fix(browser): render XX and XY sums in variant table

browser/src/VariantList/mergeExomeAndGenomeData.spec.ts

@@ -1,48 +1,22 @@
 import { describe, it, expect } from '@jest/globals'
 
-import { populationFactory, variantFactory } from '../__factories__/Variant'
+import { createAncestryGroupObjects, variantFactory } from '../__factories__/Variant'
 import { Population } from '../VariantPage/VariantPage'
 
 import {
   mergeExomeGenomeAndJointPopulationData,
   mergeExomeAndGenomeData,
 } from './mergeExomeAndGenomeData'
 
-type AncestryGroupShorthand = {
-  id: string
-  value: number
-}
-
-const createAncestryGroupObjects = (
-  shorthands: AncestryGroupShorthand[],
-  includeJointFields: boolean
-) => {
-  const geneticAncestryGroupObjects: Population[] = shorthands.map((shorthand) => {
-    const populationFields: any = {
-      id: shorthand.id,
-      ac: shorthand.value,
-      an: shorthand.value * 10,
-      ac_hemi: shorthand.value + 1,
-      ac_hom: shorthand.value + 2,
-    }
-
-    if (includeJointFields) {
-      populationFields.hemizygote_count = shorthand.value + 1
-      populationFields.homozygote_count = shorthand.value + 2
-    }
-    return populationFactory.build(populationFields)
-  })
-
-  return geneticAncestryGroupObjects
-}
-
 describe('mergeExomeGenomeAndJointPopulationData', () => {
   it('returns expected values when exomes and genomes have the same populations', () => {
     const geneticAncestryGroupObjects = createAncestryGroupObjects(
       [
         { id: 'afr', value: 1 },
         { id: 'remaining', value: 2 },
         { id: 'eur', value: 4 },
+        { id: 'XX', value: 8 },
+        { id: 'XY', value: 16 },
       ],
       false
     )
@@ -62,6 +36,8 @@ describe('mergeExomeGenomeAndJointPopulationData', () => {
       { ac: 2, ac_hemi: 4, ac_hom: 6, an: 20, id: 'afr' },
       { ac: 4, ac_hemi: 6, ac_hom: 8, an: 40, id: 'remaining' },
       { ac: 8, ac_hemi: 10, ac_hom: 12, an: 80, id: 'eur' },
+      { ac: 16, ac_hemi: 18, ac_hom: 20, an: 160, id: 'XX' },
+      { ac: 32, ac_hemi: 34, ac_hom: 36, an: 320, id: 'XY' },
     ]
 
     expect(result).toStrictEqual(expected)
@@ -250,15 +226,19 @@ describe('mergeExomeGenomeAndJointPopulationData', () => {
         { id: 'eur', value: 1 },
         { id: 'afr', value: 2 },
         { id: 'remaining', value: 4 },
+        { id: 'XX', value: 8 },
+        { id: 'XY', value: 16 },
       ],
       false
     )
 
     const genomeGeneticAncestryGroupObjects = createAncestryGroupObjects(
       [
-        { id: 'afr', value: 8 },
-        { id: 'remaining', value: 16 },
-        { id: 'eur', value: 32 },
+        { id: 'afr', value: 32 },
+        { id: 'remaining', value: 64 },
+        { id: 'eur', value: 128 },
+        { id: 'XX', value: 256 },
+        { id: 'XY', value: 512 },
       ],
       false
     )
@@ -270,6 +250,8 @@ describe('mergeExomeGenomeAndJointPopulationData', () => {
       { ac: 32, hemizygote_count: 33, homozygote_count: 34, an: 320, id: 'remaining' },
       { ac: 64, hemizygote_count: 65, homozygote_count: 66, an: 640, id: 'eur' },
       { ac: 128, hemizygote_count: 129, homozygote_count: 130, an: 1280, id: 'mid' },
+      { ac: 256, hemizygote_count: 257, homozygote_count: 258, an: 2560, id: 'XX' },
+      { ac: 512, hemizygote_count: 513, homozygote_count: 514, an: 5120, id: 'XY' },
     ]
 
