fix: more comprehensive usage of types (#64)

src/api/annonars/client.spec.ts

@@ -4,7 +4,9 @@ import { beforeEach, describe, expect, it, vi } from 'vitest'
 import createFetchMock from 'vitest-fetch-mock'
 
 import { LinearStrucvarImpl, SeqvarImpl } from '../../lib/genomicVars'
+import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base'
 import { AnnonarsClient } from './client'
+import { ClinvarSvQueryResponse, GeneSearchResponse, SeqvarInfoResponse } from './types'
 
 const geneInfoBrca1Json = JSON.parse(
   fs.readFileSync(
@@ -82,7 +84,9 @@ describe.concurrent('AnnonarsClient.fetchVariantInfo()', () => {
     const result = await client.fetchVariantInfo(seqvar)
 
     // assert:
-    expect(JSON.stringify(result)).toEqual(JSON.stringify(variantInfoBrca1Json))
+    expect(JSON.stringify(result)).toEqual(
+      JSON.stringify(SeqvarInfoResponse.fromJson(variantInfoBrca1Json))
+    )
   })
 
   it('do removes chr prefix from chromosome if genome release is grch38', async () => {
@@ -99,7 +103,9 @@ describe.concurrent('AnnonarsClient.fetchVariantInfo()', () => {
     const result = await client.fetchVariantInfo(seqvar)
 
     // assert:
-    expect(JSON.stringify(result)).toEqual(JSON.stringify(variantInfoBrca1Json))
+    expect(JSON.stringify(result)).toEqual(
+      JSON.stringify(SeqvarInfoResponse.fromJson(variantInfoBrca1Json))
+    )
   })
 
   it('fails to fetch variant info with wrong variant', async () => {
@@ -179,7 +185,9 @@ describe.concurrent('AnnonarsClient.fetchGenes()', () => {
     )
 
     // assert:
-    expect(JSON.stringify(result)).toEqual(JSON.stringify(searchInfoInfoEmpJson))
+    expect(JSON.stringify(result)).toEqual(
+      JSON.stringify(GeneSearchResponse.fromJson(searchInfoInfoEmpJson))
+    )
   })
 
   it('fails to fetch genes with wrong query', async () => {
@@ -218,7 +226,9 @@ describe.concurrent('AnnonarsClient.fetchGeneInfos()', () => {
     const result = await client.fetchGeneInfos(['BRCA1', 'BRCA2'])
 
     // assert:
-    expect(JSON.stringify(result)).toMatch(JSON.stringify([geneInfoBrca1Json]))
+    expect(JSON.stringify(result)).toMatch(
+      JSON.stringify([GeneInfoRecord.fromJson(geneInfoBrca1Json)])
+    )
   })
 
   it('fails to fetch gene infos with wrong HGNC id', async () => {
@@ -254,7 +264,9 @@ describe.concurrent('AnnonarsClient.fetchClinvarStrucvars()', () => {
     const result = await client.fetchClinvarStrucvars(strucVar)
 
     // assert:
-    expect(JSON.stringify(result)).toMatch(JSON.stringify(clinvarStrucvarResponseBrca1Json))
+    expect(JSON.stringify(result)).toMatch(
+      JSON.stringify(ClinvarSvQueryResponse.fromJson(clinvarStrucvarResponseBrca1Json))
+    )
   })
 
   it('fails to overlapping ClinVar Strucvars if query fails', async () => {

src/api/annonars/client.ts

@@ -3,7 +3,12 @@ import { chunks } from '@reactgular/chunks'
 import type { LinearStrucvar, Seqvar } from '../../lib/genomicVars'
 import { ClinvarPerGeneRecord } from '../../pbs/annonars/clinvar/per_gene'
 import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base'
-import { GeneInfoResult } from './types'
+import {
+  ClinvarSvQueryResponse,
+  GeneInfoResult,
+  GeneSearchResponse,
+  SeqvarInfoResponse
+} from './types'
 
 /** Base URL for annonars API access */
 const API_BASE_URL = '/internal/proxy/annonars/'
@@ -35,7 +40,7 @@ export class AnnonarsClient {
    *
    * @param seqvar The variant to retrieve the information for.
    */
-  async fetchVariantInfo(seqvar: Seqvar): Promise<any> {
+  async fetchVariantInfo(seqvar: Seqvar): Promise<SeqvarInfoResponse> {
     const { genomeBuild, chrom, pos, del, ins } = seqvar
     let chromosome = chrom.replace('chr', '')
     if (genomeBuild !== 'grch37') {
@@ -53,7 +58,8 @@ export class AnnonarsClient {
     if (!response.ok) {
       throw new Error(`failed to fetch variant info: ${response.statusText}`)
     }
-    return await response.json()
+    const responseJson = await response.json()
+    return SeqvarInfoResponse.fromJson(responseJson)
   }
 
