@genspectrum/dashboard-components 1.1.0 → 1.3.0

package/src/query/queryRelativeGrowthAdvantage.ts

@@ -13,20 +13,16 @@ export class NotEnoughDataToComputeFitError extends Error {
     }
 }
 
-export async function queryRelativeGrowthAdvantage<LapisDateField extends string>(
+export async function queryRelativeGrowthAdvantage(
     numerator: LapisFilter,
     denominator: LapisFilter,
     generationTime: number,
     lapis: string,
-    lapisDateField: LapisDateField,
+    lapisDateField: string,
     signal?: AbortSignal,
 ) {
-    const fetchNumerator = new FetchAggregatedOperator<{
-        [key in LapisDateField]: string | null;
-    }>(numerator, [lapisDateField]);
-    const fetchDenominator = new FetchAggregatedOperator<{
-        [key in LapisDateField]: string | null;
-    }>(denominator, [lapisDateField]);
+    const fetchNumerator = new FetchAggregatedOperator<Record<string, string | null>>(numerator, [lapisDateField]);
+    const fetchDenominator = new FetchAggregatedOperator<Record<string, string | null>>(denominator, [lapisDateField]);
     const mapToFixedDateKeyNumerator = new RenameFieldOperator(fetchNumerator, lapisDateField, 'date');
     const mapToFixedDateKeyDenominator = new RenameFieldOperator(fetchDenominator, lapisDateField, 'date');
     const mapNumerator = new MapOperator(mapToFixedDateKeyNumerator, toYearMonthDay);
@@ -36,7 +32,7 @@ export async function queryRelativeGrowthAdvantage<LapisDateField extends string
         mapDenominator.evaluate(lapis, signal),
     ]);
     const { min: minDate, max: maxDate } = getMinMaxTemporal(denominatorData.content.map((d) => d.date));
-    if (!minDate && !maxDate) {
+    if (!minDate) {
         return null;
     }
 

package/src/query/queryWastewaterMutationsOverTime.ts

@@ -41,7 +41,7 @@ export async function queryWastewaterMutationsOverTime(
             };
         } catch (e) {
             throw new Error(
-                `Failed to parse row of wastewater data: ${JSON.stringify(row)}: ${(e as Error)?.message ?? 'Unknown error'}`,
+                `Failed to parse row of wastewater data: ${JSON.stringify(row)}: ${(e as Error | null)?.message ?? 'Unknown error'}`,
             );
         }
     });

package/src/types.ts

@@ -28,7 +28,7 @@ export const namedLapisFilterSchema = z.object({
 });
 export type NamedLapisFilter = z.infer<typeof namedLapisFilterSchema>;
 
-export const lapisLocationFilterSchema = z.record(z.union([z.string(), z.undefined()]));
+export const lapisLocationFilterSchema = z.record(z.union([z.string(), z.undefined(), z.null()]));
 export type LapisLocationFilter = z.infer<typeof lapisLocationFilterSchema>;
 
 export const temporalGranularitySchema = z.union([

package/src/utils/mutations.ts

@@ -33,8 +33,8 @@ export class SubstitutionClass implements MutationClass, Substitution {
         readonly position: number,
     ) {
         const segmentString = this.segment ? `${this.segment}:` : '';
-        const valueAtReferenceString = this.valueAtReference ? `${this.valueAtReference}` : '';
-        const substitutionValueString = this.substitutionValue ? `${this.substitutionValue}` : '';
+        const valueAtReferenceString = this.valueAtReference ?? '';
+        const substitutionValueString = this.substitutionValue ?? '';
         this.code = `${segmentString}${valueAtReferenceString}${this.position}${substitutionValueString}`;
     }
 
