chore: refactoring tests

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

@@ -2,7 +2,7 @@ import { beforeEach, describe, expect, it, vi } from 'vitest'
 import createFetchMock from 'vitest-fetch-mock'
 
 import { AcmgSeqVarClient } from '@/api/acmgseqvar'
-import { type AcmgRatingBackend } from '@/stores/variantAcmgRating'
+import { type AcmgRatingBackend } from '@/stores/seqVarAcmgRating'
 
 const fetchMocker = createFetchMock(vi)
 

frontend/src/api/acmgseqvar.ts

@@ -1,5 +1,5 @@
 import { API_V1_BASE_PREFIX } from '@/api/common'
-import { type AcmgRatingBackend } from '@/stores/variantAcmgRating'
+import { type AcmgRatingBackend } from '@/stores/seqVarAcmgRating'
 
 /**
  * Access to the seqvar part of the API.

frontend/src/components/Profile/SeqVarsACMGCard.vue

@@ -1,9 +1,9 @@
 <script setup lang="ts">
 import { onMounted } from 'vue'
 
-import { useVariantAcmgRatingStore } from '@/stores/variantAcmgRating'
+import { useSeqVarAcmgRatingStore } from '@/stores/seqVarAcmgRating'
 
-const acmgRatingStore = useVariantAcmgRatingStore()
+const acmgRatingStore = useSeqVarAcmgRatingStore()
 
 const getPresentCriterias = (criterias: any) =>
   criterias.filter((criteria: any) => criteria.presence === 'Present')

frontend/src/components/SeqvarDetails/ClinsigCard.vue

@@ -19,7 +19,7 @@ import {
 } from '@/lib/acmgSeqVar'
 import { type Seqvar } from '@/lib/genomicVars'
 import { StoreState } from '@/stores/misc'
-import { useVariantAcmgRatingStore } from '@/stores/variantAcmgRating'
+import { useSeqVarAcmgRatingStore } from '@/stores/seqVarAcmgRating'
 
 /** Data type used for component's props. */
 interface Props {
@@ -36,7 +36,7 @@ const emit = defineEmits<{
 }>()
 
 /** Store to use for ACMG ratings of sequence variants. */
-const acmgRatingStore = useVariantAcmgRatingStore()
+const acmgRatingStore = useSeqVarAcmgRatingStore()
 
 /** Component state: error message to display, if any. */
 const errorMessage = ref<string>('')

frontend/src/components/StrucvarDetails/ClinsigCard.vue

@@ -20,7 +20,7 @@ import CnLoss from '@/components/StrucvarDetails/ClinsigCard/CnLoss.vue'
 import SummarySheet from '@/components/StrucvarDetails/ClinsigCard/SummarySheet.vue'
 import type { Strucvar } from '@/lib/genomicVars'
 import { StoreState } from '@/stores/misc'
-import { useSvAcmgRatingStore } from '@/stores/svAcmgRating'
+import { useStrucVarAcmgRatingStore } from '@/stores/strucVarAcmgRating'
 
 /** Data type used for component's props. */
 interface Props {
@@ -37,7 +37,7 @@ const emit = defineEmits<{
 }>()
 
 /** Store to use for ACMG ratings of structural variants. */
-const acmgRatingStore = useSvAcmgRatingStore()
+const acmgRatingStore = useStrucVarAcmgRatingStore()
 
 /** Component state: whether display of conflicting sections is enabled. */
 const showConflictingSections = ref<boolean>(false)

frontend/src/components/StrucvarDetails/ClinsigCard/CnGain.vue

@@ -6,7 +6,7 @@ import {
   Presence,
   StateSourceCNV
 } from '@/components/StrucvarDetails/ClinsigCard.c'
-import { useSvAcmgRatingStore } from '@/stores/svAcmgRating'
+import { useStrucVarAcmgRatingStore } from '@/stores/strucVarAcmgRating'
 
 const emit = defineEmits<{
   (e: 'switchCriteria', criteria: AcmgCriteriaCNVGain, presence: Presence): void
@@ -22,7 +22,7 @@ const props = withDefaults(
   }
 )
 
