@genspectrum/dashboard-components 0.10.2 → 0.10.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +19 -19
- package/custom-elements.json +377 -33
- package/dist/assets/mutationOverTimeWorker-BjjkMGzd.js.map +1 -0
- package/dist/components.d.ts +217 -59
- package/dist/components.js +1365 -177
- package/dist/components.js.map +1 -1
- package/dist/{dateRangeOption-du8H7LWu.js → dateRangeOption-Doo6WHKu.js} +17 -3
- package/dist/dateRangeOption-Doo6WHKu.js.map +1 -0
- package/dist/style.css +16 -6
- package/dist/util.d.ts +107 -41
- package/dist/util.js +1 -1
- package/package.json +10 -4
- package/src/preact/aggregatedData/aggregate.stories.tsx +14 -0
- package/src/preact/aggregatedData/aggregate.tsx +17 -15
- package/src/preact/components/error-boundary.stories.tsx +24 -3
- package/src/preact/components/error-boundary.tsx +3 -4
- package/src/preact/components/error-display.tsx +38 -17
- package/src/preact/components/tabs.tsx +2 -2
- package/src/preact/dateRangeSelector/date-range-selector.stories.tsx +1 -1
- package/src/preact/lineageFilter/lineage-filter.stories.tsx +1 -1
- package/src/preact/locationFilter/location-filter.stories.tsx +1 -1
- package/src/preact/map/__mockData__/aggregatedGermany.json +83 -0
- package/src/preact/map/__mockData__/aggregatedWorld.json +259 -0
- package/src/preact/map/__mockData__/germanyMap.json +9083 -0
- package/src/preact/map/__mockData__/howToGenerateWorldMap.md +9 -0
- package/src/preact/map/__mockData__/worldAtlas.json +497127 -0
- package/src/preact/map/leafletStyleModifications.css +3 -0
- package/src/preact/map/sequences-by-location-map.tsx +202 -0
- package/src/preact/map/sequences-by-location-table.tsx +18 -0
- package/src/preact/map/sequences-by-location.stories.tsx +144 -0
- package/src/preact/map/sequences-by-location.tsx +151 -0
- package/src/preact/map/useGeoJsonMap.tsx +62 -0
- package/src/preact/mutationComparison/mutation-comparison.tsx +1 -1
- package/src/preact/mutationFilter/mutation-filter.tsx +26 -13
- package/src/preact/mutations/mutations.tsx +16 -12
- package/src/preact/mutationsOverTime/mutations-over-time.stories.tsx +14 -0
- package/src/preact/mutationsOverTime/mutations-over-time.tsx +18 -14
- package/src/preact/numberSequencesOverTime/number-sequences-over-time.stories.tsx +14 -0
- package/src/preact/numberSequencesOverTime/number-sequences-over-time.tsx +22 -14
- package/src/preact/prevalenceOverTime/prevalence-over-time.stories.tsx +14 -0
- package/src/preact/prevalenceOverTime/prevalence-over-time.tsx +28 -19
- package/src/preact/relativeGrowthAdvantage/relative-growth-advantage.stories.tsx +14 -0
- package/src/preact/relativeGrowthAdvantage/relative-growth-advantage.tsx +18 -15
- package/src/preact/shared/charts/confideceInterval.ts +10 -8
- package/src/preact/shared/charts/getYAxisMax.ts +10 -5
- package/src/preact/shared/stories/expectErrorMessage.ts +21 -0
- package/src/preact/statistic/statistics.tsx +10 -8
- package/src/preact/textInput/text-input.stories.tsx +14 -0
- package/src/preact/textInput/text-input.tsx +16 -11
- package/src/preact/useQuery.ts +9 -1
- package/src/query/queryAggregateData.ts +2 -1
- package/src/styles/tailwind.css +1 -1
- package/src/types.ts +13 -1
- package/src/utilEntrypoint.ts +7 -0
- package/src/web-components/app.stories.ts +17 -2
- package/src/web-components/app.ts +17 -5
- package/src/web-components/input/gs-mutation-filter.stories.ts +2 -0
- package/src/web-components/input/gs-text-input.tsx +2 -2
- package/src/web-components/introduction.mdx +4 -4
- package/src/web-components/visualization/data_visualization_statistical_analysis.mdx +3 -3
- package/src/web-components/visualization/gs-mutations-over-time.tsx +1 -3
- package/src/web-components/visualization/gs-mutations.tsx +1 -3
- package/src/web-components/visualization/gs-number-sequences-over-time.tsx +1 -3
- package/src/web-components/visualization/gs-prevalence-over-time.tsx +3 -6
- package/src/web-components/visualization/gs-relative-growth-advantage.tsx +1 -5
- package/src/web-components/visualization/gs-sequences-by-location.stories.ts +234 -0
- package/src/web-components/visualization/gs-sequences-by-location.tsx +253 -0
- package/src/web-components/visualization/index.ts +1 -0
- package/standalone-bundle/assets/mutationOverTimeWorker-DoUBht2e.js.map +1 -0
- package/standalone-bundle/dashboard-components.js +16223 -9292
- package/standalone-bundle/dashboard-components.js.map +1 -1
- package/standalone-bundle/style.css +1 -1
- package/dist/assets/mutationOverTimeWorker-Di6yP1e6.js.map +0 -1
- package/dist/dateRangeOption-du8H7LWu.js.map +0 -1
- package/src/preact/shared/stories/expectInvalidAttributesErrorMessage.ts +0 -13
- package/standalone-bundle/assets/mutationOverTimeWorker-cIyshfj_.js.map +0 -1
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import { type FunctionComponent } from 'preact';
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import { type Dispatch, type StateUpdater, useContext, useState } from 'preact/hooks';
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import z from 'zod';
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import { getInsertionsTableData } from './getInsertionsTableData';
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import { getMutationsTableData } from './getMutationsTableData';
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type InsertionEntry,
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views,
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import { LapisUrlContext } from '../LapisUrlContext';
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import { CsvDownloadButton } from '../components/csv-download-button';
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const mutationsPropsSchema = z.object({
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lapisFilter: lapisFilterSchema,
