- {displayMutations !== undefined && displayMutations.length === 0 ? (
+ {displayMutations?.length === 0 ? (
= ({ wastewaterOrganism, current
customColumns={customColumns}
/>
)}
+ {analysis.mode === 'variant' && config.variantAnalysisModeEnabled && (
+
)}
@@ -130,6 +144,71 @@ const NoDataHelperText = ({ analysisFilter }: { analysisFilter: WasapAnalysisFil
);
};
+/**
+ * Info stat about the amount of sequences used during the computation of the clinical variant signature.
+ * Will also show a warning of the count is small.
+ */
+const VariantFetchInfo = ({
+ analysis,
+ clinicalLapisBaseUrl,
+ clinicalLapisLineageField,
+ clinicalLapisDateField,
+ warningThreshold,
+}: {
+ analysis: WasapVariantFilter;
+ clinicalLapisBaseUrl: string;
+ clinicalLapisLineageField: string;
+ clinicalLapisDateField: string;
+ warningThreshold: number;
+}) => {
+ const lapisFilter = {
+ ...getLapisFilterForTimeFrame(analysis.timeFrame, clinicalLapisDateField),
+ [clinicalLapisLineageField]: analysis.variant,
+ };
+
+ const { data, isPending, isError, error } = useQuery({
+ queryKey: ['variantFetchInfo'],
+ queryFn: () => getTotalCount(clinicalLapisBaseUrl, lapisFilter),
+ });
+
+ const isHighlighted = data !== undefined && data < warningThreshold;
+
+ let message = `The number of clinical sequences for ${analysis.variant}`;
+ if (analysis.timeFrame !== 'all') {
+ message += ` during the past ${variantTimeFrameLabel(analysis.timeFrame)}`;
+ }
+ if (isHighlighted) {
+ message += '. Clinical signature calculation with this few sequences is not recommended.';
+ }
+
+ return (
+
Amplicon sequences
-
{isPending ? '…' : isError ? 'Error' : data.toLocaleString()}
+
+ {isPending ? '…' : isError ? 'Error' : data.toLocaleString('en-us')}
+
{isPending
? 'Loading total amplicon sequences count…'
@@ -173,10 +254,3 @@ const DateRange = ({ config }: { config: WasapPageConfig }) => {
);
};
-
-const WasapStats = ({ config }: { config: WasapPageConfig }) => (
-
-
-);
diff --git a/website/src/components/views/wasap/useWasapPageData.ts b/website/src/components/views/wasap/useWasapPageData.ts
index ef7f9297a..309a169f9 100644
--- a/website/src/components/views/wasap/useWasapPageData.ts
+++ b/website/src/components/views/wasap/useWasapPageData.ts
@@ -1,10 +1,23 @@
-import type { CustomColumn } from '@genspectrum/dashboard-components/util';
+import type { CustomColumn, LapisFilter } from '@genspectrum/dashboard-components/util';
import { useQuery } from '@tanstack/react-query';
+import dayjs from 'dayjs';
-import type { WasapAnalysisFilter, WasapPageConfig } from './wasapPageConfig';
+import type { VariantTimeFrame, WasapAnalysisFilter, WasapPageConfig } from './wasapPageConfig';
import { getCladeLineages } from '../../../lapis/getCladeLineages';
import { getMutations, getMutationsForVariant } from '../../../lapis/getMutations';
+/**
+ * Hook that fetches and returns `WasapPageData` for the W-ASAP page,
+ * depending on the analysis mode and analysis mode settings.
+ */
+export function useWasapPageData(config: WasapPageConfig, analysis: WasapAnalysisFilter) {
+ return useQuery({
+ queryKey: ['wasap', analysis],
+ queryFn: () =>
+ fetchMutationSelection(config, analysis).then((data) => wasapPageDataFromMutationSelection(data)),
+ });
+}
+
type AllMutations = {
type: 'all';
};
@@ -47,6 +60,7 @@ async function fetchMutationSelection(
analysis.minProportion,
analysis.minCount,
analysis.minJaccard,
+ getLapisFilterForTimeFrame(analysis.timeFrame, config.clinicalLapis.dateField),
).then((r) => ({ type: 'jaccard', mutationsWithScore: r }));
case 'resistance':
if (!config.resistanceAnalysisModeEnabled) {
@@ -97,6 +111,26 @@ async function fetchMutationSelection(
}
}
+export function getLapisFilterForTimeFrame(timeFrame: VariantTimeFrame, dateFieldName: string): LapisFilter {
+ let fromDate = undefined;
+ switch (timeFrame) {
+ case 'all':
+ break;
+ case '6months':
+ fromDate = dayjs().subtract(6, 'month').format('YYYY-MM-DD');
+ break;
+ case '3months':
+ fromDate = dayjs().subtract(3, 'month').format('YYYY-MM-DD');
+ break;
+ }
+ if (fromDate === undefined) {
+ return {};
+ }
+ return {
+ [`${dateFieldName}From`]: fromDate,
+ };
+}
+
/**
* The W-ASAP page data consists of the mutations to display in the mutations-over-time component,
* and the additional custom columns that might optionally be displayed.
@@ -139,15 +173,3 @@ function wasapPageDataFromMutationSelection(mutationSelection: MutationSelection
};
}
}
-
-/**
- * Hook that fetches and returns `WasapPageData` for the W-ASAP page,
- * depending on the analysis mode and analysis mode settings.
