feat: improve HPO lookup result quality with latest viguno (#338) (#346)

bihealth · Dec 27, 2023 · 84d2c7b · 84d2c7b
1 parent 096cc85
commit 84d2c7b
Show file tree

Hide file tree

Showing 5 changed files with 16 additions and 11 deletions.
diff --git a/frontend/src/api/viguno.ts b/frontend/src/api/viguno.ts
@@ -69,8 +69,8 @@ export class VigunoClient {
     return await response.json()
   }
 
-  async queryHpoTermsByName(query: string, matchType: string = 'contains'): Promise<any> {
-    const url = `${this.apiBaseUrl}hpo/terms?name=${query}&match=${matchType}`
+  async queryHpoTermsByName(query: string): Promise<any> {
+    const url = `${this.apiBaseUrl}hpo/terms?name=${query}`
     const response = await fetch(url, {
       method: 'GET'
     })

diff --git a/frontend/src/components/CaseInformationCard.vue b/frontend/src/components/CaseInformationCard.vue
@@ -168,7 +168,7 @@ watch(
                   :items="termsStore.omimTerms"
                   :loading="omimIsLoading"
                   label="Disease"
-                  item-title="name"
+                  :item-title="(item) => item.name"
                   :item-value="(item) => item"
                   multiple
                   chips
@@ -187,8 +187,14 @@ watch(
                   :items="termsStore.hpoTerms"
                   :loading="hpoIsLoading"
                   label="HPO Terms"
-                  item-title="name"
+                  :item-title="(item) => `${item.name} (${item.term_id})`"
                   :item-value="(item) => item"
+                  :item-props="
+                    (item) => ({
+                      subtitle: item.definition
+                    })
+                  "
+                  :no-filter="true"
                   multiple
                   chips
                   closable-chips

diff --git a/frontend/src/stores/__tests__/terms.spec.ts b/frontend/src/stores/__tests__/terms.spec.ts
@@ -43,14 +43,14 @@ describe.concurrent('Terms Store', () => {
   })
 
   it('fetches HPO term by ID', async () => {
-    const mockHpoTerm = { term_id: 'HP:0000118', name: 'Phenotypic abnormality' }
-    fetchMocker.mockResponseOnce(JSON.stringify({ result: mockHpoTerm }))
+    const mockHpoTerms = [{ term_id: 'HP:0000118', name: 'Phenotypic abnormality' }]
+    fetchMocker.mockResponseOnce(JSON.stringify({ result: mockHpoTerms }))
 
     const store = useTermsStore()
     await store.fetchHpoTerms('HP:0000118')
 
     expect(store.storeState).toBe(StoreState.Active)
-    expect(store.hpoTerms).toEqual([mockHpoTerm])
+    expect(store.hpoTerms).toEqual(mockHpoTerms)
   })
 
   it('handles error when fetching HPO terms', async () => {

diff --git a/frontend/src/stores/case.ts b/frontend/src/stores/case.ts
@@ -105,6 +105,7 @@ export const ZygosityLabels = new Map<Zygosity, string>([
 export interface HpoTerm {
   term_id: string
   name: string
+  definition?: string
 }
 
 /** Interface for storing one OMIM term, for storage and API. */

diff --git a/frontend/src/stores/terms.ts b/frontend/src/stores/terms.ts
@@ -33,10 +33,8 @@ export const useTermsStore = defineStore('terms', () => {
     try {
       // Check if query matches the pattern for HPO ID
       if (hpoIdPattern.test(query)) {
-        // Extract only the digits part if "HPO:" is present
-        const hpoId = query.replace(/^HP:/, '')
-        const response = await vigunoClient.resolveHpoTermById(hpoId)
-        hpoTerms.value = [response.result as HpoTerm]
+        const response = await vigunoClient.resolveHpoTermById(query)
+        hpoTerms.value = response.result as HpoTerm[]
       } else {
         const response = await vigunoClient.queryHpoTermsByName(query)
         hpoTerms.value = response.result.map((item: any) => item as HpoTerm)