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fix(components): use null values instead of undefined for wastewater-over-time plots #1081

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Merged
fhennig merged 1 commit into from
Feb 4, 2026
Merged

fix(components): use null values instead of undefined for wastewater-over-time plots #1081

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12 changes: 10 additions & 2 deletions components/src/preact/components/features-over-time-grid.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ export type CustomColumn = z.infer<typeof customColumnSchema>;
export interface FeatureRenderer<D> {
asString(value: D): string;
renderRowLabel(value: D): JSX.Element;
renderTooltip(value: D, temporal: Temporal, proportionValue: ProportionValue | undefined): JSX.Element;
renderTooltip(value: D, temporal: Temporal, proportionValue: ProportionValue): JSX.Element;
}

export interface FeaturesOverTimeGridProps<F> {
Expand Down Expand Up @@ -99,12 +99,20 @@ function FeaturesOverTimeGrid<F>({
</div>
),
cell: ({ getValue, row, column, table }) => {
const value = getValue();
const valueRaw = getValue();
const value = valueRaw ?? null;
const rowIndex = row.index;
const columnIndex = column.getIndex();
const numberOfRows = table.getRowModel().rows.length;
const numberOfColumns = table.getAllColumns().length;

if (valueRaw === undefined) {
// eslint-disable-next-line no-console -- We want to warn that something might be wrong.
console.error(
`Found undefined value for ${row.original.feature} - ${date.dateString}. This shouldn't happen.`,
);
}

const tooltip = featureRenderer.renderTooltip(row.original.feature, date, value);

return (
Expand Down
55 changes: 55 additions & 0 deletions ...ct/wastewater/mutationsOverTime/computeWastewaterMutationsOverTimeDataPerLocation.spec.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -156,4 +156,59 @@ describe('groupMutationDataByLocation', () => {

expect(location1Data.getFirstAxisKeys()).to.deep.equal([mutation1, mutation2, mutation3]);
});

test('should backfill missing mutation-date combinations with explicit null', () => {
const input: WastewaterData = [
{
location: location1,
date: temporalCache.getYearMonthDay('2025-01-01'),
nucleotideMutationFrequency: [
{ mutation: mutation1, proportion: 0.1 },
// mutation2 missing for this date
],
aminoAcidMutationFrequency: [],
},
{
location: location1,
date: temporalCache.getYearMonthDay('2025-01-02'),
nucleotideMutationFrequency: [
// mutation1 missing for this date
{ mutation: mutation2, proportion: 0.2 },
],
aminoAcidMutationFrequency: [],
},
];

const result = groupMutationDataByLocation(input, 'nucleotide');

expect(result).to.have.length(1);
const location1Data = result[0].data;

// Both mutations should appear in all dates
expect(location1Data.getFirstAxisKeys()).to.deep.equal([mutation1, mutation2]);
expect(location1Data.getSecondAxisKeys()).to.deep.equal([
temporalCache.getYearMonthDay('2025-01-01'),
temporalCache.getYearMonthDay('2025-01-02'),
]);

// Verify backfilled nulls (not undefined)
expect(location1Data.get(mutation1, temporalCache.getYearMonthDay('2025-01-02'))).to.equal(null);
expect(location1Data.get(mutation2, temporalCache.getYearMonthDay('2025-01-01'))).to.equal(null);

// Verify actual values still present
expect(location1Data.get(mutation1, temporalCache.getYearMonthDay('2025-01-01'))).to.deep.equal({
type: 'wastewaterValue',
proportion: 0.1,
});
expect(location1Data.get(mutation2, temporalCache.getYearMonthDay('2025-01-02'))).to.deep.equal({
type: 'wastewaterValue',
proportion: 0.2,
});

// Verify the complete grid with getAsArray
expect(location1Data.getAsArray()).to.deep.equal([
[{ type: 'wastewaterValue', proportion: 0.1 }, null],
[null, { type: 'wastewaterValue', proportion: 0.2 }],
]);
});
});
26 changes: 26 additions & 0 deletions .../preact/wastewater/mutationsOverTime/computeWastewaterMutationsOverTimeDataPerLocation.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -21,15 +21,26 @@ export async function computeWastewaterMutationsOverTimeDataPerLocation(

export function groupMutationDataByLocation(data: WastewaterData, sequenceType: 'nucleotide' | 'amino acid') {
const locationMap = new Map<string, MutationOverTimeDataMap<TemporalClass>>();
// Track all unique mutations and dates per location for backfilling
const locationMutations = new Map<string, Set<string>>();
const locationDates = new Map<string, Set<string>>();

// First pass: populate sparse data and track all keys
for (const row of data) {
if (!locationMap.has(row.location)) {
locationMap.set(row.location, new BaseMutationOverTimeDataMap<TemporalClass>());
locationMutations.set(row.location, new Set());
locationDates.set(row.location, new Set());
}
const map = locationMap.get(row.location)!;
const mutations = locationMutations.get(row.location)!;
const dates = locationDates.get(row.location)!;

const mutationFrequencies =
sequenceType === 'nucleotide' ? row.nucleotideMutationFrequency : row.aminoAcidMutationFrequency;
for (const mutation of mutationFrequencies) {
dates.add(row.date.dateString);
mutations.add(mutation.mutation.code);
map.set(
mutation.mutation,
row.date,
Expand All @@ -38,6 +49,21 @@ export function groupMutationDataByLocation(data: WastewaterData, sequenceType:
}
}

// Second pass: backfill missing cells with explicit null
for (const [location, map] of locationMap.entries()) {
const allMutations = Array.from(locationMutations.get(location)!);
const allDates = Array.from(locationDates.get(location)!).map((dateStr) => map.keysSecondAxis.get(dateStr)!);

for (const mutationCode of allMutations) {
const mutation = map.keysFirstAxis.get(mutationCode)!;
for (const date of allDates) {
if (map.get(mutation, date) === undefined) {
map.set(mutation, date, null);
}
}
}
}

return [...locationMap.entries()].map(([location, data]) => ({
location,
data: new SortedMap2d(
Expand Down