@genspectrum/dashboard-components 0.6.13 → 0.6.15

package/src/preact/lineageFilter/lineage-filter.tsx

@@ -12,8 +12,8 @@ import { useQuery } from '../useQuery';
 
 export interface LineageFilterInnerProps {
     lapisField: string;
-    placeholderText?: string;
-    initialValue?: string;
+    placeholderText: string;
+    initialValue: string;
 }
 
 export interface LineageFilterProps extends LineageFilterInnerProps {

package/src/preact/locationFilter/fetchAutocompletionList.ts

@@ -1,6 +1,4 @@
-import { LapisError } from '../../lapisApi/lapisApi';
 import { FetchAggregatedOperator } from '../../operator/FetchAggregatedOperator';
-import { UserFacingError } from '../components/error-display';
 
 export async function fetchAutocompletionList(fields: string[], lapis: string, signal?: AbortSignal) {
     const toAncestorInHierarchyOverwriteValues = Array(fields.length - 1)
@@ -10,18 +8,7 @@ export async function fetchAutocompletionList(fields: string[], lapis: string, s
 
     const fetchAggregatedOperator = new FetchAggregatedOperator<Record<string, string | null>>({}, fields);
 
-    let data;
-    try {
-        data = (await fetchAggregatedOperator.evaluate(lapis, signal)).content;
-    } catch (error) {
-        if (error instanceof LapisError) {
-            throw new UserFacingError(
-                `Failed to fetch autocomplete list from LAPIS: ${error.problemDetail.status} ${error.problemDetail.title ?? ''}`,
-                error.problemDetail.detail ?? error.message,
-            );
-        }
-        throw error;
-    }
+    const data = (await fetchAggregatedOperator.evaluate(lapis, signal)).content;
 
     const locationValues = data
         .map((entry) => fields.reduce((acc, field) => ({ ...acc, [field]: entry[field] }), {}))

package/src/preact/locationFilter/location-filter.stories.tsx

@@ -1,8 +1,8 @@
-import { withActions } from '@storybook/addon-actions/decorator';
 import { type Meta, type StoryObj } from '@storybook/preact';
 
 import data from './__mockData__/aggregated.json';
 import { LocationFilter, type LocationFilterProps } from './location-filter';
+import { previewHandles } from '../../../.storybook/preview';
 import { AGGREGATED_ENDPOINT, LAPIS_URL } from '../../constants';
 import { LapisUrlContext } from '../LapisUrlContext';
 
@@ -28,7 +28,7 @@ const meta: Meta<LocationFilterProps> = {
             ],
         },
         actions: {
-            handles: ['gs-location-changed'],
+            handles: ['gs-location-changed', ...previewHandles],
         },
     },
     args: {
@@ -59,7 +59,6 @@ const meta: Meta<LocationFilterProps> = {
             },
         },
     },
-    decorators: [withActions],
 };
 
 export default meta;

package/src/preact/locationFilter/location-filter.tsx

@@ -11,8 +11,8 @@ import { ResizeContainer } from '../components/resize-container';
 import { useQuery } from '../useQuery';
 
 export interface LocationFilterInnerProps {
-    initialValue?: string;
-    placeholderText?: string;
+    initialValue: string;
+    placeholderText: string;
     fields: string[];
 }
 

package/src/preact/mutationFilter/mutation-filter.stories.tsx

@@ -1,9 +1,9 @@
-import { withActions } from '@storybook/addon-actions/decorator';
 import { type Meta, type PreactRenderer, type StoryObj } from '@storybook/preact';
 import { expect, fireEvent, fn, userEvent, waitFor, within } from '@storybook/test';
 import { type StepFunction } from '@storybook/types';
 
