bihealth · holtgrewe · Feb 5, 2024 · Feb 5, 2024 · Feb 5, 2024 · Feb 5, 2024
diff --git a/src/api/cadaPrio/__snapshots__/client.spec.ts.snap b/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":[{"geneSymbol":"WNT7A"},{"geneSymbol":"SMARCA2"},{"geneSymbol":"EFL1"},{"geneSymbol":"SRP54"},{"geneSymbol":"HPGD"},{"geneSymbol":"GALNS"},{"geneSymbol":"DNAJC21"},{"geneSymbol":"NOG"},{"geneSymbol":"ESCO2"},{"geneSymbol":"COL11A1"},{"geneSymbol":"PTDSS1"},{"geneSymbol":"VAC14"},{"geneSymbol":"TBX3"},{"geneSymbol":"GRIA3"},{"geneSymbol":"RNU4ATAC"},{"geneSymbol":"GDF5"},{"geneSymbol":"TRAPPC2"},{"geneSymbol":"IHH"},{"geneSymbol":"PCNT"}]}"`;
+exports[`CadaPrioClient > throws in case of fetching problems 1`] = `"{"entries":[{"hgncId":"HGNC:12786","ncbiGeneId":"7476","rank":1,"score":76.84823608398438},{"hgncId":"HGNC:11098","ncbiGeneId":"6595","rank":2,"score":76.46592712402344},{"hgncId":"HGNC:25789","ncbiGeneId":"79631","rank":3,"score":69.20905303955078},{"hgncId":"HGNC:11301","ncbiGeneId":"6729","rank":4,"score":65.58743286132812},{"hgncId":"HGNC:5154","ncbiGeneId":"3248","rank":5,"score":63.857845306396484},{"hgncId":"HGNC:4122","ncbiGeneId":"2588","rank":6,"score":63.840911865234375},{"hgncId":"HGNC:27030","ncbiGeneId":"134218","rank":7,"score":63.35689926147461},{"hgncId":"HGNC:7866","ncbiGeneId":"9241","rank":8,"score":63.207393646240234},{"hgncId":"HGNC:27230","ncbiGeneId":"157570","rank":9,"score":63.09525680541992},{"hgncId":"HGNC:2186","ncbiGeneId":"1301","rank":10,"score":61.24506378173828},{"hgncId":"HGNC:9587","ncbiGeneId":"9791","rank":11,"score":60.995365142822266},{"hgncId":"HGNC:25507","ncbiGeneId":"55697","rank":12,"score":60.21630859375},{"hgncId":"HGNC:11602","ncbiGeneId":"6926","rank":13,"score":59.911136627197266},{"hgncId":"HGNC:4573","ncbiGeneId":"2892","rank":14,"score":59.312957763671875},{"hgncId":"HGNC:34016","ncbiGeneId":"100151683","rank":15,"score":59.29935836791992},{"hgncId":"HGNC:4220","ncbiGeneId":"8200","rank":16,"score":58.710994720458984},{"hgncId":"HGNC:23068","ncbiGeneId":"6399","rank":17,"score":56.57151412963867},{"hgncId":"HGNC:5956","ncbiGeneId":"3549","rank":18,"score":55.67450714111328},{"hgncId":"HGNC:16068","ncbiGeneId":"5116","rank":19,"score":55.3505859375}]}"`;
diff --git a/src/api/cadaPrio/types.ts b/src/api/cadaPrio/types.ts
@@ -2,34 +2,39 @@
  * 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
+  /** HGNC ID */
+  hgnc_id: string
+  /** NCBI Gene ID */
+  ncbi_gene_id: string
+  /** Rank */
+  rank: number
+  /** Score */
+  score: number
 }
 
 /**
  * One entry of the result.
  */
 export interface ResponseEntry {
-  /** The HPO term. */
-  hpoTerm: string
-  /** The gene symbol. */
-  geneSymbol: string
-  /** The predicted impact. */
-  impact: string
+  /** HGNC ID */
+  hgncId: string
+  /** NCBI Gene ID */
+  ncbiGeneId: string
+  /** Rank */
+  rank: number
+  /** Score */
+  score: number
 }
 
 /** 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
+      hgncId: data.hgnc_id,
+      ncbiGeneId: data.ncbi_gene_id,
+      rank: data.rank,
+      score: data.score
     }
   }
 }