- */
-export function useWasapPageData(config: WasapPageConfig, analysis: WasapAnalysisFilter) {
- return useQuery({
- queryKey: ['wasap', analysis],
- queryFn: () =>
- fetchMutationSelection(config, analysis).then((data) => wasapPageDataFromMutationSelection(data)),
- });
-}
diff --git a/website/src/components/views/wasap/wasapPageConfig.ts b/website/src/components/views/wasap/wasapPageConfig.ts
index bf5c0af01..1ff438119 100644
--- a/website/src/components/views/wasap/wasapPageConfig.ts
+++ b/website/src/components/views/wasap/wasapPageConfig.ts
@@ -1,4 +1,4 @@
-import type { DateRangeOption, SequenceType } from '@genspectrum/dashboard-components/util';
+import type { DateRangeOption, SequenceType, TemporalGranularity } from '@genspectrum/dashboard-components/util';
import type { ResistanceMutationSet } from './resistanceMutations';
@@ -71,11 +71,13 @@ type VariantAnalysisModeConfig =
variantAnalysisModeEnabled: true;
clinicalLapis: {
lapisBaseUrl: string;
+ dateField: string;
lineageField: string;
};
filterDefaults: {
variant: WasapVariantFilter;
};
+ clinicalSequenceCountWarningThreshold: number;
};
type ResistanceAnalysisModeConfig =
@@ -143,7 +145,7 @@ export type WasapAnalysisMode = 'manual' | 'variant' | 'resistance' | 'untracked
export type WasapBaseFilter = {
locationName?: string;
samplingDate?: DateRangeOption;
- granularity: string;
+ granularity: TemporalGranularity;
excludeEmpty: boolean;
};
@@ -157,6 +159,25 @@ export type WasapManualFilter = {
mutations?: string[];
};
+export const VARIANT_TIME_FRAME = {
+ all: 'all',
+ sixMonths: '6months',
+ threeMonths: '3months',
+} as const;
+
+export type VariantTimeFrame = (typeof VARIANT_TIME_FRAME)[keyof typeof VARIANT_TIME_FRAME];
+
+export function variantTimeFrameLabel(timeFrame: VariantTimeFrame): string {
+ switch (timeFrame) {
+ case VARIANT_TIME_FRAME.all:
+ return 'All';
+ case VARIANT_TIME_FRAME.sixMonths:
+ return '6 months';
+ case VARIANT_TIME_FRAME.threeMonths:
+ return '3 months';
+ }
+}
+
export type WasapVariantFilter = {
mode: 'variant';
sequenceType: SequenceType;
@@ -164,6 +185,7 @@ export type WasapVariantFilter = {
minProportion: number;
minCount: number;
minJaccard: number;
+ timeFrame: VariantTimeFrame;
};
export type WasapResistanceFilter = {
diff --git a/website/src/lapis/getMutations.spec.ts b/website/src/lapis/getMutations.spec.ts
index eeed16228..394b30edd 100644
--- a/website/src/lapis/getMutations.spec.ts
+++ b/website/src/lapis/getMutations.spec.ts
@@ -41,6 +41,28 @@ describe('getMutations', () => {
expect(result).toEqual(['A123C', 'G234T']);
});
+ test('should return filtered mutations with multiple filters', async () => {
+ lapisRouteMocker.mockPostNucleotideMutations(
+ { minProportion: 0.1, pangoLineage: 'B.1.1.7', dateFrom: '2023-05-01' },
+ {
+ data: [
+ { mutation: 'A123C', count: 5 },
+ { mutation: 'G234T', count: 2 },
+ ],
+ },
+ );
+
+ const result = await getMutations(
+ DUMMY_LAPIS_URL,
+ 'nucleotide',
+ { pangoLineage: 'B.1.1.7', dateFrom: '2023-05-01' },
+ 0.1,
+ 3,
+ );
+
+ expect(result).toEqual(['A123C']);
+ });
+
test('should throw on failed request', async () => {
lapisRouteMocker.mockPostNucleotideMutations(
{ minProportion: 0.1 },
@@ -105,6 +127,50 @@ describe('getMutationsForVariant', () => {
0.1,
5,
0.9,
+ {},
+ );
+
+ expect(result).toEqual([{ mutation: 'A2C', jaccardIndex: 1 }]);
+ });
+
+ test('should set date filter correctly', async () => {
+ // Setup:
+ // - Variant FOO has 20 sequences
+ // - A1C: in 20 FOO sequences, 40 total -> Jaccard = 20/(20+40-20) = 20/40 = 0.5 (excluded, < 0.9)
+ // - A2C: in 20 FOO sequences, 20 total -> Jaccard = 20/(20+20-20) = 20/20 = 1.0 (included, >= 0.9)
+ // - A3C: in 2 FOO sequences (excluded by minCount < 5)
+ lapisRouteMocker.mockPostAggregated({ pangoLineage: 'FOO', dateFrom: '2025-01-01' }, { data: [{ count: 20 }] });
+ lapisRouteMocker.mockPostNucleotideMutationsMulti([
+ {
+ body: { minProportion: 0.1, pangoLineage: 'FOO', dateFrom: '2025-01-01' },
+ response: {
+ data: [
+ { mutation: 'A1C', count: 20 },
+ { mutation: 'A2C', count: 20 },
+ { mutation: 'A3C', count: 2 },
+ ],
+ },
+ },
+ {
+ body: { minProportion: 0, dateFrom: '2025-01-01' },
+ response: {
+ data: [
+ { mutation: 'A1C', count: 40 },
+ { mutation: 'A2C', count: 20 },
+ { mutation: 'A3C', count: 2 },
+ ],
+ },
+ },
+ ]);
+
+ const result = await getMutationsForVariant(
+ DUMMY_LAPIS_URL,
+ 'nucleotide',
+ { pangoLineage: 'FOO' },
+ 0.1,
+ 5,
+ 0.9,
+ { dateFrom: '2025-01-01' },
);
expect(result).toEqual([{ mutation: 'A2C', jaccardIndex: 1 }]);
@@ -137,6 +203,7 @@ describe('getMutationsForVariant', () => {
0.05,
5,
0.6,
+ {},
);
expect(result).toEqual([{ mutation: 'T100C', jaccardIndex: 10 / 15 }]);
@@ -169,6 +236,7 @@ describe('getMutationsForVariant', () => {
0.01,
5,
0.01,
+ {},
);
expect(result).toEqual([]);
@@ -211,6 +279,7 @@ describe('getMutationsForVariant', () => {
0.05,
5,
0.75,
+ {},
);
expect(result).toEqual([
@@ -247,6 +316,7 @@ describe('getMutationsForVariant', () => {
0.05,
5,
0.9,
+ {},
);
expect(result).toEqual([{ mutation: 'S:L452R', jaccardIndex: 1 }]);
@@ -279,6 +349,7 @@ describe('getMutationsForVariant', () => {
0.05,
5,
0.9,
+ {},
);
expect(result).toEqual([{ mutation: 'S:L452R', jaccardIndex: 1 }]);
diff --git a/website/src/lapis/getMutations.ts b/website/src/lapis/getMutations.ts
index b82b22cb4..27b7ffe2a 100644
--- a/website/src/lapis/getMutations.ts
+++ b/website/src/lapis/getMutations.ts
@@ -54,18 +54,19 @@ export async function getMutationsForVariant(
minProportion: number,
minCount: number,
minJaccardIndex: number,
+ dateFilter: LapisFilter | undefined,
) {
return Promise.all([
// sequence counts WITH mutation and WITH lineage
- getMutationsInternal(lapisUrl, mutationType, lineageFilter, minProportion).then((r) =>
+ getMutationsInternal(lapisUrl, mutationType, { ...lineageFilter, ...dateFilter }, minProportion).then((r) =>
r.filter((item) => item.count >= minCount),
),
// sequence counts WITH mutation (only)
- getMutationsInternal(lapisUrl, mutationType, undefined, 0).then((r) =>
+ getMutationsInternal(lapisUrl, mutationType, dateFilter, 0).then((r) =>
Object.fromEntries(r.map((item) => [item.mutation, item.count])),
),
// sequence count WITH lineage (only)