@@ -55,8 +55,8 @@ export class SubstitutionClass implements MutationClass, Substitution {
     }
 
     static parse(mutationStr: string): SubstitutionClass | null {
-        const match = mutationStr.match(substitutionRegex);
-        if (match === null || match.groups === undefined) {
+        const match = substitutionRegex.exec(mutationStr);
+        if (match?.groups === undefined) {
             return null;
         }
         return new SubstitutionClass(
@@ -85,7 +85,7 @@ export class DeletionClass implements MutationClass, Deletion {
         readonly position: number,
     ) {
         const segmentString = this.segment ? `${this.segment}:` : '';
-        const valueAtReferenceString = this.valueAtReference ? `${this.valueAtReference}` : '';
+        const valueAtReferenceString = this.valueAtReference ?? '';
         this.code = `${segmentString}${valueAtReferenceString}${this.position}-`;
     }
 
@@ -105,8 +105,8 @@ export class DeletionClass implements MutationClass, Deletion {
     }
 
     static parse(mutationStr: string): DeletionClass | null {
-        const match = mutationStr.match(deletionRegex);
-        if (match === null || match.groups === undefined) {
+        const match = deletionRegex.exec(mutationStr);
+        if (match?.groups === undefined) {
             return null;
         }
 
@@ -154,8 +154,8 @@ export class InsertionClass implements MutationClass {
     }
 
     static parse(mutationStr: string): InsertionClass | null {
-        const match = mutationStr.match(insertionRegexp);
-        if (match === null || match.groups === undefined) {
+        const match = insertionRegexp.exec(mutationStr);
+        if (match?.groups === undefined) {
             return null;
         }
 
@@ -204,7 +204,7 @@ export function toSubstitutionOrDeletion(mutation: SubstitutionClass | DeletionC
     }
 }
 
-export const bases: { [P in SequenceType]: string[] } = {
+export const bases: Record<SequenceType, string[]> = {
     nucleotide: ['A', 'C', 'G', 'T', '-'],
     'amino acid': [
         'I',

package/src/utils/type-utils.ts

@@ -7,7 +7,7 @@ export type NumberFields<S> = keyof S & { [P in keyof S]: S[P] extends number ?
 /**
  * MappedType<K, T> is a type that represents an object with keys of type K and values of type T.
  */
-export type MappedType<K extends string | number | symbol, T> = { [P in K]: T };
+export type MappedType<K extends string | number | symbol, T> = Record<K, T>;
 
 /**
  * MappedNumber<K> is a type that represents an object with keys of type K and values of type number.

package/src/utils/typeAssertions.spec.ts

@@ -2,7 +2,7 @@ import { describe, it } from 'vitest';
 
 import { type Equals, type Expect } from './typeAssertions';
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 describe('Expect', () => {
     it('should only accept true', () => {
         type ShouldBeTrue = Expect<true>;

package/src/web-components/gs-app.spec-d.ts

@@ -4,7 +4,7 @@ import { AppComponent } from './gs-app';
 import { type MutationAnnotations } from './mutation-annotations-context';
 
 describe('gs-app types', () => {
-    test('mutationAnnotations type should match', ({}) => {
+    test('mutationAnnotations type should match', () => {
         expectTypeOf(AppComponent.prototype).toHaveProperty('mutationAnnotations').toEqualTypeOf<MutationAnnotations>();
     });
 });

package/src/web-components/gs-app.stories.ts

@@ -129,7 +129,7 @@ export const FailsToFetchReferenceGenome: StoryObj<StoryProps> = {
 };
 
 @customElement('gs-app-display')
-// eslint-disable-next-line no-unused-vars,@typescript-eslint/no-unused-vars -- it is used in the story above
+// eslint-disable-next-line @typescript-eslint/no-unused-vars -- it is used in the story above
 class AppDisplay extends LitElement {
     @consume({ context: lapisContext })
     lapis: string = '';

package/src/web-components/input/gs-date-range-filter.tsx

@@ -151,7 +151,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type CustomSelectOptionsMatches = Expect<
     Equals<typeof DateRangeFilterComponent.prototype.dateRangeOptions, DateRangeFilterProps['dateRangeOptions']>
 >;
@@ -160,4 +160,4 @@ type WidthMatches = Expect<Equals<typeof DateRangeFilterComponent.prototype.widt
 type DateColumnMatches = Expect<
     Equals<typeof DateRangeFilterComponent.prototype.lapisDateField, DateRangeFilterProps['lapisDateField']>
 >;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/input/gs-lineage-filter.tsx