   /**
@@ -76,16 +82,18 @@ export class AnnonarsClient {
    * Search for genes, e.g., by symbol, via annonars REST API.
    *
    * @param query Query string to search for.
-   * @returns
+   * @returns Promise with gene search response.
+   * @throws Error if the request fails.
    */
-  async fetchGenes(query: string): Promise<any> {
+  async fetchGenes(query: string): Promise<GeneSearchResponse> {
     const response = await fetch(`${this.apiBaseUrl}genes/search?q=${query}`, {
       method: 'GET'
     })
     if (!response.ok) {
       throw new Error(`failed to fetch genes: ${response.statusText}`)
     }
-    return await response.json()
+    const responseJson = await response.json()
+    return GeneSearchResponse.fromJson(responseJson)
   }
 
   /**
@@ -98,7 +106,7 @@ export class AnnonarsClient {
   async fetchGeneInfos(hgncIds: string[], chunkSize?: number): Promise<GeneInfoRecord[]> {
     const hgncIdChunks = chunks(hgncIds, chunkSize ?? 10)
 
-    const promises = hgncIdChunks.map(async (chunk: any) => {
+    const promises = hgncIdChunks.map(async (chunk) => {
       const url = `${this.apiBaseUrl}genes/info?hgnc_id=${chunk.join(',')}`
 
       const response = await fetch(url, {
@@ -111,12 +119,13 @@ export class AnnonarsClient {
     })
 
     const responses = await Promise.all(promises)
-    const results = await Promise.all(responses.map((response: any) => response.json()))
+    const resultJsons = await Promise.all(responses.map((response) => response.json()))
 
-    const result: any = []
-    results.forEach((chunk: any) => {
+    const result: GeneInfoRecord[] = []
+    resultJsons.forEach((chunk: any) => {
       for (const value of Object.values(chunk.genes)) {
-        result.push(value)
+        // @ts-ignore
+        result.push(GeneInfoRecord.fromJson(value as JsonValue))
       }
     })
     return result
@@ -129,7 +138,7 @@ export class AnnonarsClient {
     strucvar: LinearStrucvar,
     pageSize: number = 1000,
     minOverlap: number = 0.1
-  ): Promise<any> {
+  ): Promise<ClinvarSvQueryResponse> {
     const { genomeBuild, chrom, start, stop } = strucvar
     const url =
       `${this.apiBaseUrl}clinvar-sv/query?genomeRelease=${genomeBuild}&` +
@@ -142,6 +151,7 @@ export class AnnonarsClient {
     if (!response.ok) {
       throw new Error(`failed to fetch clinvar strucvars: ${response.statusText}`)
     }
-    return await response.json()
+    const responseJson = await response.json()
+    return ClinvarSvQueryResponse.fromJson(responseJson)
   }
 }

src/api/annonars/types.ts

@@ -1,6 +1,7 @@
 import { JsonValue } from '@protobuf-ts/runtime'
 
-import { Record as ClinvarRecord } from '../../pbs/annonars/clinvar/minimal'
+import { Record as ClinvarSeqvarRecord } from '../../pbs/annonars/clinvar/minimal'
+import { Record as ClinvarStrucvarRecord } from '../../pbs/annonars/clinvar/sv'
 import { Record as UcscConservationRecord } from '../../pbs/annonars/cons/base'
 import { Record as DbsnpRecord } from '../../pbs/annonars/dbsnp/base'
 import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base'
@@ -10,6 +11,147 @@ import { Record as Gnomad4Record } from '../../pbs/annonars/gnomad/gnomad4'
 import { Record as GnomadMtdnaRecord } from '../../pbs/annonars/gnomad/mtdna'
 import { Record as HelixmtdbRecord } from '../../pbs/annonars/helixmtdb/base'
 