-const acmgRatingStore = useSvAcmgRatingStore()
+const acmgRatingStore = useStrucVarAcmgRatingStore()
 </script>
 
 <template>

frontend/src/components/StrucvarDetails/ClinsigCard/CnLoss.vue

@@ -6,7 +6,7 @@ import {
   Presence,
   StateSourceCNV
 } from '@/components/StrucvarDetails/ClinsigCard.c'
-import { useSvAcmgRatingStore } from '@/stores/svAcmgRating'
+import { useStrucVarAcmgRatingStore } from '@/stores/strucVarAcmgRating'
 
 const emit = defineEmits<{
   (e: 'switchCriteria', criteria: AcmgCriteriaCNVLoss, presence: Presence): void
@@ -22,7 +22,7 @@ const props = withDefaults(
   }
 )
 
-const acmgRatingStore = useSvAcmgRatingStore()
+const acmgRatingStore = useStrucVarAcmgRatingStore()
 </script>
 
 <template>

frontend/src/components/StrucvarDetails/ClinvarCard.vue

@@ -9,7 +9,7 @@ import {
 } from '@/components/SeqvarDetails/ClinvarCard.c'
 import { type Strucvar } from '@/lib/genomicVars'
 import { roundIt } from '@/lib/utils'
-import { useSvInfoStore } from '@/stores/svInfo'
+import { useStrucVarInfoStore } from '@/stores/strucVarInfo'
 
 /** Type for this component's props. */
 interface Props {
@@ -18,7 +18,7 @@ interface Props {
 
 const props = defineProps<Props>()
 
-const svInfoStore = useSvInfoStore()
+const svInfoStore = useStrucVarInfoStore()
 
 const vcvUrl = (vcv: string): string => {
   const stripped = vcv.replace(/^VCV0+/, '')

frontend/src/components/StrucvarDetails/GeneListCard.vue

@@ -5,7 +5,7 @@ import { onMounted } from 'vue'
 import GeneListEntry from '@/components/StrucvarDetails/GeneListCard/GeneListEntry.vue'
 import { type Strucvar } from '@/lib/genomicVars'
 import { StoreState } from '@/stores/misc'
-import { type Consequence } from '@/stores/svInfo'
+import { type Consequence } from '@/stores/strucVarInfo'
 
 /** `GeneInfo` is a type alias for easier future interface definition. */
 type GeneInfo = any

frontend/src/components/__tests__/Profile/SeqVarsACMGCard.spec.ts

@@ -4,7 +4,7 @@ import { describe, expect, it, vi } from 'vitest'
 import SeqVarACMGCard from '@/components/Profile/SeqVarsACMGCard.vue'
 import { setupMountedComponents } from '@/lib/test-utils'
 import { StoreState } from '@/stores/misc'
-import { useVariantAcmgRatingStore } from '@/stores/variantAcmgRating'
+import { useSeqVarAcmgRatingStore } from '@/stores/seqVarAcmgRating'
 
 // Example ACMG Rating data
 const exampleAcmgRating = {
@@ -23,7 +23,7 @@ const exampleAcmgRating = {
 describe.concurrent('SeqVarACMGCard', async () => {
   it('renders the SeqVarACMGCard information with ACMG ratings.', async () => {
     const pinia = createTestingPinia({ createSpy: vi.fn })
-    const acmgRatingStore = useVariantAcmgRatingStore(pinia)
+    const acmgRatingStore = useSeqVarAcmgRatingStore(pinia)
     const mockListAcmgRatings = vi.fn().mockImplementation(() => {
       acmgRatingStore.acmgRatings = [exampleAcmgRating]
     })
@@ -32,7 +32,7 @@ describe.concurrent('SeqVarACMGCard', async () => {
       { component: SeqVarACMGCard, template: false },
       {
         initialStoreState: {
-          variantAcmgRating: {
+          seqVarAcmgRating: {
             storeState: StoreState.Active,
             acmgRatings: []
           }
@@ -46,7 +46,7 @@ describe.concurrent('SeqVarACMGCard', async () => {
 