@@ -105,7 +105,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type InitialValueMatches = Expect<Equals<typeof LineageFilterComponent.prototype.value, LineageFilterProps['value']>>;
 type LapisFieldMatches = Expect<
     Equals<typeof LineageFilterComponent.prototype.lapisField, LineageFilterProps['lapisField']>
@@ -117,4 +117,4 @@ type PlaceholderTextMatches = Expect<
     Equals<typeof LineageFilterComponent.prototype.placeholderText, LineageFilterProps['placeholderText']>
 >;
 type WidthMatches = Expect<Equals<typeof LineageFilterComponent.prototype.width, LineageFilterProps['width']>>;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/input/gs-location-filter.tsx

@@ -37,7 +37,7 @@ export class LocationFilterComponent extends PreactLitAdapter {
      * The initial value to use for this location filter.
      */
     @property({ type: Object })
-    value: Record<string, string | undefined> | undefined = undefined;
+    value: Record<string, string | null | undefined> | undefined = undefined;
 
     /**
      * Required.
@@ -109,7 +109,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type InitialValueMatches = Expect<Equals<typeof LocationFilterComponent.prototype.value, LocationFilterProps['value']>>;
 type FieldsMatches = Expect<Equals<typeof LocationFilterComponent.prototype.fields, LocationFilterProps['fields']>>;
 type LapisFilterMatches = Expect<
@@ -119,4 +119,4 @@ type PlaceholderTextMatches = Expect<
     Equals<typeof LocationFilterComponent.prototype.placeholderText, LocationFilterProps['placeholderText']>
 >;
 type WidthMatches = Expect<Equals<typeof LocationFilterComponent.prototype.width, LocationFilterProps['width']>>;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/input/gs-mutation-filter.tsx

@@ -109,9 +109,9 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type InitialValueMatches = Expect<
     Equals<typeof MutationFilterComponent.prototype.initialValue, MutationFilterProps['initialValue']>
 >;
 type WidthMatches = Expect<Equals<typeof MutationFilterComponent.prototype.width, MutationFilterProps['width']>>;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/input/gs-number-range-filter.spec.ts

@@ -4,7 +4,7 @@ import { NumberRangeFilterComponent } from './gs-number-range-filter';
 import { type NumberRangeFilterProps } from '../../preact/numberRangeFilter/number-range-filter';
 
 describe('gs-number-range-filter types', () => {
-    test('should match', ({}) => {
+    test('should match', () => {
         expectTypeOf(NumberRangeFilterComponent.prototype)
             .toHaveProperty('value')
             .toEqualTypeOf<NumberRangeFilterProps['value']>();

package/src/web-components/input/gs-text-filter.tsx

@@ -99,7 +99,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type InitialValueMatches = Expect<Equals<typeof TextFilterComponent.prototype.value, TextFilterProps['value']>>;
 type LapisFieldMatches = Expect<Equals<typeof TextFilterComponent.prototype.lapisField, TextFilterProps['lapisField']>>;
 type LapisFilterMatches = Expect<
@@ -109,4 +109,4 @@ type PlaceholderTextMatches = Expect<
     Equals<typeof TextFilterComponent.prototype.placeholderText, TextFilterProps['placeholderText']>
 >;
 type WidthMatches = Expect<Equals<typeof TextFilterComponent.prototype.width, TextFilterProps['width']>>;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/visualization/gs-aggregate.tsx

@@ -138,7 +138,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type FieldsMatches = Expect<Equals<typeof AggregateComponent.prototype.fields, AggregateProps['fields']>>;
 type ViewsMatches = Expect<Equals<typeof AggregateComponent.prototype.views, AggregateProps['views']>>;
 type FilterMatches = Expect<Equals<typeof AggregateComponent.prototype.lapisFilter, AggregateProps['lapisFilter']>>;
@@ -154,4 +154,4 @@ type PageSizeMatches = Expect<Equals<typeof AggregateComponent.prototype.pageSiz
 type MaxNumberOfBarsMatches = Expect<
     Equals<typeof AggregateComponent.prototype.maxNumberOfBars, AggregateProps['maxNumberOfBars']>
 >;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/visualization/gs-genome-data-viewer.spec-d.ts