+/**
+ * Interface for Clinvar Strucvars query response as returned by
+ */
+export interface ClinvarSvQueryResponse$Api {
+  records: ClinvarStrucvarRecord[]
+}
+
+/**
+ * Interface for Clinvar Strucvars query result.
+ */
+export interface ClinvarSvQueryResponse {
+  records: ClinvarStrucvarRecord[]
+}
+
+/**
+ * Helper class to convert `ClinvarSvQueryResponse$Api` to `ClinvarSvQueryResponse`.
+ */
+class ClinvarSvQueryResponse$Type {
+  fromJson(apiResponse: ClinvarSvQueryResponse$Api): ClinvarSvQueryResponse {
+    return {
+      records: apiResponse.records
+    }
+  }
+}
+
+/**
+ * Helper instance to convert `ClinvarSvQueryResponse$Api` to `ClinvarSvQueryResponse`.
+ */
+export const ClinvarSvQueryResponse = new ClinvarSvQueryResponse$Type()
+
+/**
+ * Interface for gene names as returned by `genes/search` API.
+ */
+export interface GeneNames$Api {
+  hgnc_id: string
+  symbol: string
+  name: string
+  alias_symbol: string[]
+  alias_name: string[]
+  ensembl_gene_id?: string
+  ncbi_gene_id?: string
+}
+
+/**
+ * Interface for gene names results.
+ */
+export interface GeneNames {
+  hgncId: string
+  symbol: string
+  name: string
+  aliasSymbol: string[]
+  aliasName: string[]
+  ensemblGeneId?: string
+  ncbiGeneId?: string
+}
+
+/**
+ * Helper class to convert `GeneNames$Api` to `GeneNames`.
+ */
+class GeneNames$Type {
+  fromJson(apiGene: GeneNames$Api): GeneNames {
+    return {
+      hgncId: apiGene.hgnc_id,
+      symbol: apiGene.symbol,
+      name: apiGene.name,
+      aliasSymbol: apiGene.alias_symbol,
+      aliasName: apiGene.alias_name,
+      ensemblGeneId: apiGene.ensembl_gene_id,
+      ncbiGeneId: apiGene.ncbi_gene_id
+    }
+  }
+}
+
+/**
+ * Helper instance to convert `GeneNames$Api` to `GeneNames`.
+ */
+export const GeneNames = new GeneNames$Type()
+
+/**
+ * Interface for scored gene names as returned by `genes/search` API.
+ */
+export interface ScoreGeneNames$Api {
+  score: number
+  data: GeneNames$Api
+}
+
+/**
+ * Interface for scored gene names results.
+ */
+export interface ScoreGeneNames {
+  score: number
+  data: GeneNames
+}
+
+/**
+ * Helper class to convert `ScoreGeneNames$Api` to `ScoreGeneNames`.
+ */
+class ScoreGeneNames$Type {
+  fromJson(apiGene: ScoreGeneNames$Api): ScoreGeneNames {
+    return {
+      score: apiGene.score,
+      data: GeneNames.fromJson(apiGene.data)
+    }
+  }
+}
+
+/**
+ * Helper instance to convert `ScoreGeneNames$Api` to `ScoreGeneNames`.
+ */
+export const ScoreGeneNames = new ScoreGeneNames$Type()
+
+/**
+ * Interface for gene search query response as returned by API.
+ */
+export interface GeneSearchResponse$Api {
+  genes: ScoreGeneNames$Api[]
+}
+
+/**
+ * Interface for gene search query result.
+ */
+export interface GeneSearchResponse {
+  genes: ScoreGeneNames[]
+}
+
+/**
+ * Helper class to convert `GeneSearchResponse$Api` to `GeneSearchResponse`.
+ */
+class GeneSearchResponse$Type {
+  fromJson(apiResponse: GeneSearchResponse$Api): GeneSearchResponse {
+    return {
+      genes: apiResponse.genes.map((gene) => ScoreGeneNames.fromJson(gene))
+    }
+  }
+}
+
+/**
+ * Helper instance to convert `GeneSearchResponse$Api` to `GeneSearchResponse`.
+ */
+export const GeneSearchResponse = new GeneSearchResponse$Type()
+
 /**
  * Interface for gene info result.
  */
@@ -91,7 +233,7 @@ export interface SeqvarInfoResult {
   gnomadGenomes?: Gnomad2Record | Gnomad3Record | Gnomad4Record
   helixmtdb?: HelixmtdbRecord
   ucscConservation: UcscConservationRecord[][]
-  clinvar?: ClinvarRecord
+  clinvar?: ClinvarSeqvarRecord
 }
 
 /**
@@ -129,7 +271,7 @@ class SeqvarInfoResult$Type {
         apiResult.clinvar === null
           ? undefined
           : // @ts-ignore
-            ClinvarRecord.fromJson(apiResult.clinvar as JsonValue)
+            ClinvarSeqvarRecord.fromJson(apiResult.clinvar as JsonValue)
     }
   }
 }