- getTotalCount(lapisUrl, lineageFilter),
+ getTotalCount(lapisUrl, { ...lineageFilter, ...dateFilter }),
]).then(([intersectionCounts, totalCounts, variantCount]) =>
intersectionCounts
.map(({ mutation, count }) => ({
diff --git a/website/src/layouts/OrganismPage/DataPageLayout.astro b/website/src/layouts/OrganismPage/DataPageLayout.astro
index 4cca64d02..fbd92a1cf 100644
--- a/website/src/layouts/OrganismPage/DataPageLayout.astro
+++ b/website/src/layouts/OrganismPage/DataPageLayout.astro
@@ -1,11 +1,11 @@
---
import type { ComponentProps } from 'astro/types';
-import AccessionsDownloadButton from './AccessionsDownloadButton.astro';
-import LastUpdatedInfo from './LastUpdatedInfo.astro';
import LapisUnreachableWrapperClient from '../../components/LapisUnreachableWrapperClient';
-import type { DataOrigin } from '../../types/dataOrigins';
import { type BreadcrumbElement, Breadcrumbs } from '../Breadcrumbs';
+import AccessionsDownloadButton from './AccessionsDownloadButton.astro';
+import LastUpdatedInfo from './LastUpdatedInfo.astro';
+import type { DataOrigin } from '../../types/dataOrigins.ts';
import BaseLayout from '../base/BaseLayout.astro';
import DataInfo from '../base/footer/DataInfo.astro';
@@ -22,23 +22,27 @@ const { title, breadcrumbs, dataOrigins, lapisUrl, downloadLinks = [], accession
---
-
-
-
-
-
- {
- downloadLinks.length > 0 && (
-
- )
- }
-
-
+
+
+
+
+
+
+
+
+ {
+ downloadLinks.length > 0 && (
+
+ )
+ }
+
+
+
diff --git a/website/src/layouts/OrganismPage/OrganismViewPageLayout.astro b/website/src/layouts/OrganismPage/OrganismViewPageLayout.astro
index 38d752847..11d51ab7b 100644
--- a/website/src/layouts/OrganismPage/OrganismViewPageLayout.astro
+++ b/website/src/layouts/OrganismPage/OrganismViewPageLayout.astro
@@ -24,5 +24,10 @@ const { view, downloadLinks } = Astro.props;
lapisUrl={getLapisUrl(view.organismConstants.organism)}
accessionDownloadFields={view.organismConstants.accessionDownloadFields}
>
-
+
+
diff --git a/website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.astro b/website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.astro
index 2841b7624..514a91a78 100644
--- a/website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.astro
+++ b/website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.astro
@@ -3,7 +3,6 @@ import type { ComponentProps } from 'astro/types';
import AccessionsDownloadButton from './AccessionsDownloadButton.astro';
import OrganismViewPageLayout from './OrganismViewPageLayout.astro';
-import { getLapisUrl } from '../../config';
import type { OrganismConstants } from '../../views/OrganismConstants';
import type { View } from '../../views/View';
import { type PageStateHandler } from '../../views/pageStateHandlers/PageStateHandler';
@@ -17,15 +16,10 @@ const { view, downloadLinks } = Astro.props;
---
-
-
-
-
-
+
diff --git a/website/src/layouts/base/BaseLayout.astro b/website/src/layouts/base/BaseLayout.astro
index 8f8bccc9c..bcf85d40f 100644
--- a/website/src/layouts/base/BaseLayout.astro
+++ b/website/src/layouts/base/BaseLayout.astro
@@ -34,14 +34,13 @@ const { title, forceLoggedOutState = false } = Astro.props;
-
+
+
-
diff --git a/website/src/layouts/base/footer/Footer.astro b/website/src/layouts/base/footer/Footer.astro
index 0b90db516..918a8612d 100644
--- a/website/src/layouts/base/footer/Footer.astro
+++ b/website/src/layouts/base/footer/Footer.astro
@@ -1,12 +1,8 @@
---
import PrimaryFooter from './PrimaryFooter.astro';
-import SecondaryFooter from './SecondaryFooter.astro';
---
-
-
diff --git a/website/src/layouts/base/footer/SecondaryFooter.astro b/website/src/layouts/base/footer/SecondaryFooter.astro
deleted file mode 100644
index 1725a6973..000000000
--- a/website/src/layouts/base/footer/SecondaryFooter.astro
+++ /dev/null
@@ -1,7 +0,0 @@
----
-
----
-
-
-
diff --git a/website/src/pages/covid/compare-side-by-side.astro b/website/src/pages/covid/compare-side-by-side.astro
index 85799976f..159e32004 100644
--- a/website/src/pages/covid/compare-side-by-side.astro
+++ b/website/src/pages/covid/compare-side-by-side.astro
@@ -1,130 +1,6 @@
---
-import GsAggregate from '../../components/genspectrum/GsAggregate.astro';
-import GsMutations from '../../components/genspectrum/GsMutations.astro';
-import GsPrevalenceOverTime from '../../components/genspectrum/GsPrevalenceOverTime.astro';
-import GsRelativeGrowthAdvantage from '../../components/genspectrum/GsRelativeGrowthAdvantage.astro';
-import { CompareSideBySidePageStateSelector } from '../../components/pageStateSelectors/CompareSideBySidePageStateSelector';
-import { CompareSideBySideSelectorFallback } from '../../components/pageStateSelectors/FallbackElement';
-import { toDownloadLink } from '../../components/views/compareSideBySide/toDownloadLink';
-import { isStaging, getDashboardsConfig, getLapisUrl } from '../../config';
-import OrganismViewPageLayout from '../../layouts/OrganismPage/OrganismViewPageLayout.astro';
-import { chooseGranularityBasedOnDateRange } from '../../util/chooseGranularityBasedOnDateRange';
-import { ComponentHeight } from '../../views/OrganismConstants';
-import { toLapisFilterWithoutVariant } from '../../views/pageStateHandlers/toLapisFilterWithoutVariant';
-import type { OrganismViewKey } from '../../views/routing';
-import { ServerSide } from '../../views/serverSideRouting';
-
-const organismViewKey: OrganismViewKey = 'covid.compareSideBySideView';
-const view = ServerSide.routing.getOrganismView(organismViewKey);
-
-const pageState = view.pageStateHandler.parsePageStateFromUrl(Astro.url);
-
-const downloadLinks = [...pageState.filters.entries()].map(
- toDownloadLink(view.pageStateHandler, view.organismConstants.organism),
-);
+import GenericCompareSideBySidePage from '../../components/views/compareSideBySide/GenericCompareSideBySidePage.astro';
+import { Organisms } from '../../types/Organism';
---
-
-
-
- {
- Array.from(pageState.filters).map(([id, { variantFilter, datasetFilter }]) => {
- const baselineLapisFilter = toLapisFilterWithoutVariant(
- datasetFilter,
- view.organismConstants.additionalFilters,
- );
- const timeGranularity = chooseGranularityBasedOnDateRange({
- earliestDate: new Date(view.organismConstants.earliestDate),
- dateRange: datasetFilter.dateFilters[view.organismConstants.mainDateField],