@@ -4,7 +4,7 @@ import { GenomeDataViewerComponent } from './gs-genome-data-viewer';
 import type { GenomeDataViewerProps } from '../../preact/genomeViewer/genome-data-viewer';
 
 describe('gs-app types', () => {
-    test('mutationAnnotations type should match', ({}) => {
+    test('mutationAnnotations type should match', () => {
         expectTypeOf(GenomeDataViewerComponent.prototype)
             .toHaveProperty('gff3Source')
             .toEqualTypeOf<GenomeDataViewerProps['gff3Source']>();

package/src/web-components/visualization/gs-mutation-comparison.tsx

@@ -134,7 +134,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type LapisFiltersMatches = Expect<
     Equals<typeof MutationComparisonComponent.prototype.lapisFilters, MutationComparisonProps['lapisFilters']>
 >;
@@ -153,4 +153,4 @@ type HeightMatches = Expect<
 type PageSizeMatches = Expect<
     Equals<typeof MutationComparisonComponent.prototype.pageSize, MutationComparisonProps['pageSize']>
 >;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/visualization/gs-mutations-over-time.spec-d.ts

@@ -32,6 +32,9 @@ describe('gs-mutations-over-time', () => {
         expectTypeOf<typeof MutationsOverTimeComponent.prototype.initialMeanProportionInterval>().toEqualTypeOf<
             MutationsOverTimeProps['initialMeanProportionInterval']
         >();
+        expectTypeOf<typeof MutationsOverTimeComponent.prototype.useNewEndpoint>().toEqualTypeOf<
+            MutationsOverTimeProps['useNewEndpoint']
+        >();
         expectTypeOf<typeof MutationsOverTimeComponent.prototype.pageSizes>().toEqualTypeOf<
             MutationsOverTimeProps['pageSizes']
         >();

package/src/web-components/visualization/gs-mutations-over-time.stories.ts

@@ -42,6 +42,7 @@ const meta: Meta<Required<MutationsOverTimeProps>> = {
         lapisDateField: { control: 'text' },
         displayMutations: { control: 'object' },
         initialMeanProportionInterval: { control: 'object' },
+        useNewEndpoint: { control: 'boolean' },
         pageSizes: { control: 'object' },
     },
     args: {
@@ -52,6 +53,7 @@ const meta: Meta<Required<MutationsOverTimeProps>> = {
         granularity: 'month',
         lapisDateField: 'date',
         initialMeanProportionInterval: { min: 0.05, max: 0.9 },
+        useNewEndpoint: false,
         pageSizes: [10, 20, 30, 40, 50],
     },
     parameters: withComponentDocs({
@@ -99,6 +101,7 @@ const Template: StoryObj<Required<MutationsOverTimeProps>> = {
                 .displayMutations=${args.displayMutations}
                 .initialMeanProportionInterval=${args.initialMeanProportionInterval}
                 .pageSizes=${args.pageSizes}
+                .useNewEndpoint=${args.useNewEndpoint}
             ></gs-mutations-over-time>
         </gs-app>
     `,

package/src/web-components/visualization/gs-mutations-over-time.tsx

@@ -113,6 +113,14 @@ export class MutationsOverTimeComponent extends PreactLitAdapterWithGridJsStyles
     @property({ type: Object })
     initialMeanProportionInterval: { min: number; max: number } = { min: 0.05, max: 0.9 };
 