   it('renders the SeqVarACMGCard information with no ACMG ratings.', async () => {
     const pinia = createTestingPinia({ createSpy: vi.fn })
-    const acmgRatingStore = useVariantAcmgRatingStore(pinia)
+    const acmgRatingStore = useSeqVarAcmgRatingStore(pinia)
     const mockListAcmgRatings = vi.fn().mockImplementation(() => {
       acmgRatingStore.acmgRatings = []
     })
@@ -55,7 +55,7 @@ describe.concurrent('SeqVarACMGCard', async () => {
       { component: SeqVarACMGCard, template: false },
       {
         initialStoreState: {
-          variantAcmgRating: {
+          seqVarAcmgRating: {
             storeState: StoreState.Active,
             acmgRatings: []
           }

frontend/src/components/__tests__/SeqvarDetails/BeaconNetworkCard.spec.ts

@@ -1,16 +1,16 @@
 import { describe, expect, it } from 'vitest'
 
 import BeaconNetwork from '@/components/SeqvarDetails/BeaconNetworkCard.vue'
+import type { Seqvar } from '@/lib/genomicVars'
 import { setupMountedComponents } from '@/lib/test-utils'
 
-const smallVariantInfo = {
-  release: 'grch37',
-  chromosome: 'chr17',
-  start: '43044295',
-  end: '43044295',
-  reference: 'G',
-  alternative: 'A',
-  hgnc_id: 'HGNC:1100'
+const seqvarInfo: Seqvar = {
+  genomeBuild: 'grch37',
+  chrom: '17',
+  pos: 43044295,
+  del: 'G',
+  ins: 'A',
+  userRepr: 'grch37-17-43044295-G-A'
 }
 
 describe.concurrent('BeaconNetwork', async () => {
@@ -19,7 +19,7 @@ describe.concurrent('BeaconNetwork', async () => {
       { component: BeaconNetwork, template: false },
       {
         props: {
-          smallVariant: smallVariantInfo
+          seqvar: seqvarInfo
         }
       }
     )
@@ -33,7 +33,7 @@ describe.concurrent('BeaconNetwork', async () => {
       { component: BeaconNetwork, template: false },
       {
         props: {
-          smallVariant: smallVariantInfo
+          seqvar: seqvarInfo
         }
       }
     )

frontend/src/components/__tests__/SeqvarDetails/ClinsigCard.spec.ts

@@ -8,7 +8,7 @@ import { AcmgCriteria, MultiSourceAcmgCriteriaState, Presence, StateSource } fro
 import type { Seqvar } from '@/lib/genomicVars'
 import { deepCopy, setupMountedComponents } from '@/lib/test-utils'
 import { StoreState } from '@/stores/misc'
-import { useVariantAcmgRatingStore } from '@/stores/variantAcmgRating'
+import { useSeqVarAcmgRatingStore } from '@/stores/seqVarAcmgRating'
 
 const seqvarInfo: Seqvar = {
   genomeBuild: 'grch37',
@@ -21,7 +21,7 @@ const seqvarInfo: Seqvar = {
 
 const makeWrapper = () => {
   const pinia = createTestingPinia({ createSpy: vi.fn })
-  const store = useVariantAcmgRatingStore(pinia)
+  const store = useSeqVarAcmgRatingStore(pinia)
 
   const mockRetrieveAcmgRating = vi.fn().mockImplementation(async () => {
     store.storeState = StoreState.Active

frontend/src/components/__tests__/SeqvarDetails/ClinvarCard.spec.ts

@@ -5,7 +5,7 @@ import ClinVar from '@/components/SeqvarDetails/ClinvarCard.vue'
 import { setupMountedComponents } from '@/lib/test-utils'
 
 describe.concurrent('ClinVar', async () => {
-  it.skip('renders the ClinVar info', async () => {
+  it('renders the ClinVar info', async () => {
     const { wrapper } = await setupMountedComponents(
       { component: ClinVar, template: false },
       {
@@ -14,14 +14,15 @@ describe.concurrent('ClinVar', async () => {
         }
       }
     )
+    expect(wrapper.text()).toContain('ClinVar')
     expect(wrapper.text()).toContain('VCV000055407')
     const stars = wrapper.findAll('.mdi-star')
-    expect(stars.length).toBe(18)
+    expect(stars.length).toBe(15)
     const starsOutline = wrapper.findAll('.mdi-star-outline')
-    expect(starsOutline.length).toBe(27)
+    expect(starsOutline.length).toBe(30)
   })
 