- });
- const numeratorFilter = {
- ...variantFilter.lineages,
- ...variantFilter.mutations,
- variantQuery: variantFilter.variantQuery,
- ...baselineLapisFilter,
- };
-
- return (
-
-
-
-
-
-
-
- {view.organismConstants.aggregatedVisualizations.compareSideBySide.map(
- ({ label, fields, views }) => (
-
- ),
- )}
-
- );
- })
- }
-
- Add column
-
-
-
+
+
diff --git a/website/src/types/wastewaterConfig.spec.ts b/website/src/types/wastewaterConfig.spec.ts
new file mode 100644
index 000000000..e1b58e06b
--- /dev/null
+++ b/website/src/types/wastewaterConfig.spec.ts
@@ -0,0 +1,13 @@
+import { describe, expect, test } from 'vitest';
+
+import { wastewaterOrganismConfigs } from './wastewaterConfig';
+
+describe.each(Object.entries(wastewaterOrganismConfigs))('wastewaterConfig %s', (_configName, config) => {
+ test('default resistance set name is valid', () => {
+ if (config.resistanceAnalysisModeEnabled) {
+ const resistanceSetNames = config.resistanceMutationSets.map((s) => s.name);
+ const defaultSetName = config.filterDefaults.resistance.resistanceSet;
+ expect(resistanceSetNames).include(defaultSetName);
+ }
+ });
+});
diff --git a/website/src/types/wastewaterConfig.ts b/website/src/types/wastewaterConfig.ts
index 5fb496f42..1c95f9cbd 100644
--- a/website/src/types/wastewaterConfig.ts
+++ b/website/src/types/wastewaterConfig.ts
@@ -1,7 +1,7 @@
import type { MutationAnnotation } from '@genspectrum/dashboard-components/util';
import { covidResistanceMutations } from '../components/views/wasap/resistanceMutations';
-import type { WasapPageConfig } from '../components/views/wasap/wasapPageConfig';
+import { VARIANT_TIME_FRAME, type WasapPageConfig } from '../components/views/wasap/wasapPageConfig';
export const wastewaterOrganisms = {
covid: 'covid',
@@ -33,12 +33,14 @@ export const wastewaterOrganismConfigs: Record
,
-> implements View
-{
+> implements View {
public readonly pathname;
public readonly viewTitle;
public readonly viewBreadcrumbEntries;
diff --git a/website/src/views/pageStateHandlers/SequencingEffortsPageStateHandler.ts b/website/src/views/pageStateHandlers/SequencingEffortsPageStateHandler.ts
index 9016e37fc..6cb6acae8 100644
--- a/website/src/views/pageStateHandlers/SequencingEffortsPageStateHandler.ts
+++ b/website/src/views/pageStateHandlers/SequencingEffortsPageStateHandler.ts
@@ -16,9 +16,9 @@ import { parseTextFiltersFromUrl, setSearchFromTextFilters } from './textFilterF
import { advancedQueryUrlParam } from '../../components/genspectrum/AdvancedQueryFilter.tsx';
import { formatUrl } from '../../util/formatUrl.ts';
-export class SequencingEffortsStateHandler
- implements PageStateHandler
-{
+export class SequencingEffortsStateHandler<
+ PageState extends DatasetAndVariantData = DatasetAndVariantData,
+> implements PageStateHandler {
protected readonly pathname;
constructor(
diff --git a/website/src/views/pageStateHandlers/SingleVariantPageStateHandler.ts b/website/src/views/pageStateHandlers/SingleVariantPageStateHandler.ts
index 7577f0f0c..79518b758 100644
--- a/website/src/views/pageStateHandlers/SingleVariantPageStateHandler.ts
+++ b/website/src/views/pageStateHandlers/SingleVariantPageStateHandler.ts
@@ -19,9 +19,9 @@ import { toLapisFilterWithoutVariant } from './toLapisFilterWithoutVariant.ts';
import { advancedQueryUrlParam } from '../../components/genspectrum/AdvancedQueryFilter.tsx';
import { formatUrl } from '../../util/formatUrl.ts';
-export class SingleVariantPageStateHandler
- implements PageStateHandler
-{
+export class SingleVariantPageStateHandler<
+ PageState extends DatasetAndVariantData = DatasetAndVariantData,
+> implements PageStateHandler {
protected readonly pathname;
constructor(
diff --git a/website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts b/website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts
new file mode 100644
index 000000000..4a8edb987
--- /dev/null
+++ b/website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts
@@ -0,0 +1,323 @@
+import { describe, expect, it } from 'vitest';
+
+import { WasapPageStateHandler } from './WasapPageStateHandler';
+import { covidResistanceMutations } from '../../components/views/wasap/resistanceMutations';
+import {
+ VARIANT_TIME_FRAME,
+ type WasapManualFilter,
+ type WasapPageConfig,
+ type WasapResistanceFilter,
+ type WasapUntrackedFilter,
+ type WasapVariantFilter,
+} from '../../components/views/wasap/wasapPageConfig';
+
+const config: WasapPageConfig = {
+ name: 'SARS-CoV-2',
+ path: `/wastewater/covid`,
+ description: 'Analyze SARS-CoV-2 data that was collected by the WISE project.',
+ linkTemplate: {
+ nucleotideMutation:
+ 'https://open.cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nucMutations={{mutation}}',
+ aminoAcidMutation:
+ 'https://open.cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?aaMutations={{mutation}}',
+ },
+ manualAnalysisModeEnabled: true,
+ variantAnalysisModeEnabled: true,
+ resistanceAnalysisModeEnabled: true,
+ untrackedAnalysisModeEnabled: true,
+ resistanceMutationSets: covidResistanceMutations,
+ lapisBaseUrl: 'https://lapis.wasap.genspectrum.org',
+ samplingDateField: 'samplingDate',
+ locationNameField: 'locationName',
+ clinicalLapis: {
+ lapisBaseUrl: 'https://lapis.cov-spectrum.org/open/v2',
+ cladeField: 'nextstrainClade',
+ lineageField: 'nextcladePangoLineage',
+ dateField: 'date',
+ },
+ browseDataUrl: 'https://db.wasap.genspectrum.org/covid/search',
+ browseDataDescription: 'Browse the data in the W-ASAP Loculus instance.',
+ defaultLocationName: 'Zürich (ZH)',
+ clinicalSequenceCountWarningThreshold: 50,
+ filterDefaults: {
+ manual: {
+ mode: 'manual',
+ sequenceType: 'nucleotide',
+ mutations: undefined,
+ },
+ variant: {
+ mode: 'variant',
+ sequenceType: 'nucleotide',
+ variant: 'XFG*',
+ minProportion: 0.8,
+ minCount: 15,
+ minJaccard: 0.75,
+ timeFrame: VARIANT_TIME_FRAME.all,
+ },
+ resistance: {
+ mode: 'resistance',
+ sequenceType: 'amino acid',
+ resistanceSet: '3CLpro',
+ },
+ untracked: {
+ mode: 'untracked',
+ sequenceType: 'nucleotide',
+ excludeSet: 'predefined',
+ },
+ },
+};
+
+describe('WasapPageStateHandler', () => {
+ const handler = new WasapPageStateHandler(config);
+
+ describe('default URL', () => {
