feat: make components more robust in case of store/api errors (#160) (#…

…161)

src/api/annonars/client.spec.ts

@@ -1,9 +1,10 @@
 import fs from 'fs'
 import path from 'path'
-import { beforeEach, describe, expect, it, vi } from 'vitest'
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest'
 import createFetchMock from 'vitest-fetch-mock'
 
 import { LinearStrucvarImpl, SeqvarImpl } from '../../lib/genomicVars'
+import { setupUrlConfigForTesting, urlConfig } from '../../lib/urlConfig'
 import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base'
 import { AnnonarsClient } from './client'
 import { ClinvarSvQueryResponse } from './types'
@@ -32,6 +33,38 @@ const fetchMocker = createFetchMock(vi)
 /** Example Sequence Variant */
 const seqvar = new SeqvarImpl('grch37', '1', 123, 'A', 'G')
 
+describe.concurrent('AnnonarsClient.construct()', () => {
+  afterEach(() => {
+    setupUrlConfigForTesting()
+  })
+
+  it('constructs correctly with default base URL', () => {
+    // act:
+    const client = new AnnonarsClient()
+
+    // assert:
+    expect(client).toBeDefined()
+  })
+
+  it('constructs correctly with custom base URL', () => {
+    // act:
+    const client = new AnnonarsClient('http://localhost:8080')
+
+    // assert:
+    expect(client).toBeDefined()
+  })
+
+  it('throws error if no base URL is configured', () => {
+    // arrange:
+    urlConfig.baseUrlAnnonars = undefined
+
+    // (guarded)
+    expect(() => new AnnonarsClient(undefined)).toThrow(
+      'Configuration error: API base URL not configured'
+    )
+  })
+})
+
 describe.concurrent('AnnonarsClient.fetchGeneInfo()', () => {
   beforeEach(() => {
     fetchMocker.enableMocks()

src/api/annonars/client.ts

@@ -4,6 +4,7 @@ import type { Seqvar, Strucvar } from '../../lib/genomicVars'
 import { urlConfig } from '../../lib/urlConfig'
 import { ClinvarPerGeneRecord } from '../../pbs/annonars/clinvar/per_gene'
 import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base'
+import { ConfigError, InvalidResponseContent, StatusCodeNotOk } from '../common'
 import {
   ClinvarSvQueryResponse,
   GeneInfoResult,
@@ -21,34 +22,47 @@ export class AnnonarsClient {
    * @param apiBaseUrl
    *            API base to the backend, excluding trailing `/`.
    *            The default is declared in '@/lib/urlConfig`.
-   * @throws Error if the API base URL is not configured.
+   * @throws ConfigError if the API base URL is not configured.
    */
   constructor(apiBaseUrl?: string) {
     if (apiBaseUrl !== undefined || urlConfig.baseUrlAnnonars !== undefined) {
       // @ts-ignore
       this.apiBaseUrl = apiBaseUrl ?? urlConfig.baseUrlAnnonars
     } else {
-      throw new Error('Configuration error: API base URL not configured')
+      throw new ConfigError('Configuration error: API base URL not configured')
     }
   }
 
   /**
    * Fetch gene information via annonars REST API.
    *
    * @param hgncId HGNC ID, e.g., `"HGNC:26467"`.
+   * @returns Promise with gene information.
+   * @throws StatusCodeNotOk if the request fails.
+   * @throws InvalidResponseContent if the response is not valid JSON.
    */
   async fetchGeneInfo(hgncId: string): Promise<GeneInfoResult> {
     const response = await fetch(`${this.apiBaseUrl}/genes/info?hgnc_id=${hgncId}`, {
       method: 'GET'
     })
-    const responseJson = await response.json()
-    return GeneInfoResult.fromJson(responseJson)
+    if (!response.ok) {
+      throw new StatusCodeNotOk(`failed to fetch gene info: ${response.statusText}`)
+    }
+    try {
+      const responseJson = await response.json()
+      return GeneInfoResult.fromJson(responseJson)
+    } catch (e) {
+      throw new InvalidResponseContent(`failed to parse gene info response: ${e}`)
+    }
   }
 
