tests

backend/app/main.py

@@ -64,7 +64,6 @@
     "bp5": False,
     "bp6": False,
     "bp7": False,
-    "class_override": None,
 }
 
 app = FastAPI()
@@ -158,7 +157,7 @@ async def variantvalidator(request: Request, path: str):
 
 # Register app for retrieving ACMG classification.
 @app.get("/acmg/{path:path}")
-async def acmg(request: Request, path: str):
+async def acmg(request: Request):
     """Implement searching for ACMG classification."""
     query_params = request.query_params
     chromosome = query_params.get("chromosome")
@@ -167,14 +166,20 @@ async def acmg(request: Request, path: str):
     alternative = query_params.get("alternative")
     build = query_params.get("release")
 
-    url = f"http://wintervar.wglab.org/api_new.php?queryType=position&chr={chromosome}&pos={position}&ref={reference}&alt={alternative}&build={build}"
+    if not chromosome or not position or not reference or not alternative or not build:
+        return Response(status_code=400, content="Missing query parameters")
+
+    url = (
+        f"http://wintervar.wglab.org/api_new.php?"
+        f"queryType=position&chr={chromosome}&pos={position}"
+        f"&ref={reference}&alt={alternative}&build={build}"
+    )
     backend_req = client.build_request(method="GET", url=url)
     backend_resp = await client.send(backend_req)
     if backend_resp.status_code != 200:
         return Response(status_code=backend_resp.status_code, content=backend_resp.content)
 
     acmg_rating = ACMG_RATING.copy()
-    acmg_rating["class_override"] = query_params.get("class_override", None)
     for key, value in backend_resp.json().items():
         if key.lower() in acmg_rating:
             acmg_rating[key.lower()] = True if value == 1 else False

backend/tests/test_main.py

@@ -99,7 +99,7 @@ async def test_version_no_version(monkeypatch, fp):
 
 
 @pytest.mark.asyncio
-async def test_variantvalidator(monkeypatch, httpx_mock):
+async def test_variantvalidator(httpx_mock):
     """Test variant validator endpoint."""
     variantvalidator_url = "https://rest.variantvalidator.org/VariantValidator/variantvalidator"
     httpx_mock.add_response(
@@ -113,6 +113,31 @@ async def test_variantvalidator(monkeypatch, httpx_mock):
     assert response.text == "Mocked response"
 
 
+@pytest.mark.asyncio
+async def test_acmg(httpx_mock):
+    """Test ACMG endpoint."""
+    acmg_url = "http://wintervar.wglab.org/api_new.php"
+    acmg_qury_params = "?chromosome=1&position=123&reference=A&alternative=T&release=hg19"
+    httpx_mock.add_response(
+        url=f"{acmg_url}?queryType=position&chr=1&pos=123&ref=A&alt=T&build=hg19",
+        method="GET",
+        json={"acmg": "Mocked response"},
+    )
+
+    response = client.get(f"/acmg/{acmg_qury_params}")
+    assert response.status_code == 200
+    print("Main", main.ACMG_RATING)
+    assert response.json() == main.ACMG_RATING
+
+
+@pytest.mark.asyncio
+async def test_acmg_missing_query_params():
+    """Test ACMG endpoint with missing query parameters."""
+    response = client.get("/acmg")
+    assert response.status_code == 400
+    assert response.text == "Missing query parameters"
+
+
 @pytest.mark.asyncio
 async def test_favicon():
     """Test favicon endpoint."""

frontend/src/components/VariantDetails/AcmgRating.vue

@@ -38,8 +38,7 @@ const emptyAcmgRatingTemplate: any = {
   bp4: false,
   bp5: false,
   bp6: false,
-  bp7: false,
-  class_override: null
+  bp7: false
 }
 
 const acmgRatingToSubmit = ref({ ...emptyAcmgRatingTemplate })
@@ -79,7 +78,6 @@ const resetAcmgRating = () => {
     acmgRatingToSubmit.value.bp5 = acmgRatingStore.acmgRating.bp5
     acmgRatingToSubmit.value.bp6 = acmgRatingStore.acmgRating.bp6
     acmgRatingToSubmit.value.bp7 = acmgRatingStore.acmgRating.bp7
-    acmgRatingToSubmit.value.class_override = acmgRatingStore.acmgRating.class_override
   } else {
     unsetAcmgRating()
   }
@@ -158,14 +156,6 @@ const calculateAcmgRating = computed(() => {
   return computedClassAuto
 })
 
