From 7b5f1314f8865cf18d4c410bfd2201add7a29779 Mon Sep 17 00:00:00 2001
From: gromdimon <grom.dima.grom@gmail.com>
Date: Sat, 9 Dec 2023 11:55:15 +0100
Subject: [PATCH] tests

---
 .../components/SeqvarDetails/FreqsCard.vue    |  2 +-
 .../FreqsCard/MitochondrialFreqs.vue          |  4 +-
 .../ClinsigCard/CriterionSwitch.spec.ts       | 41 +++++++++++++++++
 .../ClinsigCard/SummarySheet.spec.ts          | 20 +++++++++
 .../FreqsCard/MitochondrialFreqs.spec.ts      | 24 +++++-----
 frontend/src/lib/__tests__/utils.spec.ts      | 45 +++++++++++++------
 frontend/src/lib/utils.ts                     | 19 ++++----
 7 files changed, 118 insertions(+), 37 deletions(-)

diff --git a/frontend/src/components/SeqvarDetails/FreqsCard.vue b/frontend/src/components/SeqvarDetails/FreqsCard.vue
index b1603a10..a6b5521a 100644
--- a/frontend/src/components/SeqvarDetails/FreqsCard.vue
+++ b/frontend/src/components/SeqvarDetails/FreqsCard.vue
@@ -24,7 +24,7 @@ const props = defineProps<{
     <v-card-title class="mb-0">Population Frequencies</v-card-title>
     <v-card-text>
       <VariantDetailsFreqsMitochondrial
-        v-if="isVariantMt(seqvar)"
+        v-if="isVariantMt(seqvar as Seqvar)"
         :seqvar="seqvar"
         :var-annos="varAnnos"
       />
diff --git a/frontend/src/components/SeqvarDetails/FreqsCard/MitochondrialFreqs.vue b/frontend/src/components/SeqvarDetails/FreqsCard/MitochondrialFreqs.vue
index b9b322b7..2e630079 100644
--- a/frontend/src/components/SeqvarDetails/FreqsCard/MitochondrialFreqs.vue
+++ b/frontend/src/components/SeqvarDetails/FreqsCard/MitochondrialFreqs.vue
@@ -29,12 +29,12 @@ const gnomadMtDna = computed(() => {
 </script>
 
 <template>
-  <template v-if="seqVar">
+  <template v-if="!seqVar">
     <v-skeleton-loader type="table" />
   </template>
   <template v-else>
     <div>
-      <div v-if="!isVariantMtHomopolymer(seqVar)">
+      <div v-if="!isVariantMtHomopolymer(seqVar as Seqvar)">
         <small>
           <v-icon>mdi-alert-circle-outline</v-icon>
           Variant in homopolymeric region
diff --git a/frontend/src/components/__tests__/SeqvarDetails/ClinsigCard/CriterionSwitch.spec.ts b/frontend/src/components/__tests__/SeqvarDetails/ClinsigCard/CriterionSwitch.spec.ts
index e69de29b..35a879b1 100644
--- a/frontend/src/components/__tests__/SeqvarDetails/ClinsigCard/CriterionSwitch.spec.ts
+++ b/frontend/src/components/__tests__/SeqvarDetails/ClinsigCard/CriterionSwitch.spec.ts
@@ -0,0 +1,41 @@
+import { describe, expect, it } from 'vitest'
+
+import CriterionSwitch from '@/components/SeqvarDetails/ClinsigCard/CriterionSwitch.vue'
+import {
+  AcmgCriteria,
+  AcmgEvidenceLevel,
+  MultiSourceAcmgCriteriaState,
+  Presence,
+  StateSource
+} from '@/lib/acmgSeqVar'
+import { setupMountedComponents } from '@/lib/test-utils'
+
+describe.concurrent('CriterionSwitch', async () => {
+  it('renders the CriterionSwitch', async () => {
+    const acmgRating = new MultiSourceAcmgCriteriaState()
+    acmgRating.setPresence(StateSource.User, AcmgCriteria.Pm1, Presence.Present)
+    const { wrapper } = await setupMountedComponents(
+      { component: CriterionSwitch, template: false },
+      {
+        props: {
+          acmgRating: acmgRating,
+          criteria: AcmgCriteria.Pm1,
+          criteriaState: {
+            criteria: AcmgCriteria.Pm1,
+            presence: Presence.Present,
+            evidenceLevel: AcmgEvidenceLevel.PathogenicModerate
+          }
+        }
+      }
+    )
+
+    expect(wrapper.text()).contains('Pm1')
+    expect(wrapper.text()).contains('Pathogenic Moderate')
+    const vSwitch = wrapper.findComponent({ name: 'VSwitch' })
+    const vTooltip = wrapper.findComponent({ name: 'VTooltip' })
+    const vSelect = wrapper.findComponent({ name: 'VSelect' })
+    expect(vSwitch.exists()).toBe(true)
+    expect(vTooltip.exists()).toBe(true)
+    expect(vSelect.exists()).toBe(true)
+  })
+})
diff --git a/frontend/src/components/__tests__/SeqvarDetails/ClinsigCard/SummarySheet.spec.ts b/frontend/src/components/__tests__/SeqvarDetails/ClinsigCard/SummarySheet.spec.ts
index e69de29b..0e5ea841 100644
--- a/frontend/src/components/__tests__/SeqvarDetails/ClinsigCard/SummarySheet.spec.ts
+++ b/frontend/src/components/__tests__/SeqvarDetails/ClinsigCard/SummarySheet.spec.ts
@@ -0,0 +1,20 @@
+import { describe, expect, it } from 'vitest'
+
+import SummarySheet from '@/components/SeqvarDetails/ClinsigCard/SummarySheet.vue'
+import { setupMountedComponents } from '@/lib/test-utils'
+
+describe.concurrent('SummarySheet', async () => {
+  it('renders the SummarySheet', async () => {
+    const { wrapper } = await setupMountedComponents(
+      { component: SummarySheet, template: false },
+      {
+        props: {
+          calculatedAcmgClass: 'Pathogenic'
+        }
+      }
+    )
+
+    expect(wrapper.text()).contains('Semi-Automated ACMG Pathogenicity Prediction')
+    expect(wrapper.text()).contains('Pathogenic')
+  })
+})
diff --git a/frontend/src/components/__tests__/SeqvarDetails/FreqsCard/MitochondrialFreqs.spec.ts b/frontend/src/components/__tests__/SeqvarDetails/FreqsCard/MitochondrialFreqs.spec.ts
index 87accda4..4394910d 100644
--- a/frontend/src/components/__tests__/SeqvarDetails/FreqsCard/MitochondrialFreqs.spec.ts
+++ b/frontend/src/components/__tests__/SeqvarDetails/FreqsCard/MitochondrialFreqs.spec.ts
@@ -1,16 +1,16 @@
 import { describe, expect, it } from 'vitest'
 
