Change populations to ancestry_groups in variant page

Author: phildarnowsky-broad

browser/src/VariantList/ExportVariantsButton.tsx

@@ -22,8 +22,8 @@ const getValueGivenProperty = (
   variant: VariantTableVariant,
   property: Property
 ) => {
-  return variant.populations.filter((v) => v.id === popId)[0]
-    ? JSON.stringify(variant.populations.filter((v) => v.id === popId)[0][property])
+  return variant.ancestry_groups.filter((v) => v.id === popId)[0]
+    ? JSON.stringify(variant.ancestry_groups.filter((v) => v.id === popId)[0][property])
     : ''
 }
 
@@ -342,7 +342,7 @@ export type VariantTableVariant = {
   hgvs?: string
   hgvsc?: string
   hgvsp?: string
-  populations: Population[]
+  ancestry_groups: Population[]
   pos: number
   rsids?: string[]
   transcript_id: string

browser/src/VariantList/mergeExomeAndGenomeData.spec.ts

@@ -26,7 +26,7 @@ const createAncestryGroupObjects = (shorthands: AncestryGroupShorthand[]) => {
 }
 
 describe('mergeExomeAndGenomePopulationData', () => {
-  it('returns expected values when exomes and genomes have the same populations', () => {
+  it('returns expected values when exomes and genomes have the same ancestry_groups', () => {
     const geneticAncestryGroupObjects = createAncestryGroupObjects([
       { id: 'afr', value: 1 },
       { id: 'remaining', value: 2 },
@@ -35,8 +35,8 @@ describe('mergeExomeAndGenomePopulationData', () => {
 
     const testVariant = variantFactory.build({
       variant_id: 'test_variant',
-      exome: { populations: geneticAncestryGroupObjects },
-      genome: { populations: geneticAncestryGroupObjects },
+      exome: { ancestry_groups: geneticAncestryGroupObjects },
+      genome: { ancestry_groups: geneticAncestryGroupObjects },
     })
 
     const result = mergeExomeAndGenomePopulationData(testVariant.exome!, testVariant.genome!)
@@ -50,7 +50,7 @@ describe('mergeExomeAndGenomePopulationData', () => {
     expect(result).toStrictEqual(expected)
   })
 
-  it('returns expected values when exomes have less populations than genomes', () => {
+  it('returns expected values when exomes have less ancestry_groups than genomes', () => {
     const exomeGeneticAncestryGroupObjects = createAncestryGroupObjects([
       { id: 'afr', value: 1 },
       { id: 'remaining', value: 2 },
@@ -66,8 +66,8 @@ describe('mergeExomeAndGenomePopulationData', () => {
 
     const testVariant = variantFactory.build({
       variant_id: 'test_variant',
-      exome: { populations: exomeGeneticAncestryGroupObjects },
-      genome: { populations: genomeGeneticAncestryGroupObjects },
+      exome: { ancestry_groups: exomeGeneticAncestryGroupObjects },
+      genome: { ancestry_groups: genomeGeneticAncestryGroupObjects },
     })
 
     const result = mergeExomeAndGenomePopulationData(testVariant.exome!, testVariant.genome!)
@@ -82,7 +82,7 @@ describe('mergeExomeAndGenomePopulationData', () => {
     expect(result).toStrictEqual(expected)
   })
 
-  it('returns expected values exomes have more populations than genomes', () => {
+  it('returns expected values exomes have more ancestry_groups than genomes', () => {
     const exomeGeneticAncestryGroupObjects = createAncestryGroupObjects([
       { id: 'afr', value: 1 },
       { id: 'remaining', value: 2 },
@@ -98,8 +98,8 @@ describe('mergeExomeAndGenomePopulationData', () => {
 
     const testVariant = variantFactory.build({
       variant_id: 'test_variant',
-      exome: { populations: exomeGeneticAncestryGroupObjects },
-      genome: { populations: genomeGeneticAncestryGroupObjects },
+      exome: { ancestry_groups: exomeGeneticAncestryGroupObjects },
+      genome: { ancestry_groups: genomeGeneticAncestryGroupObjects },
     })
 
     const result = mergeExomeAndGenomePopulationData(testVariant.exome!, testVariant.genome!)
@@ -114,7 +114,7 @@ describe('mergeExomeAndGenomePopulationData', () => {
     expect(result).toStrictEqual(expected)
   })
 
