url =
-      `${this.apiBaseUrl}annos/variant?genome_release=${genomeRelease}&` +
-      `chromosome=${chrom}&pos=${pos}&reference=${reference}&` +
-      `alternative=${alternative}`
+      `${this.apiBaseUrl}annos/variant?genome_release=${genomeBuild}&` +
+      `chromosome=${chromosome}&pos=${pos}&reference=${del}&` +
+      `alternative=${ins}`
 
     const response = await fetch(url, {
       method: 'GET'
@@ -105,16 +97,14 @@ export class AnnonarsClient {
    * Fetch overlapping ClinVar strucvars via annonars REST API.
    */
   async fetchClinvarStrucvars(
-    genomeRelease: string,
-    chromosome: string,
-    start: number,
-    end: number,
+    strucvar: LinearStrucvar,
     pageSize: number = 1000,
     minOverlap: number = 0.1
   ): Promise<any> {
+    const { genomeBuild, chrom, start, stop } = strucvar
     const url =
-      `${this.apiBaseUrl}clinvar-sv/query?genomeRelease=${genomeRelease}&` +
-      `chromosome=${chromosome}&start=${start}&stop=${end}&pageSize=${pageSize}&` +
+      `${this.apiBaseUrl}clinvar-sv/query?genomeRelease=${genomeBuild}&` +
+      `chromosome=${chrom}&start=${start}&stop=${stop}&pageSize=${pageSize}&` +
       `minOverlap=${minOverlap}`
 
     const response = await fetch(url, {

diff --git a/frontend/src/api/mehari.ts b/frontend/src/api/mehari.ts
@@ -1,4 +1,5 @@
 import { API_INTERNAL_BASE_PREFIX_MEHARI } from '@/api/common'
+import type { LinearStrucvar, Seqvar } from '@/lib/genomicVars'
 
 const API_BASE_URL = `${API_INTERNAL_BASE_PREFIX_MEHARI}/`
 
@@ -11,36 +12,25 @@ export class MehariClient {
     this.csrfToken = csrfToken ?? null
   }
 
-  async retrieveSeqvarsCsq(
-    genomeRelease: string,
-    chromosome: string,
-    pos: number,
-    reference: string,
-    alternative: string,
-    hgnc_id?: string
-  ): Promise<any> {
+  async retrieveSeqvarsCsq(seqvar: Seqvar, hgnc_id?: string): Promise<any> {
+    const { genomeBuild, chrom, pos, del, ins } = seqvar
     const hgncSuffix = hgnc_id ? `&hgnc_id=${hgnc_id}` : ''
     const url =
-      `${this.apiBaseUrl}seqvars/csq?genome_release=${genomeRelease}&` +
-      `chromosome=${chromosome}&position=${pos}&reference=${reference}&` +
-      `alternative=${alternative}${hgncSuffix}`
+      `${this.apiBaseUrl}seqvars/csq?genome_release=${genomeBuild}&` +
+      `chromosome=${chrom}&position=${pos}&reference=${del}&` +
+      `alternative=${ins}${hgncSuffix}`
 
     const response = await fetch(url, {
       method: 'GET'
     })
     return await response.json()
   }
 
-  async retrieveStrucvarsCsq(
-    genomeRelease: string,
-    chromosome: string,
-    start: number,
-    stop: number,
-    sv_type: string
-  ): Promise<any> {
+  async retrieveStrucvarsCsq(strucvar: LinearStrucvar): Promise<any> {
+    const { genomeBuild, chrom, start, stop, svType } = strucvar
     const url =
-      `${this.apiBaseUrl}strucvars/csq?genome_release=${genomeRelease}&` +
-      `chromosome=${chromosome}&start=${start}&stop=${stop}&sv_type=${sv_type}`
+      `${this.apiBaseUrl}strucvars/csq?genome_release=${genomeBuild}&` +
+      `chromosome=${chrom}&start=${start}&stop=${stop}&sv_type=${svType}`
     const response = await fetch(url, {
       method: 'GET'
     })