diff --git a/src/store/cadaPrio/__snapshots__/store.spec.ts.snap b/src/store/cadaPrio/__snapshots__/store.spec.ts.snap
@@ -1,201 +1,120 @@
 // Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
-exports[`Cada Prio Store > should handle error when predicting gene impact 1`] = `
-[
-  {
-    "geneSymbol": "WNT7A",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "SMARCA2",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "EFL1",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "SRP54",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "HPGD",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "GALNS",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "DNAJC21",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "NOG",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "ESCO2",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "COL11A1",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "PTDSS1",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "VAC14",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "TBX3",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "GRIA3",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "RNU4ATAC",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "GDF5",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "TRAPPC2",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "IHH",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-  {
-    "geneSymbol": "PCNT",
-    "hpoTerm": undefined,
-    "impact": undefined,
-  },
-]
-`;
-
 exports[`Cada Prio Store > should predict gene impact 1`] = `
 [
   {
-    "geneSymbol": "WNT7A",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:12786",
+    "ncbiGeneId": "7476",
+    "rank": 1,
+    "score": 76.84823608398438,
   },
   {
-    "geneSymbol": "SMARCA2",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:11098",
+    "ncbiGeneId": "6595",
+    "rank": 2,
+    "score": 76.46592712402344,
   },
   {
-    "geneSymbol": "EFL1",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:25789",
+    "ncbiGeneId": "79631",
+    "rank": 3,
+    "score": 69.20905303955078,
   },
   {
-    "geneSymbol": "SRP54",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:11301",
+    "ncbiGeneId": "6729",
+    "rank": 4,
+    "score": 65.58743286132812,
   },
   {
-    "geneSymbol": "HPGD",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:5154",
+    "ncbiGeneId": "3248",
+    "rank": 5,
+    "score": 63.857845306396484,
   },
   {
-    "geneSymbol": "GALNS",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:4122",
+    "ncbiGeneId": "2588",
+    "rank": 6,
+    "score": 63.840911865234375,
   },
   {
-    "geneSymbol": "DNAJC21",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:27030",
+    "ncbiGeneId": "134218",
+    "rank": 7,
+    "score": 63.35689926147461,
   },
   {
-    "geneSymbol": "NOG",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:7866",
+    "ncbiGeneId": "9241",
+    "rank": 8,
+    "score": 63.207393646240234,
   },
   {
-    "geneSymbol": "ESCO2",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:27230",
+    "ncbiGeneId": "157570",
+    "rank": 9,
+    "score": 63.09525680541992,
   },
   {
-    "geneSymbol": "COL11A1",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:2186",
+    "ncbiGeneId": "1301",
+    "rank": 10,
+    "score": 61.24506378173828,
   },
   {
-    "geneSymbol": "PTDSS1",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:9587",
+    "ncbiGeneId": "9791",
+    "rank": 11,
+    "score": 60.995365142822266,
   },
   {
-    "geneSymbol": "VAC14",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:25507",
+    "ncbiGeneId": "55697",
+    "rank": 12,
+    "score": 60.21630859375,
   },
   {
-    "geneSymbol": "TBX3",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:11602",
+    "ncbiGeneId": "6926",
+    "rank": 13,
+    "score": 59.911136627197266,
   },
   {
-    "geneSymbol": "GRIA3",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:4573",
+    "ncbiGeneId": "2892",
+    "rank": 14,
+    "score": 59.312957763671875,
   },
   {
-    "geneSymbol": "RNU4ATAC",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:34016",
+    "ncbiGeneId": "100151683",
+    "rank": 15,
+    "score": 59.29935836791992,
   },
   {
-    "geneSymbol": "GDF5",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:4220",
+    "ncbiGeneId": "8200",
+    "rank": 16,
+    "score": 58.710994720458984,
   },
   {
-    "geneSymbol": "TRAPPC2",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:23068",
+    "ncbiGeneId": "6399",
+    "rank": 17,
+    "score": 56.57151412963867,
   },
   {
-    "geneSymbol": "IHH",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:5956",
+    "ncbiGeneId": "3549",
+    "rank": 18,
+    "score": 55.67450714111328,
   },
   {
-    "geneSymbol": "PCNT",
-    "hpoTerm": undefined,
-    "impact": undefined,
+    "hgncId": "HGNC:16068",
+    "ncbiGeneId": "5116",
+    "rank": 19,
+    "score": 55.3505859375,
   },
 ]
 `;
diff --git a/src/store/cadaPrio/index.ts b/src/store/cadaPrio/index.ts
@@ -1 +1,2 @@
 export * from './store'
+export * from './types'
diff --git a/src/store/cadaPrio/store.ts b/src/store/cadaPrio/store.ts
@@ -6,8 +6,9 @@
 import { defineStore } from 'pinia'
 import { ref } from 'vue'
 
-import { CadaPrioClient, ResponseEntry } from '../../api/cadaPrio'
+import { CadaPrioClient } from '../../api/cadaPrio'
 import { StoreState } from '../../store'
+import { GeneRank } from './types'
 
 /** Options for `loadData()` */
 export interface LoadDataOptions {
@@ -22,8 +23,11 @@ export const useCadaPrioStore = defineStore('cadaPrio', () => {
   const storeState = ref<StoreState>(StoreState.Initial)
 
   /** The current gene Ranking. */
-  const geneRanking = ref<ResponseEntry[] | undefined>(undefined)
+  const geneRanking = ref<GeneRank[] | undefined>(undefined)
 
+  /**
+   * Clear all data from store and reset it into initial state.
+   */
   function clearData() {
     storeState.value = StoreState.Initial
     geneRanking.value = undefined

diff --git a/src/store/cadaPrio/types.ts b/src/store/cadaPrio/types.ts
@@ -0,0 +1 @@
+export { ResponseEntry as GeneRank } from '../../api/cadaPrio'
diff --git a/src/store/index.ts b/src/store/index.ts
@@ -1 +1,5 @@
+import { createPinia } from 'pinia'
+
 export * from './types'
+
+export const pinia = createPinia()
diff --git a/tsconfig.node.json b/tsconfig.node.json
@@ -5,5 +5,5 @@
     "moduleResolution": "Node",
     "allowSyntheticDefaultImports": true
   },
-  "include": ["vite.config.ts"]
+  "include": ["vite.config.mts"]
 }
diff --git a/vite.config.mts b/vite.config.mts
@@ -23,7 +23,7 @@ export default defineConfig({
           declarationMap: true
         }
       },
-      exclude: ['vite.config.ts']
+      exclude: ['vite.config.mts']
     })
   ],
   build: {
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		export { ResponseEntry as GeneRank } from '../../api/cadaPrio'