   /**
    * Fetch variant information via annonars and mehari REST APIs.
    *
    * @param seqvar The variant to retrieve the information for.
+   * @returns Promise with variant information.
+   * @throws StatusCodeNotOk if the request fails.
+   * @throws InvalidResponseContent if the response is not valid JSON.
    */
   async fetchVariantInfo(seqvar: Seqvar): Promise<SeqvarInfoResponse> {
     const { genomeBuild, chrom, pos, del, ins } = seqvar
@@ -66,30 +80,40 @@ export class AnnonarsClient {
       method: 'GET'
     })
     if (!response.ok) {
-      throw new Error(`failed to fetch variant info: ${response.statusText}`)
+      throw new StatusCodeNotOk(`failed to fetch variant info: ${response.statusText}`)
+    }
+    try {
+      const responseJson = await response.json()
+      return SeqvarInfoResponse.fromJson(responseJson)
+    } catch (e) {
+      throw new InvalidResponseContent(`failed to parse variant info response: ${e}`)
     }
-    const responseJson = await response.json()
-    return SeqvarInfoResponse.fromJson(responseJson)
   }
 
   /**
    * Fetch per-gene ClinVar information via annonars REST API.
    *
-   * @param hgncId
-   * @returns
+   * @param hgncId HGNC ID, e.g., `"HGNC:26467"`.
+   * @returns Promise with per-gene ClinVar information.
+   * @throws StatusCodeNotOk if the request fails.
+   * @throws InvalidResponseContent if the response is not valid JSON.
    */
   async fetchGeneClinvarInfo(hgncId: string): Promise<ClinvarPerGeneRecord> {
     const response = await fetch(`${this.apiBaseUrl}/genes/clinvar?hgnc_id=${hgncId}`, {
       method: 'GET'
     })
     if (!response.ok) {
-      throw new Error(`failed to fetch gene clinvar info: ${response.statusText}`)
+      throw new StatusCodeNotOk(`failed to fetch gene clinvar info: ${response.statusText}`)
     }
     const responseJson = await response.json()
     if (responseJson?.genes && responseJson?.genes[hgncId]) {
-      return ClinvarPerGeneRecord.fromJson(responseJson.genes[hgncId])
+      try {
+        return ClinvarPerGeneRecord.fromJson(responseJson.genes[hgncId])
+      } catch (e) {
+        throw new InvalidResponseContent(`failed to parse gene clinvar info response: ${e}`)
+      }
     } else {
-      throw new Error(`failed to fetch gene clinvar info for HGNC ID: ${hgncId}`)
+      throw new InvalidResponseContent(`failed to fetch gene clinvar info for HGNC ID: ${hgncId}`)
     }
   }
 
@@ -98,17 +122,22 @@ export class AnnonarsClient {
    *
    * @param query Query string to search for.
    * @returns Promise with gene search response.
-   * @throws Error if the request fails.
+   * @throws StatusCodeNotOk if the request fails.
+   * @throws InvalidResponseContent if the response is not valid JSON.
    */
   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}`)
+      throw new StatusCodeNotOk(`failed to fetch genes: ${response.statusText}`)
+    }
+    try {
+      const responseJson = await response.json()
+      return GeneSearchResponse.fromJson(responseJson)
+    } catch (e) {
+      throw new InvalidResponseContent(`failed to parse gene search response: ${e}`)
     }
-    const responseJson = await response.json()
-    return GeneSearchResponse.fromJson(responseJson)
   }
 
   /**
@@ -117,6 +146,8 @@ export class AnnonarsClient {
    * @param hgncIds Array of HGNC IDs to use, e.g., `["HGNC:26467"]`.
    * @param chunkSize How many IDs to send in one request.
    * @returns Promise with an array of gene information objects.
+   * @throws StatusCodeNotOk if the request fails.
+   * @throws InvalidResponseContent if the response is not valid JSON.
    */
   async fetchGeneInfos(hgncIds: string[], chunkSize?: number): Promise<GeneInfoRecord[]> {
     const hgncIdChunks = chunks(hgncIds, chunkSize ?? 10)
@@ -128,26 +159,35 @@ export class AnnonarsClient {
         method: 'GET'
       })
       if (!response.ok) {
-        throw new Error(`failed to fetch gene infos: ${response.statusText}`)
+        throw new StatusCodeNotOk(`failed to fetch gene infos: ${response.statusText}`)
       }
       return response
     })
 