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sequenceType: sequenceTypeSchema,
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views: viewSchema.array(),
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pageSize: z.union([z.boolean(), z.number()]),
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export type MutationsProps = z.infer<typeof mutationsPropsSchema>;
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export const Mutations: FunctionComponent<MutationsProps> = (componentProps) => {
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import referenceGenome from '../../lapisApi/__mockData__/referenceGenome.json';
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import { LapisUrlContext } from '../LapisUrlContext';
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import { ReferenceGenomeContext } from '../ReferenceGenomeContext';
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const meta: Meta<MutationsOverTimeProps> = {
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title: 'Visualization/Mutation over time',
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export const WithNoLapisDateFieldField: StoryObj<MutationsOverTimeProps> = {
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// @ts-expect-error -- uses subpath imports and vite worker import
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import MutationsOverTimeGrid from './mutations-over-time-grid';
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temporalGranularitySchema,
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views,
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import { type Deletion, type Substitution } from '../../utils/mutations';
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import { toTemporalClass } from '../../utils/temporalClass';
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sequenceType: sequenceTypeSchema,
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pageSize: z.union([z.boolean(), z.number()]),
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@@ -6,6 +6,7 @@ import numerator from './__mockData__/numeratorFilter.json';
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import { RelativeGrowthAdvantage, type RelativeGrowthAdvantageProps } from './relative-growth-advantage';
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title: 'Visualization/RelativeGrowthAdvantage',
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...Primary,
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args: {
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play: async ({ canvasElement, step }) => {
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await expectInvalidAttributesErrorMessage(canvasElement, 'String must contain at least 1 character(s)');
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queryRelativeGrowthAdvantage,
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type RelativeGrowthAdvantageData,
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} from '../../query/queryRelativeGrowthAdvantage';
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import {
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import {
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import { yAxisMaxConfigSchema } from '../shared/charts/getYAxisMax';
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const viewSchema = z.literal(views.line);
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export type View = z.infer<typeof viewSchema>;
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|
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export const relativeGrowthAdvantagePropsSchema = z.object({
|
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width: z.string(),
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height: z.string(),
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numeratorFilter: lapisFilterSchema,
|
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denominatorFilter: lapisFilterSchema,
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+
generationTime: z.number(),
|
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|
+
views: z.array(viewSchema),
|
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|
+
lapisDateField: z.string().min(1),
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|
+
yAxisMaxConfig: yAxisMaxConfigSchema,
|
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+
});
|
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|
+
export type RelativeGrowthAdvantageProps = z.infer<typeof relativeGrowthAdvantagePropsSchema>;
|
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|
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|
export const RelativeGrowthAdvantage: FunctionComponent<RelativeGrowthAdvantageProps> = (componentProps) => {
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const { width, height } = componentProps;
|
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|
const size = { height, width };
|
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return (
|
|
42
|
-
<ErrorBoundary size={size}>
|
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+
<ErrorBoundary size={size} schema={relativeGrowthAdvantagePropsSchema} componentProps={componentProps}>
|
|
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46
|
<ResizeContainer size={size}>
|
|
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|
<RelativeGrowthAdvantageInner {...componentProps} />
|
|
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</ResizeContainer>
|
|
@@ -1,10 +1,11 @@
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import z from 'zod';
|
|
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|
+
|
|
3
|
+
/*
|
|
4
|
+
* calculateWilsonInterval calculates the Wilson score interval for 95% confidence.