-const convertEmptyToNull = (classOverride: any) => {
-  if (classOverride === '' || classOverride === null) {
-    acmgRatingToSubmit.value.class_override = null
-  } else {
-    acmgRatingToSubmit.value.class_override = classOverride
-  }
-}
-
 const onSubmitAcmgRating = async () => {
   await acmgRatingStore.submitAcmgRating(props.smallVariant, acmgRatingToSubmit.value)
 }
@@ -249,7 +239,7 @@ const acmgCriteriaInfo = {
           id: 'pm2',
           description:
             'Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium',
-          hint: 'rare in 1:20.000 in ExAC'
+          hint: 'rare; < 1:20.000 in ExAC'
         },
         {
           name: 'PM3',
@@ -301,7 +291,7 @@ const acmgCriteriaInfo = {
           id: 'pp3',
           description:
             'Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)',
-          hint: 'predicted pathogenic'
+          hint: 'predicted pathogenic >= 2'
         },
         {
           name: 'PP4',
@@ -386,34 +376,34 @@ const acmgCriteriaInfo = {
           id: 'bp3',
           description:
             'In-frame deletions/insertions in a repetitive region without a known function',
-          hint: 'in-frame del/ins in repeat'
+          hint: 'in-frame indel in repeat'
         },
         {
           name: 'BP4',
           id: 'bp4',
           description:
             'Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary,splicing impact, etc.)',
-          hint: 'predicted benign'
+          hint: 'prediction: benign'
         },
         {
           name: 'BP5',
           id: 'bp5',
           description: 'Variant found in a case with an alternate molecular basis for disease',
-          hint: 'other variant is causative'
+          hint: 'different gene in other case'
         },
         {
           name: 'BP6',
           id: 'bp6',
           description:
             'Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation',
-          hint: 'reliable source: benign'
+          hint: 'reputable source: benign'
         },
         {
           name: 'BP7',
           id: 'bp7',
           description:
             'A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved',
-          hint: 'synonymous: no splice effect'
+          hint: 'silent, no splicing/conservation'
         }
       ]
     }
@@ -482,21 +472,6 @@ const acmgCriteriaInfo = {
           {{ calculateAcmgRating }}
         </h1>
       </div>
-      <div title="Manually override the automatically determined class">
-        <div>
-          <label for="acmg-class-override"><strong>ACMG class override</strong></label>
-        </div>
-        <div style="margin-bottom: 12px">
-          <v-text-field
-            label="Label"
-            variant="outlined"
-            id="acmg-class-override"
-            style="width: 135px; height: 50px"
-            @change="convertEmptyToNull(acmgRatingToSubmit.class_override)"
-            v-model.number="acmgRatingToSubmit.class_override"
-          />
-        </div>
-      </div>
       <div>
         <div>
           <label for="acmg-class"><strong>Score explanation:</strong></label>
@@ -522,9 +497,7 @@ const acmgCriteriaInfo = {
       <div class="button-group">
         <v-btn @click="unsetAcmgRating()"> Clear </v-btn>
         <v-btn @click="resetAcmgRating()"> Reset </v-btn>
-        <v-btn prepend-icon="mdi-star-check" @click="onSubmitAcmgRating()">
-          Submit to ClinVar
-        </v-btn>
+        <v-btn prepend-icon="mdi-star-check" @click="onSubmitAcmgRating()"> Save changes </v-btn>
       </div>
       <div v-if="acmgRatingConflicting">
         <div>
@@ -539,15 +512,11 @@ const acmgCriteriaInfo = {
           <div>
             <v-icon>mdi-information</v-icon>
             Select all fulfilled criteria to get the classification following Richards
-            <i>et al.</i> (2015). If necessary, you can also specify a manual override.
-            <span class="badge badge-primary">Submit</span> indicates that there are changes not yet
-            submitted, while <span class="badge badge-success">Submit</span> indicates that changes
-            have been submitted or not made at all.
-            <span class="badge badge-warning">Submit</span> indicates that there are conflicting
-            variant interpretations. In that case, submission is possible, but not recommended.
-            Press <span class="badge badge-secondary">Reset</span> to reset the form to the last
-            submitted state. Press <span class="badge badge-secondary">Clear</span> and
-            <span class="badge badge-primary">Submit</span> to delete ACMG rating.
+            <i>et al.</i> (2015). If necessary, you can also specify a manual override. Press
+            <span style="background-color: wheat">Reset</span> to reset the form to the last
+            submitted state. Press <span style="background-color: wheat">Clear</span> to delete ACMG
+            rating and <span style="background-color: wheat">Submit</span> to submit rating to
+            ClinVar.
           </div>
         </div>
       </div>