-    const responses = await Promise.all(promises)
-    const resultJsons = await Promise.all(responses.map((response) => response.json()))
+    try {
+      const responses = await Promise.all(promises)
+      const resultJsons = await Promise.all(responses.map((response) => response.json()))
 
-    const result: GeneInfoRecord[] = []
-    resultJsons.forEach((chunk: any) => {
-      for (const value of Object.values(chunk.genes)) {
-        // @ts-ignore
-        result.push(GeneInfoRecord.fromJson(value as JsonValue))
-      }
-    })
-    return result
+      const result: GeneInfoRecord[] = []
+      resultJsons.forEach((chunk: any) => {
+        for (const value of Object.values(chunk.genes)) {
+          // @ts-ignore
+          result.push(GeneInfoRecord.fromJson(value as JsonValue))
+        }
+      })
+      return result
+    } catch (e) {
+      throw new InvalidResponseContent(`failed to parse gene infos response: ${e}`)
+    }
   }
 
   /**
    * Fetch overlapping ClinVar strucvars via annonars REST API.
+   *
+   * @param strucvar The structural variant to retrieve the information for.
+   * @param pageSize The maximum number of records to return.
+   * @param minOverlap The minimum overlap required for a record to be returned.
+   * @returns Promise with ClinVar structural variant query response.
    */
   async fetchClinvarStrucvars(
     strucvar: Strucvar,
@@ -172,9 +212,13 @@ export class AnnonarsClient {
       method: 'GET'
     })
     if (!response.ok) {
-      throw new Error(`failed to fetch clinvar strucvars: ${response.statusText}`)
+      throw new StatusCodeNotOk(`failed to fetch clinvar strucvars: ${response.statusText}`)
+    }
+    try {
+      const responseJson = await response.json()
+      return ClinvarSvQueryResponse.fromJson(responseJson)
+    } catch (e) {
+      throw new InvalidResponseContent(`failed to parse clinvar strucvars response: ${e}`)
     }
-    const responseJson = await response.json()
-    return ClinvarSvQueryResponse.fromJson(responseJson)
   }
 }