 import FreqsMitochondrial from '@/components/SeqvarDetails/FreqsCard/MitochondrialFreqs.vue'
+import { type Seqvar } from '@/lib/genomicVars'
 import { setupMountedComponents } from '@/lib/test-utils'
 
-const smallVariantInfo = {
-  release: 'grch37',
-  chromosome: 'chrM',
-  start: '70',
-  end: '70',
-  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'
 }
 
 const variantInfo = {
@@ -37,7 +37,7 @@ describe.concurrent('FreqsMitochondrial', async () => {
       { component: FreqsMitochondrial, template: false },
       {
         props: {
-          smallVar: smallVariantInfo,
+          seqVar: seqvarInfo,
           varAnnos: variantInfo
         }
       }
@@ -55,7 +55,7 @@ describe.concurrent('FreqsMitochondrial', async () => {
       { component: FreqsMitochondrial, template: false },
       {
         props: {
-          smallVar: smallVariantInfo,
+          seqVar: seqvarInfo,
           varAnnos: variantInfoNoHelixmtdb
         }
       }
@@ -73,7 +73,7 @@ describe.concurrent('FreqsMitochondrial', async () => {
       { component: FreqsMitochondrial, template: false },
       {
         props: {
-          smallVar: smallVariantInfo,
+          seqVar: seqvarInfo,
           varAnnos: variantInfoNoGnomad
         }
       }
@@ -89,7 +89,7 @@ describe.concurrent('FreqsMitochondrial', async () => {
       { component: FreqsMitochondrial, template: false },
       {
         props: {
-          smallVar: smallVariantInfo,
+          seqVar: seqvarInfo,
           varAnnos: {}
         }
       }
diff --git a/frontend/src/lib/__tests__/utils.spec.ts b/frontend/src/lib/__tests__/utils.spec.ts
index ef3df4d7..8596a4e4 100644
--- a/frontend/src/lib/__tests__/utils.spec.ts
+++ b/frontend/src/lib/__tests__/utils.spec.ts
@@ -1,5 +1,8 @@
 import { describe, expect, it } from 'vitest'
 
+import { type GenomeBuild } from '@/lib/genomeBuilds'
+import { type Seqvar } from '@/lib/genomicVars'
+
 import {
   copy,
   infoFromQuery,
@@ -10,6 +13,16 @@ import {
   separateIt
 } from '../utils'
 
