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Change references to "populations" in API to "ancestry groups" #1457

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Change references to "populations" in API to "ancestry groups" #1457

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5130327
Update schema and API to prefer term "ancestry group" to "population"
phildarnowsky-broad Mar 26, 2024
9b524e4
Clean up CopyNumberVariant associated types
phildarnowsky-broad Mar 26, 2024
f218a0e
Change populations to ancestry_groups in CNV page query and associate…
phildarnowsky-broad Mar 26, 2024
540099a
Change populations to ancestry_groups in mitochondrial variant query …
phildarnowsky-broad Mar 26, 2024
a42e0e3
Change populations to ancestry_groups in short tandem repat page quer…
phildarnowsky-broad Mar 26, 2024
99641ff
Change populations to ancestry_groups in structural variant page
phildarnowsky-broad Mar 27, 2024
1c390b2
Change populations to ancestry_groups in variant cooccurrence page
phildarnowsky-broad Mar 27, 2024
12869f6
Change populations to ancestry_groups in variant page
phildarnowsky-broad Mar 27, 2024
586e726
Revert frontend references to new ancestry_groups fields
phildarnowsky-broad Apr 2, 2024
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1 change: 0 additions & 1 deletion browser/src/CopyNumberVariantList/CopyNumberVariantPlot.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@ type Props = {
variant: {
pos: number
end: number
type: string
}
width: number
}
Expand Down
61 changes: 0 additions & 61 deletions browser/src/CopyNumberVariantList/CopyNumberVariantPropType.ts
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This file was deleted.

6 changes: 3 additions & 3 deletions browser/src/CopyNumberVariantList/CopyNumberVariantTracks.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ import { Track } from '@gnomad/region-viewer'

import Link from '../Link'
import CopyNumberVariantPlot from './CopyNumberVariantPlot'
import CopyNumberVariantPropType from './CopyNumberVariantPropType'
import { CopyNumberVariant } from '../CopyNumberVariantPage/CopyNumberVariantPage'

type RowProps = {
data: {
Expand All @@ -15,7 +15,7 @@ type RowProps = {
onHover: (...args: any[]) => any
scalePosition: (...args: any[]) => any
trackColor: (...args: any[]) => any
variants: CopyNumberVariantPropType[]
variants: CopyNumberVariant[]
width: number
}
index: number
Expand Down Expand Up @@ -67,7 +67,7 @@ type OwnCopyNumberVariantTracksProps = {
onScroll: (...args: any[]) => any
trackColor: (...args: any[]) => any
trackHeight: number
variants: CopyNumberVariantPropType[]
variants: CopyNumberVariant[]
}

// @ts-expect-error TS(2456) FIXME: Type alias 'OwnCopyNumberVariantTracksProps' circular... Remove this comment to see the full error message
Expand Down
4 changes: 2 additions & 2 deletions browser/src/CopyNumberVariantList/CopyNumberVariants.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ import filterCopyNumberVariants from './filterCopyNumberVariants'
import CopyNumberVariantFilterControls from './CopyNumberVariantFilterControls'

import { cnvTypeColors } from './copyNumberVariantTypes'
import CopyNumberVariantPropType from './CopyNumberVariantPropType'
import { CopyNumberVariant } from '../CopyNumberVariantPage/CopyNumberVariantPage'
import copyNumberVariantTableColumns, {
getColumnsForContext,
} from './copyNumberVariantTableColumns'
Expand Down Expand Up @@ -48,7 +48,7 @@ export interface Context {
type CopyNumberVariantsProps = {
context: Context
exportFileName: string
variants: CopyNumberVariantPropType[]
variants: CopyNumberVariant[]
}

