feat: integration of meahri 0.8.0 (#56)

This provides access to all affected genes in a SV. Note that
this also changes keys from kebab-case to snake_case.

frontend/src/api/__tests__/common.spec.ts

@@ -1,7 +1,7 @@
 import { describe, expect, it } from 'vitest'
 
 import {
-  API_INTERNALBASE_PREFIX_MEHARI,
+  API_INTERNAL_BASE_PREFIX_MEHARI,
   API_INTERNAL_BASE_PREFIX,
   API_INTERNAL_BASE_PREFIX_ANNONARS,
   API_INTERNAL_BASE_PREFIX_NGINX
@@ -22,7 +22,7 @@ describe.concurrent('API_BASE_PREFIX constants', () => {
 
   it('returns the correct API base prefix for mehari in production mode', () => {
     const originalMode = import.meta.env.MODE
-    expect(API_INTERNALBASE_PREFIX_MEHARI).toBe('/internal/proxy/mehari')
+    expect(API_INTERNAL_BASE_PREFIX_MEHARI).toBe('/internal/proxy/mehari')
     import.meta.env.MODE = originalMode
   })
 

frontend/src/api/common.ts

@@ -6,7 +6,7 @@ export const API_INTERNAL_BASE_PREFIX_ANNONARS = '/internal/proxy/annonars'
 //   ? `//localhost:8080/internal/proxy/annonars`
 //   : '/internal/proxy/annonars'
 
-export const API_INTERNALBASE_PREFIX_MEHARI = '/internal/proxy/mehari'
+export const API_INTERNAL_BASE_PREFIX_MEHARI = '/internal/proxy/mehari'
 // import.meta.env.MODE == 'development'
 //   ? '//localhost:8080/internal/proxy/mehari'
 //   : '/internal/proxy/mehari'

frontend/src/api/mehari.ts

@@ -1,6 +1,6 @@
-import { API_INTERNALBASE_PREFIX_MEHARI } from '@/api/common'
+import { API_INTERNAL_BASE_PREFIX_MEHARI } from '@/api/common'
 
-const API_BASE_URL = `${API_INTERNALBASE_PREFIX_MEHARI}/`
+const API_BASE_URL = `${API_INTERNAL_BASE_PREFIX_MEHARI}/`
 
 export class MehariClient {
   private apiBaseUrl: string
@@ -19,9 +19,9 @@ export class MehariClient {
     alternative: string,
     hgnc_id?: string
   ): Promise<any> {
-    const hgncSuffix = hgnc_id ? `&hgnc-id=${hgnc_id}` : ''
+    const hgncSuffix = hgnc_id ? `&hgnc_id=${hgnc_id}` : ''
     const url =
-      `${this.apiBaseUrl}tx/csq?genome-release=${genomeRelease}&` +
+      `${this.apiBaseUrl}seqvars/csq?genome_release=${genomeRelease}&` +
       `chromosome=${chromosome}&position=${pos}&reference=${reference}&` +
       `alternative=${alternative}${hgncSuffix}`
 

frontend/src/stores/__tests__/variantInfo.spec.ts

@@ -64,7 +64,7 @@ describe.concurrent('geneInfo Store', () => {
     fetchMocker.mockResponse((req) => {
       if (req.url.includes('annos/variant')) {
         return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
-      } else if (req.url.includes('tx/csq')) {
+      } else if (req.url.includes('seqvars/csq')) {
         return Promise.resolve(JSON.stringify(BRCA1TxInfo))
       } else if (req.url.includes('genes/info')) {
         return Promise.resolve(JSON.stringify(BRCA1GeneInfo))
@@ -110,7 +110,7 @@ describe.concurrent('geneInfo Store', () => {
         return Promise.resolve(
           JSON.stringify({ result: { cadd: null, dbnsfp: null, dbscsnv: null } })
         )
-      } else if (req.url.includes('tx/csq')) {
+      } else if (req.url.includes('seqvars/csq')) {
         return Promise.resolve(JSON.stringify(BRCA1TxInfo))
       } else if (req.url.includes('genes/info')) {
         return Promise.resolve(JSON.stringify(BRCA1GeneInfo))
@@ -143,7 +143,7 @@ describe.concurrent('geneInfo Store', () => {
     fetchMocker.mockResponse((req) => {
       if (req.url.includes('annos/variant')) {
         return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
-      } else if (req.url.includes('tx/csq')) {
+      } else if (req.url.includes('seqvars/csq')) {
         return Promise.resolve(JSON.stringify({ result: [] }))
       } else if (req.url.includes('genes/info')) {
         return Promise.resolve(JSON.stringify(BRCA1GeneInfo))
@@ -176,7 +176,7 @@ describe.concurrent('geneInfo Store', () => {
     fetchMocker.mockResponse((req) => {
       if (req.url.includes('annos/variant')) {
         return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
-      } else if (req.url.includes('tx/csq')) {
+      } else if (req.url.includes('seqvars/csq')) {
         return Promise.resolve(JSON.stringify(BRCA1TxInfo))
       } else if (req.url.includes('genes/info')) {
         return Promise.resolve(JSON.stringify({ genes: null }))
@@ -207,7 +207,7 @@ describe.concurrent('geneInfo Store', () => {
     fetchMocker.mockResponse((req) => {
       if (req.url.includes('annos/variant')) {
         return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
-      } else if (req.url.includes('tx/csq')) {
+      } else if (req.url.includes('seqvars/csq')) {
         return Promise.resolve(JSON.stringify(BRCA1TxInfo))
       } else if (req.url.includes('genes/info')) {
         return Promise.resolve(JSON.stringify(BRCA1GeneInfo))

frontend/src/stores/variantAcmgRating.ts

@@ -64,7 +64,7 @@ export const useVariantAcmgRatingStore = defineStore('variantAcmgRating', () =>
       const ref = smallVar.reference
       const alt = smallVar.alternative
       const response = await fetch(
-        `${API_BASE_URL}internal/remote/acmg/?release=${release}&chromosome=${chromosome}` +
+        `${API_BASE_URL}remote/acmg/?release=${release}&chromosome=${chromosome}` +
           `&position=${pos}&reference=${ref}&alternative=${alt}`,
         { method: 'GET' }
       )

frontend/src/stores/variantInfo.ts

@@ -101,7 +101,7 @@ export const useVariantInfoStore = defineStore('variantInfo', () => {
         txCsq.value = txCsqData.result
       }
 
-      const hgncId: string = txCsqData.result[0]['gene-id']
+      const hgncId: string = txCsqData.result[0]['gene_id']
       const geneData = await annonarsClient.fetchGeneInfo(hgncId)
       if (geneData?.genes === null) {
         throw new Error('No gene data found.')