-  it('returns expected values when exome and genome populations are in a different order', () => {
+  it('returns expected values when exome and genome ancestry_groups are in a different order', () => {
     const exomeGeneticAncestryGroupObjects = createAncestryGroupObjects([
       { id: 'eur', value: 1 },
       { id: 'afr', value: 2 },
@@ -129,8 +129,8 @@ describe('mergeExomeAndGenomePopulationData', () => {
 
     const testVariant = variantFactory.build({
       variant_id: 'test_variant',
-      exome: { populations: exomeGeneticAncestryGroupObjects },
-      genome: { populations: genomeGeneticAncestryGroupObjects },
+      exome: { ancestry_groups: exomeGeneticAncestryGroupObjects },
+      genome: { ancestry_groups: genomeGeneticAncestryGroupObjects },
     })
 
     const result = mergeExomeAndGenomePopulationData(testVariant.exome!, testVariant.genome!)

browser/src/VariantList/mergeExomeAndGenomeData.ts

@@ -7,10 +7,10 @@ export const mergeExomeAndGenomePopulationData = (
   exome: SequencingType,
   genome: SequencingType
 ) => {
-  const populations: { [key: string]: Population } = {}
+  const ancestry_groups: { [key: string]: Population } = {}
 
-  exome.populations.forEach((exomePopulation: Population) => {
-    populations[exomePopulation.id] = {
+  exome.ancestry_groups.forEach((exomePopulation: Population) => {
+    ancestry_groups[exomePopulation.id] = {
       id: exomePopulation.id,
       ac: exomePopulation.ac,
       an: exomePopulation.an,
@@ -19,18 +19,18 @@ export const mergeExomeAndGenomePopulationData = (
     }
   })
 
-  genome.populations.forEach((genomePopulation: Population) => {
-    if (genomePopulation.id in populations) {
-      const entry = populations[genomePopulation.id]
-      populations[genomePopulation.id] = {
+  genome.ancestry_groups.forEach((genomePopulation: Population) => {
+    if (genomePopulation.id in ancestry_groups) {
+      const entry = ancestry_groups[genomePopulation.id]
+      ancestry_groups[genomePopulation.id] = {
         id: genomePopulation.id,
         ac: add(entry.ac, genomePopulation.ac),
         an: add(entry.an, genomePopulation.an),
         ac_hemi: add(entry.ac_hemi, genomePopulation.ac_hemi),
         ac_hom: add(entry.ac_hom, genomePopulation.ac_hom),
       }
     } else {
-      populations[genomePopulation.id] = {
+      ancestry_groups[genomePopulation.id] = {
         id: genomePopulation.id,
         ac: genomePopulation.ac,
         an: genomePopulation.an,
@@ -40,7 +40,7 @@ export const mergeExomeAndGenomePopulationData = (
     }
   })
 
-  return Object.values(populations)
+  return Object.values(ancestry_groups)
 }
 
 const mergeExomeAndGenomeData = (variants: any) =>
@@ -74,7 +74,7 @@ const mergeExomeAndGenomeData = (variants: any) =>
       ac_hemi: add(exome.ac_hemi, genome.ac_hemi),
       ac_hom: add(exome.ac_hom, genome.ac_hom),
       filters: exome.filters.concat(genome.filters),
-      populations: mergeExomeAndGenomePopulationData(exome!, genome!),
+      ancestry_groups: mergeExomeAndGenomePopulationData(exome!, genome!),
     }
   })
 

browser/src/VariantPage/VariantPage.tsx

@@ -194,8 +194,8 @@ export type SequencingType = {
   hemizygote_count: number | null
   faf95: Faf95
   filters: string[]
-  populations: Population[]
-  local_ancestry_populations: LocalAncestryPopulation[]
+  ancestry_groups: Population[]
+  local_ancestry_groups: LocalAncestryPopulation[]
   age_distribution: AgeDistribution | null
   quality_metrics: VariantQualityMetrics
 }
@@ -348,7 +348,7 @@ export const VariantPageContent = ({ datasetId, variant }: VariantPageContentPro
           Genetic Ancestry Group Frequencies <InfoButton topic="ancestry" />
         </h2>
         {hasLocalAncestryPopulations(datasetId) &&
-          ((variant.genome && variant.genome.local_ancestry_populations) || []).length > 0 && (
+          ((variant.genome && variant.genome.local_ancestry_groups) || []).length > 0 && (
             <div
               style={{
                 padding: '0 1em',
@@ -495,14 +495,14 @@ query ${operationName}($variantId: String!, $datasetId: DatasetId!, $referenceGe
         popmax_population
       }
       filters
-      populations {
+      ancestry_groups {
         id
         ac
         an
         ac_hemi
         ac_hom
       }
-      local_ancestry_populations @include(if: $includeLocalAncestry) {
+      local_ancestry_groups @include(if: $includeLocalAncestry) {
         id
         ac
         an
@@ -574,14 +574,14 @@ query ${operationName}($variantId: String!, $datasetId: DatasetId!, $referenceGe
         popmax_population
       }
       filters
-      populations {
+      ancestry_groups {
         id
         ac
         an
         ac_hemi
         ac_hom
       }
-      local_ancestry_populations @include(if: $includeLocalAncestry) {
+      local_ancestry_groups @include(if: $includeLocalAncestry) {
         id
         ac
         an