const CopyNumberVariants = ({ context, exportFileName, variants }: CopyNumberVariantsProps) => {
Expand Down
27 changes: 18 additions & 9 deletions browser/src/CopyNumberVariantList/__snapshots__/CopyNumberVariants.spec.tsx.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -14,18 +14,19 @@ exports[`CopyNumberVariants has no unexpected changes 1`] = `
[
{
"alts": null,
"ancestry_groups": [],
"chrom": "21",
"end": 456,
"endmax": 100168742,
"endmin": 100168738,
"filters": [],
"genes": [],
"length": 333,
"populations": [],
"pos": 123,
"posmax": 100121284,
"posmin": 100121281,
"qual": 99,
"reference_genome": "GRCh38",
"sc": 123,
"sf": 0.5,
"sn": 345,
Expand All @@ -34,18 +35,19 @@ exports[`CopyNumberVariants has no unexpected changes 1`] = `
},
{
"alts": null,
"ancestry_groups": [],
"chrom": "21",
"end": 456,
"endmax": 100168742,
"endmin": 100168738,
"filters": [],
"genes": [],
"length": 333,
"populations": [],
"pos": 123,
"posmax": 100121284,
"posmin": 100121281,
"qual": 99,
"reference_genome": "GRCh38",
"sc": 123,
"sf": 0.5,
"sn": 345,
Expand All @@ -54,18 +56,19 @@ exports[`CopyNumberVariants has no unexpected changes 1`] = `
},
{
"alts": null,
"ancestry_groups": [],
"chrom": "21",
"end": 456,
"endmax": 100168742,
"endmin": 100168738,
"filters": [],
"genes": [],
"length": 333,
"populations": [],
"pos": 123,
"posmax": 100121284,
"posmin": 100121281,
"qual": 99,
"reference_genome": "GRCh38",
"sc": 123,
"sf": 0.5,
"sn": 345,
Expand Down Expand Up @@ -108,18 +111,19 @@ exports[`CopyNumberVariants has no unexpected changes 1`] = `
[
{
"alts": null,
"ancestry_groups": [],
"chrom": "21",
"end": 456,
"endmax": 100168742,
"endmin": 100168738,
"filters": [],
"genes": [],
"length": 333,
"populations": [],
"pos": 123,
"posmax": 100121284,
"posmin": 100121281,
"qual": 99,
"reference_genome": "GRCh38",
"sc": 123,
"sf": 0.5,
"sn": 345,
Expand All @@ -128,18 +132,19 @@ exports[`CopyNumberVariants has no unexpected changes 1`] = `
},
{
"alts": null,
"ancestry_groups": [],
"chrom": "21",
"end": 456,
"endmax": 100168742,
"endmin": 100168738,
"filters": [],
"genes": [],
"length": 333,
"populations": [],
"pos": 123,
"posmax": 100121284,
"posmin": 100121281,
"qual": 99,
"reference_genome": "GRCh38",
"sc": 123,
"sf": 0.5,
"sn": 345,
Expand All @@ -148,18 +153,19 @@ exports[`CopyNumberVariants has no unexpected changes 1`] = `
},
{
"alts": null,
"ancestry_groups": [],
"chrom": "21",
"end": 456,
"endmax": 100168742,
"endmin": 100168738,
"filters": [],
"genes": [],
"length": 333,
"populations": [],
"pos": 123,
"posmax": 100121284,
"posmin": 100121281,
"qual": 99,
"reference_genome": "GRCh38",
"sc": 123,
"sf": 0.5,
"sn": 345,
Expand Down Expand Up @@ -287,18 +293,19 @@ exports[`CopyNumberVariants has no unexpected changes 1`] = `
[
{
"alts": null,
"ancestry_groups": [],
"chrom": "21",
"end": 456,
"endmax": 100168742,
"endmin": 100168738,
"filters": [],
"genes": [],
"length": 333,
"populations": [],
"pos": 123,
"posmax": 100121284,
"posmin": 100121281,
"qual": 99,
"reference_genome": "GRCh38",
"sc": 123,
"sf": 0.5,
"sn": 345,
Expand All @@ -307,18 +314,19 @@ exports[`CopyNumberVariants has no unexpected changes 1`] = `
},
{
"alts": null,
"ancestry_groups": [],
"chrom": "21",
"end": 456,
"endmax": 100168742,
"endmin": 100168738,
"filters": [],
"genes": [],
"length": 333,
"populations": [],
"pos": 123,
"posmax": 100121284,
"posmin": 100121281,
"qual": 99,
"reference_genome": "GRCh38",
"sc": 123,
"sf": 0.5,
"sn": 345,
Expand All @@ -327,18 +335,19 @@ exports[`CopyNumberVariants has no unexpected changes 1`] = `
},
{
"alts": null,
"ancestry_groups": [],
"chrom": "21",
"end": 456,
"endmax": 100168742,
"endmin": 100168738,
"filters": [],
"genes": [],
"length": 333,
"populations": [],
"pos": 123,
"posmax": 100121284,
"posmin": 100121281,
"qual": 99,
"reference_genome": "GRCh38",
"sc": 123,
"sf": 0.5,
"sn": 345,
Expand Down
2 changes: 1 addition & 1 deletion browser/src/CopyNumberVariantList/copyNumberVariantTableColumns.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ const copyNumberVariantTableColumns = [
if (variant.length === -1) {
s = '—'
} else {
const size = variant.length
const size = variant.length || 0
if (size >= 1e6) {
s = `${(size / 1e6).toPrecision(3)} Mb`
} else if (size >= 1e3) {
Expand Down
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