 import { MutationFilter, type MutationFilterProps } from './mutation-filter';
+import { previewHandles } from '../../../.storybook/preview';
 import { LAPIS_URL } from '../../constants';
 import referenceGenome from '../../lapisApi/__mockData__/referenceGenome.json';
 import { LapisUrlContext } from '../LapisUrlContext';
@@ -14,7 +14,7 @@ const meta: Meta<MutationFilterProps> = {
     component: MutationFilter,
     parameters: {
         actions: {
-            handles: ['gs-mutation-filter-changed', 'gs-mutation-filter-on-blur'],
+            handles: ['gs-mutation-filter-changed', 'gs-mutation-filter-on-blur', ...previewHandles],
         },
         fetchMock: {},
     },
@@ -26,7 +26,6 @@ const meta: Meta<MutationFilterProps> = {
             },
         },
     },
-    decorators: [withActions],
 };
 
 export default meta;

package/src/preact/mutationsOverTime/__mockData__/aggregated_2024_01.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 25800
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_2024_02.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 16673
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_2024_03.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 7931
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_2024_04.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 2947
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_2024_05.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 2424
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_2024_06.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 2890
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_2024_07.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 0
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_20_01_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 456
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_21_01_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 533
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_22_01_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 1107
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_23_01_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 1020
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_24_01_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 880
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_25_01_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 832
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_26_01_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 635
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_tooManyMutations_total.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 503198
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_week3_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 5213
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_week4_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 5311
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_week5_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 5264
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/__mockData__/aggregated_week6_2024.json

@@ -0,0 +1,13 @@
+{
+    "data": [
+        {
+            "count": 4954
+        }
+    ],
+    "info": {
+        "dataVersion": "1722452937",
+        "requestId": "aede768e-d9d1-4273-9a74-992986554995",
+        "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-08-02T06:57:09.319474043",
+        "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report."
+    }
+}

package/src/preact/mutationsOverTime/getFilteredMutationsOverTime.spec.ts

@@ -15,10 +15,12 @@ describe('getFilteredMutationOverTimeData', () => {
             data.set(new Substitution('someSegment', 'A', 'T', 123), yearMonthDay('2021-01-01'), {
                 count: 1,
                 proportion: 0.1,
+                totalCount: 10,
             });
             data.set(new Substitution('someOtherSegment', 'A', 'T', 123), yearMonthDay('2021-01-01'), {
                 count: 2,
                 proportion: 0.2,
+                totalCount: 10,
             });
 
             filterDisplayedSegments(
@@ -41,10 +43,12 @@ describe('getFilteredMutationOverTimeData', () => {
             data.set(new Substitution('someSegment', 'A', 'T', 123), yearMonthDay('2021-01-01'), {
                 count: 1,
                 proportion: 0.1,
+                totalCount: 10,
             });
             data.set(new Deletion('someOtherSegment', 'A', 123), yearMonthDay('2021-01-01'), {
                 count: 2,
                 proportion: 0.2,
+                totalCount: 10,
             });
 
             filterMutationTypes(
@@ -76,7 +80,13 @@ describe('getFilteredMutationOverTimeData', () => {
 
             filterProportion(data, getOverallMutationData(belowFilter), proportionInterval);
 
-            expect(data.getAsArray({ count: 0, proportion: 0 })).to.toHaveLength(0);
+            expect(
+                data.getAsArray({
+                    count: 0,
+                    proportion: 0,
+                    totalCount: 10,
+                }),
+            ).to.toHaveLength(0);
         });
 
         it('should remove mutations where overall proportion is above filter', () => {
@@ -84,7 +94,13 @@ describe('getFilteredMutationOverTimeData', () => {
 
             filterProportion(data, getOverallMutationData(aboveFilter), proportionInterval);
 
-            expect(data.getAsArray({ count: 0, proportion: 0 })).to.toHaveLength(0);
+            expect(
+                data.getAsArray({
+                    count: 0,
+                    proportion: 0,
+                    totalCount: 10,
+                }),
+            ).to.toHaveLength(0);
         });
 
         it('should remove mutations where overall proportion is missing', () => {
@@ -92,7 +108,13 @@ describe('getFilteredMutationOverTimeData', () => {
 
             filterProportion(data, getOverallMutationData(aboveFilter, someOtherMutation), proportionInterval);
 
