feat: adding api/cadaPrio (#37)

src/api/cadaPrio/client.spec.ts

@@ -0,0 +1,52 @@
+import fs from 'fs'
+import path from 'path'
+import { beforeEach, describe, expect, it, vi } from 'vitest'
+import createFetchMock from 'vitest-fetch-mock'
+
+import { CadaPrioClient } from './client'
+import { Response } from './types'
+
+/** Fixture with prediction results. */
+const cadaPrioPredictResultJson = JSON.parse(
+  fs.readFileSync(path.resolve(__dirname, './fixture.predictResponse.json'), 'utf8')
+)
+
+/** Initialize mock for `fetch()`. */
+const fetchMocker = createFetchMock(vi)
+
+describe.concurrent('CadaPrioClient', () => {
+  beforeEach(() => {
+    fetchMocker.enableMocks()
+    fetchMocker.resetMocks()
+  })
+
+  it('returns the correct result', async () => {
+    // arrange:
+    fetchMocker.mockResponseOnce(JSON.stringify(cadaPrioPredictResultJson))
+
+    // act:
+    const client = new CadaPrioClient()
+    const result = await client.predictGeneImpact(['HP:0000001'])
+
+    // assert:
+    expect(JSON.stringify(result)).toEqual(
+      JSON.stringify(Response.fromJson(cadaPrioPredictResultJson))
+    )
+  })
+
+  it('throws in case of fetching problems', async () => {
+    // arrange:
+    fetchMocker.mockResponse(() => {
+      return Promise.reject(new Error('failed to run cada-prio'))
+    })
+
+    // act:
+    const client = new CadaPrioClient()
+    // (with guard)
+    await expect(async () => await client.predictGeneImpact(['HP:0000001'])).rejects.toThrow(
+      'failed to run cada-prio'
+    )
+
+    // assert:
+  })
+})

src/api/cadaPrio/client.ts

@@ -0,0 +1,34 @@
+import { Response } from './types'
+
+/** Default API base URL to use. */
+const API_BASE_URL = '/internal/proxy/cada-prio/'
+
+/**
+ * Client for the CADA-Prio API.
+ */
+export class CadaPrioClient {
+  private apiBaseUrl: string
+
+  constructor(apiBaseUrl?: string) {
+    this.apiBaseUrl = apiBaseUrl ?? API_BASE_URL
+  }
+
+  /**
+   * Predict similarity of genes with list of HPO terms.
+   *
+   * @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.
+   */
+  async predictGeneImpact(hpoTerms: string[], geneSymbols?: string[]): Promise<Response> {
+    const geneSuffix = geneSymbols ? `&gene_symbols=${geneSymbols.join(',')}` : ''
+    const url = `${this.apiBaseUrl}api/v1/predict?hpo_terms=${hpoTerms.join(',')}${geneSuffix}`
+
+    const response = await fetch(url, {
+      method: 'GET'
+    })
+    const responseJson = await response.json()
+    return Response.fromJson(responseJson)
+  }
+}