+ it('should return the default page URL', () => {
+ const url = handler.getDefaultPageUrl();
+ expect(url).toBe('/wastewater/covid');
+ });
+ });
+
+ describe('base filter', () => {
+ it('parses base filter with all fields', () => {
+ const url =
+ '/wastewater/covid?' +
+ 'locationName=Berlin&' +
+ 'samplingDate=2024-01-01--2024-12-31&' +
+ 'granularity=week&' +
+ 'excludeEmpty=false&' +
+ 'analysisMode=manual&' +
+ 'sequenceType=nucleotide&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ expect(filter.base.locationName).toBe('Berlin');
+ expect(filter.base.samplingDate).toEqual({
+ label: 'Custom',
+ dateFrom: '2024-01-01',
+ dateTo: '2024-12-31',
+ });
+ expect(filter.base.granularity).toBe('week');
+ expect(filter.base.excludeEmpty).toBe(false);
+ });
+
+ it('defaults base filter fields when missing from URL', () => {
+ const url = '/wastewater/covid?analysisMode=manual&sequenceType=nucleotide&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ expect(filter.base.locationName).toBe('Zürich (ZH)');
+ expect(filter.base.samplingDate).toBeUndefined();
+ expect(filter.base.granularity).toBe('day');
+ expect(filter.base.excludeEmpty).toBe(true);
+ });
+
+ it('encodes excludeEmpty=false in URL but omits when true', () => {
+ const filterTrue = handler.parsePageStateFromUrl(
+ new URL('http://example.com/wastewater/covid?analysisMode=manual&sequenceType=nucleotide&'),
+ );
+ const filterFalse = handler.parsePageStateFromUrl(
+ new URL(
+ 'http://example.com/wastewater/covid?analysisMode=manual&sequenceType=nucleotide&excludeEmpty=false&',
+ ),
+ );
+
+ const urlTrue = handler.toUrl(filterTrue);
+ const urlFalse = handler.toUrl(filterFalse);
+
+ expect(urlTrue).not.toContain('excludeEmpty');
+ expect(urlFalse).toContain('excludeEmpty=false');
+ });
+
+ it('parses excludeEmpty string "false" as boolean false', () => {
+ const url = '/wastewater/covid?analysisMode=manual&sequenceType=nucleotide&excludeEmpty=false&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ expect(typeof filter.base.excludeEmpty).toBe('boolean');
+ expect(filter.base.excludeEmpty).toBe(false);
+ });
+ });
+
+ describe('manual mode', () => {
+ it('parses and encodes manual filter', () => {
+ const url =
+ '/wastewater/covid?' +
+ 'locationName=Z%C3%BCrich+%28ZH%29&' +
+ 'granularity=day&' +
+ 'analysisMode=manual&' +
+ 'sequenceType=nucleotide&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+ expect(filter.base.locationName).toBe('Zürich (ZH)');
+ expect(filter.base.granularity).toBe('day');
+ expect(filter.analysis.mode).toBe('manual');
+ expect(filter.analysis.sequenceType).toBe('nucleotide');
+
+ const newUrl = handler.toUrl(filter);
+ expect(newUrl).toBe(url);
+ });
+
+ it('parses manual mode with multiple mutations', () => {
+ const url =
+ '/wastewater/covid?' +
+ 'analysisMode=manual&' +
+ 'sequenceType=nucleotide&' +
+ 'mutations=A23T%7CS:E44H%7CORFla:T123A&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ expect(filter.analysis.mode).toBe('manual');
+ const analysis = filter.analysis as WasapManualFilter;
+ expect(analysis.mutations).toEqual(['A23T', 'S:E44H', 'ORFla:T123A']);
+ });
+
+ it('manual mode with no mutations specified', () => {
+ const url = '/wastewater/covid?analysisMode=manual&sequenceType=amino+acid&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ expect(filter.analysis.mode).toBe('manual');
+ const analysis = filter.analysis as WasapManualFilter;
+ expect(analysis.sequenceType).toBe('amino acid');
+ expect(analysis.mutations).toBeUndefined();
+ });
+ });
+
+ describe('variant mode', () => {
+ it('parses and encodes variant filter with all parameters', () => {
+ const url =
+ '/wastewater/covid?' +
+ 'locationName=Berlin&' +
+ 'granularity=week&' +
+ 'analysisMode=variant&' +
+ 'sequenceType=nucleotide&' +
+ 'variant=BA.2*&' +
+ 'minProportion=0.5&' +
+ 'minCount=10&' +
+ 'minJaccard=0.6&' +
+ 'timeFrame=3months&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ expect(filter.analysis.mode).toBe('variant');
+ const analysis = filter.analysis as WasapVariantFilter;
+ expect(analysis.variant).toBe('BA.2*');
+ expect(typeof analysis.minProportion).toBe('number');
+ expect(analysis.minProportion).toBe(0.5);
+ expect(typeof analysis.minCount).toBe('number');
+ expect(analysis.minCount).toBe(10);
+ expect(typeof analysis.minJaccard).toBe('number');
+ expect(analysis.minJaccard).toBe(0.6);
+ expect(analysis.timeFrame).toBe(VARIANT_TIME_FRAME.threeMonths);
+
+ const newUrl = handler.toUrl(filter);
+ expect(newUrl).toBe(url);
+ });
+
+ it('converts numeric string parameters to numbers', () => {
+ const url =
+ '/wastewater/covid?' +
+ 'analysisMode=variant&' +
+ 'minProportion=0.5&' +
+ 'minCount=10&' +
+ 'minJaccard=0.6&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ const analysis = filter.analysis as WasapVariantFilter;
+ expect(typeof analysis.minProportion).toBe('number');
+ expect(typeof analysis.minCount).toBe('number');
+ expect(typeof analysis.minJaccard).toBe('number');
+ });
+
+ it('variant mode round-trip preserves numeric precision', () => {
+ const url =
+ '/wastewater/covid?' + 'analysisMode=variant&' + 'minProportion=0.123456&' + 'minJaccard=0.789012&';
+ const filter1 = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+ const url2 = handler.toUrl(filter1);
+ const filter2 = handler.parsePageStateFromUrl(new URL(`http://example.com${url2}`));
+
+ const analysis1 = filter1.analysis as WasapVariantFilter;
+ const analysis2 = filter2.analysis as WasapVariantFilter;
+ expect(analysis2.minProportion).toBe(analysis1.minProportion);
+ expect(analysis2.minJaccard).toBe(analysis1.minJaccard);
+ });
+ });
+
+ describe('resistance mode', () => {
+ it('parses and encodes resistance filter', () => {
+ const url =
+ '/wastewater/covid?' +
+ 'locationName=Z%C3%BCrich+%28ZH%29&' +
+ 'granularity=day&' +
+ 'analysisMode=resistance&' +
+ 'resistanceSet=3CLpro&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ expect(filter.analysis.mode).toBe('resistance');
+ const analysis = filter.analysis as WasapResistanceFilter;
+ expect(analysis.resistanceSet).toBe('3CLpro');
+
+ const newUrl = handler.toUrl(filter);
+ expect(newUrl).toBe(url);
+ });
+
+ it('resistance mode always uses amino acid sequence type', () => {
