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fix: workaround because custom useQuery doesn't immediately update th…
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…e data

This is a workaround for a weird bug: When changing to amino acids, the plot crashes.
On the first update run, the old data for nucleotides would still be returned by useQuery.
Only on the second run, it returns the new data.

Also make the unit test independent of local time.
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@fengelniederhammer
fengelniederhammer committed May 17, 2023
1 parent caf89c7 commit 3ddd9c8
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Showing 6 changed files with 255 additions and 161 deletions.
217 changes: 91 additions & 126 deletions src/components/NucleotideEntropy/__tests__/hooks.test.ts
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Original file line number Diff line number Diff line change
@@ -1,11 +1,14 @@
import { act, renderHook } from '@testing-library/react';
import { useNucleotideEntropyDataByPosition, useNucleotideEntropyDataByTime } from '../hooks';
import { MutationProportionData } from '../../../data/MutationProportionDataset';
import { SamplingStrategy } from '../../../data/SamplingStrategy';
import { addDefaultHostAndQc } from '../../../data/HostAndQcSelector';
import { FixedDateRangeSelector } from '../../../data/DateRangeSelector';
import { globalDateCache } from '../../../helpers/date-cache';
import { DateRange } from '../../../data/DateRange';
import { SequenceType } from '../../../data/SequenceType';
import {
ALL_GENES_SELECTED,
DEFAULT_DATE_RANGE,
DEFAULT_SELECTOR,
expectedTicks,
getSelector,
} from '../testUtils';

jest.mock('../../../data/api');

Expand All @@ -16,42 +19,12 @@ beforeEach(() => {
jest.resetAllMocks();
});

const DEFAULT_SELECTOR = {
location: {},
samplingStrategy: SamplingStrategy.AllSamples,
};

const ALL_GENES_SELECTED = {
value: 'All',
label: 'All',
startPosition: 0,
endPosition: 29903,
aaSeq: '',
color: 'some color',
};

function getSelector(dateRange: DateRange) {
return addDefaultHostAndQc({
location: {},
samplingStrategy: SamplingStrategy.AllSamples,
dateRange: new FixedDateRangeSelector(dateRange),
});
}

describe('useNucleotideEntropyDataByPosition', () => {
test('should return undefined if backend request fails', async () => {
mutationProportionDataMock.mockRejectedValue('no data');

const { result } = renderHook(() =>
useNucleotideEntropyDataByPosition(
getSelector({
dateFrom: globalDateCache.getDay('2023-05-01'),
dateTo: globalDateCache.getDay('2023-05-15'),
}),
'aa',
false,
false
)
useNucleotideEntropyDataByPosition(getSelector(DEFAULT_DATE_RANGE), 'aa', false, false)
);
await act(() => {});

Expand All @@ -68,15 +41,7 @@ describe('useNucleotideEntropyDataByPosition', () => {
});

const { result } = renderHook(() =>
useNucleotideEntropyDataByPosition(
getSelector({
dateFrom: globalDateCache.getDay('2023-05-01'),
dateTo: globalDateCache.getDay('2023-05-15'),
}),
'nuc',
false,
false
)
useNucleotideEntropyDataByPosition(getSelector(DEFAULT_DATE_RANGE), 'nuc', false, false)
);
await act(() => {});

Expand All @@ -103,15 +68,7 @@ describe('useNucleotideEntropyDataByPosition', () => {
});

const { result } = renderHook(() =>
useNucleotideEntropyDataByPosition(
getSelector({
dateFrom: globalDateCache.getDay('2023-05-01'),
dateTo: globalDateCache.getDay('2023-05-15'),
}),
'nuc',
false,
false
)
useNucleotideEntropyDataByPosition(getSelector(DEFAULT_DATE_RANGE), 'nuc', false, false)
);
await act(() => {});

Expand All @@ -135,15 +92,7 @@ describe('useNucleotideEntropyDataByPosition', () => {
});

const { result } = renderHook(() =>
useNucleotideEntropyDataByPosition(
getSelector({
dateFrom: globalDateCache.getDay('2023-05-01'),
dateTo: globalDateCache.getDay('2023-05-15'),
}),
'nuc',
false,
true
)
useNucleotideEntropyDataByPosition(getSelector(DEFAULT_DATE_RANGE), 'nuc', false, true)
);
await act(() => {});

Expand All @@ -168,15 +117,7 @@ describe('useNucleotideEntropyDataByPosition', () => {
});

const { result } = renderHook(() =>
useNucleotideEntropyDataByPosition(
getSelector({
dateFrom: globalDateCache.getDay('2023-05-01'),
dateTo: globalDateCache.getDay('2023-05-15'),
}),
'aa',
false,
false
)
useNucleotideEntropyDataByPosition(getSelector(DEFAULT_DATE_RANGE), 'aa', false, false)
);
await act(() => {});