+    /**
+     * Whether to use the mutationsOverTime endpoint from LAPIS.
+     * If true, use the endpoint, if false, compute component data as before.
+     * Eventually, the new endpoint will become the default.
+     */
+    @property({ type: Boolean })
+    useNewEndpoint?: boolean = false;
+
     /**
      * The number of rows per page, which can be selected by the user.
      */
@@ -138,6 +146,7 @@ export class MutationsOverTimeComponent extends PreactLitAdapterWithGridJsStyles
                     lapisDateField={this.lapisDateField}
                     displayMutations={this.displayMutations}
                     initialMeanProportionInterval={this.initialMeanProportionInterval}
+                    useNewEndpoint={this.useNewEndpoint}
                     pageSizes={this.pageSizes}
                 />
             </MutationAnnotationsContextProvider>

package/src/web-components/visualization/gs-mutations.tsx

@@ -166,7 +166,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type LapisFilterMatches = Expect<
     Equals<typeof MutationsComponent.prototype.lapisFilter, MutationsProps['lapisFilter']>
 >;
@@ -180,4 +180,4 @@ type ViewsMatches = Expect<Equals<typeof MutationsComponent.prototype.views, Mut
 type WidthMatches = Expect<Equals<typeof MutationsComponent.prototype.width, MutationsProps['width']>>;
 type HeightMatches = Expect<Equals<typeof MutationsComponent.prototype.height, MutationsProps['height']>>;
 type PageSizeMatches = Expect<Equals<typeof MutationsComponent.prototype.pageSize, MutationsProps['pageSize']>>;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/visualization/gs-number-sequences-over-time.tsx

@@ -133,7 +133,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type LapisFilterMatches = Expect<
     Equals<typeof NumberSequencesOverTimeComponent.prototype.lapisFilters, NumberSequencesOverTimeProps['lapisFilters']>
 >;
@@ -164,4 +164,4 @@ type SmoothingWindowMatches = Expect<
 type PageSizeMatches = Expect<
     Equals<typeof NumberSequencesOverTimeComponent.prototype.pageSize, NumberSequencesOverTimeProps['pageSize']>
 >;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/visualization/gs-prevalence-over-time.tsx

@@ -200,7 +200,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type NumeratorMatches = Expect<
     Equals<typeof PrevalenceOverTimeComponent.prototype.numeratorFilters, PrevalenceOverTimeProps['numeratorFilters']>
 >;
@@ -243,4 +243,4 @@ type YAxisMaxLogarithmicMatches = Expect<
         PrevalenceOverTimeProps['yAxisMaxLogarithmic']
     >
 >;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/visualization/gs-relative-growth-advantage.tsx

@@ -154,7 +154,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type NumeratorMatches = Expect<
     Equals<
         typeof RelativeGrowthAdvantageComponent.prototype.numeratorFilter,
@@ -200,4 +200,4 @@ type YAxisMaxLogarithmicMatches = Expect<
         RelativeGrowthAdvantageProps['yAxisMaxLogarithmic']
     >
 >;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/visualization/gs-sequences-by-location.tsx

@@ -226,7 +226,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type LapisFilterMatches = Expect<
     Equals<typeof SequencesByLocationComponent.prototype.lapisFilter, SequencesByLocationProps['lapisFilter']>
 >;
@@ -261,4 +261,4 @@ type OffsetXMatches = Expect<
 type OffsetYMatches = Expect<
     Equals<typeof SequencesByLocationComponent.prototype.offsetY, SequencesByLocationProps['offsetY']>
 >;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */

package/src/web-components/visualization/gs-statistics.tsx

@@ -83,7 +83,7 @@ declare global {
     }
 }
 
-/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 type WidthMatches = Expect<Equals<typeof StatisticsComponent.prototype.width, StatisticsProps['width']>>;
 type HeightMatches = Expect<Equals<typeof StatisticsComponent.prototype.height, StatisticsProps['height']>>;
 type DenominatorFilterMatches = Expect<
@@ -92,4 +92,4 @@ type DenominatorFilterMatches = Expect<
 type NumeratorFilterMatches = Expect<
     Equals<typeof StatisticsComponent.prototype.numeratorFilter, StatisticsProps['numeratorFilter']>
 >;
-/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */
+/* eslint-enable @typescript-eslint/no-unused-vars */