-            expect(data.getAsArray({ count: 0, proportion: 0 })).to.toHaveLength(0);
+            expect(
+                data.getAsArray({
+                    count: 0,
+                    proportion: 0,
+                    totalCount: 10,
+                }),
+            ).to.toHaveLength(0);
         });
 
         it('should not remove mutation where overall proportion is at lower border of filter', () => {
@@ -100,7 +122,13 @@ describe('getFilteredMutationOverTimeData', () => {
 
             filterProportion(data, getOverallMutationData(inFilter), proportionInterval);
 
-            expect(data.getRow(someSubstitution, { count: 0, proportion: 0 })).to.toHaveLength(2);
+            expect(
+                data.getRow(someSubstitution, {
+                    count: 0,
+                    proportion: 0,
+                    totalCount: 10,
+                }),
+            ).to.toHaveLength(2);
         });
 
         it('should not remove mutation where overall proportion is within filter', () => {
@@ -108,7 +136,13 @@ describe('getFilteredMutationOverTimeData', () => {
 
             filterProportion(data, getOverallMutationData(inFilter), proportionInterval);
 
-            expect(data.getRow(someSubstitution, { count: 0, proportion: 0 })).to.toHaveLength(2);
+            expect(
+                data.getRow(someSubstitution, {
+                    count: 0,
+                    proportion: 0,
+                    totalCount: 10,
+                }),
+            ).to.toHaveLength(2);
         });
 
         it('should not remove mutation where overall proportion is at upper border of filter', () => {
@@ -116,13 +150,27 @@ describe('getFilteredMutationOverTimeData', () => {
 
             filterProportion(data, getOverallMutationData(inFilter), proportionInterval);
 
-            expect(data.getRow(someSubstitution, { count: 0, proportion: 0 })).to.toHaveLength(2);
+            expect(
+                data.getRow(someSubstitution, {
+                    count: 0,
+                    proportion: 0,
+                    totalCount: 10,
+                }),
+            ).to.toHaveLength(2);
         });
 
         function getMutationOverTimeData() {
             const data = new Map2dBase<Substitution | Deletion, Temporal, MutationOverTimeMutationValue>();
-            data.set(someSubstitution, yearMonthDay('2021-01-01'), { count: 1, proportion: 0.1 });
-            data.set(someSubstitution, yearMonthDay('2021-02-02'), { count: 99, proportion: 0.99 });
+            data.set(someSubstitution, yearMonthDay('2021-01-01'), {
+                count: 1,
+                proportion: 0.1,
+                totalCount: 10,
+            });
+            data.set(someSubstitution, yearMonthDay('2021-02-02'), {
+                count: 99,
+                proportion: 0.99,
+                totalCount: 10,
+            });
             return data;
         }
 

package/src/preact/mutationsOverTime/mutations-over-time-grid.tsx

@@ -56,7 +56,7 @@ const MutationsOverTimeGrid: FunctionComponent<MutationsOverTimeGridProps> = ({
                                 <MutationCell mutation={mutation} />
                             </div>
                             {dates.map((date, columnIndex) => {
-                                const value = data.get(mutation, date) ?? { proportion: 0, count: 0 };
+                                const value = data.get(mutation, date) ?? { proportion: 0, count: 0, totalCount: 0 };
                                 const tooltipPosition = getTooltipPosition(
                                     rowIndex,
                                     shownMutations.length,
@@ -136,7 +136,9 @@ const ProportionCell: FunctionComponent<{
             <p>({timeIntervalDisplay(date)})</p>
             <p>{mutation.code}</p>
             <p>Proportion: {formatProportion(value.proportion)}</p>
-            <p>Count: {value.count}</p>
+            <p>
+                Count: {value.count} / {value.totalCount} total
+            </p>
         </div>
     );