|
|
5
|
+
*This function is based on https://github.com/erikfox/wilson-interval, but without high precision math.
|
|
6
|
+
* observed - number of observed positive outcomes
|
|
7
|
+
* sample - number of experiments or size of the sample
|
|
8
|
+
*/
|
|
8
9
|
export function wilson95PercentConfidenceInterval(observed: number, sample: number) {
|
|
9
10
|
const p = observed / sample;
|
|
10
11
|
const n = sample;
|
|
@@ -31,4 +32,5 @@ export const confidenceIntervalDataLabel = (
|
|
|
31
32
|
return `${label}${value.toFixed(3)} (${lowerLimit?.toFixed(3)} - ${upperLimit?.toFixed(3)})`;
|
|
32
33
|
};
|
|
33
34
|
|
|
34
|
-
export
|
|
35
|
+
export const confidenceIntervalMethodSchema = z.union([z.literal('wilson'), z.literal('none')]);
|
|
36
|
+
export type ConfidenceIntervalMethod = z.infer<typeof confidenceIntervalMethodSchema>;
|
|
@@ -1,9 +1,14 @@
|
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1
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-
|
|
2
|
-
linear?: AxisMax;
|
|
3
|
-
logarithmic?: AxisMax;
|
|
4
|
-
}
|
|
1
|
+
import z from 'zod';
|
|
5
2
|
|
|
6
|
-
export
|
|
3
|
+
export const axisMaxSchema = z.union([z.literal('maxInData'), z.literal('limitTo1'), z.number()]);
|
|
4
|
+
export type AxisMax = z.infer<typeof axisMaxSchema>;
|
|
5
|
+
|
|
6
|
+
export const yAxisMaxConfigSchema = z.object({
|
|
7
|
+
linear: axisMaxSchema.optional(),
|
|
8
|
+
logarithmic: axisMaxSchema.optional(),
|
|
9
|
+
});
|
|
10
|
+
|
|
11
|
+
export type YAxisMaxConfig = z.infer<typeof yAxisMaxConfigSchema>;
|
|
7
12
|
|
|
8
13
|
export const getYAxisMax = (maxInData: number, axisMax?: AxisMax) => {
|
|
9
14
|
if (!axisMax) {
|
|
@@ -0,0 +1,21 @@
|
|
|
1
|
+
import { expect, waitFor, within } from '@storybook/test';
|
|
2
|
+
|
|
3
|
+
export function playThatExpectsErrorMessage(errorTitle: string, errorMessage: string) {
|
|
4
|
+
return async ({ canvasElement }: { canvasElement: HTMLElement }) => {
|
|
5
|
+
await expectErrorMessage(canvasElement, errorTitle, errorMessage);
|
|
6
|
+
};
|
|
7
|
+
}
|
|
8
|
+
|
|
9
|
+
export async function expectErrorMessage(canvasElement: HTMLElement, errorTitle: string, errorMessage: string) {
|
|
10
|
+
const canvas = within(canvasElement);
|
|
11
|
+
|
|
12
|
+
await waitFor(() => expect(canvas.getByText(errorTitle, { exact: false })).toBeInTheDocument());
|
|
13
|
+
|
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14
|
+
canvas.getByRole('button', { name: 'Show details.' }).click();
|
|
15
|
+
|
|
16
|
+
await waitFor(() => expect(canvas.getByText(errorMessage, { exact: false })).toBeVisible());
|
|
17
|
+
}
|
|
18
|
+
|
|
19
|
+
export async function expectInvalidAttributesErrorMessage(canvasElement: HTMLElement, errorMessage: string) {
|
|
20
|
+
await expectErrorMessage(canvasElement, 'Error - Invalid component attributes', errorMessage);
|
|
21
|
+
}
|
|
@@ -1,8 +1,9 @@
|
|
|
1
1
|
import { type FunctionComponent } from 'preact';
|
|
2
2
|
import { useContext } from 'preact/hooks';
|
|
3
|
+
import z from 'zod';