frontend/src/components/__tests__/AcmgRating.spec.ts

@@ -0,0 +1,106 @@
+import { describe, expect, it, vi } from 'vitest'
+import { mount } from '@vue/test-utils'
+import { createRouter, createWebHistory } from 'vue-router'
+import { routes } from '@/router'
+
+import { createTestingPinia } from '@pinia/testing'
+import { useVariantAcmgRatingStore } from '@/stores/variantAcmgRating'
+import { StoreState } from '@/stores/misc'
+
+import { createVuetify } from 'vuetify'
+import * as components from 'vuetify/components'
+import * as directives from 'vuetify/directives'
+
+import AcmgRating from '@/components/VariantDetails/AcmgRating.vue'
+
+const vuetify = createVuetify({
+  components,
+  directives
+})
+
+const router = createRouter({
+  history: createWebHistory(import.meta.env.BASE_URL),
+  routes: routes
+})
+// Mock router push
+router.push = vi.fn()
+
+const smallVariantInfo = {
+  release: 'grch37',
+  chromosome: 'chr17',
+  start: '43044295',
+  end: '43044295',
+  reference: 'G',
+  alternative: 'A',
+  hgnc_id: 'HGNC:1100'
+}
+
+export const AcmgRatingInfo = {
+  pvs1: false,
+  ps1: false,
+  ps2: false,
+  ps3: false,
+  ps4: false,
+  pm1: false,
+  pm2: false,
+  pm3: false,
+  pm4: false,
+  pm5: false,
+  pm6: false,
+  pp1: false,
+  pp2: false,
+  pp3: false,
+  pp4: false,
+  pp5: false,
+  ba1: false,
+  bs1: false,
+  bs2: false,
+  bs3: false,
+  bs4: false,
+  bp1: false,
+  bp2: false,
+  bp3: false,
+  bp4: false,
+  bp5: false,
+  bp6: false,
+  bp7: false
+}
+
+const makeWrapper = () => {
+  const pinia = createTestingPinia({ createSpy: vi.fn() })
+  const store = useVariantAcmgRatingStore(pinia)
+
+  const mockRetrieveAcmgRating = vi.fn().mockImplementation(async () => {
+    store.storeState = StoreState.Active
+    store.smallVariant = JSON.parse(JSON.stringify(smallVariantInfo))
+    store.acmgRating = JSON.parse(JSON.stringify(AcmgRatingInfo))
+  })
+  store.retrieveAcmgRating = mockRetrieveAcmgRating
+
+  store.storeState = StoreState.Active
+  store.smallVariant = JSON.parse(JSON.stringify(smallVariantInfo))
+  store.acmgRating = JSON.parse(JSON.stringify(AcmgRatingInfo))
+
+  return mount(AcmgRating, {
+    props: {
+      smallVariant: smallVariantInfo
+    },
+    global: {
+      plugins: [vuetify, router, pinia],
+      components: {
+        AcmgRating
+      }
+    }
+  })
+}
+
+describe.concurrent('AcmgRating', async () => {
+  it('renders the AcmgRating info', async () => {
+    const wrapper = makeWrapper()
+    expect(wrapper.text()).toContain('Pathogenic')
+    expect(wrapper.text()).toContain('Benign')
+
+    const switchers = wrapper.findAll('.v-switch')
+    expect(switchers.length).toBe(28)
+  })
+})