     const testVariant = variantFactory.build({
@@ -294,6 +276,8 @@ describe('mergeExomeGenomeAndJointPopulationData', () => {
         { id: 'remaining', value: 32 },
         { id: 'eur', value: 64 },
         { id: 'mid', value: 128 },
+        { id: 'XX', value: 256 },
+        { id: 'XY', value: 512 },
       ],
       true
     )
@@ -346,6 +330,8 @@ describe('mergeExomeAndGenomeData', () => {
         { id: 'afr', value: 1 },
         { id: 'remaining', value: 2 },
         { id: 'eur', value: 4 },
+        { id: 'XX', value: 8 },
+        { id: 'XY', value: 16 },
       ],
       false
     )

browser/src/VariantList/mergeExomeAndGenomeData.ts

@@ -32,7 +32,12 @@ const addMissingAncestries = (
       findAncestries(versionAncestry, currentAncestries) || emptyAncestries(versionAncestry)
   )
 
-  return fullAncestries
+  const totalXX = currentAncestries.filter((ancestry) => ancestry.id === 'XX')
+  const totalXY = currentAncestries.filter((ancestry) => ancestry.id === 'XY')
+
+  const fullAncestriesWithTotalKaryotypes = fullAncestries.concat(totalXX, totalXY)
+
+  return fullAncestriesWithTotalKaryotypes
 }
 
 export const mergeExomeGenomeAndJointPopulationData = ({

browser/src/VariantPage/GnomadPopulationsTable.spec.tsx

@@ -0,0 +1,71 @@
+import React from 'react'
+import { describe, expect, test } from '@jest/globals'
+import renderer from 'react-test-renderer'
+
+import { GnomadPopulationsTable } from './GnomadPopulationsTable'
+import { allDatasetIds } from '@gnomad/dataset-metadata/metadata'
+import { createAncestryGroupObjects } from '../__factories__/Variant'
+
+describe('GnomadPopulationsTable', () => {
+  describe.each(allDatasetIds)('with a dataset of %s', (dataset: any) => {
+    test('has no unexpected changes', () => {
+      const exomeGeneticAncestryGroupObjexts = createAncestryGroupObjects(
+        [
+          { id: 'afr', value: 1 },
+          { id: 'remaining', value: 2 },
+          { id: 'eur', value: 4 },
+          { id: 'XX', value: 8 },
+          { id: 'XY', value: 16 },
+        ],
+        false
+      )
+
+      const genomeGeneticAncestryGroupObjexts = createAncestryGroupObjects(
+        [
+          { id: 'afr', value: 32 },
+          { id: 'remaining', value: 64 },
+          { id: 'eur', value: 128 },
+          { id: 'XX', value: 256 },
+          { id: 'XY', value: 512 },
+        ],
+        false
+      )
+
+      const tree = renderer.create(
+        <GnomadPopulationsTable
+          datasetId={dataset}
+          exomePopulations={exomeGeneticAncestryGroupObjexts}
+          genomePopulations={genomeGeneticAncestryGroupObjexts}
+          jointPopulations={null}
+          showHemizygotes={false}
+        />
+      )
+
+      expect(tree).toMatchSnapshot()
+    })
+    test('has no unexpected changes when missing genetic ancestry groups are filled in', () => {
+      const jointGeneticAncestryGroupObjects = createAncestryGroupObjects(
+        [
+          { id: 'afr', value: 1 },
+          { id: 'remaining', value: 2 },
+          { id: 'eur', value: 4 },
+          { id: 'XX', value: 8 },
+          { id: 'XY', value: 16 },
+        ],
+        true
+      )
+
+      const tree = renderer.create(
+        <GnomadPopulationsTable
+          datasetId={dataset}
+          exomePopulations={[]}
+          genomePopulations={[]}
+          jointPopulations={jointGeneticAncestryGroupObjects}
+          showHemizygotes={false}
+        />
+      )
+
+      expect(tree).toMatchSnapshot()
+    })
+  })
+})