From 4476c13a31229959909eac13b5225673c690f3ff Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Thu, 1 Feb 2024 09:15:13 +0100
Subject: [PATCH] fix: api/annonars type GeneInfoResult (#68)

---
 src/api/annonars/client.spec.ts |  9 +++++++--
 src/api/annonars/client.ts      |  3 ++-
 src/api/annonars/types.ts       | 23 +++++++++++++++++++++++
 3 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/src/api/annonars/client.spec.ts b/src/api/annonars/client.spec.ts
index 6638203..1c99e50 100644
--- a/src/api/annonars/client.spec.ts
+++ b/src/api/annonars/client.spec.ts
@@ -6,7 +6,12 @@ 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'
+import {
+  ClinvarSvQueryResponse,
+  GeneInfoResult,
+  GeneSearchResponse,
+  SeqvarInfoResponse
+} from './types'
 
 const geneInfoBrca1Json = JSON.parse(
   fs.readFileSync(
@@ -45,7 +50,7 @@ describe.concurrent('AnnonarsClient.fetchGeneInfo()', () => {
 
     // assert:
     expect(JSON.stringify(result)).toEqual(
-      JSON.stringify({ genes: { 'HGNC:1100': geneInfoBrca1Json } })
+      JSON.stringify(GeneInfoResult.fromJson({ genes: { 'HGNC:1100': geneInfoBrca1Json } }))
     )
   })
 
diff --git a/src/api/annonars/client.ts b/src/api/annonars/client.ts
index dec163f..7ed639d 100644
--- a/src/api/annonars/client.ts
+++ b/src/api/annonars/client.ts
@@ -41,7 +41,8 @@ export class AnnonarsClient {
     const response = await fetch(`${this.apiBaseUrl}/genes/info?hgnc_id=${hgncId}`, {
       method: 'GET'
     })
-    return await response.json()
+    const responseJson = await response.json()
+    return GeneInfoResult.fromJson(responseJson)
   }
 
   /**
diff --git a/src/api/annonars/types.ts b/src/api/annonars/types.ts
index 78e075e..5cb7192 100644
--- a/src/api/annonars/types.ts
+++ b/src/api/annonars/types.ts
@@ -152,6 +152,13 @@ class GeneSearchResponse$Type {
  */
 export const GeneSearchResponse = new GeneSearchResponse$Type()
 
+/**
+ * Interface for gene info result as returned by API.
+ */
+export interface GeneInfoResult$Api {
+  genes: { [key: string]: GeneInfoRecord }
+}
+
 /**
  * Interface for gene info result.
  */
@@ -160,6 +167,22 @@ export interface GeneInfoResult {
   genes: GeneInfoRecord[]
 }
 
+/**
+ * Helper class to convert `GeneInfoResult$Api` to `GeneInfoResult`.
+ */
+class GeneInfoResult$Type {
+  fromJson(apiResult: GeneInfoResult$Api): GeneInfoResult {
+    return {
+      genes: Object.values(apiResult.genes)
+    }
+  }
+}
+
+/**
+ * Helper instance to convert `GeneInfoResult$Api` to `GeneInfoResult`.
+ */
+export const GeneInfoResult = new GeneInfoResult$Type()
+
 /**
  * Interface for seqvar info query as returned by API.
  */