browser/src/VariantPage/VariantPopulationFrequencies.tsx

@@ -23,22 +23,22 @@ type Props = {
 const VariantPopulationFrequencies = ({ datasetId, variant }: Props) => {
   if (hasLocalAncestryPopulations(datasetId) && variant.genome) {
     const genome = variant.genome!
-    const genomePopulations = genome.populations.filter(
+    const genomePopulations = genome.ancestry_groups.filter(
       (pop) => !(pop.id.startsWith('hgdp:') || pop.id.startsWith('1kg:'))
     )
     const exomePopulations = variant.exome
-      ? variant.exome.populations.filter(
+      ? variant.exome.ancestry_groups.filter(
           (pop) => !(pop.id.startsWith('hgdp:') || pop.id.startsWith('1kg:'))
         )
       : []
-    const hgdpPopulations = genome.populations
+    const hgdpPopulations = genome.ancestry_groups
       .filter((pop) => pop.id.startsWith('hgdp:'))
       .map((pop) => ({ ...pop, id: pop.id.slice(5) })) // Remove hgdp: prefix
-    const tgpPopulations = genome.populations
+    const tgpPopulations = genome.ancestry_groups
       .filter((pop) => pop.id.startsWith('1kg:'))
       .map((pop) => ({ ...pop, id: pop.id.slice(4) })) // Remove 1kg: prefix
 
-    const localAncestryPopulations = genome.local_ancestry_populations || []
+    const localAncestryPopulations = genome.local_ancestry_groups || []
 
     return (
       // @ts-expect-error TS(2741) FIXME: Property 'onChange' is missing in type '{ tabs: { ... Remove this comment to see the full error message
@@ -141,8 +141,8 @@ const VariantPopulationFrequencies = ({ datasetId, variant }: Props) => {
     <TableWrapper>
       <GnomadPopulationsTable
         datasetId={datasetId}
-        exomePopulations={variant.exome ? variant.exome.populations : []}
-        genomePopulations={variant.genome ? variant.genome.populations : []}
+        exomePopulations={variant.exome ? variant.exome.ancestry_groups : []}
+        genomePopulations={variant.genome ? variant.genome.ancestry_groups : []}
         showHemizygotes={variant.chrom === 'X' || variant.chrom === 'Y'}
       />
     </TableWrapper>

browser/src/__factories__/Variant.ts

@@ -148,7 +148,7 @@ export const variantTableVariantFactory = Factory.define<VariantTableVariant>(
       hgvs = 'string',
       hgvsc = 'string',
       hgvsp = 'string',
-      populations = [],
+      ancestry_groups = [],
       pos = 1,
       rsids = [],
       variant_id = '',
@@ -177,7 +177,7 @@ export const variantTableVariantFactory = Factory.define<VariantTableVariant>(
       hgvs,
       hgvsc,
       hgvsp,
-      populations,
+      ancestry_groups,
       pos,
       rsids,
       variant_id,
@@ -198,8 +198,8 @@ export const sequencingFactory = Factory.define<SequencingType>(({ params, assoc
     homozygote_count = null,
     hemizygote_count = null,
     filters = [],
-    populations = [],
-    local_ancestry_populations = [],
+    ancestry_groups = [],
+    local_ancestry_groups = [],
     ac_hemi = 1,
     ac_hom = 1,
   } = params
@@ -226,8 +226,8 @@ export const sequencingFactory = Factory.define<SequencingType>(({ params, assoc
     homozygote_count,
     hemizygote_count,
     filters,
-    populations,
-    local_ancestry_populations,
+    ancestry_groups,
+    local_ancestry_groups,
     age_distribution,
     quality_metrics,
     faf95,