src/api/cadaPrio/fixture.predictResponse.json

@@ -0,0 +1,135 @@
+[
+  {
+    "rank": 1,
+    "score": 76.84823608398438,
+    "gene_symbol": "WNT7A",
+    "ncbi_gene_id": "7476",
+    "hgnc_id": "HGNC:12786"
+  },
+  {
+    "rank": 2,
+    "score": 76.46592712402344,
+    "gene_symbol": "SMARCA2",
+    "ncbi_gene_id": "6595",
+    "hgnc_id": "HGNC:11098"
+  },
+  {
+    "rank": 3,
+    "score": 69.20905303955078,
+    "gene_symbol": "EFL1",
+    "ncbi_gene_id": "79631",
+    "hgnc_id": "HGNC:25789"
+  },
+  {
+    "rank": 4,
+    "score": 65.58743286132812,
+    "gene_symbol": "SRP54",
+    "ncbi_gene_id": "6729",
+    "hgnc_id": "HGNC:11301"
+  },
+  {
+    "rank": 5,
+    "score": 63.857845306396484,
+    "gene_symbol": "HPGD",
+    "ncbi_gene_id": "3248",
+    "hgnc_id": "HGNC:5154"
+  },
+  {
+    "rank": 6,
+    "score": 63.840911865234375,
+    "gene_symbol": "GALNS",
+    "ncbi_gene_id": "2588",
+    "hgnc_id": "HGNC:4122"
+  },
+  {
+    "rank": 7,
+    "score": 63.35689926147461,
+    "gene_symbol": "DNAJC21",
+    "ncbi_gene_id": "134218",
+    "hgnc_id": "HGNC:27030"
+  },
+  {
+    "rank": 8,
+    "score": 63.207393646240234,
+    "gene_symbol": "NOG",
+    "ncbi_gene_id": "9241",
+    "hgnc_id": "HGNC:7866"
+  },
+  {
+    "rank": 9,
+    "score": 63.09525680541992,
+    "gene_symbol": "ESCO2",
+    "ncbi_gene_id": "157570",
+    "hgnc_id": "HGNC:27230"
+  },
+  {
+    "rank": 10,
+    "score": 61.24506378173828,
+    "gene_symbol": "COL11A1",
+    "ncbi_gene_id": "1301",
+    "hgnc_id": "HGNC:2186"
+  },
+  {
+    "rank": 11,
+    "score": 60.995365142822266,
+    "gene_symbol": "PTDSS1",
+    "ncbi_gene_id": "9791",
+    "hgnc_id": "HGNC:9587"
+  },
+  {
+    "rank": 12,
+    "score": 60.21630859375,
+    "gene_symbol": "VAC14",
+    "ncbi_gene_id": "55697",
+    "hgnc_id": "HGNC:25507"
+  },
+  {
+    "rank": 13,
+    "score": 59.911136627197266,
+    "gene_symbol": "TBX3",
+    "ncbi_gene_id": "6926",
+    "hgnc_id": "HGNC:11602"
+  },
+  {
+    "rank": 14,
+    "score": 59.312957763671875,
+    "gene_symbol": "GRIA3",
+    "ncbi_gene_id": "2892",
+    "hgnc_id": "HGNC:4573"
+  },
+  {
+    "rank": 15,
+    "score": 59.29935836791992,
+    "gene_symbol": "RNU4ATAC",
+    "ncbi_gene_id": "100151683",
+    "hgnc_id": "HGNC:34016"
+  },
+  {
+    "rank": 16,
+    "score": 58.710994720458984,
+    "gene_symbol": "GDF5",
+    "ncbi_gene_id": "8200",
+    "hgnc_id": "HGNC:4220"
+  },
+  {
+    "rank": 17,
+    "score": 56.57151412963867,
+    "gene_symbol": "TRAPPC2",
+    "ncbi_gene_id": "6399",
+    "hgnc_id": "HGNC:23068"
+  },
+  {
+    "rank": 18,
+    "score": 55.67450714111328,
+    "gene_symbol": "IHH",
+    "ncbi_gene_id": "3549",
+    "hgnc_id": "HGNC:5956"
+  },
+  {
+    "rank": 19,
+    "score": 55.3505859375,
+    "gene_symbol": "PCNT",
+    "ncbi_gene_id": "5116",
+    "hgnc_id": "HGNC:16068"
+  }
+]

src/api/cadaPrio/index.ts

@@ -0,0 +1,2 @@
+export * from './types'
+export * from './client'

src/api/cadaPrio/types.ts

@@ -0,0 +1,57 @@
+/**
+ * One entry of the result as returned by the API.
+ */
+export interface ResponseEntry$Api {
+  /** The HPO term. */
+  hpo_term: string
+  /** The gene symbol. */
+  gene_symbol: string
+  /** The predicted impact. */
+  impact: string
+}
+
+/**
+ * One entry of the result.
+ */
+export interface ResponseEntry {
+  /** The HPO term. */
+  hpoTerm: string
+  /** The gene symbol. */
+  geneSymbol: string
+  /** The predicted impact. */
+  impact: string
+}
+
+/** Helper class for converting `ResponseEntry$Api` to `ResponseEntry`. */
+class ResponseEntry$Type {
+  /** Converts `ResponseEntry$Api` to `ResponseEntry`. */
+  fromJson(data: ResponseEntry$Api): ResponseEntry {
+    return {
+      hpoTerm: data.hpo_term,
+      geneSymbol: data.gene_symbol,
+      impact: data.impact
+    }
+  }
+}
+
+/** Helper instance for converting `ResponseEntry$Api` to `ResponseEntry`. */
+export const ResponseEntry = new ResponseEntry$Type()
+
+/** Type for the response of the `predict` endpoint. */
+export interface Response {
+  /** The result entries. */
+  entries: ResponseEntry[]
+}
+
+/** Helper class for converting JSON from API to `Response`. */
+class Response$Type {
+  /** Converts JSON from API to `Response`. */
+  fromJson(data: any[]): Response {
+    return {
+      entries: data.map((entry) => ResponseEntry.fromJson(entry))
+    }
+  }
+}
+
+/** Helper instance for converting JSON to `Response`. */
+export const Response = new Response$Type()