src/api/cadaPrio/__snapshots__/client.spec.ts.snap

@@ -1,3 +1,3 @@
 // Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
-exports[`CadaPrioClient > throws in case of fetching problems 1`] = `"{"entries":[{"hgncId":"HGNC:12786","ncbiGeneId":"7476","geneSymbol":"WNT7A","rank":1,"score":76.84823608398438},{"hgncId":"HGNC:11098","ncbiGeneId":"6595","geneSymbol":"SMARCA2","rank":2,"score":76.46592712402344},{"hgncId":"HGNC:25789","ncbiGeneId":"79631","geneSymbol":"EFL1","rank":3,"score":69.20905303955078},{"hgncId":"HGNC:11301","ncbiGeneId":"6729","geneSymbol":"SRP54","rank":4,"score":65.58743286132812},{"hgncId":"HGNC:5154","ncbiGeneId":"3248","geneSymbol":"HPGD","rank":5,"score":63.857845306396484},{"hgncId":"HGNC:4122","ncbiGeneId":"2588","geneSymbol":"GALNS","rank":6,"score":63.840911865234375},{"hgncId":"HGNC:27030","ncbiGeneId":"134218","geneSymbol":"DNAJC21","rank":7,"score":63.35689926147461},{"hgncId":"HGNC:7866","ncbiGeneId":"9241","geneSymbol":"NOG","rank":8,"score":63.207393646240234},{"hgncId":"HGNC:27230","ncbiGeneId":"157570","geneSymbol":"ESCO2","rank":9,"score":63.09525680541992},{"hgncId":"HGNC:2186","ncbiGeneId":"1301","geneSymbol":"COL11A1","rank":10,"score":61.24506378173828},{"hgncId":"HGNC:9587","ncbiGeneId":"9791","geneSymbol":"PTDSS1","rank":11,"score":60.995365142822266},{"hgncId":"HGNC:25507","ncbiGeneId":"55697","geneSymbol":"VAC14","rank":12,"score":60.21630859375},{"hgncId":"HGNC:11602","ncbiGeneId":"6926","geneSymbol":"TBX3","rank":13,"score":59.911136627197266},{"hgncId":"HGNC:4573","ncbiGeneId":"2892","geneSymbol":"GRIA3","rank":14,"score":59.312957763671875},{"hgncId":"HGNC:34016","ncbiGeneId":"100151683","geneSymbol":"RNU4ATAC","rank":15,"score":59.29935836791992},{"hgncId":"HGNC:4220","ncbiGeneId":"8200","geneSymbol":"GDF5","rank":16,"score":58.710994720458984},{"hgncId":"HGNC:23068","ncbiGeneId":"6399","geneSymbol":"TRAPPC2","rank":17,"score":56.57151412963867},{"hgncId":"HGNC:5956","ncbiGeneId":"3549","geneSymbol":"IHH","rank":18,"score":55.67450714111328},{"hgncId":"HGNC:16068","ncbiGeneId":"5116","geneSymbol":"PCNT","rank":19,"score":55.3505859375}]}"`;
+exports[`CadaPrioClient.predictGeneImpact() > throws in case of fetching problems 1`] = `"{"entries":[{"hgncId":"HGNC:12786","ncbiGeneId":"7476","geneSymbol":"WNT7A","rank":1,"score":76.84823608398438},{"hgncId":"HGNC:11098","ncbiGeneId":"6595","geneSymbol":"SMARCA2","rank":2,"score":76.46592712402344},{"hgncId":"HGNC:25789","ncbiGeneId":"79631","geneSymbol":"EFL1","rank":3,"score":69.20905303955078},{"hgncId":"HGNC:11301","ncbiGeneId":"6729","geneSymbol":"SRP54","rank":4,"score":65.58743286132812},{"hgncId":"HGNC:5154","ncbiGeneId":"3248","geneSymbol":"HPGD","rank":5,"score":63.857845306396484},{"hgncId":"HGNC:4122","ncbiGeneId":"2588","geneSymbol":"GALNS","rank":6,"score":63.840911865234375},{"hgncId":"HGNC:27030","ncbiGeneId":"134218","geneSymbol":"DNAJC21","rank":7,"score":63.35689926147461},{"hgncId":"HGNC:7866","ncbiGeneId":"9241","geneSymbol":"NOG","rank":8,"score":63.207393646240234},{"hgncId":"HGNC:27230","ncbiGeneId":"157570","geneSymbol":"ESCO2","rank":9,"score":63.09525680541992},{"hgncId":"HGNC:2186","ncbiGeneId":"1301","geneSymbol":"COL11A1","rank":10,"score":61.24506378173828},{"hgncId":"HGNC:9587","ncbiGeneId":"9791","geneSymbol":"PTDSS1","rank":11,"score":60.995365142822266},{"hgncId":"HGNC:25507","ncbiGeneId":"55697","geneSymbol":"VAC14","rank":12,"score":60.21630859375},{"hgncId":"HGNC:11602","ncbiGeneId":"6926","geneSymbol":"TBX3","rank":13,"score":59.911136627197266},{"hgncId":"HGNC:4573","ncbiGeneId":"2892","geneSymbol":"GRIA3","rank":14,"score":59.312957763671875},{"hgncId":"HGNC:34016","ncbiGeneId":"100151683","geneSymbol":"RNU4ATAC","rank":15,"score":59.29935836791992},{"hgncId":"HGNC:4220","ncbiGeneId":"8200","geneSymbol":"GDF5","rank":16,"score":58.710994720458984},{"hgncId":"HGNC:23068","ncbiGeneId":"6399","geneSymbol":"TRAPPC2","rank":17,"score":56.57151412963867},{"hgncId":"HGNC:5956","ncbiGeneId":"3549","geneSymbol":"IHH","rank":18,"score":55.67450714111328},{"hgncId":"HGNC:16068","ncbiGeneId":"5116","geneSymbol":"PCNT","rank":19,"score":55.3505859375}]}"`;

src/api/cadaPrio/client.spec.ts

@@ -1,8 +1,9 @@
 import fs from 'fs'
 import path from 'path'
-import { beforeEach, describe, expect, it, vi } from 'vitest'
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest'
 import createFetchMock from 'vitest-fetch-mock'
 