|
|
3
4
|
|
|
4
5
|
import { queryGeneralStatistics } from '../../query/queryGeneralStatistics';
|
|
5
|
-
import {
|
|
6
|
+
import { lapisFilterSchema } from '../../types';
|
|
6
7
|
import { LapisUrlContext } from '../LapisUrlContext';
|
|
7
8
|
import { ErrorBoundary } from '../components/error-boundary';
|
|
8
9
|
import { LoadingDisplay } from '../components/loading-display';
|
|
@@ -11,19 +12,20 @@ import { ResizeContainer } from '../components/resize-container';
|
|
|
11
12
|
import { formatProportion } from '../shared/table/formatProportion';
|
|
12
13
|
import { useQuery } from '../useQuery';
|
|
13
14
|
|
|
14
|
-
|
|
15
|
-
width: string
|
|
16
|
-
height: string
|
|
17
|
-
numeratorFilter:
|
|
18
|
-
denominatorFilter:
|
|
19
|
-
};
|
|
15
|
+
const statisticsPropsSchema = z.object({
|
|
16
|
+
width: z.string(),
|
|
17
|
+
height: z.string(),
|
|
18
|
+
numeratorFilter: lapisFilterSchema,
|
|
19
|
+
denominatorFilter: lapisFilterSchema,
|
|
20
|
+
});
|
|
21
|
+
export type StatisticsProps = z.infer<typeof statisticsPropsSchema>;
|
|
20
22
|
|
|
21
23
|
export const Statistics: FunctionComponent<StatisticsProps> = (componentProps) => {
|
|
22
24
|
const { width, height } = componentProps;
|
|
23
25
|
const size = { height, width };
|
|
24
26
|
|
|
25
27
|
return (
|
|
26
|
-
<ErrorBoundary size={size}>
|
|
28
|
+
<ErrorBoundary size={size} schema={statisticsPropsSchema} componentProps={componentProps}>
|
|
27
29
|
<ResizeContainer size={size}>
|
|
28
30
|
<StatisticsInner {...componentProps} />
|
|
29
31
|
</ResizeContainer>
|
|
@@ -6,6 +6,7 @@ import { TextInput, type TextInputProps } from './text-input';
|
|
|
6
6
|
import { previewHandles } from '../../../.storybook/preview';
|
|
7
7
|
import { AGGREGATED_ENDPOINT, LAPIS_URL } from '../../constants';
|
|
8
8
|
import { LapisUrlContext } from '../LapisUrlContext';
|
|
9
|
+
import { expectInvalidAttributesErrorMessage } from '../shared/stories/expectErrorMessage';
|
|
9
10
|
|
|
10
11
|
const meta: Meta<TextInputProps> = {
|
|
11
12
|
title: 'Input/TextInput',
|
|
@@ -93,3 +94,16 @@ export const WithInitialValue: StoryObj<TextInputProps> = {
|
|
|
93
94
|
});
|
|
94
95
|
},
|
|
95
96
|
};
|
|
97
|
+
|
|
98
|
+
export const WithNoLapisField: StoryObj<TextInputProps> = {
|
|
99
|
+
...Default,
|
|
100
|
+
args: {
|
|
101
|
+
...Default.args,
|
|
102
|
+
lapisField: '',
|
|
103
|
+
},
|
|
104
|
+
play: async ({ canvasElement, step }) => {
|
|
105
|
+
step('expect error message', async () => {
|
|
106
|
+
await expectInvalidAttributesErrorMessage(canvasElement, 'String must contain at least 1 character(s)');
|
|
107
|
+
});
|
|
108
|
+
},
|
|
109
|
+
};
|
|
@@ -1,5 +1,6 @@
|
|
|
1
1
|
import { type FunctionComponent } from 'preact';
|
|
2
2
|
import { useContext, useRef } from 'preact/hooks';
|
|
3
|
+
import z from 'zod';
|
|
3
4
|
|
|
4
5
|
import { fetchAutocompleteList } from './fetchAutocompleteList';
|
|
5
6
|
import { LapisUrlContext } from '../LapisUrlContext';
|
|