+ const url = '/wastewater/covid?analysisMode=resistance&resistanceSet=3CLpro&sequenceType=nucleotide&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ expect(filter.analysis.mode).toBe('resistance');
+ const analysis = filter.analysis as WasapResistanceFilter;
+ expect(analysis.sequenceType).toBe('amino acid');
+ });
+ });
+
+ describe('untracked mode', () => {
+ it('parses and encodes untracked filter with predefined excludeSet', () => {
+ const url =
+ '/wastewater/covid?' +
+ 'locationName=Z%C3%BCrich+%28ZH%29&' +
+ 'granularity=day&' +
+ 'analysisMode=untracked&' +
+ 'sequenceType=nucleotide&' +
+ 'excludeSet=predefined&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ expect(filter.analysis.mode).toBe('untracked');
+ const analysis = filter.analysis as WasapUntrackedFilter;
+ expect(analysis.excludeSet).toBe('predefined');
+ expect(analysis.excludeVariants).toBeUndefined();
+
+ const newUrl = handler.toUrl(filter);
+ expect(newUrl).toBe(url);
+ });
+
+ it('parses and encodes untracked filter with custom excludeSet and variants', () => {
+ const url =
+ '/wastewater/covid?' +
+ 'locationName=Z%C3%BCrich+%28ZH%29&' +
+ 'granularity=day&' +
+ 'analysisMode=untracked&' +
+ 'sequenceType=nucleotide&' +
+ 'excludeSet=custom&' +
+ 'excludeVariants=XBB.1.5*%7CBA.2*%7CJN.1&';
+ const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+
+ expect(filter.analysis.mode).toBe('untracked');
+ const analysis = filter.analysis as WasapUntrackedFilter;
+ expect(analysis.excludeSet).toBe('custom');
+ expect(analysis.excludeVariants).toEqual(['XBB.1.5*', 'BA.2*', 'JN.1']);
+
+ const newUrl = handler.toUrl(filter);
+ expect(newUrl).toBe(url);
+ });
+
+ it('untracked mode round-trip with pipe-separated variants', () => {
+ const url =
+ '/wastewater/covid?' +
+ 'analysisMode=untracked&' +
+ 'sequenceType=nucleotide&' +
+ 'excludeSet=custom&' +
+ 'excludeVariants=XBB*%7CBA.2*%7CJN.1%7CXFG*&';
+ const filter1 = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`));
+ const url2 = handler.toUrl(filter1);
+ const filter2 = handler.parsePageStateFromUrl(new URL(`http://example.com${url2}`));
+
+ const analysis1 = filter1.analysis as WasapUntrackedFilter;
+ const analysis2 = filter2.analysis as WasapUntrackedFilter;
+ expect(analysis2.excludeVariants).toEqual(analysis1.excludeVariants);
+ });
+ });
+});
diff --git a/website/src/views/pageStateHandlers/WasapPageStateHandler.ts b/website/src/views/pageStateHandlers/WasapPageStateHandler.ts
index e4c17247e..d16b8e31f 100644
--- a/website/src/views/pageStateHandlers/WasapPageStateHandler.ts
+++ b/website/src/views/pageStateHandlers/WasapPageStateHandler.ts
@@ -1,12 +1,13 @@
-import { type SequenceType } from '@genspectrum/dashboard-components/util';
+import { type SequenceType, type TemporalGranularity } from '@genspectrum/dashboard-components/util';
import { type PageStateHandler } from './PageStateHandler';
import { parseDateRangesFromUrl, setSearchFromDateRange } from './dateFilterFromToUrl';
import { parseTextFiltersFromUrl } from './textFilterFromToUrl';
-import { type BaselineFilterConfig } from '../../components/pageStateSelectors/BaselineSelector';
+import type { BaselineFilterConfig } from '../../components/pageStateSelectors/BaselineSelector';
import {
enabledAnalysisModes,
type ExcludeSetName,
+ type VariantTimeFrame,
type WasapAnalysisFilter,
type WasapAnalysisMode,
type WasapBaseFilter,
@@ -62,6 +63,9 @@ export class WasapPageStateHandler implements PageStateHandler {
minProportion: Number(texts.minProportion ?? this.config.filterDefaults.variant.minProportion),
minCount: Number(texts.minCount ?? this.config.filterDefaults.variant.minCount),
minJaccard: Number(texts.minJaccard ?? this.config.filterDefaults.variant.minJaccard),
+ timeFrame:
+ (texts.timeFrame as VariantTimeFrame | undefined) ??
+ this.config.filterDefaults.variant.timeFrame,
};
break;
case 'resistance':
@@ -92,7 +96,7 @@ export class WasapPageStateHandler implements PageStateHandler {
const base: WasapBaseFilter = {
locationName: texts.locationName ?? this.config.defaultLocationName,
samplingDate: dateRanges.samplingDate,
- granularity: texts.granularity ?? 'day',
+ granularity: (texts.granularity as TemporalGranularity | undefined) ?? 'day',
excludeEmpty: texts.excludeEmpty !== 'false',
};
@@ -126,6 +130,7 @@ export class WasapPageStateHandler implements PageStateHandler {
setSearchFromString(search, 'minProportion', String(analysis.minProportion));
setSearchFromString(search, 'minCount', String(analysis.minCount));
setSearchFromString(search, 'minJaccard', String(analysis.minJaccard));
+ setSearchFromString(search, 'timeFrame', analysis.timeFrame);
break;
case 'resistance':
setSearchFromString(search, 'resistanceSet', analysis.resistanceSet);
@@ -195,6 +200,10 @@ function generateWasapFilterConfig(pageConfig: WasapPageConfig): BaselineFilterC
type: 'text',
lapisField: 'minJaccard',
},
+ {
+ type: 'text',
+ lapisField: 'timeFrame',
+ },
{
type: 'text',
lapisField: 'resistanceSet',
diff --git a/website/tests/CompareSideBySidePage.ts b/website/tests/CompareSideBySidePage.ts
new file mode 100644
index 000000000..3b93102a0
--- /dev/null
+++ b/website/tests/CompareSideBySidePage.ts
@@ -0,0 +1,50 @@
+import { expect } from '@playwright/test';
+
+import { ViewPage } from './ViewPage.ts';
+import { paths } from '../src/types/Organism.ts';
+import { type OrganismWithViewKey } from '../src/views/routing';
+import { compareSideBySideViewKey } from '../src/views/viewKeys';
+
+export class CompareSideBySidePage extends ViewPage {
+ public readonly removeColumnButton = this.page.getByRole('link', { name: 'Remove column' });
+ public readonly addColumnButton = this.page.getByRole('link', { name: 'Add column' });
+ public readonly mutationField = this.page.getByRole('combobox', { name: 'Enter a mutation', exact: false });
+
+ public async goto(organism: OrganismWithViewKey) {
+ await this.page.goto(`${paths[organism].basePath}/compare-side-by-side`);
+ }
+
+ public async addColumn(options: {
+ dateRangeOption: string;
+ expectedColumnCount: number;
+ lineage?: string;
+ lineageFieldPlaceholder?: string;
+ mutation?: string;
+ }) {
+ await expect(this.addColumnButton).toBeVisible();
+
+ await this.addColumnButton.click();