+import { setupUrlConfigForTesting, urlConfig } from '../../lib/urlConfig'
 import { CadaPrioClient } from './client'
 
 /** Fixture with prediction results. */
@@ -13,7 +14,39 @@ const cadaPrioPredictResultJson = JSON.parse(
 /** Initialize mock for `fetch()`. */
 const fetchMocker = createFetchMock(vi)
 
-describe.concurrent('CadaPrioClient', () => {
+describe.concurrent('CadaPrioClient.construct()', () => {
+  afterEach(() => {
+    setupUrlConfigForTesting()
+  })
+
+  it('constructs correctly with default base URL', () => {
+    // act:
+    const client = new CadaPrioClient()
+
+    // assert:
+    expect(client).toBeDefined()
+  })
+
+  it('constructs correctly with custom base URL', () => {
+    // act:
+    const client = new CadaPrioClient('http://localhost:8080')
+
+    // assert:
+    expect(client).toBeDefined()
+  })
+
+  it('throws error if no base URL is configured', () => {
+    // arrange:
+    urlConfig.baseUrlCadaPrio = undefined
+
+    // (guarded)
+    expect(() => new CadaPrioClient(undefined)).toThrow(
+      'Configuration error: API base URL not configured'
+    )
+  })
+})
+
+describe.concurrent('CadaPrioClient.predictGeneImpact()', () => {
   beforeEach(() => {
     fetchMocker.enableMocks()
     fetchMocker.resetMocks()

src/api/cadaPrio/client.ts

@@ -1,4 +1,5 @@
 import { urlConfig } from '../../lib/urlConfig'
+import { ConfigError, InvalidResponseContent, StatusCodeNotOk } from '../common'
 import { Response } from './types'
 
 /**
@@ -11,14 +12,14 @@ export class CadaPrioClient {
    * @param apiBaseUrl
    *            API base to the backend, excluding trailing `/`.
    *            The default is declared in '@/lib/urlConfig`.
-   * @throws Error if the API base URL is not configured.
+   * @throws ConfigError if the API base URL is not configured.
    */
   constructor(apiBaseUrl?: string) {
     if (apiBaseUrl !== undefined || urlConfig.baseUrlCadaPrio !== undefined) {
       // @ts-ignore
       this.apiBaseUrl = apiBaseUrl ?? urlConfig.baseUrlCadaPrio
     } else {
-      throw new Error('Configuration error: API base URL not configured')
+      throw new ConfigError('Configuration error: API base URL not configured')
     }
   }
 
@@ -28,7 +29,8 @@ export class CadaPrioClient {
    * @param hpoTerms HPO term IDs (e.g. `HP:0000001`)
    * @param geneSymbols Gene symbols (e.g. `BRCA1`)
    * @returns Promise with response of impact prediction.
-   * @throws Error if the API returns an error.
+   * @throws StatusCodeNotOk if the request fails.
+   * @throws InvalidResponseContent if the response is not valid JSON.
    */
   async predictGeneImpact(hpoTerms: string[], geneSymbols?: string[]): Promise<Response> {
     const geneSuffix = geneSymbols ? `&gene_symbols=${geneSymbols.join(',')}` : ''
@@ -37,7 +39,14 @@ export class CadaPrioClient {
     const response = await fetch(url, {
       method: 'GET'
     })
-    const responseJson = await response.json()
-    return Response.fromJson(responseJson)
+    if (!response.ok) {
+      throw new StatusCodeNotOk(`failed to fetch gene impact prediction: ${response.statusText}`)
+    }
+    try {
+      const responseJson = await response.json()
+      return Response.fromJson(responseJson)
+    } catch (e) {
+      throw new InvalidResponseContent(`failed to parse gene impact prediction response: ${e}`)
+    }
   }
 }