@@ -9,21 +10,25 @@ import { NoDataDisplay } from '../components/no-data-display';
|
|
|
9
10
|
import { ResizeContainer } from '../components/resize-container';
|
|
10
11
|
import { useQuery } from '../useQuery';
|
|
11
12
|
|
|
12
|
-
|
|
13
|
-
lapisField: string
|
|
14
|
-
placeholderText: string
|
|
15
|
-
initialValue: string
|
|
16
|
-
}
|
|
13
|
+
const textInputInnerPropsSchema = z.object({
|
|
14
|
+
lapisField: z.string().min(1),
|
|
15
|
+
placeholderText: z.string().optional(),
|
|
16
|
+
initialValue: z.string().optional(),
|
|
17
|
+
});
|
|
17
18
|
|
|
18
|
-
|
|
19
|
-
width: string
|
|
20
|
-
}
|
|
19
|
+
const textInputPropsSchema = textInputInnerPropsSchema.extend({
|
|
20
|
+
width: z.string(),
|
|
21
|
+
});
|
|
21
22
|
|
|
22
|
-
export
|
|
23
|
+
export type TextInputInnerProps = z.infer<typeof textInputInnerPropsSchema>;
|
|
24
|
+
export type TextInputProps = z.infer<typeof textInputPropsSchema>;
|
|
25
|
+
|
|
26
|
+
export const TextInput: FunctionComponent<TextInputProps> = (props) => {
|
|
27
|
+
const { width, ...innerProps } = props;
|
|
23
28
|
const size = { width, height: '3rem' };
|
|
24
29
|
|
|
25
30
|
return (
|
|
26
|
-
<ErrorBoundary size={size} layout='horizontal'>
|
|
31
|
+
<ErrorBoundary size={size} layout='horizontal' componentProps={props} schema={textInputPropsSchema}>
|
|
27
32
|
<ResizeContainer size={size}>
|
|
28
33
|
<TextInputInner {...innerProps} />
|
|
29
34
|
</ResizeContainer>
|
|
@@ -76,7 +81,7 @@ const TextInputInner: FunctionComponent<TextInputInnerProps> = ({ lapisField, pl
|
|
|
76
81
|
<input
|
|
77
82
|
type='text'
|
|
78
83
|
class='input input-bordered w-full'
|
|
79
|
-
placeholder={placeholderText
|
|
84
|
+
placeholder={placeholderText ?? lapisField}
|
|
80
85
|
onInput={onInput}
|
|
81
86
|
ref={inputRef}
|
|
82
87
|
list={lapisField}
|
package/src/preact/useQuery.ts
CHANGED
|
@@ -23,5 +23,13 @@ export function useQuery<Data>(fetchDataCallback: () => Promise<Data>, dependenc
|
|
|
23
23
|
// eslint-disable-next-line react-hooks/exhaustive-deps
|
|
24
24
|
}, [JSON.stringify(dependencies)]);
|
|
25
25
|
|
|
26
|
-
|
|
26
|
+
if (isLoading) {
|
|
27
|
+
return { isLoading: true } as const;
|
|
28
|
+
}
|
|
29
|
+
|
|
30
|
+
if (error !== null) {
|
|
31
|
+
return { error, isLoading: false as const };
|
|
32
|
+
}
|
|
33
|
+
|
|
34
|
+
return { data: data!, error: null, isLoading: false as const };
|
|
27
35
|
}
|
|
@@ -1,8 +1,9 @@
|
|
|
1
1
|
import { FetchAggregatedOperator } from '../operator/FetchAggregatedOperator';
|
|
2
2
|
import { SortOperator } from '../operator/SortOperator';
|
|
3
|
-
import { type InitialSort } from '../preact/aggregatedData/aggregate';
|
|
4
3
|
import { type LapisFilter } from '../types';
|
|
5
4
|
|
|
5
|
+
export type InitialSort = { field: string; direction: 'ascending' | 'descending' };
|
|
6
|
+
|
|
6
7
|
export type AggregateData = (Record<string, string | null | number | boolean> & {
|
|
7
8
|
count: number;
|
|
8
9
|
proportion: number;
|
package/src/styles/tailwind.css
CHANGED