-  it.skip('renders the ClinVar info with stars', async () => {
+  it('renders the ClinVar info with stars', async () => {
     const clinVarInfoStars = structuredClone(clinVarInfo)
     clinVarInfoStars.referenceAssertions[0].reviewStatus =
       'REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED'
@@ -35,9 +36,9 @@ describe.concurrent('ClinVar', async () => {
     )
     expect(wrapper.text()).toContain('VCV000055407')
     const stars = wrapper.findAll('.mdi-star')
-    expect(stars.length).toBe(12)
+    expect(stars.length).toBe(9)
     const starsOutline = wrapper.findAll('.mdi-star-outline')
-    expect(starsOutline.length).toBe(33)
+    expect(starsOutline.length).toBe(36)
   })
 
   it('renders the ClinVar info (not found)', async () => {

frontend/src/components/__tests__/SeqvarDetails/FreqsCard/MitochondrialFreqs.spec.ts

@@ -13,7 +13,7 @@ const seqvarInfo: Seqvar = {
   userRepr: 'grch37-17-43044295-G-A'
 }
 
-const variantInfo = {
+const seqVarInfo = {
   helixmtdb: {
     num_total: 1,
     num_het: 1,
@@ -38,7 +38,7 @@ describe.concurrent('FreqsMitochondrial', async () => {
       {
         props: {
           seqVar: seqvarInfo,
-          varAnnos: variantInfo
+          varAnnos: seqVarInfo
         }
       }
     )
@@ -49,7 +49,7 @@ describe.concurrent('FreqsMitochondrial', async () => {
   })
 
   it('renders the FreqsMitochondrial info with no helixmtdb', async () => {
-    const variantInfoNoHelixmtdb: any = structuredClone(variantInfo)
+    const variantInfoNoHelixmtdb: any = structuredClone(seqVarInfo)
     variantInfoNoHelixmtdb.helixmtdb = {}
     const { wrapper } = await setupMountedComponents(
       { component: FreqsMitochondrial, template: false },
@@ -67,7 +67,7 @@ describe.concurrent('FreqsMitochondrial', async () => {
   })
 
   it('renders the FreqsMitochondrial info with no gnomad-mtdna', async () => {
-    const variantInfoNoGnomad: any = structuredClone(variantInfo)
+    const variantInfoNoGnomad: any = structuredClone(seqVarInfo)
     variantInfoNoGnomad['gnomad-mtdna'] = {}
     const { wrapper } = await setupMountedComponents(
       { component: FreqsMitochondrial, template: false },

frontend/src/components/__tests__/SeqvarDetails/VariantScoresCard.spec.ts

@@ -4,28 +4,29 @@ import * as BRCA1VariantInfo from '@/assets/__tests__/BRCA1VariantInfo.json'
 import VariantTools from '@/components/SeqvarDetails/VariantScoresCard.vue'
 import { setupMountedComponents } from '@/lib/test-utils'
 
-const smallVariantInfo = {
-  release: 'grch37',
-  chromosome: 'chr17',
-  start: '43044295',
-  end: '43044295',
-  reference: 'G',
-  alternative: 'A',
-  hgnc_id: 'HGNC:1100'
-}
-
 describe.concurrent('VariantTools', async () => {
   it('renders the Variant Tools info', async () => {
     const { wrapper } = await setupMountedComponents(
       { component: VariantTools, template: false },
       {
         props: {
-          smallVar: smallVariantInfo,
           varAnnos: BRCA1VariantInfo['result']
         }
       }
     )
     expect(wrapper.text()).toContain('Scoring Method')
     expect(wrapper.text()).toContain('BayesDel')
   })
+
+  it('renders the Variant Tools info with empty variance information', async () => {
+    const { wrapper } = await setupMountedComponents(
+      { component: VariantTools, template: false },
+      {
+        props: {
+          varAnnos: undefined
+        }
+      }
+    )
+    expect(wrapper.text()).toContain('No UCSC conservation data available.')
+  })
 })