+/** Example Sequence variant. */
+const seqVar: Seqvar = {
+  genomeBuild: 'grch37' as GenomeBuild,
+  chrom: '1',
+  pos: 12345,
+  del: 'A',
+  ins: 'G',
+  userRepr: 'chr1:12345:A:G'
+}
+
 describe.concurrent('roundIt method', () => {
   it('should round a positive value with default digits', () => {
     const result = roundIt(3.14159)
@@ -71,10 +84,14 @@ describe.concurrent('separateIt method', () => {
 
 describe.concurrent('isVariantMt method', () => {
   it('should return true if mitochondrial chromosome', () => {
-    const result_MT = isVariantMt({ chromosome: 'MT' })
-    const result_M = isVariantMt({ chromosome: 'M' })
-    const result_chrMT = isVariantMt({ chromosome: 'chrMT' })
-    const result_chrM = isVariantMt({ chromosome: 'chrM' })
+    seqVar.chrom = 'MT'
+    const result_MT = isVariantMt(seqVar)
+    seqVar.chrom = 'M'
+    const result_M = isVariantMt(seqVar)
+    seqVar.chrom = 'chrMT'
+    const result_chrMT = isVariantMt(seqVar)
+    seqVar.chrom = 'chrM'
+    const result_chrM = isVariantMt(seqVar)
     expect(result_MT).toBe(true)
     expect(result_M).toBe(true)
     expect(result_chrMT).toBe(true)
@@ -82,29 +99,31 @@ describe.concurrent('isVariantMt method', () => {
   })
 
   it('should return false if not mitochondrial chromosome', () => {
-    const result = isVariantMt({ chromosome: '1' })
+    seqVar.chrom = '1'
+    const result = isVariantMt(seqVar)
     expect(result).toBe(false)
   })
 })
 
 describe.concurrent('isVariantMtHomopolymer method', () => {
   it('should return true if mitochondrial homopolymer', () => {
-    const result = isVariantMtHomopolymer({ chromosome: 'MT', start: 70 })
+    seqVar.chrom = 'MT'
+    seqVar.pos = 70
+    const result = isVariantMtHomopolymer(seqVar)
     expect(result).toBe(true)
   })
 
   it('should return false if not mitochondrial homopolymer (chromosome)', () => {
-    const result = isVariantMtHomopolymer({ chromosome: '1', start: 70 })
+    seqVar.chrom = '1'
+    seqVar.pos = 70
+    const result = isVariantMtHomopolymer(seqVar)
     expect(result).toBe(false)
   })
 
   it('should return false if not mitochondrial homopolymer (position)', () => {
-    const result = isVariantMtHomopolymer({ chromosome: 'MT', start: 1 })
-    expect(result).toBe(false)
-  })
-
-  it('should return false for NaN', () => {
-    const result = isVariantMtHomopolymer(NaN)
+    seqVar.chrom = 'MT'
+    seqVar.pos = 1
+    const result = isVariantMtHomopolymer(seqVar)
     expect(result).toBe(false)
   })
 })
diff --git a/frontend/src/lib/utils.ts b/frontend/src/lib/utils.ts
index 5475c1f6..60a90733 100644
--- a/frontend/src/lib/utils.ts
+++ b/frontend/src/lib/utils.ts
@@ -1,6 +1,7 @@
 import { type RouteLocationNormalizedLoaded, type RouteLocationRaw, type Router } from 'vue-router'
 
 import { type GenomeBuild } from '@/lib/genomeBuilds'
+import { type Seqvar } from '@/lib/genomicVars'
 import { type BookmarkData } from '@/stores/bookmarks'
 
 /**
@@ -50,24 +51,24 @@ export const separateIt = (value: number, separator: string = ' '): string => {
 /**
  * Returns whether the given variant looks mitochondrial.
  *
- * @param smallVar Small variant to check.
+ * @param seqvar Small variant to check.
  * @returns whether the position is on the mitochondrial genome
  */
-export const isVariantMt = (smallVar: any): boolean => {
-  return ['MT', 'M', 'chrMT', 'chrM'].includes(smallVar?.chrom)
+export const isVariantMt = (seqvar: Seqvar): boolean => {
+  return ['MT', 'M', 'chrMT', 'chrM'].includes(seqvar?.chrom)
 }
 
 /**
  * Returns whether the given position is in a homopolymer on the mitochondrial chromosome.
  *
- * @param smallVar Small variant to check.
+ * @param seqvar Small variant to check.
  * @returns whether the position is in a mitochondrial homopolymer
  */
-export const isVariantMtHomopolymer = (smallVar: any): boolean => {
-  if (!smallVar) {
+export const isVariantMtHomopolymer = (seqvar: Seqvar): boolean => {
+  if (!seqvar) {
     return false
   }
-  const { start, end } = smallVar
+  const { pos } = seqvar
   const positionCheck = (pos: number) => {
     return (
       (pos >= 66 && pos <= 71) ||
@@ -78,8 +79,8 @@ export const isVariantMtHomopolymer = (smallVar: any): boolean => {
       (pos >= 16182 && pos <= 16194)
     )
   }
-  if (isVariantMt(smallVar)) {
-    return positionCheck(start) || positionCheck(end)
+  if (isVariantMt(seqvar)) {
+    return positionCheck(pos)
   } else {
     return false
   }