+ await expect(this.mutationField).toHaveCount(options.expectedColumnCount);
+
+ await this.page
+ .locator('gs-date-range-filter')
+ .getByRole('combobox')
+ .last()
+ .selectOption(options.dateRangeOption);
+
+ if (options.lineage && options.lineageFieldPlaceholder) {
+ const { lineage, lineageFieldPlaceholder } = options;
+
+ const lineageFieldLocator = this.page.getByPlaceholder(lineageFieldPlaceholder);
+ await expect(lineageFieldLocator).toHaveCount(options.expectedColumnCount);
+
+ await this.fillLineageField(lineageFieldLocator.last(), lineage);
+ }
+
+ if (options.mutation) {
+ await this.fillMutationField(this.mutationField.last(), options.mutation);
+ }
+
+ await this.page.getByRole('button', { name: 'Apply filters' }).last().click();
+ }
+}
diff --git a/website/tests/CompareToBaselinePage.ts b/website/tests/CompareToBaselinePage.ts
new file mode 100644
index 000000000..a5a091b3b
--- /dev/null
+++ b/website/tests/CompareToBaselinePage.ts
@@ -0,0 +1,34 @@
+import { type Page } from '@playwright/test';
+
+import { CompareVariantsPage } from './CompareVariantsPage.ts';
+import { paths } from '../src/types/Organism.ts';
+import { type OrganismWithViewKey } from '../src/views/routing';
+import { compareToBaselineViewKey } from '../src/views/viewKeys';
+
+export class CompareToBaselinePage extends CompareVariantsPage {
+ public readonly selectVariantsMessage;
+ public readonly mutationField;
+
+ constructor(page: Page) {
+ super(page);
+ this.selectVariantsMessage = this.page.getByText('Analyze a variant compared to a baseline', { exact: false });
+ this.mutationField = this.page.getByRole('combobox', { name: 'Enter a mutation', exact: false });
+ }
+
+ public async goto(organism: OrganismWithViewKey) {
+ await this.page.goto(`${paths[organism].basePath}/compare-to-baseline`);
+ }
+
+ public async selectBaseline(options: { lineage?: string; lineageFieldPlaceholder?: string; mutation?: string }) {
+ if (options.lineage && options.lineageFieldPlaceholder) {
+ const { lineage, lineageFieldPlaceholder } = options;
+
+ const lineageFieldLocator = this.page.getByPlaceholder(lineageFieldPlaceholder);
+ await this.fillLineageField(lineageFieldLocator.first(), lineage);
+ }
+
+ if (options.mutation) {
+ await this.fillMutationField(this.mutationField.first(), options.mutation);
+ }
+ }
+}
diff --git a/website/tests/CompareVariantsPage.ts b/website/tests/CompareVariantsPage.ts
index 16b7585aa..d566f074c 100644
--- a/website/tests/CompareVariantsPage.ts
+++ b/website/tests/CompareVariantsPage.ts
@@ -33,15 +33,11 @@ export class CompareVariantsPage extends ViewPage {
const lineageFieldLocator = this.page.getByPlaceholder(lineageFieldPlaceholder);
await expect(lineageFieldLocator).toHaveCount(numberMutationFields + 1);
- await lineageFieldLocator.last().fill(lineage);
-
- const selectedLineage = this.page.getByRole('option', { name: lineage, exact: false });
- await selectedLineage.first().click();
+ await this.fillLineageField(lineageFieldLocator.last(), lineage);
}
if (options.mutation) {
- await this.mutationField.last().fill(options.mutation);
- await this.mutationField.last().press('Enter');
+ await this.fillMutationField(this.mutationField.last(), options.mutation);
}
}
}
diff --git a/website/tests/ViewPage.ts b/website/tests/ViewPage.ts
index be146eb78..43ee2549e 100644
--- a/website/tests/ViewPage.ts
+++ b/website/tests/ViewPage.ts
@@ -1,4 +1,4 @@
-import { expect, type Page } from '@playwright/test';
+import { expect, type Locator, type Page } from '@playwright/test';
import { type Organism } from '../src/types/Organism.ts';
@@ -23,4 +23,15 @@ export abstract class ViewPage {
public async selectDateRange(dateRangeOption: string) {
await this.page.locator('gs-date-range-filter').getByRole('combobox').first().selectOption(dateRangeOption);
}
+
+ public async fillLineageField(locator: Locator, lineage: string) {
+ await locator.fill(lineage);
+ const selectedLineage = this.page.getByRole('option', { name: lineage, exact: false });
+ await selectedLineage.first().click();
+ }
+
+ public async fillMutationField(locator: Locator, mutation: string) {
+ await locator.first().fill(mutation);
+ await locator.first().press('Enter');
+ }
}
diff --git a/website/tests/compareSideBySide.spec.ts b/website/tests/compareSideBySide.spec.ts
new file mode 100644
index 000000000..2ccfa925e
--- /dev/null
+++ b/website/tests/compareSideBySide.spec.ts
@@ -0,0 +1,38 @@
+import { expect } from '@playwright/test';
+
+import { test } from './e2e.fixture.ts';
+import { organismOptions, organismsWithView } from './helpers.ts';
+import { compareSideBySideViewKey } from '../src/views/viewKeys';
+
+test.describe('The Compare Side-By-Side page', () => {
+ for (const organism of organismsWithView(compareSideBySideViewKey)) {
+ test(`should show diagrams after selecting a variant in both columns - ${organism}`, async ({
+ compareSideBySidePage,
+ }) => {
+ const options = organismOptions[organism];
+
+ await compareSideBySidePage.goto(organism);
+ await expect(compareSideBySidePage.removeColumnButton).not.toBeVisible();
+ await expect(compareSideBySidePage.addColumnButton).toBeVisible();
+
+ await expect(compareSideBySidePage.diagramTitle('Prevalence Over Time')).not.toBeVisible();
+
+ await compareSideBySidePage.addColumn({
+ dateRangeOption: 'All times',
+ expectedColumnCount: 1,
+ ...options,
+ });
+ await expect(compareSideBySidePage.removeColumnButton).not.toBeVisible();
+
+ await compareSideBySidePage.addColumn({
+ dateRangeOption: 'All times',
+ expectedColumnCount: 2,
+ ...options,
+ });
+ await expect(compareSideBySidePage.removeColumnButton).toHaveCount(2);
+
+ await expect(compareSideBySidePage.diagramTitle('Prevalence Over Time')).toHaveCount(2);
+ await compareSideBySidePage.expectToSeeNoComponentErrors();
+ });
+ }
+});
diff --git a/website/tests/compareToBaseline.spec.ts b/website/tests/compareToBaseline.spec.ts
new file mode 100644
index 000000000..b78929117
--- /dev/null
+++ b/website/tests/compareToBaseline.spec.ts
@@ -0,0 +1,27 @@
+import { expect } from '@playwright/test';
+
+import { test } from './e2e.fixture.ts';
+import { organismOptions, organismsWithView } from './helpers.ts';
+import { compareToBaselineViewKey } from '../src/views/viewKeys';
+