Expand All @@ -193,22 +134,44 @@ describe('useNucleotideEntropyDataByPosition', () => {
]);
});

test('should switch between nucleotide and amino acids', async () => {
mutationProportionDataMock.mockResolvedValueOnce({
selector: DEFAULT_SELECTOR,
payload: [{ mutation: 'T671G', proportion: 0.3, count: 42 }],
});

const { result, rerender } = renderHook(
(sequenceType: SequenceType) =>
useNucleotideEntropyDataByPosition(getSelector(DEFAULT_DATE_RANGE), sequenceType, false, false),
{ initialProps: 'nuc' }
);
await act(() => {});

expect(result.current).toHaveLength(1);

mutationProportionDataMock.mockResolvedValueOnce({
selector: DEFAULT_SELECTOR,
payload: [
{ mutation: 'ORF8:R101C', proportion: 0.3, count: 42 },
{ mutation: 'ORF8:R102C', proportion: 0.3, count: 42 },
],
});

await act(() => {
rerender('aa');
});

expect(result.current).toHaveLength(2);
});

test('should compute entropy for an amino acid mutation including zero entropy positions', async () => {
mutationProportionDataMock.mockResolvedValue({
selector: DEFAULT_SELECTOR,
payload: [{ mutation: 'ORF8:R101C', proportion: 0.3, count: 42 }],
});

const { result } = renderHook(() =>
useNucleotideEntropyDataByPosition(
getSelector({
dateFrom: globalDateCache.getDay('2023-05-01'),
dateTo: globalDateCache.getDay('2023-05-15'),
}),
'aa',
false,
true
)
useNucleotideEntropyDataByPosition(getSelector(DEFAULT_DATE_RANGE), 'aa', false, true)
);
await act(() => {});

Expand All @@ -234,15 +197,7 @@ describe('useNucleotideEntropyDataByTime', () => {
mutationProportionDataMock.mockRejectedValue('no data');

const { result } = renderHook(() =>
useNucleotideEntropyDataByTime(
getSelector({
dateFrom: globalDateCache.getDay('2023-05-01'),
dateTo: globalDateCache.getDay('2023-05-15'),
}),
'aa',
[ALL_GENES_SELECTED],
false
)
useNucleotideEntropyDataByTime(getSelector(DEFAULT_DATE_RANGE), 'aa', [ALL_GENES_SELECTED], false)
);
await act(() => {});

Expand All @@ -259,28 +214,20 @@ describe('useNucleotideEntropyDataByTime', () => {
});

const { result } = renderHook(() =>
useNucleotideEntropyDataByTime(
getSelector({
dateFrom: globalDateCache.getDay('2023-05-01'),
dateTo: globalDateCache.getDay('2023-05-15'),
}),
'nuc',
[ALL_GENES_SELECTED],
false
)
useNucleotideEntropyDataByTime(getSelector(DEFAULT_DATE_RANGE), 'nuc', [ALL_GENES_SELECTED], false)
);
await act(() => {});

expect(result.current).toStrictEqual({
ticks: [1682892000000, 1683496800000, 1684101600000],
ticks: expectedTicks,
timeData: [
{
All: 0,
day: 1682892000000,
day: expectedTicks[0],
},
{
All: 0,
day: 1683496800000,
day: expectedTicks[1],
},
],
});
Expand All @@ -293,28 +240,20 @@ describe('useNucleotideEntropyDataByTime', () => {
});

const { result } = renderHook(() =>
useNucleotideEntropyDataByTime(
getSelector({
dateFrom: globalDateCache.getDay('2023-05-01'),
dateTo: globalDateCache.getDay('2023-05-15'),
}),
'nuc',
[ALL_GENES_SELECTED],
false
)
useNucleotideEntropyDataByTime(getSelector(DEFAULT_DATE_RANGE), 'nuc', [ALL_GENES_SELECTED], false)
);
await act(() => {});

expect(result.current).toStrictEqual({
ticks: [1682892000000, 1683496800000, 1684101600000],
ticks: expectedTicks,
timeData: [
{
All: 0.000020428194564254205,
day: 1682892000000,
day: expectedTicks[0],
},
{
All: 0.000020428194564254205,
day: 1683496800000,
day: expectedTicks[1],
},
],
});
Expand All @@ -327,30 +266,56 @@ describe('useNucleotideEntropyDataByTime', () => {
});

const { result } = renderHook(() =>
useNucleotideEntropyDataByTime(
getSelector({
dateFrom: globalDateCache.getDay('2023-05-01'),
dateTo: globalDateCache.getDay('2023-05-15'),
}),
'aa',
[ALL_GENES_SELECTED],
false
)
useNucleotideEntropyDataByTime(getSelector(DEFAULT_DATE_RANGE), 'aa', [ALL_GENES_SELECTED], false)
);
await act(() => {});

expect(result.current).toStrictEqual({
ticks: [1682892000000, 1683496800000, 1684101600000],
ticks: expectedTicks,
timeData: [
{
All: 0.00006224417180098772,
day: 1682892000000,
day: expectedTicks[0],
},
{
All: 0.00006224417180098772,
day: 1683496800000,
day: expectedTicks[1],
},
],
});
});

test('should switch between nucleotide and amino acids', async () => {
mutationProportionDataMock.mockResolvedValue({
selector: DEFAULT_SELECTOR,
payload: [{ mutation: 'T671G', proportion: 0.5, count: 42 }],
});

const { result, rerender } = renderHook(
(sequenceType: SequenceType) =>
useNucleotideEntropyDataByTime(
getSelector(DEFAULT_DATE_RANGE),
sequenceType,
[ALL_GENES_SELECTED],
false
),
{ initialProps: 'nuc' }
);
await act(() => {});

expect(result.current?.timeData[0]?.All).toBeGreaterThan(0);

mutationProportionDataMock.mockReset();
mutationProportionDataMock.mockResolvedValue({
selector: DEFAULT_SELECTOR,
payload: [
{ mutation: 'ORF8:R101C', proportion: 1, count: 42 },
{ mutation: 'ORF8:R102C', proportion: 1, count: 42 },
],
});

await act(() => rerender('aa'));

expect(result.current?.timeData[0]?.All).toBe(0);
});
});
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