+test.describe('The Compare To Baseline page', () => {
+ for (const organism of organismsWithView(compareToBaselineViewKey)) {
+ test(`should show diagrams after selecting two variants and a baseline - ${organism}`, async ({
+ compareToBaselinePage,
+ }) => {
+ const options = organismOptions[organism];
+
+ await compareToBaselinePage.goto(organism);
+ await expect(compareToBaselinePage.selectVariantsMessage).toBeVisible();
+ await expect(compareToBaselinePage.diagramTitle('Prevalence Over Time')).not.toBeVisible();
+
+ await compareToBaselinePage.selectDateRange('All times');
+ await compareToBaselinePage.selectBaseline(options);
+ await compareToBaselinePage.addVariant(options);
+ await compareToBaselinePage.submitFilters();
+
+ await expect(compareToBaselinePage.diagramTitle('Prevalence Over Time')).toBeVisible();
+ await compareToBaselinePage.expectToSeeNoComponentErrors();
+ });
+ }
+});
diff --git a/website/tests/compareVariants.spec.ts b/website/tests/compareVariants.spec.ts
index eef8b89c7..8ffbdd53f 100644
--- a/website/tests/compareVariants.spec.ts
+++ b/website/tests/compareVariants.spec.ts
@@ -1,30 +1,9 @@
import { expect } from '@playwright/test';
import { test } from './e2e.fixture.ts';
-import { organismsWithView } from './helpers.ts';
-import { Organisms } from '../src/types/Organism.ts';
+import { organismOptions, organismsWithView } from './helpers.ts';
import { compareVariantsViewKey } from '../src/views/viewKeys';
-const organismOptions = {
- [Organisms.covid]: { lineage: 'JN.1*', lineageFieldPlaceholder: 'Nextclade pango lineage' },
- [Organisms.h5n1]: { lineage: '2.3.4.4b', lineageFieldPlaceholder: 'Clade' },
- [Organisms.h1n1pdm]: { lineage: '6B.1A.5a.2a.1', lineageFieldPlaceholder: 'Clade HA' },
- [Organisms.h3n2]: { lineage: '3C.2a1b', lineageFieldPlaceholder: 'Clade HA' },
- [Organisms.victoria]: { lineage: 'V1A.3a.2', lineageFieldPlaceholder: 'Clade HA' },
- [Organisms.westNile]: { lineage: '1A', lineageFieldPlaceholder: 'Lineage' },
- [Organisms.rsvA]: { lineage: 'A.D.5.2', lineageFieldPlaceholder: 'Lineage' },
- [Organisms.rsvB]: { lineage: 'B.D.E.1', lineageFieldPlaceholder: 'Lineage' },
- [Organisms.mpox]: { lineage: 'F.1', lineageFieldPlaceholder: 'Lineage' },
- [Organisms.ebolaSudan]: { mutation: 'G5902T' },
- [Organisms.ebolaZaire]: { mutation: 'T18365C' },
- [Organisms.cchf]: { mutation: 'M:G3565A' },
- [Organisms.denv1]: { lineage: '1I_K.1.1', lineageFieldPlaceholder: 'Clade' },
- [Organisms.denv2]: { lineage: '2II_F.1.1', lineageFieldPlaceholder: 'Clade' },
- [Organisms.denv3]: { lineage: '3III_B.3.2', lineageFieldPlaceholder: 'Clade' },
- [Organisms.denv4]: { lineage: '4II_B.1.2', lineageFieldPlaceholder: 'Clade' },
- [Organisms.measles]: { lineage: 'B3', lineageFieldPlaceholder: 'Genotype' },
-};
-
test.describe('The Compare Variants page', () => {
for (const organism of organismsWithView(compareVariantsViewKey)) {
test(`should show diagrams after selecting two variants ${organism}`, async ({ compareVariantsPage }) => {
diff --git a/website/tests/e2e.fixture.ts b/website/tests/e2e.fixture.ts
index 561452517..3e4dbf6dc 100644
--- a/website/tests/e2e.fixture.ts
+++ b/website/tests/e2e.fixture.ts
@@ -1,11 +1,15 @@
import { test as base } from '@playwright/test';
+import { CompareSideBySidePage } from './CompareSideBySidePage.ts';
+import { CompareToBaselinePage } from './CompareToBaselinePage.ts';
import { CompareVariantsPage } from './CompareVariantsPage.ts';
import { SequencingEffortsPage } from './SequencingEffortsPage.ts';
type E2EFixture = {
compareVariantsPage: CompareVariantsPage;
sequencingEffortsPage: SequencingEffortsPage;
+ compareToBaselinePage: CompareToBaselinePage;
+ compareSideBySidePage: CompareSideBySidePage;
};
export const test = base.extend({
@@ -15,4 +19,10 @@ export const test = base.extend({
sequencingEffortsPage: async ({ page }, use) => {
await use(new SequencingEffortsPage(page));
},
+ compareToBaselinePage: async ({ page }, use) => {
+ await use(new CompareToBaselinePage(page));
+ },
+ compareSideBySidePage: async ({ page }, use) => {
+ await use(new CompareSideBySidePage(page));
+ },
});
diff --git a/website/tests/helpers.ts b/website/tests/helpers.ts
index 55120cbc5..5dfda525f 100644
--- a/website/tests/helpers.ts
+++ b/website/tests/helpers.ts
@@ -1,7 +1,29 @@
-import { allOrganisms } from '../src/types/Organism.ts';
+import { allOrganisms, Organisms } from '../src/types/Organism.ts';
import type { OrganismWithViewKey } from '../src/views/routing.ts';
import { ServerSide } from '../src/views/serverSideRouting.ts';
export function organismsWithView(viewKey: ViewKey): OrganismWithViewKey[] {
return allOrganisms.filter((organism) => ServerSide.routing.isOrganismWithViewKey(organism, viewKey));
}
+
+export const organismOptions = {
+ [Organisms.covid]: { lineage: 'JN.1*', lineageFieldPlaceholder: 'Nextclade pango lineage' },
+ [Organisms.influenzaA]: { lineage: 'H1', lineageFieldPlaceholder: 'HA subtype' },
+ [Organisms.h5n1]: { lineage: '2.3.4.4b', lineageFieldPlaceholder: 'Clade' },
+ [Organisms.h1n1pdm]: { lineage: '6B.1A.5a.2a.1', lineageFieldPlaceholder: 'Clade HA' },
+ [Organisms.h3n2]: { lineage: '3C.2a1b', lineageFieldPlaceholder: 'Clade HA' },
+ [Organisms.influenzaB]: { lineage: 'vic', lineageFieldPlaceholder: 'Lineage' },
+ [Organisms.victoria]: { lineage: 'V1A.3a.2', lineageFieldPlaceholder: 'Clade HA' },
+ [Organisms.westNile]: { lineage: '1A', lineageFieldPlaceholder: 'Lineage' },
+ [Organisms.rsvA]: { lineage: 'A.D.5.2', lineageFieldPlaceholder: 'Lineage' },
+ [Organisms.rsvB]: { lineage: 'B.D.E.1', lineageFieldPlaceholder: 'Lineage' },
+ [Organisms.mpox]: { lineage: 'F.1', lineageFieldPlaceholder: 'Lineage' },
+ [Organisms.ebolaSudan]: { mutation: 'G5902T' },
+ [Organisms.ebolaZaire]: { mutation: 'T18365C' },
+ [Organisms.cchf]: { mutation: 'M:G3565A' },
+ [Organisms.denv1]: { lineage: '1I_K.1.1', lineageFieldPlaceholder: 'Clade' },
+ [Organisms.denv2]: { lineage: '2II_F.1.1', lineageFieldPlaceholder: 'Clade' },
+ [Organisms.denv3]: { lineage: '3III_B.3.2', lineageFieldPlaceholder: 'Clade' },
+ [Organisms.denv4]: { lineage: '4II_B.1.2', lineageFieldPlaceholder: 'Clade' },
+ [Organisms.measles]: { lineage: 'B3', lineageFieldPlaceholder: 'Genotype' },
+};